2018 Index IEEE/ACM Transactions on Computational Biology ... · IEEE/ACM Transactions on Computational Biology and Bioinformatics Vol. 15 This index covers all technical items—papers,

2018 IndexIEEE/ACM Transactions on Computational Biology and Bioinformatics

Vol. 15

This index covers all technical items—papers, correspondence, reviews,etc.—that appeared in this periodical during 2018, and items from previousyears that were commented upon or corrected in 2018. Departments and otheritems may also be covered if they have been judged to have archival value.

The Author Index contains the primary entry for each item, listed under thefirst author’s name. The primary entry includes the coauthors’ names, the title ofthe paper or other item, and its location, specified by the publication abbrevia-tion, year, month, and inclusive pagination. The Subject Index contains entriesdescribing the item under all appropriate subject headings, plus the first author’sname, the publication abbreviation, month, and year, and inclusive pages. Notethat the item title is found only under the primary entry in the Author Index.

AUTHOR INDEX

A

Abbas, A., see Alazmi, M., TCBB Nov.-Dec. 2018 1999-2008Abdallah, A.B., seeWang, H., TCBB Nov.-Dec. 2018 1968-1978Acharyya, S., see Biswas, S., TCBB Nov.-Dec. 2018 2053-2059Afzal, M.T., see Ikram, N., TCBB May -June 2018 905-912Ahmad, A., see Noor, A., TCBB March-April 2018 387-395Ahn, C.K., see Ali, M.S., TCBB Jan.-Feb. 2018 271-285Akutsu, T., see Tamura, T., TCBB Nov.-Dec. 2018 1853-1862Akutsu, T., see Li, J., TCBB March-April 2018 633-646Al-Ouran, R., Schmidt, R., Naik, A., Jones, J., Drews, F., Juedes, D., Elnitski,

L., and Welch, L., Discovering Gene Regulatory Elements Using Cover-age-Based Heuristics; TCBB July-Aug. 2018 1290-1300

Alazmi, M., Abbas, A., Guo, X., Fan, M., Li, L., and Gao, X., A Slice-based13C-detected NMR Spin System Forming and Resonance AssignmentMethod; TCBB Nov.-Dec. 2018 1999-2008

Ali, M.S., Gunasekaran, N., Ahn, C.K., and Shi, P., Sampled-Data Stabiliza-tion for Fuzzy Genetic Regulatory Networks with Leakage Delays; TCBBJan.-Feb. 2018 271-285

Alim, M.A., Ay, A., Hasan, M.M., Thai, M.T., and Kahveci, T., Constructionof Signaling Pathways with RNAi Data and Multiple Reference Networks;TCBB July-Aug. 2018 1079-1091

Allman, E.S., Degnan, J.H., and Rhodes, J.A., Species Tree Inference fromGene Splits by Unrooted STAR Methods; TCBB Jan.-Feb. 2018 337-342

Alves, P., Liu, S., Wang, D., and Gerstein, M., Multiple-Swarm Ensembles:Improving the Predictive Power and Robustness of Predictive Modelsand Its Use in Computational Biology; TCBB May -June 2018 926-933

An, S., Wang, J., and Wei, J., Local-Nearest-Neighbors-Based FeatureWeighting for Gene Selection; TCBB Sept.-Oct. 2018 1538-1548

Anders, G., Hassiepen, U., Theisgen, S., Heymann, S., Muller, L., Panigada,T., Huster, D., and Samsonov, S.A., The Intrinsic Pepsin Resistance ofInterleukin-8 Can Be Explained from a Combined Bioinformatical andExperimental Approach; TCBB Jan.-Feb. 2018 300-308

Arruda, T.d.S., Dias, U., and Dias, Z., AGRASP-BasedHeuristic for the Sortingby Length-Weighted Inversions Problem; TCBBMarch-April 2018 352-363

Arshad, O.A., see Ghaffari, N., TCBB March-April 2018 494-505Avcu, N., Pekergin, N., Pekergin, F., and Guzelis, C., Aggregation for

Computing Multi-Modal Stationary Distributions in 1-D Gene RegulatoryNetworks; TCBB May -June 2018 813-827

Avidan, M., seeWang, H., TCBB Nov.-Dec. 2018 1968-1978Avila, A., see Iglesias, A., TCBB Nov.-Dec. 2018 1929-1942Awdeh, A., Phenix, H., Karn, M., and Perkins, T.J., Dynamics in Epistasis

Analysis; TCBB May -June 2018 878-891Ay, A., see Alim, M.A., TCBB July-Aug. 2018 1079-1091Ayday, E., see Deznabi, I., TCBB July-Aug. 2018 1333-1343Ayday, E., Jiang, X., and Malin, B., GenoPri’16: International Workshop on

Genome Privacy and Security; TCBB Sept.-Oct. 2018 1403-1404

B

Backenk€ohler, M., Bortolussi, L., and Wolf, V., Moment-Based ParameterEstimation for Stochastic Reaction Networks in Equilibrium; TCBB July-Aug. 2018 1180-1192

Backes, M., Berrang, P., Humbert, M., Shen, X., and Wolf, V., Simulating theLarge-Scale Erosion of Genomic Privacy Over Time; TCBB Sept.-Oct.2018 1405-1412

Bahadorinejad, A., and Braga-Neto, U.M., Optimal Fault Detection andDiagnosis in Transcriptional Circuits Using Next-Generation Sequencing;TCBB March-April 2018 516-525

Balasubramaniam, S., seeMartins, D.P., TCBB Nov.-Dec. 2018 2017-2027Bandyopadhyay, S., and Mallik, S., Integrating Multiple Data Sources for

Combinatorial Marker Discovery: A Study in Tumorigenesis; TCBBMarch-April 2018 673-687

Banga, J.R., see Villaverde, A.F., TCBB July-Aug. 2018 1193-1202Bao, F., Deng, Y., and Dai, Q., ACID: Association Correction for Imbalanced

Data in GWAS; TCBB Jan.-Feb. 2018 316-322Bao, W., Yuan, C., Zhang, Y., Han, K., Nandi, A.K., Honig, B., and Huang,

D., Mutli-Features Prediction of Protein Translational Modification Sites;TCBB Sept.-Oct. 2018 1453-1460

Bapat, S., see Vyas, R., TCBB Jan.-Feb. 2018 27-37Barros, M.T., seeMartins, D.P., TCBB Nov.-Dec. 2018 2017-2027Bartocci, E., Lio, P., and Paoletti, N., Guest Editors’ Introduction to the Spe-

cial Section on the 14th International Conference on Computational Meth-ods in Systems Biology (CMSB 2016); TCBB July-Aug. 2018 1122-1123

Basu, S., see Dutta, P., TCBB May -June 2018 839-849Bay�a, A.E., see Leale, G., TCBB Jan.-Feb. 2018 168-180Beasley, R., see Singh, R., TCBB March-April 2018 469-481Becker, K., see Villaverde, A.F., TCBB July-Aug. 2018 1193-1202Behinaein, B., Rudie, K., and Sangrar, W., Petri Net Siphon Analysis and

Graph Theoretic Measures for Identifying Combination Therapies in Can-cer; TCBB Jan.-Feb. 2018 231-243

Bei, E.S., see Chlis, N., TCBB Jan.-Feb. 2018 181-190Bennamoun, M., see Khan, S., TCBB Jan.-Feb. 2018 244-250Bernt, M., see Hartmann, T., TCBB Jan.-Feb. 2018 83-95Bernt, M., see Hartmann, T., TCBB Sept.-Oct. 2018 1585-1593Berrang, P., see Backes, M., TCBB Sept.-Oct. 2018 1405-1412Bevilacqua, V., see Huang, D., TCBB Sept.-Oct. 2018 1433-1435Billey, S.C., seeMatsen, F.A., TCBB Jan.-Feb. 2018 343-349Biswas, S., and Acharyya, S., A Bi-Objective RNN Model to Reconstruct

Gene Regulatory Network: A Modified Multi-Objective SimulatedAnnealing Approach; TCBB Nov.-Dec. 2018 2053-2059

Bogdanov, D., Kamm, L., Laur, S., and Sokk, V., Implementation and Evalua-tion of an Algorithm for Cryptographically Private Principal ComponentAnalysis on Genomic Data; TCBB Sept.-Oct. 2018 1427-1432

Borges, V.R.P., Oliveira, M.C.F.d., Silva, T.G., Vieira, A.A.H., and Hamann,B., Region Growing for Segmenting Green Microalgae Images; TCBBJan.-Feb. 2018 257-270

Borguesan, B., see Correa, L., TCBB May -June 2018 690-704Bortolussi, L., see Backenk€ohler, M., TCBB July-Aug. 2018 1180-1192Boscarino, R., see Russo, G., TCBB Sept.-Oct. 2018 1492-1499Bowman, F.D., see Zhang, L., TCBB March-April 2018 570-580Braga-Neto, U., see Karbalayghareh, A., TCBB Jan.-Feb. 2018 68-82Braga-Neto, U.M., see Bahadorinejad, A., TCBB March-April 2018 516-525Brauer Massirer, K., see Sato, J.R., TCBB March-April 2018 581-587Brzyski, D., see Gossmann, A., TCBB July-Aug. 2018 1066-1078

C

Caffrey, C.R., see Singh, R., TCBB March-April 2018 469-481Cai, M., see Ren, S., TCBB Sept.-Oct. 2018 1660-1668Calebe Vidal, M., see Sato, J.R., TCBB March-April 2018 581-587Calhoun, V.D., see Deng, S., TCBB Sept.-Oct. 2018 1480-1491Cao, B., see Luo, J., TCBB Jan.-Feb. 2018 309-315

IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS, VOL. 16, NO. 1, JANUARY/FEBRUARY 2019 1

Cao, C., seeWu, H., TCBB Sept.-Oct. 2018 1445-1452Cao, S., see Gossmann, A., TCBB July-Aug. 2018 1066-1078Chai, H., see Zhang, J., TCBB Jan.-Feb. 2018 147-156Chan, K.C., see He, T., TCBB May -June 2018 892-904Chan, S., seeWu, H., TCBB Nov.-Dec. 2018 2039-2052Chapkin, R.S., see Knight, J.M., TCBB March-April 2018 484-493Chaterji, S., see Ghoshal, A., TCBB July-Aug. 2018 1037-1051Chauve, C., see Luhmann, N., TCBB Nov.-Dec. 2018 2094-2100Chauve, C., see Lafond, M., TCBB Sept.-Oct. 2018 1560-1570Chen, F., see Yuan, L., TCBB March-April 2018 551-561Chen, J., see Hu, B., TCBB Nov.-Dec. 2018 1765-1773Chen, J., see Yu, C., TCBB Sept.-Oct. 2018 1683-1691Chen, J.Y., see Yue, Z., TCBB Nov.-Dec. 2018 1991-1998Chen, J.Y., see Gao, X., TCBB Nov.-Dec. 2018 1951-1952Chen, S., Liu, M., Zhang, X., Long, R., Wang, Y., Han, Y., Zhang, S., Xu, M.,

and Gu, J., A Study of Cell-Free DNA Fragmentation Pattern and ItsApplication in DNA Sample Type Classification; TCBB Sept.-Oct. 20181718-1722

Chen, Y., see Chiu, Y., TCBB Nov.-Dec. 2018 1754-1764Chen, Y., seeWang, H., TCBB Nov.-Dec. 2018 1968-1978Chen, Y., see Cui, X., TCBB March-April 2018 526-534Chen, Y.P., see Cheng, Z., TCBB Nov.-Dec. 2018 1832-1843Chen, Y.P., see Tang, J., TCBB March-April 2018 396-397Chen, Y.P., seeWang, L., TCBB Sept.-Oct. 2018 1513-1514Chen, Z., Feng, Q., Shen, C., Wang, J., and Wang, L., Algorithms for Pedigree

Comparison; TCBB March-April 2018 422-431Cheng, J., see Guo, Y., TCBB Nov.-Dec. 2018 1891-1903Cheng, J., see Gao, S., TCBB July-Aug. 2018 1365-1378Cheng, S., seeWang, A., TCBB Nov.-Dec. 2018 1960-1967Cheng, X., Hou, Y., Nie, Y., Zhang, Y., Huang, H., Liu, H., and Sun, X.,

Nucleosome Positioning of Intronless Genes in the Human Genome;TCBB July-Aug. 2018 1111-1121

Cheng, Y., see Liu, J., TCBB Sept.-Oct. 2018 1500-1512Cheng, Z., Zhou, S., Wang, Y., Liu, H., Guan, J., and Chen, Y.P., Effectively

Identifying Compound-Protein Interactions by Learning from Positiveand Unlabeled Examples; TCBB Nov.-Dec. 2018 1832-1843

Chicco, D., Palluzzi, F., and Masseroli, M., Novelty Indicator for EnhancedPrioritization of Predicted Gene Ontology Annotations; TCBB May -June2018 954-965

Chiu, Y., Hsiao, T., Wang, L., Chen, Y., and Chuang, E.Y., Analyzing Differ-ential Regulatory Networks Modulated by Continuous-State GenomicFeatures in Glioblastoma Multiforme; TCBB Nov.-Dec. 2018 1754-1764

Chlis, N., Bei, E.S., and Zervakis, M., Introducing a Stable Bootstrap Valida-tion Framework for Reliable Genomic Signature Extraction; TCBB Jan.-Feb. 2018 181-190

Cho, S., see Pal, J.K., TCBB March-April 2018 659-672Choi, G., see Raisaro, J.L., TCBB Sept.-Oct. 2018 1413-1426Choi, H., see Park, S., TCBB March-April 2018 441-451Choi, S., see Kim, H., TCBB Jan.-Feb. 2018 129-146Chu, A., see Hartmann, T., TCBB Jan.-Feb. 2018 83-95Chu, X., see Niu, B., TCBB Nov.-Dec. 2018 1865-1876Chuang, E.Y., see Chiu, Y., TCBB Nov.-Dec. 2018 1754-1764Chun, J., see Park, S., TCBB March-April 2018 441-451Coleman, J.R., see Papamichail, D., TCBB March-April 2018 452-459Colsenet, R., see Raisaro, J.L., TCBB Sept.-Oct. 2018 1413-1426Correa, L., Borguesan, B., Farf�an, C., Inostroza-Ponta, M., and Dorn, M., A

Memetic Algorithm for 3D Protein Structure Prediction Problem; TCBBMay -June 2018 690-704

Couprie, C., see Pirayre, A., TCBB May -June 2018 850-860Criscitiello, M.F., see Ghaffari, N., TCBB March-April 2018 494-505Cui, X., Zhang, L., Meng, J., Rao, M.K., Chen, Y., and Huang, Y., MeTDiff: A

Novel Differential RNA Methylation Analysis for MeRIP-Seq Data;TCBB March-April 2018 526-534

Cui, X., see Liu, J., TCBB Sept.-Oct. 2018 1500-1512Cui, Z., seeWang, H., TCBB Nov.-Dec. 2018 1968-1978Czapla, R., Random Sets of Stadiums in Square and Collective Behavior of

Bacteria; TCBB Jan.-Feb. 2018 251-256Czeizler, E., Wu, K., Gratie, C., Kanhaiya, K., and Petre, I., Structural Target

Controllability of Linear Networks; TCBB July-Aug. 2018 1217-1228

D

Dai, J., see Liu, K., TCBB July-Aug. 2018 1107-1110Dai, Q., see Bao, F., TCBB Jan.-Feb. 2018 316-322Dai, Y., see Hu, B., TCBB Nov.-Dec. 2018 1765-1773

Datta, A., see Ghaffari, N., TCBB March-April 2018 494-505Datta, A., see Ghosh, B.K., TCBB March-April 2018 482-483Datta, S., see Pesonen, M., TCBB May -June 2018 760-773Datta, S., see Pesonen, M., TCBB May -June 2018 760-773Davidson, R., Lawhorn, M., Rusinko, J., and Weber, N., Efficient Quartet

Representations of Trees and Applications to Supertree and SummaryMethods; TCBB May -June 2018 1010-1015

De Jong, K.A., see Sapin, E., TCBB May -June 2018 719-731de Siqueira Santos, S., see Sato, J.R., TCBB March-April 2018 581-587Dediu, A., and Martin-Vide, C., Selected Papers of the First International Con-

ference on Algorithms for Computational Biology (AlCoB 2014); TCBBMarch-April 2018 350-351

Degnan, J.H., see Allman, E.S., TCBB Jan.-Feb. 2018 337-342Dehghannasiri, R., seeMohsenizadeh, D.N., TCBB Jan.-Feb. 2018 218-230Deng, H., see Gossmann, A., TCBB July-Aug. 2018 1066-1078Deng, S., Hu, W., Calhoun, V.D., and Wang, Y., Integrating Imaging Genomic

Data in the Quest for Biomarkers of Schizophrenia Disease; TCBB Sept.-Oct. 2018 1480-1491

Deng, Y., see Bao, F., TCBB Jan.-Feb. 2018 316-322Deris, S., see Fotoohifiroozabadi, S., TCBB May -June 2018 934-943Deshpande, G., see Zhang, J., TCBB March-April 2018 535-536Deznabi, I., Mobayen, M., Jafari, N., Tastan, O., and Ayday, E., An Inference

Attack on Genomic Data Using Kinship, Complex Correlations, and Phe-notype Information; TCBB July-Aug. 2018 1333-1343

Diallo, A.B., see Halioui, A., TCBB Nov.-Dec. 2018 1979-1990Dias, U., see Arruda, T.d.S., TCBB March-April 2018 352-363Dias, Z., see Arruda, T.d.S., TCBB March-April 2018 352-363Ding, L., see Tang, Q., TCBB Nov.-Dec. 2018 1943-1950Dittrich, P., seeMu, C., TCBB July-Aug. 2018 1152-1166Djeddi, W.E., Yahia, S.B., and Nguifo, E.M., A Novel Computational

Approach for Global Alignment for Multiple Biological Networks; TCBBNov.-Dec. 2018 2060-2066

Dong, W., see Li, J., TCBB Nov.-Dec. 2018 2028-2038Dorn, M., see Correa, L., TCBB May -June 2018 690-704Dougherty, E.R., seeMohsenizadeh, D.N., TCBB Jan.-Feb. 2018 218-230Dougherty, E.R., see Karbalayghareh, A., TCBB Jan.-Feb. 2018 68-82Dougherty, E.R., see Knight, J.M., TCBB March-April 2018 484-493Drews, F., see Al-Ouran, R., TCBB July-Aug. 2018 1290-1300Du, G., see Zhang, L., TCBB March-April 2018 570-580Du, J., see Liu, J., TCBB Sept.-Oct. 2018 1500-1512Du, W., see Peng, X., TCBB May -June 2018 788-801Duarte-Sanchez, J.E., Velasco-Medina, J., and Moreno, P.A., Hardware

Accelerator for the Multifractal Analysis of DNA Sequences; TCBBSept.-Oct. 2018 1611-1624

Dutta, P., Basu, S., and Kundu, M., Assessment of Semantic Similaritybetween Proteins Using Information Content and Topological Propertiesof the Gene Ontology Graph; TCBB May -June 2018 839-849

Duval, L., see Pirayre, A., TCBB May -June 2018 850-860

E

El-Mabrouk, N., see Lafond, M., TCBB Sept.-Oct. 2018 1560-1570Eladawy, M., see Hashem, S., TCBB May -June 2018 861-868Elakel, W., see Hashem, S., TCBB May -June 2018 861-868Elhadad, A., see Hamad, S., TCBB Sept.-Oct. 2018 1605-1610Elhefnawi, M., see Hashem, S., TCBB May -June 2018 861-868ElHefnawi, M., see Hashem, S., TCBB May -June 2018 861-868Elmsallati, A., Msalati, A., and Kalita, J., Index-Based Network Aligner of

Protein-Protein Interaction Networks; TCBB Jan.-Feb. 2018 330-336Elnitski, L., see Al-Ouran, R., TCBB July-Aug. 2018 1290-1300Eslinger, P.J., see Zhang, L., TCBB March-April 2018 570-580Esmat, G., see Hashem, S., TCBB May -June 2018 861-868Eulenstein, O., see G�orecki, P., TCBB Sept.-Oct. 2018 1723-1727Euler, R., see Lin, C., TCBB March-April 2018 377-386

F

Fages, F., Martinez, T., Rosenblueth, D.A., and Soliman, S., Influence Net-works Compared with Reaction Networks: Semantics, Expressivity andAttractors; TCBB July-Aug. 2018 1138-1151

Fan, M., see Alazmi, M., TCBB Nov.-Dec. 2018 1999-2008Fan, X., Ji, X., and Jiang, R., Guest Editorial for Special Section on the Sixth

National Conference on Bioinformatics and System Biology of China;TCBB July-Aug. 2018 1092

2 IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS, VOL. 16, NO. 1, JANUARY/FEBRUARY 2019

+ Check author entry for coauthors

Farf�an, C., see Correa, L., TCBB May -June 2018 690-704Fathy, M., see Sedaghat, N., TCBB Sept.-Oct. 2018 1594-1604Feng, Q., see Chen, Z., TCBB March-April 2018 422-431Feng, Y., see Zhou, X., TCBB May -June 2018 802-812Feret, J., and L�y, K.Q., Local Traces: An Over-Approximation of the

Behavior of the Proteins in Rule-Based Models; TCBB July-Aug. 20181124-1137

Ferro, J.M., seeMonteiro, M., TCBB Nov.-Dec. 2018 1953-1959Fober, T., see Leinweber, M., TCBB May -June 2018 740-752Fonseca, A.C., seeMonteiro, M., TCBB Nov.-Dec. 2018 1953-1959Forman, J., seeMa, W., TCBB March-April 2018 411-421Fortier, P., see Poirier, C., TCBB May -June 2018 1003-1009Fotoohifiroozabadi, S., Mohamad, M.S., and Deris, S., NAHAL-Flex:

A Numerical and Alphabetical Hinge Detection Algorithm for FlexibleProtein Structure Alignment; TCBB May -June 2018 934-943

Francisco, A.P., seeMonteiro, M., TCBB Nov.-Dec. 2018 1953-1959Freisleben, B., see Leinweber, M., TCBB May -June 2018 740-752Freitas, A.T., seeMonteiro, M., TCBB Nov.-Dec. 2018 1953-1959Frith, M.C., and Shrestha, A.M.S., A Simplified Description of Child Tables

for Sequence Similarity Search; TCBB Nov.-Dec. 2018 2067-2073Fu, G., see Yu, G., TCBB July-Aug. 2018 1390-1402Fujita, A., see Sato, J.R., TCBB March-April 2018 581-587Fukui, K., see Suryanto, C.H., TCBB Jan.-Feb. 2018 286-299

G

G�alvez, A., see Iglesias, A., TCBB Nov.-Dec. 2018 1929-1942Ganapathiraju, M.K., see Roth, A., TCBB July-Aug. 2018 1239-1246Gao, B., see Zhang, J., TCBB Jan.-Feb. 2018 147-156Gao, C., Liang, M., Li, X., Zhang, Z., Wang, Z., and Zhou, Z., Network

Community Detection Based on the Physarum-Inspired ComputationalFramework; TCBB Nov.-Dec. 2018 1916-1928

Gao, L., seeMa, X., TCBB March-April 2018 647-658Gao, S., Song, S., Cheng, J., Todo, Y., and Zhou, M., Incorporation of Solvent

Effect into Multi-Objective Evolutionary Algorithm for Improved ProteinStructure Prediction; TCBB July-Aug. 2018 1365-1378

Gao, X., Chen, J.Y., and Zaki, M.J., Multiscale and Multimodal Analysis forComputational Biology; TCBB Nov.-Dec. 2018 1951-1952

Gao, X., see Alazmi, M., TCBB Nov.-Dec. 2018 1999-2008Gao, Y., see Liu, J., TCBB May -June 2018 974-987Gerstein, M., see Alves, P., TCBB May -June 2018 926-933Ghaffari, N., Arshad, O.A., Jeong, H., Thiltges, J., Criscitiello, M.F., Yoon,

B., Datta, A., and Johnson, C.D., Examining De Novo TranscriptomeAssemblies via a Quality Assessment Pipeline; TCBB March-April 2018494-505

Ghosh, B.K., Datta, A., and Pal, R., Deep Sequencing Data Analysis; TCBBMarch-April 2018 482-483

Ghoshal, A., Zhang, J., Roth, M.A., Xia, K.M., Grama, A.Y., and Chaterji, S.,A Distributed Classifier for MicroRNA Target Prediction with ValidationThrough TCGA Expression Data; TCBB July-Aug. 2018 1037-1051

Goel, P., see Vyas, R., TCBB Jan.-Feb. 2018 27-37Gong, D., see Xu, B., TCBB Nov.-Dec. 2018 1877-1890Gong, D., see Guo, Y., TCBB Nov.-Dec. 2018 1891-1903Gong, M., see Huang, J., TCBB May -June 2018 705-718Gonz�alez-Dom�ınguez, J., and Martin, M.J., MPIGeneNet: Parallel Calcula-

tion of Gene Co-Expression Networks on Multicore Clusters; TCBBSept.-Oct. 2018 1732-1737

Gopalan, R.P., see Uppu, S., TCBB March-April 2018 599-612G�orecki, P., seeMykowiecka, A., TCBB Sept.-Oct. 2018 1571-1578G�orecki, P., and Eulenstein, O., Bijective Diameters of Gene Tree Parsimony

Costs; TCBB Sept.-Oct. 2018 1723-1727G�orecki, P., see Paszek, J., TCBB Sept.-Oct. 2018 1515-1524Gosselin, B., see Poirier, C., TCBB May -June 2018 1003-1009Gossmann, A., Cao, S., Brzyski, D., Zhao, L., Deng, H., and Wang, Y., A

Sparse Regression Method for Group-Wise Feature Selection with FalseDiscovery Rate Control; TCBB July-Aug. 2018 1066-1078

Gould, N., see Papamichail, D., TCBB March-April 2018 452-459Grama, A.Y., see Ghoshal, A., TCBB July-Aug. 2018 1037-1051Granitto, P.M., see Leale, G., TCBB Jan.-Feb. 2018 168-180Gratie, C., see Czeizler, E., TCBB July-Aug. 2018 1217-1228Gromiha, M.M., see Kulandaisamy, A., TCBB Sept.-Oct. 2018 1436-1444Gromiha, M.M., see Huang, D., TCBB Sept.-Oct. 2018 1433-1435Grosse, I., see Hedtke, I., TCBB March-April 2018 364-376Gu, J., see Chen, S., TCBB Sept.-Oct. 2018 1718-1722Guan, J., see Cheng, Z., TCBB Nov.-Dec. 2018 1832-1843

Gunasekaran, N., see Ali, M.S., TCBB Jan.-Feb. 2018 271-285Guo, W., Si, C., Xue, Y., Mao, Y., Wang, L., and Wu, Q., A Grouping Particle

Swarm Optimizer with Personal-Best-Position Guidance for Large ScaleOptimization; TCBB Nov.-Dec. 2018 1904-1915

Guo, X., see Alazmi, M., TCBB Nov.-Dec. 2018 1999-2008Guo, X., seeMa, X., TCBB March-April 2018 647-658Guo, Y., see Xu, B., TCBB Nov.-Dec. 2018 1877-1890Guo, Y., Cheng, J., Luo, S., Gong, D., and Xue, Y., Robust Dynamic Multi-

Objective Vehicle Routing Optimization Method; TCBB Nov.-Dec. 20181891-1903

Guzelis, C., see Avcu, N., TCBB May -June 2018 813-827

H

Habashy, S., see Hashem, S., TCBB May -June 2018 861-868Hahn, M.W., see Ramalho, R.F., TCBB July-Aug. 2018 1284-1289Halioui, A., Valtchev, P., and Diallo, A.B., Bioinformatic Workflow Extrac-

tion from Scientific Texts based on Word Sense Disambiguation; TCBBNov.-Dec. 2018 1979-1990

Hamad, S., Elhadad, A., and Khalifa, A., DNA Watermarking Using CodonPostfix Technique; TCBB Sept.-Oct. 2018 1605-1610

Hamann, B., see Borges, V.R.P., TCBB Jan.-Feb. 2018 257-270Han, K., see Xia, C., TCBB July-Aug. 2018 1315-1324Han, K., see Lee, W., TCBB Sept.-Oct. 2018 1461-1469Han, K., see Bao, W., TCBB Sept.-Oct. 2018 1453-1460Han, Y., see Chen, S., TCBB Sept.-Oct. 2018 1718-1722Handl, J., Shehu, A., and Santos Reyes, J., Advances in the Application and

Development of Non-Linear Global Optimization Techniques in Compu-tational Structural Biology; TCBB May -June 2018 688-689

Hartmann, T., Chu, A., Middendorf, M., and Bernt, M., Combinatorics ofTandem Duplication Random Loss Mutations on Circular Genomes;TCBB Jan.-Feb. 2018 83-95

Hartmann, T., Wieseke, N., Sharan, R., Middendorf, M., and Bernt, M.,Genome Rearrangement with ILP; TCBB Sept.-Oct. 2018 1585-1593

Hasan, M.M., see Alim, M.A., TCBB July-Aug. 2018 1079-1091Hashem, S., Esmat, G., Elakel, W., Habashy, S., Raouf, S.A., Elhefnawi, M.,

Eladawy, M., and ElHefnawi, M., Comparison of Machine LearningApproaches for Prediction of Advanced Liver Fibrosis in Chronic Hepati-tis C Patients; TCBB May -June 2018 861-868

Hashemikhabir, S., Xia, R., Xiang, Y., and Janga, S.C., A Framework forIdentifying Genotypic Information from Clinical Records: ExploitingIntegrated Ontology Structures to Transfer Annotations between ICDCodes and Gene Ontologies; TCBB July-Aug. 2018 1259-1269

Hassiepen, U., see Anders, G., TCBB Jan.-Feb. 2018 300-308Hautaniemi, S., see Liu, C., TCBB May -June 2018 1022-1027He, T., and Chan, K.C., Evolutionary Graph Clustering for Protein Complex

Identification; TCBB May -June 2018 892-904He, W., see Peng, X., TCBB May -June 2018 788-801He, X., see Xie, Q., TCBB July-Aug. 2018 1344-1350He, X., Li, L., Liu, Y., Yu, X., and Meng, J., A Two-Stage Biomedical Event

Trigger Detection Method Integrating Feature Selection and WordEmbeddings; TCBB July-Aug. 2018 1325-1332

He, Y., see Liu, M., TCBB Sept.-Oct. 2018 1706-1717Hedtke, I., Lemnian, I., Grosse, I., and Muller-Hannemann, M., Optimal

Block-Based Trimming for Next Generation Sequencing; TCBB March-April 2018 364-376

Heymann, S., see Anders, G., TCBB Jan.-Feb. 2018 300-308Hirose, O., Kawaguchi, S., Tokunaga, T., Toyoshima, Y., Teramoto, T., Kuge,

S., Ishihara, T., Iino, Y., and Yoshida, R., SPF-CellTracker: TrackingMultiple Cells with Strongly-Correlated Moves Using a Spatial ParticleFilter; TCBB Nov.-Dec. 2018 1822-1831

Honig, B., see Bao, W., TCBB Sept.-Oct. 2018 1453-1460Hou, S., see Liu, K., TCBB July-Aug. 2018 1107-1110Hou, Y., see Cheng, X., TCBB July-Aug. 2018 1111-1121Hsiao, T., see Chiu, Y., TCBB Nov.-Dec. 2018 1754-1764Hu, B., Li, X., Sun, S., and Ratcliffe, M., Attention Recognition in EEG-Based

Affective Learning Research Using CFS+KNN Algorithm; TCBB Jan.-Feb. 2018 38-45

Hu, B., Dai, Y., Su, Y., Moore, P., Zhang, X., Mao, C., Chen, J., and Xu, L.,Feature Selection for Optimized High-Dimensional Biomedical DataUsing an Improved Shuffled Frog Leaping Algorithm; TCBB Nov.-Dec.2018 1765-1773

Hu, B., see Liu, J., TCBB Sept.-Oct. 2018 1649-1659Hu, D., see Yuan, L., TCBB March-April 2018 551-561



Hu, M., Li, W., and Liang, H., A Copula-Based Granger Causality Measurefor the Analysis of Neural Spike Train Data; TCBB March-April 2018562-569

Hu, S., see Zhou, X., TCBB May -June 2018 802-812Hu, W., see Deng, S., TCBB Sept.-Oct. 2018 1480-1491Hu, X., see Xu, T., TCBB Nov.-Dec. 2018 2079-2085Hua, J., see Karbalayghareh, A., TCBB Jan.-Feb. 2018 68-82Huang, D., see Zhang, H., TCBB Nov.-Dec. 2018 1810-1820Huang, D., see Zhu, L., TCBB May -June 2018 913-925Huang, D., see Liang, X., TCBB May -June 2018 1016-1021Huang, D., see Bao, W., TCBB Sept.-Oct. 2018 1453-1460Huang, D., Bevilacqua, V., and Gromiha, M.M., Guest Editorial for Special

Section on the 12th International Conference on Intelligent Computing(ICIC); TCBB Sept.-Oct. 2018 1433-1435

Huang, H., see Cheng, X., TCBB July-Aug. 2018 1111-1121Huang, H., see Nguyen, N., TCBB Sept.-Oct. 2018 1625-1635Huang, J., see Tian, T., TCBB Nov.-Dec. 2018 1752-1753Huang, J., Gong, M., and Ma, L., A Global Network Alignment Method Using

Discrete Particle Swarm Optimization; TCBB May -June 2018 705-718Huang, W., see Luo, J., TCBB Jan.-Feb. 2018 309-315Huang, X., see Zhang, L., TCBB March-April 2018 570-580Huang, Y., see Cui, X., TCBB March-April 2018 526-534Hubaux, J., see Raisaro, J.L., TCBB Sept.-Oct. 2018 1413-1426Hujdurovi�c, A., Ka�car, U., Milani�c, M., Ries, B., and Tomescu, A.I., Com-

plexity and Algorithms for Finding a Perfect Phylogeny from MixedTumor Samples; TCBB Jan.-Feb. 2018 96-108

Humbert, M., see Backes, M., TCBB Sept.-Oct. 2018 1405-1412Huson, D.H., and Linz, S., Autumn Algorithm—Computation of Hybridiza-

tion Networks for Realistic Phylogenetic Trees; TCBB March-April 2018398-410

Huster, D., see Anders, G., TCBB Jan.-Feb. 2018 300-308

I

Iglesias, A., G�alvez, A., and Avila, A., Immunological Approach for FullNURBS Reconstruction of Outline Curves from Noisy Data Points inMedical Imaging; TCBB Nov.-Dec. 2018 1929-1942

Iino, Y., see Hirose, O., TCBB Nov.-Dec. 2018 1822-1831Ikram, N., Qadir, M.A., and Afzal, M.T., Investigating Correlation between

Protein Sequence Similarity and Semantic Similarity Using GeneOntology Annotations; TCBB May -June 2018 905-912

Inostroza-Ponta, M., see Correa, L., TCBB May -June 2018 690-704Ironi, L., and Lanzarone, E., A Model-Based Tool for the Analysis and Design

of Gene Regulatory Networks; TCBB July-Aug. 2018 1301-1314Ishihara, T., see Hirose, O., TCBB Nov.-Dec. 2018 1822-1831Ismail, H.D., Saigo, H., and KC, D.B., RF-NR: Random Forest Based

Approach for Improved Classification of Nuclear Receptors; TCBB Nov.-Dec. 2018 1844-1852

Ivanov, I., see Knight, J.M., TCBB March-April 2018 484-493Izawa, T., see Patra, P., TCBB July-Aug. 2018 1270-1283

J

Jacquemont, N., see Raisaro, J.L., TCBB Sept.-Oct. 2018 1413-1426Jafari, N., see Deznabi, I., TCBB July-Aug. 2018 1333-1343Jakubowski, R., see Rydzewski, J., TCBB May -June 2018 732-739Jamil, H.M., Optimizing Phylogenetic Queries for Performance; TCBB Sept.-

Oct. 2018 1692-1705Jang, D., see Shin, M., TCBB March-April 2018 432-440Janga, S.C., see Hashemikhabir, S., TCBB July-Aug. 2018 1259-1269Janga, S.C., seeMilenkovi�c, T., TCBB July-Aug. 2018 1229-1230Jansson, J., Rajaby, R., Shen, C., and Sung, W., Algorithms for the Majority

Rule (+) Consensus Tree and the Frequency Difference Consensus Tree;TCBB Jan.-Feb. 2018 15-26

Jeong, H., see Ghaffari, N., TCBB March-April 2018 494-505Jetten, L., and van Iersel, L., Nonbinary Tree-Based Phylogenetic Networks;

TCBB Jan.-Feb. 2018 205-217Ji, X., see Fan, X., TCBB July-Aug. 2018 1092Jiang, N., Rong, W., Nie, Y., Shen, Y., and Xiong, Z., Biological Event

Trigger Identification with Noise Contrastive Estimation; TCBB Sept.-Oct. 2018 1549-1559

Jiang, R., see Fan, X., TCBB July-Aug. 2018 1092Jiang, X., see Ayday, E., TCBB Sept.-Oct. 2018 1403-1404

Jiao, H., Shi, M., Shen, Q., Zhu, J., and Shi, P., Filter Design with Adaptationto Time-Delay Parameters for Genetic Regulatory Networks; TCBB Jan.-Feb. 2018 323-329

Jiao, H., Zhang, L., Shen, Q., Zhu, J., and Shi, P., Robust Gene Circuit ControlDesign for Time-Delayed Genetic Regulatory Networks Without SUMRegulatory Logic; TCBB Nov.-Dec. 2018 2086-2093

Johnson, C.D., see Ghaffari, N., TCBB March-April 2018 494-505Jones, J., see Al-Ouran, R., TCBB July-Aug. 2018 1290-1300Joveini, M.B.Z., and Sadri, J., Application of Fractal Theory on Motifs

Counting in Biological Networks; TCBB March-April 2018 613-623Juedes, D., see Al-Ouran, R., TCBB July-Aug. 2018 1290-1300

K

Kacar, U., see Hujdurovi�c, A., TCBB Jan.-Feb. 2018 96-108Kahveci, T., see Alim, M.A., TCBB July-Aug. 2018 1079-1091Kalita, J., see Elmsallati, A., TCBB Jan.-Feb. 2018 330-336Kamm, L., see Bogdanov, D., TCBB Sept.-Oct. 2018 1427-1432Kandhavelu, M., seeMartins, D.P., TCBB Nov.-Dec. 2018 2017-2027Kang, J., see Zhao, Y., TCBB March-April 2018 537-550Kanhaiya, K., see Czeizler, E., TCBB July-Aug. 2018 1217-1228Karbalayghareh, A., Braga-Neto, U., Hua, J., and Dougherty, E.R., Classifi-

cation of State Trajectories in Gene Regulatory Networks; TCBB Jan.-Feb. 2018 68-82

Karn, M., see Awdeh, A., TCBB May -June 2018 878-891Karthikeyan, M., see Vyas, R., TCBB Jan.-Feb. 2018 27-37Kas, A., seeMatsen, F.A., TCBB Jan.-Feb. 2018 343-349Kawaguchi, S., see Hirose, O., TCBB Nov.-Dec. 2018 1822-1831KC, D.B., see Ismail, H.D., TCBB Nov.-Dec. 2018 1844-1852Khalid, Z., and Sezerman, O.U., Prediction of HIV Drug Resistance by Com-

bining Sequence and Structural Properties; TCBBMay -June 2018 966-973Khalifa, A., see Hamad, S., TCBB Sept.-Oct. 2018 1605-1610Khan, I.K., see Yerneni, S., TCBB July-Aug. 2018 1247-1258Khan, S., Naseem, I., Togneri, R., and Bennamoun, M., RAFP-Pred: Robust

Prediction of Antifreeze Proteins Using Localized Analysis of n-PeptideCompositions; TCBB Jan.-Feb. 2018 244-250

Kihara, D., see Yerneni, S., TCBB July-Aug. 2018 1247-1258Kim, H., Choi, S., and Park, S., GSEH: A Novel Approach to Select Prostate

Cancer-Associated Genes Using Gene Expression Heterogeneity; TCBBJan.-Feb. 2018 129-146

Kim, M., Zhang, H., Woloshuk, C., Shim, W., and Yoon, B., ComputationalPrediction of Pathogenic Network Modules in Fusarium verticillioides;TCBB March-April 2018 506-515

Kim, S., Editorial for Selected Papers of a Joint Conferences, Genome Infor-matics Workshop/International Conference on Bioinformatics (GIW/InCoB) 2015; TCBB Nov.-Dec. 2018 1821

Kimber, M., see Zamanighomi, M., TCBB July-Aug. 2018 1093-1106Klimentova, X., see Ushakov, A.V., TCBB Jan.-Feb. 2018 46-59Knight, J.M., Ivanov, I., Triff, K., Chapkin, R.S., and Dougherty, E.R.,

Detecting Multivariate Gene Interactions in RNA-Seq Data Using Opti-mal Bayesian Classification; TCBB March-April 2018 484-493

Kong, Y., see Liu, J., TCBB Sept.-Oct. 2018 1500-1512Konvalinka, M., seeMatsen, F.A., TCBB Jan.-Feb. 2018 343-349Koyuturk, M., see Qiao, S., TCBB July-Aug. 2018 1052-1065Kremer, S.C., seeMa, E.Y.T., TCBB Jan.-Feb. 2018 191-204Krishna, A., see Uppu, S., TCBB March-April 2018 599-612Kronzer, A., seeWang, H., TCBB Nov.-Dec. 2018 1968-1978Kuge, S., see Hirose, O., TCBB Nov.-Dec. 2018 1822-1831Kulandaisamy, A., Srivastava, A., Kumar, P., Nagarajan, R., Priya, S.B., and

Gromiha, M.M., Identification and Analysis of Key Residues in Protein–RNA Complexes; TCBB Sept.-Oct. 2018 1436-1444

Kulkarni, B.D., see Vyas, R., TCBB Jan.-Feb. 2018 27-37Kumar, P., see Kulandaisamy, A., TCBB Sept.-Oct. 2018 1436-1444Kundu, M., see Dutta, P., TCBB May -June 2018 839-849

L

Lacey, M.R., seeMeyer, K.N., TCBB July-Aug. 2018 1379-1389Lafond, M., Chauve, C., El-Mabrouk, N., and Ouangraoua, A., Gene Tree

Construction and Correction Using SuperTree and Reconciliation; TCBBSept.-Oct. 2018 1560-1570

Lan, W., Wang, J., Li, M., Liu, J., Wu, F., and Pan, Y., Predicting MicroRNA-Disease Associations Based on Improved MicroRNA and DiseaseSimilarities; TCBB Nov.-Dec. 2018 1774-1782



Lan, W., see Liu, J., TCBB March-April 2018 624-632Lanzarone, E., see Ironi, L., TCBB July-Aug. 2018 1301-1314Laur, S., see Bogdanov, D., TCBB Sept.-Oct. 2018 1427-1432Lawhorn, M., see Davidson, R., TCBB May -June 2018 1010-1015Leale, G., Bay�a, A.E., Milone, D.H., Granitto, P.M., and Stegmayer, G., Infer-

ring Unknown Biological Function by Integration of GO Annotations andGene Expression Data; TCBB Jan.-Feb. 2018 168-180

Lee, B., see Park, S., TCBB March-April 2018 441-451Lee, D., see Shin, M., TCBB March-April 2018 432-440Lee, E., see Zhang, L., TCBB March-April 2018 570-580Lee, K.H., see Shin, M., TCBB March-April 2018 432-440Lee, W., Park, B., and Han, K., Sequence-Based Prediction of Putative Tran-

scription Factor Binding Sites in DNA Sequences of Any Length; TCBBSept.-Oct. 2018 1461-1469

Lehtonen, R., see Liu, C., TCBB May -June 2018 1022-1027Leinweber, M., Fober, T., and Freisleben, B., GPU-Based Point Cloud Super-

positioning for Structural Comparisons of Protein Binding Sites; TCBBMay -June 2018 740-752

Lemarchand, L., see Lin, C., TCBB March-April 2018 377-386Lemnian, I., see Hedtke, I., TCBB March-April 2018 364-376Lewis, M.M., see Zhang, L., TCBB March-April 2018 570-580Li, J., Dong, W., and Meng, D., Grouped Gene Selection of Cancer via Adap-

tive Sparse Group Lasso Based on Conditional Mutual Information;TCBB Nov.-Dec. 2018 2028-2038

Li, J., Nagamochi, H., and Akutsu, T., Enumerating Substituted Benzene Iso-mers of Tree-Like Chemical Graphs; TCBB March-April 2018 633-646

Li, J., Zhang, W., and Li, X., 3D Genome Reconstruction with ShRec3D+ andHi-C Data; TCBB March-April 2018 460-468

Li, L., see Alazmi, M., TCBB Nov.-Dec. 2018 1999-2008Li, L., see He, X., TCBB July-Aug. 2018 1325-1332Li, M., see Lan, W., TCBB Nov.-Dec. 2018 1774-1782Li, M., see Liu, J., TCBB March-April 2018 624-632Li, Q., see Zhou, X., TCBB May -June 2018 802-812Li, S., see Ramalho, R.F., TCBB July-Aug. 2018 1284-1289Li, S.C., seeWang, L., TCBB Sept.-Oct. 2018 1513-1514Li, W., see Hu, M., TCBB March-April 2018 562-569Li, X., see Hu, B., TCBB Jan.-Feb. 2018 38-45Li, X., see Gao, C., TCBB Nov.-Dec. 2018 1916-1928Li, X., see Li, J., TCBB March-April 2018 460-468Li, X., and Wong, K., A Comparative Study for Identifying the Chromosome-

Wide Spatial Clusters from High-Throughput Chromatin ConformationCapture Data; TCBB May -June 2018 774-787

Li, Y., see Zhang, W., TCBB Jan.-Feb. 2018 109-116Li, Y., see Tang, Q., TCBB Nov.-Dec. 2018 1943-1950Li, Y., see Zhang, W., TCBB May -June 2018 1035Li, Y., see Xie, Q., TCBB July-Aug. 2018 1344-1350Li, Y., and Zhuang, Y., fmpRPMF: AWeb Implementation for Protein Identifica-

tion byRobust PeptideMass Fingerprinting; TCBB Sept.-Oct. 2018 1728-1731Liang, H., see Hu, M., TCBB March-April 2018 562-569Liang, M., see Gao, C., TCBB Nov.-Dec. 2018 1916-1928Liang, X., Zhu, L., and Huang, D., Optimization of Gene Set Annotations Using

Robust Trace-NormMultitask Learning; TCBBMay -June 2018 1016-1021Libeskind-Hadas, R., seeMa, W., TCBB March-April 2018 411-421Lieber, R.L., seeMukund, K., TCBB Nov.-Dec. 2018 2009-2016Lim, H., seeWang, A., TCBB Nov.-Dec. 2018 1960-1967Lin, C., Lemarchand, L., Euler, R., and Sparkes, I., Modeling the Geometry

and Dynamics of the Endoplasmic Reticulum Network; TCBB March-April 2018 377-386

Lin, H., see Xu, B., TCBB Nov.-Dec. 2018 1797-1809Lin, X., and Zhang, X., Prediction of Hot Regions in PPIs Based on Improved

Local Community Structure Detecting; TCBB Sept.-Oct. 2018 1470-1479Lin, Y., see Xu, B., TCBB Nov.-Dec. 2018 1797-1809Lin, Y., see Yu, C., TCBB Sept.-Oct. 2018 1683-1691Lin, Z., see Zhou, X., TCBB May -June 2018 802-812Linz, S., see Huson, D.H., TCBB March-April 2018 398-410Lio, P., see Bartocci, E., TCBB July-Aug. 2018 1122-1123Lio’, P., seeMartins, D.P., TCBB Nov.-Dec. 2018 2017-2027Liu, C., Lehtonen, R., and Hautaniemi, S., PerPAS: Topology-Based Single

Sample Pathway Analysis Method; TCBB May -June 2018 1022-1027Liu, H., see Cheng, Z., TCBB Nov.-Dec. 2018 1832-1843Liu, H., see Papamichail, D., TCBB March-April 2018 452-459Liu, H., see Cheng, X., TCBB July-Aug. 2018 1111-1121Liu, J., see Niu, B., TCBB Nov.-Dec. 2018 1865-1876Liu, J., see Lan, W., TCBB Nov.-Dec. 2018 1774-1782Liu, J., Li, M., Lan, W., Wu, F., Pan, Y., and Wang, J., Classification of Alz-

heimer’s Disease Using Whole Brain Hierarchical Network; TCBBMarch-April 2018 624-632

Liu, J., seeMin, W., TCBB May -June 2018 944-953Liu, J., Wang, D., Gao, Y., Zheng, C., Xu, Y., and Yu, J., Regularized Non-

Negative Matrix Factorization for Identifying Differentially ExpressedGenes and Clustering Samples: A Survey; TCBB May -June 2018 974-987

Liu, J., Cheng, Y., Wang, X., Cui, X., Kong, Y., and Du, J., LowRank SubspaceClustering via Discrete Constraint and Hypergraph Regularization forTumorMolecular Pattern Discovery; TCBB Sept.-Oct. 2018 1500-1512

Liu, J., Wang, J., Tang, Z., Hu, B., Wu, F., and Pan, Y., Improving Alzheim-er’s Disease Classification by Combining Multiple Measures; TCBBSept.-Oct. 2018 1649-1659

Liu, K., Hou, S., Dai, J., and Sun, Z., PyMut: AWeb Tool for Overlapping GeneLoss-of-FunctionMutation Design; TCBB July-Aug. 2018 1107-1110

Liu, M., see Shao, W., TCBB May -June 2018 828-838Liu, M., see Chen, S., TCBB Sept.-Oct. 2018 1718-1722Liu, M., He, Y., Qian, W., Wei, Y., and Liu, X., Cell Population Tracking in a

Honeycomb Structure Using an IMM Filter Based 3D Local GraphMatching Model; TCBB Sept.-Oct. 2018 1706-1717

Liu, S., see Alves, P., TCBB May -June 2018 926-933Liu, T., see Zhang, J., TCBB March-April 2018 535-536Liu, X., see Xie, Q., TCBB July-Aug. 2018 1344-1350Liu, X., see Liu, M., TCBB Sept.-Oct. 2018 1706-1717Liu, Y., see Niu, B., TCBB Nov.-Dec. 2018 1865-1876Liu, Y., see Xie, Q., TCBB July-Aug. 2018 1344-1350Liu, Y., see He, X., TCBB July-Aug. 2018 1325-1332Long, Q., see Zhao, Y., TCBB March-April 2018 537-550Long, R., see Chen, S., TCBB Sept.-Oct. 2018 1718-1722Long, T., see Singh, R., TCBB March-April 2018 469-481L€u, Q., seeWu, H., TCBB Sept.-Oct. 2018 1445-1452Lu, W., see Tamura, T., TCBB Nov.-Dec. 2018 1853-1862Luhmann, N., Chauve, C., Stoye, J., and Wittler, R., Scaffolding of Ancient

Contigs and Ancestral Reconstruction in a Phylogenetic Framework;TCBB Nov.-Dec. 2018 2094-2100

Luo, J., Huang,W., andCao, B., ANovel Approach to Identify themiRNA-mRNACausal RegulatoryModules in Cancer; TCBB Jan.-Feb. 2018 309-315

Luo, S., see Guo, Y., TCBB Nov.-Dec. 2018 1891-1903L�y, K.Q., see Feret, J., TCBB July-Aug. 2018 1124-1137

M

Ma, E.Y.T., Ratnasingham, S., and Kremer, S.C., Machine Learned Replacementof N-Labels for Basecalled Sequences in DNA Barcoding; TCBB Jan.-Feb.2018 191-204

Ma, L., see Huang, J., TCBB May -June 2018 705-718Ma, W., Smirnov, D., Forman, J., Schweickart, A., Slocum, C., Srinivasan, S.,

and Libeskind-Hadas, R., DTL-RnB: Algorithms and Tools for Summariz-ing the Space of DTL Reconciliations; TCBBMarch-April 2018 411-421

Ma, X., Tang, W., Wang, P., Guo, X., and Gao, L., Extracting Stage-Specificand Dynamic Modules Through Analyzing Multiple Networks Associatedwith Cancer Progression; TCBB March-April 2018 647-658

Ma, X., Sun, P., and Qin, G., Identifying Condition-Specific Modules by Clus-tering Multiple Networks; TCBB Sept.-Oct. 2018 1636-1648

Ma, Y., see Xu, B., TCBB Nov.-Dec. 2018 1797-1809Ma, Z., see Zhang, J., TCBB Jan.-Feb. 2018 147-156Machado, V., see Papamichail, D., TCBB March-April 2018 452-459Malin, B., see Ayday, E., TCBB Sept.-Oct. 2018 1403-1404Mallik, S., see Bandyopadhyay, S., TCBB March-April 2018 673-687Mao, C., see Hu, B., TCBB Nov.-Dec. 2018 1765-1773Mao, Y., see Guo, W., TCBB Nov.-Dec. 2018 1904-1915Margaliot, M., see Zarai, Y., TCBB July-Aug. 2018 1351-1364Martin, M.J., see Gonz�alez-Dom�ınguez, J., TCBB Sept.-Oct. 2018 1732-1737Martin-Vide, C., see Dediu, A., TCBB March-April 2018 350-351Martinez, T., see Fages, F., TCBB July-Aug. 2018 1138-1151Martins, D.P., Barros, M.T., Pierobon, M., Kandhavelu, M., Lio’, P., and

Balasubramaniam, S., Computational Models for Trapping Ebola VirusUsing Engineered Bacteria; TCBB Nov.-Dec. 2018 2017-2027

Masseroli, M., see Chicco, D., TCBB May -June 2018 954-965Matsen, F.A., Billey, S.C., Kas, A., and Konvalinka,M., Tanglegrams: A Reduc-

tion Tool forMathematical Phylogenetics; TCBB Jan.-Feb. 2018 343-349Maulik, U., see Ray, S., TCBB May -June 2018 869-877Maximova, T., Plaku, E., and Shehu, A., Structure-Guided Protein Transition

Modeling with a Probabilistic Roadmap Algorithm; TCBB Nov.-Dec.2018 1783-1796

Meng, D., see Li, J., TCBB Nov.-Dec. 2018 2028-2038Meng, J., see Cui, X., TCBB March-April 2018 526-534Meng, J., see He, X., TCBB July-Aug. 2018 1325-1332



Meyer, K.N., and Lacey, M.R., Modeling Methylation Patterns with LongRead Sequencing Data; TCBB July-Aug. 2018 1379-1389

Middendorf, M., see Hartmann, T., TCBB Jan.-Feb. 2018 83-95Middendorf, M., see Hartmann, T., TCBB Sept.-Oct. 2018 1585-1593Milanic, M., see Hujdurovi�c, A., TCBB Jan.-Feb. 2018 96-108Milenkovi�c, T., and Janga, S.C., Great Lakes Bioinformatics Conference

(GLBIO) 2015 Special Section Editorial; TCBB July-Aug. 2018 1229-1230Milenkovi�c, T., see Vijayan, V., TCBB Sept.-Oct. 2018 1669-1682Milone, D.H., see Leale, G., TCBB Jan.-Feb. 2018 168-180Min, W., Liu, J., and Zhang, S., Network-Regularized Sparse Logistic Regres-

sion Models for Clinical Risk Prediction and Biomarker Discovery; TCBBMay -June 2018 944-953

Mirarab, S., see Shekhar, S., TCBB Sept.-Oct. 2018 1738-1747Mizera, A., Pang, J., Su, C., and Yuan, Q., ASSA-PBN: A Toolbox for

Probabilistic Boolean Networks; TCBB July-Aug. 2018 1203-1216Mizera, A., Pang, J., and Yuan, Q., Reviving the Two-State Markov Chain

Approach; TCBB Sept.-Oct. 2018 1525-1537Mobayen, M., see Deznabi, I., TCBB July-Aug. 2018 1333-1343Modarressi, M.H., see Sedaghat, N., TCBB Sept.-Oct. 2018 1594-1604Mohamad, M.S., see Fotoohifiroozabadi, S., TCBB May -June 2018 934-943Mohsenizadeh, D.N., Dehghannasiri, R., and Dougherty, E.R., Optimal

Objective-Based Experimental Design for Uncertain Dynamical GeneNetworks with Experimental Error; TCBB Jan.-Feb. 2018 218-230

Monteiro, M., Fonseca, A.C., Freitas, A.T., Pinho e Melo, T., Francisco, A.P.,Ferro, J.M., and Oliveira, A.L., Using Machine Learning to Improve thePrediction of Functional Outcome in Ischemic Stroke Patients; TCBBNov.-Dec. 2018 1953-1959

Moore, P., see Hu, B., TCBB Nov.-Dec. 2018 1765-1773Mooser, V., see Raisaro, J.L., TCBB Sept.-Oct. 2018 1413-1426Moreno, P.A., see Duarte-Sanchez, J.E., TCBB Sept.-Oct. 2018 1611-1624Msalati, A., see Elmsallati, A., TCBB Jan.-Feb. 2018 330-336Mu, C., Dittrich, P., Parker, D., and Rowe, J.E., Organisation-Oriented Coarse

Graining and Refinement of Stochastic Reaction Networks; TCBB July-Aug. 2018 1152-1166

Mukund, K., Ward, S.R., Lieber, R.L., and Subramaniam, S., Co-ExpressionNetwork Approach to Studying the Effects of Botulinum Neurotoxin-A;TCBB Nov.-Dec. 2018 2009-2016

Muller, L., see Anders, G., TCBB Jan.-Feb. 2018 300-308M€uller-Hannemann, M., see Hedtke, I., TCBB March-April 2018 364-376Murali, T.M., Guest Editorial; TCBB July-Aug. 2018 1036Mykowiecka, A., Szczesny, P., and G�orecki, P., Inferring Gene-Species Assign-

ments in the Presence of Horizontal Gene Transfer; TCBB Sept.-Oct. 20181571-1578

N

Nagamochi, H., see Li, J., TCBB March-April 2018 633-646Nagarajan, R., see Kulandaisamy, A., TCBB Sept.-Oct. 2018 1436-1444Naik, A., see Al-Ouran, R., TCBB July-Aug. 2018 1290-1300Nam, H., see Shin, M., TCBB March-April 2018 432-440Nandi, A.K., see Bao, W., TCBB Sept.-Oct. 2018 1453-1460Naseem, I., see Khan, S., TCBB Jan.-Feb. 2018 244-250Nevalainen, J., see Pesonen, M., TCBB May -June 2018 760-773Neylon, M.T., see Yue, Z., TCBB Nov.-Dec. 2018 1991-1998Nguifo, E.M., see Djeddi, W.E., TCBB Nov.-Dec. 2018 2060-2066Nguyen, N., Vo, A., Sun, H., and Huang, H., Heavy-Tailed Noise Suppression

and Derivative Wavelet Scalogram for Detecting DNA Copy NumberAberrations; TCBB Sept.-Oct. 2018 1625-1635

Nguyen, T., see Yue, Z., TCBB Nov.-Dec. 2018 1991-1998Nicosia, G., see Rydzewski, J., TCBB May -June 2018 732-739Nie, Y., see Cheng, X., TCBB July-Aug. 2018 1111-1121Nie, Y., see Jiang, N., TCBB Sept.-Oct. 2018 1549-1559Niu, B., Liu, J., Wu, T., Chu, X., Wang, Z., and Liu, Y., Coevolutionary Struc-

ture-Redesigned-Based Bacterial Foraging Optimization; TCBB Nov.-Dec. 2018 1865-1876

Noor, A., Ahmad, A., and Serpedin, E., SparseNCA: Sparse Network Compo-nent Analysis for Recovering Transcription Factor Activities with Incom-plete Prior Information; TCBB March-April 2018 387-395

Nowak, W., see Rydzewski, J., TCBB May -June 2018 732-739

O

Oliveira, A.L., seeMonteiro, M., TCBB Nov.-Dec. 2018 1953-1959Oliveira, M.C.F.d., see Borges, V.R.P., TCBB Jan.-Feb. 2018 257-270Ornamenti, M., see Pizzi, C., TCBB Jan.-Feb. 2018 117-128Ou-Yang, L., see Xu, T., TCBB Nov.-Dec. 2018 2079-2085

Ouangraoua, A., see Lafond, M., TCBB Sept.-Oct. 2018 1560-1570€Ozsoyoglu, M.Z., see Qiao, S., TCBB July-Aug. 2018 1052-1065

P

Pal, J.K., Ray, S.S., Cho, S., and Pal, S.K., Fuzzy-Rough Entropy Measureand Histogram Based Patient Selection for miRNA Ranking in Cancer;TCBB March-April 2018 659-672

Pal, R., see Ghosh, B.K., TCBB March-April 2018 482-483Pal, S.K., see Pal, J.K., TCBB March-April 2018 659-672Palluzzi, F., see Chicco, D., TCBB May -June 2018 954-965Pan, Y., see Lan, W., TCBB Nov.-Dec. 2018 1774-1782Pan, Y., see Liu, J., TCBB March-April 2018 624-632Pan, Y., see Liu, J., TCBB Sept.-Oct. 2018 1649-1659Pang, J., seeMizera, A., TCBB July-Aug. 2018 1203-1216Pang, J., seeMizera, A., TCBB Sept.-Oct. 2018 1525-1537Panigada, T., see Anders, G., TCBB Jan.-Feb. 2018 300-308Paoletti, N., see Bartocci, E., TCBB July-Aug. 2018 1122-1123Papamichail, D., Liu, H., Machado, V., Gould, N., Coleman, J.R., and Papa-

michail, G., Codon Context Optimization in Synthetic Gene Design;TCBB March-April 2018 452-459

Papamichail, G., see Papamichail, D., TCBB March-April 2018 452-459Pappalardo, F., see Russo, G., TCBB Sept.-Oct. 2018 1492-1499Parida, L., see Pizzi, C., TCBB Jan.-Feb. 2018 117-128Park, B., see Lee, W., TCBB Sept.-Oct. 2018 1461-1469Park, S., see Kim, H., TCBB Jan.-Feb. 2018 129-146Park, S., Choi, H., Lee, B., Chun, J., Won, J., and Yoon, S., hc-OTU: A Fast

and Accurate Method for Clustering Operational Taxonomic Units Basedon Homopolymer Compaction; TCBB March-April 2018 441-451

Parker, D., seeMu, C., TCBB July-Aug. 2018 1152-1166Paszek, J., and G�orecki, P., Efficient Algorithms for Genomic Duplication

Models; TCBB Sept.-Oct. 2018 1515-1524Patra, P., Izawa, T., and Pe~na-Castillo, L., REPA: Applying Pathway Analysis

to Genome-Wide Transcription Factor Binding Data; TCBB July-Aug.2018 1270-1283

Paulev�e, L., Reduction of Qualitative Models of Biological Networks forTransient Dynamics Analysis; TCBB July-Aug. 2018 1167-1179

Pease, J.B., and Rosenzweig, B.K., Encoding Data Using Biological Princi-ples: The Multisample Variant Format for Phylogenomics and PopulationGenomics; TCBB July-Aug. 2018 1231-1238

Pekergin, F., see Avcu, N., TCBB May -June 2018 813-827Pekergin, N., see Avcu, N., TCBB May -June 2018 813-827Pe~na-Castillo, L., see Patra, P., TCBB July-Aug. 2018 1270-1283Peng, X., Tang, Y., He, W., Du, W., and Qian, F., A Just-in-Time Learning

Based Monitoring and Classification Method for Hyper/HypocalcemiaDiagnosis; TCBB May -June 2018 788-801

Pennisi, M., see Russo, G., TCBB Sept.-Oct. 2018 1492-1499Perkins, T.J., see Awdeh, A., TCBB May -June 2018 878-891Pesonen, M., Nevalainen, J., Potter, S., Datta, S., and Datta, S., A Combined

PLS and Negative Binomial Regression Model for Inferring AssociationNetworks from Next-Generation Sequencing Count Data; TCBB May-June 2018 760-773

Pesquet, J., see Pirayre, A., TCBB May -June 2018 850-860Petre, I., see Czeizler, E., TCBB July-Aug. 2018 1217-1228Petzold, L., see Torshizi, A.D., TCBB May -June 2018 1028-1034Phenix, H., see Awdeh, A., TCBB May -June 2018 878-891Pierobon, M., seeMartins, D.P., TCBB Nov.-Dec. 2018 2017-2027Pinho e Melo, T., seeMonteiro, M., TCBB Nov.-Dec. 2018 1953-1959Pirayre, A., Couprie, C., Duval, L., and Pesquet, J., BRANE Clust: Cluster-

Assisted Gene Regulatory Network Inference Refinement; TCBB May-June 2018 850-860

Pizzi, C., Ornamenti, M., Spangaro, S., Rombo, S.E., and Parida, L., EfficientAlgorithms for Sequence Analysis with Entropic Profiles; TCBB Jan.-Feb. 2018 117-128

Plaku, E., seeMaximova, T., TCBB Nov.-Dec. 2018 1783-1796Poirier, C., Gosselin, B., and Fortier, P., DNA Assembly with De Bruijn

Graphs Using an FPGA Platform; TCBB May -June 2018 1003-1009Potter, S., see Pesonen, M., TCBB May -June 2018 760-773Pradervand, S., see Raisaro, J.L., TCBB Sept.-Oct. 2018 1413-1426Priya, S.B., see Kulandaisamy, A., TCBB Sept.-Oct. 2018 1436-1444

Q

Qadir, M.A., see Ikram, N., TCBB May -June 2018 905-912Qi, Y., see Xia, C., TCBB July-Aug. 2018 1315-1324



Qian, F., see Peng, X., TCBB May -June 2018 788-801Qian, W., seeWang, Y., TCBB Jan.-Feb. 2018 1-14Qian, W., see Liu, M., TCBB Sept.-Oct. 2018 1706-1717Qiao, S., Koyuturk, M., and €Ozsoyoglu, M.Z., Querying of Disparate Associa-

tion and Interaction Data in Biomedical Applications; TCBB July-Aug.2018 1052-1065

Qin, G., seeMa, X., TCBB Sept.-Oct. 2018 1636-1648

R

Radivojac, P., see Ramalho, R.F., TCBB July-Aug. 2018 1284-1289Raisaro, J.L., Choi, G., Pradervand, S., Colsenet, R., Jacquemont, N., Rosat,

N., Mooser, V., and Hubaux, J., Protecting Privacy and Security of Geno-mic Data in i2b2 with Homomorphic Encryption and Differential Privacy;TCBB Sept.-Oct. 2018 1413-1426

Rajaby, R., see Jansson, J., TCBB Jan.-Feb. 2018 15-26Ramalho, R.F., Li, S., Radivojac, P., and Hahn, M.W., Proteomic Evidence

for In-Frame and Out-of-Frame Alternatively Spliced Isoforms in Humanand Mouse; TCBB July-Aug. 2018 1284-1289

Rao, M.K., see Cui, X., TCBB March-April 2018 526-534Raouf, S.A., see Hashem, S., TCBB May -June 2018 861-868Ratcliffe, M., see Hu, B., TCBB Jan.-Feb. 2018 38-45Ratliff, T., see Yue, Z., TCBB Nov.-Dec. 2018 1991-1998Ratnasingham, S., seeMa, E.Y.T., TCBB Jan.-Feb. 2018 191-204Ray, S., and Maulik, U., Discovering Perturbation of Modular Structure in

HIV Progression by Integrating Multiple Data Sources Through Non-Neg-ative Matrix Factorization; TCBB May -June 2018 869-877

Ray, S.S., see Pal, J.K., TCBB March-April 2018 659-672Ren, S., Shi, Y., Cai, M., and Xu, W., Influence of Airway Secretion on Air-

flow Dynamics of Mechanical Ventilated Respiratory System; TCBBSept.-Oct. 2018 1660-1668

Rhodes, J.A., see Allman, E.S., TCBB Jan.-Feb. 2018 337-342Ries, B., see Hujdurovi�c, A., TCBB Jan.-Feb. 2018 96-108Roch, S., see Shekhar, S., TCBB Sept.-Oct. 2018 1738-1747Rombo, S.E., see Pizzi, C., TCBB Jan.-Feb. 2018 117-128Rong, M., see Xu, B., TCBB Nov.-Dec. 2018 1877-1890Rong, W., see Jiang, N., TCBB Sept.-Oct. 2018 1549-1559Rosat, N., see Raisaro, J.L., TCBB Sept.-Oct. 2018 1413-1426Rosenblueth, D.A., see Fages, F., TCBB July-Aug. 2018 1138-1151Rosenzweig, B.K., see Pease, J.B., TCBB July-Aug. 2018 1231-1238Roth, A., Subramanian, S., and Ganapathiraju, M.K., Towards Extracting Sup-

porting Information About Predicted Protein-Protein Interactions; TCBBJuly-Aug. 2018 1239-1246

Roth, M.A., see Ghoshal, A., TCBB July-Aug. 2018 1037-1051Rowe, J.E., seeMu, C., TCBB July-Aug. 2018 1152-1166Rudie, K., see Behinaein, B., TCBB Jan.-Feb. 2018 231-243Rusinko, J., see Davidson, R., TCBB May -June 2018 1010-1015Russo, G., Pennisi, M., Boscarino, R., and Pappalardo, F., Continuous Petri

Nets and microRNA Analysis in Melanoma; TCBB Sept.-Oct. 2018 1492-1499

Rydzewski, J., Jakubowski, R., Nicosia, G., and Nowak, W., ConformationalSampling of a Biomolecular Rugged Energy Landscape; TCBB May-June 2018 732-739

S

Sadri, J., see Joveini, M.B.Z., TCBB March-April 2018 613-623Saigo, H., see Suryanto, C.H., TCBB Jan.-Feb. 2018 286-299Saigo, H., see Ismail, H.D., TCBB Nov.-Dec. 2018 1844-1852Samsonov, S.A., see Anders, G., TCBB Jan.-Feb. 2018 300-308Sangrar, W., see Behinaein, B., TCBB Jan.-Feb. 2018 231-243Sankoff, D., see Zhang, Y., TCBB Sept.-Oct. 2018 1579-1584Santos Reyes, J., see Handl, J., TCBB May -June 2018 688-689Sapin, E., De Jong, K.A., and Shehu, A., From Optimization to Mapping: An

Evolutionary Algorithm for Protein Energy Landscapes; TCBB May -June2018 719-731

Sato, J.R., Calebe Vidal, M., de Siqueira Santos, S., Brauer Massirer, K., andFujita, A., Complex Network Measures in Autism Spectrum Disorders;TCBB March-April 2018 581-587

Schmidt, R., see Al-Ouran, R., TCBB July-Aug. 2018 1290-1300Schweickart, A., seeMa, W., TCBB March-April 2018 411-421Sedaghat, N., Fathy, M., Modarressi, M.H., and Shojaie, A., Combining

Supervised and Unsupervised Learning for Improved miRNA Target Pre-diction; TCBB Sept.-Oct. 2018 1594-1604

Serpedin, E., see Noor, A., TCBB March-April 2018 387-395Sezerman, O.U., see Khalid, Z., TCBB May -June 2018 966-973Shao, W., Liu, M., Xu, Y., Shen, H., and Zhang, D., An Organelle Correlation-

Guided Feature Selection Approach for Classifying Multi-Label Subcellu-lar Bio-Images; TCBB May -June 2018 828-838

Sharan, R., see Hartmann, T., TCBB Sept.-Oct. 2018 1585-1593Shehu, A., seeMaximova, T., TCBB Nov.-Dec. 2018 1783-1796Shehu, A., see Sapin, E., TCBB May -June 2018 719-731Shehu, A., see Handl, J., TCBB May -June 2018 688-689Shekhar, S., Roch, S., and Mirarab, S., Species Tree Estimation Using

ASTRAL: How Many Genes Are Enough?; TCBB Sept.-Oct. 2018 1738-1747

Shen, B., see Yu, C., TCBB Sept.-Oct. 2018 1683-1691Shen, C., see Jansson, J., TCBB Jan.-Feb. 2018 15-26Shen, C., see Chen, Z., TCBB March-April 2018 422-431Shen, H., see Shao, W., TCBB May -June 2018 828-838Shen, Q., see Jiao, H., TCBB Jan.-Feb. 2018 323-329Shen, Q., see Jiao, H., TCBB Nov.-Dec. 2018 2086-2093Shen, X., see Backes, M., TCBB Sept.-Oct. 2018 1405-1412Shen, Y., see Jiang, N., TCBB Sept.-Oct. 2018 1549-1559Shi, M., see Jiao, H., TCBB Jan.-Feb. 2018 323-329Shi, P., see Jiao, H., TCBB Jan.-Feb. 2018 323-329Shi, P., see Ali, M.S., TCBB Jan.-Feb. 2018 271-285Shi, P., see Jiao, H., TCBB Nov.-Dec. 2018 2086-2093Shi, Y., see Tan, Y., TCBB Nov.-Dec. 2018 1863-1864Shi, Y., see Zhou, J., TCBB May -June 2018 753-759Shi, Y., see Ren, S., TCBB Sept.-Oct. 2018 1660-1668Shim, W., see Kim, M., TCBB March-April 2018 506-515Shin, M., Jang, D., Nam, H., Lee, K.H., and Lee, D., Predicting the Absorption

Potential of Chemical Compounds Through a Deep Learning Approach;TCBB March-April 2018 432-440

Shojaie, A., see Sedaghat, N., TCBB Sept.-Oct. 2018 1594-1604Shrestha, A.M.S., see Frith, M.C., TCBB Nov.-Dec. 2018 2067-2073Si, C., see Guo, W., TCBB Nov.-Dec. 2018 1904-1915Silva, T.G., see Borges, V.R.P., TCBB Jan.-Feb. 2018 257-270Singh, R., Beasley, R., Long, T., and Caffrey, C.R., Algorithmic Mapping and

Characterization of the Drug-Induced Phenotypic-Response Space of Par-asites Causing Schistosomiasis; TCBB March-April 2018 469-481

Slocum, C., seeMa, W., TCBB March-April 2018 411-421Smirnov, D., seeMa, W., TCBB March-April 2018 411-421Sokk, V., see Bogdanov, D., TCBB Sept.-Oct. 2018 1427-1432Soliman, S., see Fages, F., TCBB July-Aug. 2018 1138-1151Song, J., see Tamura, T., TCBB Nov.-Dec. 2018 1853-1862Song, S., see Gao, S., TCBB July-Aug. 2018 1365-1378Sontag, E.D., see Zarai, Y., TCBB July-Aug. 2018 1351-1364Spangaro, S., see Pizzi, C., TCBB Jan.-Feb. 2018 117-128Sparkes, I., see Lin, C., TCBB March-April 2018 377-386Srinivasan, S., seeMa, W., TCBB March-April 2018 411-421Srivastava, A., see Kulandaisamy, A., TCBB Sept.-Oct. 2018 1436-1444Stegmayer, G., see Leale, G., TCBB Jan.-Feb. 2018 168-180Sterling, N.W., see Zhang, L., TCBB March-April 2018 570-580Stoye, J., see Luhmann, N., TCBB Nov.-Dec. 2018 2094-2100Su, C., seeMizera, A., TCBB July-Aug. 2018 1203-1216Su, Y., see Hu, B., TCBB Nov.-Dec. 2018 1765-1773Subramaniam, S., seeMukund, K., TCBB Nov.-Dec. 2018 2009-2016Subramanian, S., see Roth, A., TCBB July-Aug. 2018 1239-1246Sun, H., see Nguyen, N., TCBB Sept.-Oct. 2018 1625-1635Sun, P., seeMa, X., TCBB Sept.-Oct. 2018 1636-1648Sun, S., see Hu, B., TCBB Jan.-Feb. 2018 38-45Sun, X., see Cheng, X., TCBB July-Aug. 2018 1111-1121Sun, Z., see Liu, K., TCBB July-Aug. 2018 1107-1110Sung, W., see Jansson, J., TCBB Jan.-Feb. 2018 15-26Suryanto, C.H., Saigo, H., and Fukui, K., Structural Class Classification of 3D

Protein Structure Based on Multi-View 2D Images; TCBB Jan.-Feb. 2018286-299

Szczesny, P., seeMykowiecka, A., TCBB Sept.-Oct. 2018 1571-1578

T

Taha, K., Inferring the Functions of Proteins from the Interrelationshipsbetween Functional Categories; TCBB Jan.-Feb. 2018 157-167

Tambe, S.S., see Vyas, R., TCBB Jan.-Feb. 2018 27-37Tamura, T., Lu, W., Song, J., and Akutsu, T., Computing Minimum Reaction

Modifications in a Boolean Metabolic Network; TCBB Nov.-Dec. 20181853-1862



Tan, Y., and Shi, Y., Special Section on Swarm-Based Algorithms andApplications in Computational Biology and Bioinformatics; TCBB Nov.-Dec. 2018 1863-1864

Tang, F., see Zhou, X., TCBB May -June 2018 802-812Tang, J., Tian, L., and Chen, Y.P., Guest Editorial for the 14th Asia Pacific

Bioinformatics Conference; TCBB March-April 2018 396-397Tang, Q., Ding, L., Yu, F., Zhang, Y., Li, Y., and Tu, H., Swarm Robots

Search for Multiple Targets Based on an Improved Grouping Strategy;TCBB Nov.-Dec. 2018 1943-1950

Tang, W., seeMa, X., TCBB March-April 2018 647-658Tang, Y., see Peng, X., TCBB May -June 2018 788-801Tang, Z., see Liu, J., TCBB Sept.-Oct. 2018 1649-1659Tastan, O., see Deznabi, I., TCBB July-Aug. 2018 1333-1343Teramoto, T., see Hirose, O., TCBB Nov.-Dec. 2018 1822-1831Thai, M.T., see Alim, M.A., TCBB July-Aug. 2018 1079-1091Theisgen, S., see Anders, G., TCBB Jan.-Feb. 2018 300-308Thiltges, J., see Ghaffari, N., TCBB March-April 2018 494-505Tian, L., see Tang, J., TCBB March-April 2018 396-397Tian, T., and Huang, J., Guest Editorial for Special Section on BIBM 2015;

TCBB Nov.-Dec. 2018 1752-1753Todo, Y., see Gao, S., TCBB July-Aug. 2018 1365-1378Togneri, R., see Khan, S., TCBB Jan.-Feb. 2018 244-250Tokunaga, T., see Hirose, O., TCBB Nov.-Dec. 2018 1822-1831Tomescu, A.I., see Hujdurovi�c, A., TCBB Jan.-Feb. 2018 96-108Torshizi, A.D., and Petzold, L., Sparse Pathway-Induced Dynamic Network

Biomarker Discovery for Early Warning Signal Detection in ComplexDiseases; TCBB May -June 2018 1028-1034

Toyoshima, Y., see Hirose, O., TCBB Nov.-Dec. 2018 1822-1831Triff, K., see Knight, J.M., TCBB March-April 2018 484-493Truong, Y., see Zhang, L., TCBB March-April 2018 570-580Tu, H., see Tang, Q., TCBB Nov.-Dec. 2018 1943-1950Tuller, T., see Zarai, Y., TCBB July-Aug. 2018 1351-1364

U

Uppu, S., Krishna, A., and Gopalan, R.P., A Review on Methods for DetectingSNP Interactions in High-Dimensional Genomic Data; TCBB March-April2018 599-612

Ushakov, A.V., Klimentova, X., and Vasilyev, I., Bi-level and Bi-objective p-Median Type Problems for Integrative Clustering: Application to Analysisof Cancer Gene-Expression and Drug-Response Data; TCBB Jan.-Feb.2018 46-59

V

Valtchev, P., see Halioui, A., TCBB Nov.-Dec. 2018 1979-1990van Iersel, L., see Jetten, L., TCBB Jan.-Feb. 2018 205-217Vasilyev, I., see Ushakov, A.V., TCBB Jan.-Feb. 2018 46-59Velasco-Medina, J., seeDuarte-Sanchez, J.E., TCBB Sept.-Oct. 2018 1611-1624Vieira, A.A.H., see Borges, V.R.P., TCBB Jan.-Feb. 2018 257-270Vijayan, V., and Milenkovi�c, T., Multiple Network Alignment via Multi-

MAGNA++; TCBB Sept.-Oct. 2018 1669-1682Villaverde, A.F., Becker, K., and Banga, J.R., PREMER: A Tool to Infer

Biological Networks; TCBB July-Aug. 2018 1193-1202Viswanath, N.C., Calculating the Expected Time to Eradicate HIV-1 Using a

Markov Chain; TCBB Jan.-Feb. 2018 60-67Vo, A., see Nguyen, N., TCBB Sept.-Oct. 2018 1625-1635Vyas, R., Bapat, S., Goel, P., Karthikeyan, M., Tambe, S.S., and Kulkarni,

B.D., Application of Genetic Programming (GP) Formalism for BuildingDisease Predictive Models from Protein-Protein Interactions (PPI) Data;TCBB Jan.-Feb. 2018 27-37

W

Wagner, D., see Zhang, L., TCBB March-April 2018 570-580Wang, A., Lim, H., Cheng, S., and Xie, L., ANTENNA, a Multi-Rank, Multi-

Layered Recommender System for Inferring Reliable Drug-Gene-DiseaseAssociations: Repurposing Diazoxide as a Targeted Anti-Cancer Therapy;TCBB Nov.-Dec. 2018 1960-1967

Wang, B., A New Efficient Algorithm for the Frequent Gene Team Problem;TCBB March-April 2018 588-598

Wang, B., Zheng, X., Zhou, S., Zhou, C., Wei, X., Zhang, Q., and Wei, Z.,Constructing DNA Barcode Sets Based on Particle Swarm Optimization;TCBB May -June 2018 999-1002

Wang, D., see Alves, P., TCBB May -June 2018 926-933Wang, D., see Liu, J., TCBB May -June 2018 974-987Wang, H., Cui, Z., Chen, Y., Avidan, M., Abdallah, A.B., and Kronzer, A.,

Predicting Hospital Readmission via Cost-Sensitive Deep Learning;TCBB Nov.-Dec. 2018 1968-1978

Wang, J., see Lan, W., TCBB Nov.-Dec. 2018 1774-1782Wang, J., see Xu, B., TCBB Nov.-Dec. 2018 1797-1809Wang, J., see Chen, Z., TCBB March-April 2018 422-431Wang, J., see Liu, J., TCBB March-April 2018 624-632Wang, J., see Yu, G., TCBB July-Aug. 2018 1390-1402Wang, J., see Yu, C., TCBB Sept.-Oct. 2018 1683-1691Wang, J., see Liu, J., TCBB Sept.-Oct. 2018 1649-1659Wang, J., see An, S., TCBB Sept.-Oct. 2018 1538-1548Wang, L., see Chiu, Y., TCBB Nov.-Dec. 2018 1754-1764Wang, L., see Guo, W., TCBB Nov.-Dec. 2018 1904-1915Wang, L., see Yuan, L., TCBB March-April 2018 551-561Wang, L., see Chen, Z., TCBB March-April 2018 422-431Wang, L., Li, S.C., and Chen, Y.P., Guest Editorial for the 15th Asia Pacific

Bioinformatics Conference; TCBB Sept.-Oct. 2018 1513-1514Wang, M., see Zhang, L., TCBB March-April 2018 570-580Wang, P., seeMa, X., TCBB March-April 2018 647-658Wang, X., see Liu, J., TCBB Sept.-Oct. 2018 1500-1512Wang, Y., Qian, W., and Yuan, B., A Graphical Model of Smoking-Induced

Global Instability in Lung Cancer; TCBB Jan.-Feb. 2018 1-14Wang, Y., see Cheng, Z., TCBB Nov.-Dec. 2018 1832-1843Wang, Y., see Gossmann, A., TCBB July-Aug. 2018 1066-1078Wang, Y., see Chen, S., TCBB Sept.-Oct. 2018 1718-1722Wang, Y., see Deng, S., TCBB Sept.-Oct. 2018 1480-1491Wang, Z., see Gao, C., TCBB Nov.-Dec. 2018 1916-1928Wang, Z., see Niu, B., TCBB Nov.-Dec. 2018 1865-1876Wang, Z., see Zamanighomi, M., TCBB July-Aug. 2018 1093-1106Ward, S.R., seeMukund, K., TCBB Nov.-Dec. 2018 2009-2016Weber, N., see Davidson, R., TCBB May -June 2018 1010-1015Wei, J., see An, S., TCBB Sept.-Oct. 2018 1538-1548Wei, Q., see Yerneni, S., TCBB July-Aug. 2018 1247-1258Wei, X., seeWu, H., TCBB Nov.-Dec. 2018 2039-2052Wei, X., seeWang, B., TCBB May -June 2018 999-1002Wei, Y., see Liu, M., TCBB Sept.-Oct. 2018 1706-1717Wei, Z., seeWang, B., TCBB May -June 2018 999-1002Welch, L., see Al-Ouran, R., TCBB July-Aug. 2018 1290-1300Wieseke, N., see Hartmann, T., TCBB Sept.-Oct. 2018 1585-1593Wittler, R., see Luhmann, N., TCBB Nov.-Dec. 2018 2094-2100Wolf, V., see Backenk€ohler, M., TCBB July-Aug. 2018 1180-1192Wolf, V., see Backes, M., TCBB Sept.-Oct. 2018 1405-1412Woloshuk, C., see Kim, M., TCBB March-April 2018 506-515Won, J., see Park, S., TCBB March-April 2018 441-451Wong, K., see Li, X., TCBB May -June 2018 774-787Wu, F., see Lan, W., TCBB Nov.-Dec. 2018 1774-1782Wu, F., see Liu, J., TCBB March-April 2018 624-632Wu, F., see Liu, J., TCBB Sept.-Oct. 2018 1649-1659Wu, H., Wei, X., and Chan, S., Novel Consensus Gene Selection Criteria for

Distributed GPU Partial Least Squares-Based Gene Microarray Analysisin Diffused Large B Cell Lymphoma (DLBCL) and Related Findings;TCBB Nov.-Dec. 2018 2039-2052

Wu, H., Cao, C., Xia, X., and L€u, Q., Unified Deep Learning Architecture forModeling Biology Sequence; TCBB Sept.-Oct. 2018 1445-1452

Wu, K., see Czeizler, E., TCBB July-Aug. 2018 1217-1228Wu, Q., see Guo, W., TCBB Nov.-Dec. 2018 1904-1915Wu, T., see Niu, B., TCBB Nov.-Dec. 2018 1865-1876Wu, W., see Yu, C., TCBB Sept.-Oct. 2018 1683-1691

X

Xia, C., Han, K., Qi, Y., Zhang, Y., and Yu, D., A Self-Training SubspaceClustering Algorithm under Low-Rank Representation for Cancer Classi-fication on Gene Expression Data; TCBB July-Aug. 2018 1315-1324

Xia, K.M., see Ghoshal, A., TCBB July-Aug. 2018 1037-1051Xia, R., see Hashemikhabir, S., TCBB July-Aug. 2018 1259-1269Xia, X., seeWu, H., TCBB Sept.-Oct. 2018 1445-1452Xiang, Y., see Hashemikhabir, S., TCBB July-Aug. 2018 1259-1269Xie, L., seeWang, A., TCBB Nov.-Dec. 2018 1960-1967



Xie, Q., He, X., Yang, F., Liu, X., Li, Y., Liu, Y., Yang, Z., Yu, J., Zhang, B.,and Zhao, W., Analysis of the Genome Sequence and Prediction of B-CellEpitopes of the Envelope Protein of Middle East Respiratory Syndrome-Coronavirus; TCBB July-Aug. 2018 1344-1350

Xiong, Z., see Jiang, N., TCBB Sept.-Oct. 2018 1549-1559Xu, B., Lin, H., Lin, Y., Ma, Y., Yang, L., Wang, J., and Yang, Z., Improve

Biomedical Information Retrieval Using Modified Learning to RankMethods; TCBB Nov.-Dec. 2018 1797-1809

Xu, B., Zhang, Y., Gong, D., Guo, Y., and Rong, M., Environment Sensitivity-Based Cooperative Co-Evolutionary Algorithms for Dynamic Multi-Objective Optimization; TCBB Nov.-Dec. 2018 1877-1890

Xu, J., see Zhang, W., TCBB Jan.-Feb. 2018 109-116Xu, J., see Zhang, W., TCBB May -June 2018 1035Xu, L., see Hu, B., TCBB Nov.-Dec. 2018 1765-1773Xu, M., see Chen, S., TCBB Sept.-Oct. 2018 1718-1722Xu, T., Ou-Yang, L., Hu, X., and Zhang, X., Identifying Gene Network Rewir-

ing by Integrating Gene Expression and Gene Network Data; TCBB Nov.-Dec. 2018 2079-2085

Xu, W., see Ren, S., TCBB Sept.-Oct. 2018 1660-1668Xu, Y., see Liu, J., TCBB May -June 2018 974-987Xu, Y., see Shao, W., TCBB May -June 2018 828-838Xue, Y., see Guo, W., TCBB Nov.-Dec. 2018 1904-1915Xue, Y., see Guo, Y., TCBB Nov.-Dec. 2018 1891-1903

Y

Yahia, S.B., see Djeddi, W.E., TCBB Nov.-Dec. 2018 2060-2066Yang, F., see Zhou, X., TCBB May -June 2018 802-812Yang, F., see Xie, Q., TCBB July-Aug. 2018 1344-1350Yang, G., see Zhang, J., TCBB Jan.-Feb. 2018 147-156Yang, L., see Xu, B., TCBB Nov.-Dec. 2018 1797-1809Yang, Y., see Yu, C., TCBB Sept.-Oct. 2018 1683-1691Yang, Z., see Xu, B., TCBB Nov.-Dec. 2018 1797-1809Yang, Z., see Xie, Q., TCBB July-Aug. 2018 1344-1350Yerneni, S., Khan, I.K., Wei, Q., and Kihara, D., IAS: Interaction Specific GO

Term Associations for Predicting Protein-Protein Interaction Networks;TCBB July-Aug. 2018 1247-1258

Yoon, B., see Ghaffari, N., TCBB March-April 2018 494-505Yoon, B., see Kim, M., TCBB March-April 2018 506-515Yoon, S., see Park, S., TCBB March-April 2018 441-451Yoshida, R., see Hirose, O., TCBB Nov.-Dec. 2018 1822-1831Yu, C., Wu, W., Wang, J., Lin, Y., Yang, Y., Chen, J., Zhu, F., and Shen, B.,

NGS-FC: A Next-Generation Sequencing Data Format Converter; TCBBSept.-Oct. 2018 1683-1691

Yu, D., see Xia, C., TCBB July-Aug. 2018 1315-1324Yu, F., see Tang, Q., TCBB Nov.-Dec. 2018 1943-1950Yu, G., Fu, G., Wang, J., and Zhao, Y., NewGOA: Predicting New GO Anno-

tations of Proteins by Bi-Random Walks on a Hybrid Graph; TCBB July-Aug. 2018 1390-1402

Yu, J., see Liu, J., TCBB May -June 2018 974-987Yu, J., see Xie, Q., TCBB July-Aug. 2018 1344-1350Yu, X., see He, X., TCBB July-Aug. 2018 1325-1332Yuan, B., seeWang, Y., TCBB Jan.-Feb. 2018 1-14Yuan, C., see Bao, W., TCBB Sept.-Oct. 2018 1453-1460Yuan, L., Chen, F., Zeng, L., Wang, L., and Hu, D., Gender Identification of

Human Brain Image with A Novel 3D Descriptor; TCBB March-April2018 551-561

Yuan, Q., seeMizera, A., TCBB July-Aug. 2018 1203-1216Yuan, Q., seeMizera, A., TCBB Sept.-Oct. 2018 1525-1537Yue, Z., Neylon, M.T., Nguyen, T., Ratliff, T., and Chen, J.Y., “Super Gene

Set” Causal Relationship Discovery from Functional Genomics Data;TCBB Nov.-Dec. 2018 1991-1998

Z

Zaki, M.J., see Gao, X., TCBB Nov.-Dec. 2018 1951-1952Zamanian, M., see Zamanighomi, M., TCBB July-Aug. 2018 1093-1106Zamanighomi, M., Zamanian, M., Kimber, M., and Wang, Z., Gene Regula-

tory Network Inference from Perturbed Time-Series Expression Data viaOrdered Dynamical Expansion of Non-Steady State Actors; TCBB July-Aug. 2018 1093-1106

Zarai, Y., Margaliot, M., Sontag, E.D., and Tuller, T., Controllability Analysisand Control Synthesis for the Ribosome Flow Model; TCBB July-Aug.2018 1351-1364

Zeng, L., see Yuan, L., TCBB March-April 2018 551-561Zervakis, M., see Chlis, N., TCBB Jan.-Feb. 2018 181-190Zhang, B., see Xie, Q., TCBB July-Aug. 2018 1344-1350Zhang, D., see Shao, W., TCBB May -June 2018 828-838Zhang, H., Zhu, L., and Huang, D., DiscMLA: An Efficient Discriminative

Motif Learning Algorithm over High-Throughput Datasets; TCBB Nov.-Dec. 2018 1810-1820

Zhang, H., see Kim, M., TCBB March-April 2018 506-515Zhang, H., see Zhu, L., TCBB May -June 2018 913-925Zhang, J., Chai, H., Gao, B., Yang, G., and Ma, Z., HEMEsPred: Structure-

Based Ligand-Specific Heme Binding Residues Prediction by Using Fast-Adaptive Ensemble Learning Scheme; TCBB Jan.-Feb. 2018 147-156

Zhang, J., Liu, T., and Deshpande, G., Probabilistic Methods in Computa-tional Neuroscience; TCBB March-April 2018 535-536

Zhang, J., and Zhang, S., The Discovery of Mutated Driver Pathways in Can-cer: Models and Algorithms; TCBB May -June 2018 988-998

Zhang, J., see Ghoshal, A., TCBB July-Aug. 2018 1037-1051Zhang, L., see Jiao, H., TCBB Nov.-Dec. 2018 2086-2093Zhang, L., see Cui, X., TCBB March-April 2018 526-534Zhang, L., Wang, M., Sterling, N.W., Lee, E., Eslinger, P.J., Wagner, D., Du,

G., Lewis, M.M., Truong, Y., Bowman, F.D., and Huang, X., CorticalThinning and Cognitive Impairment in Parkinson’s Disease withoutDementia; TCBB March-April 2018 570-580

Zhang, L., see Zhou, X., TCBB May -June 2018 802-812Zhang, Q., seeWang, B., TCBB May -June 2018 999-1002Zhang, S., seeMin, W., TCBB May -June 2018 944-953Zhang, S., see Zhang, J., TCBB May -June 2018 988-998Zhang, S., see Chen, S., TCBB Sept.-Oct. 2018 1718-1722Zhang, W., Xu, J., Li, Y., and Zou, X., Detecting Essential Proteins Based on

Network Topology, Gene Expression Data, and Gene Ontology Informa-tion; TCBB Jan.-Feb. 2018 109-116

Zhang, W., see Li, J., TCBB March-April 2018 460-468Zhang, W., Xu, J., Li, Y., and Zou, X., Correction to “Detecting Essential Pro-

teins Based on Network Topology, Gene Expression Data, and GeneOntology Information”; TCBB May -June 2018 1035

Zhang, X., see Xu, T., TCBB Nov.-Dec. 2018 2079-2085Zhang, X., Altering Indispensable Proteins in Controlling Directed Human

Protein Interaction Network; TCBB Nov.-Dec. 2018 2074-2078Zhang, X., see Hu, B., TCBB Nov.-Dec. 2018 1765-1773Zhang, X., see Chen, S., TCBB Sept.-Oct. 2018 1718-1722Zhang, X., see Lin, X., TCBB Sept.-Oct. 2018 1470-1479Zhang, Y., see Tang, Q., TCBB Nov.-Dec. 2018 1943-1950Zhang, Y., see Xu, B., TCBB Nov.-Dec. 2018 1877-1890Zhang, Y., see Xia, C., TCBB July-Aug. 2018 1315-1324Zhang, Y., see Cheng, X., TCBB July-Aug. 2018 1111-1121Zhang, Y., Zheng, C., and Sankoff, D., Evolutionary Model for the Statistical

Divergence of Paralogous and Orthologous Gene Pairs Generated byWholeGenome Duplication and Speciation; TCBB Sept.-Oct. 2018 1579-1584

Zhang, Y., see Bao, W., TCBB Sept.-Oct. 2018 1453-1460Zhang, Z., see Gao, C., TCBB Nov.-Dec. 2018 1916-1928Zhao, L., see Gossmann, A., TCBB July-Aug. 2018 1066-1078Zhao, W., see Xie, Q., TCBB July-Aug. 2018 1344-1350Zhao, Y., Kang, J., and Long, Q., Bayesian Multiresolution Variable Selection

for Ultra-High Dimensional Neuroimaging Data; TCBB March-April2018 537-550

Zhao, Y., see Yu, G., TCBB July-Aug. 2018 1390-1402Zheng, C., see Liu, J., TCBB May -June 2018 974-987Zheng, C., see Zhang, Y., TCBB Sept.-Oct. 2018 1579-1584Zheng, X., seeWang, B., TCBB May -June 2018 999-1002Zhou, C., seeWang, B., TCBB May -June 2018 999-1002Zhou, J., and Shi, Y., A Bipartite Network and Resource Transfer-Based

Approach to Infer lncRNA-Environmental Factor Associations; TCBBMay -June 2018 753-759

Zhou, M., see Gao, S., TCBB July-Aug. 2018 1365-1378Zhou, S., see Cheng, Z., TCBB Nov.-Dec. 2018 1832-1843Zhou, S., seeWang, B., TCBB May -June 2018 999-1002Zhou, X., Yang, F., Feng, Y., Li, Q., Tang, F., Hu, S., Lin, Z., and Zhang, L.,

A Spatial-Temporal Method to Detect Global Influenza Epidemics UsingHeterogeneous Data Collected from the Internet; TCBB May -June 2018802-812

Zhou, Z., see Gao, C., TCBB Nov.-Dec. 2018 1916-1928Zhu, F., see Yu, C., TCBB Sept.-Oct. 2018 1683-1691Zhu, J., see Jiao, H., TCBB Jan.-Feb. 2018 323-329Zhu, J., see Jiao, H., TCBB Nov.-Dec. 2018 2086-2093Zhu, L., see Zhang, H., TCBB Nov.-Dec. 2018 1810-1820Zhu, L., Zhang, H., and Huang, D., LMMO: A Large Margin Approach for

Refining Regulatory Motifs; TCBB May -June 2018 913-925



Zhu, L., see Liang, X., TCBB May -June 2018 1016-1021Zhuang, Y., see Li, Y., TCBB Sept.-Oct. 2018 1728-1731Zou, X., see Zhang, W., TCBB Jan.-Feb. 2018 109-116Zou, X., see Zhang, W., TCBB May -June 2018 1035

SUBJECT INDEX

A

Adaptive estimationOptimal Fault Detection and Diagnosis in Transcriptional Circuits UsingNext-Generation Sequencing. Bahadorinejad, A., þ, TCBB March-April2018 516-525

Adaptive filtersFilter Design with Adaptation to Time-Delay Parameters for GeneticRegulatory Networks. Jiao, H., þ, TCBB Jan.-Feb. 2018 323-329

Algorithm design and analysisFeature Selection for Optimized High-Dimensional Biomedical Data Usingan Improved Shuffled Frog Leaping Algorithm. Hu, B., þ, TCBB Nov.-Dec. 2018 1765-1773Local-Nearest-Neighbors-Based Feature Weighting for Gene Selection. An,S., þ, TCBB Sept.-Oct. 2018 1538-1548Network Community Detection Based on the Physarum-Inspired Computa-tional Framework. Gao, C., þ, TCBB Nov.-Dec. 2018 1916-1928Structure-Guided Protein Transition Modeling with a Probabilistic Road-map Algorithm.Maximova, T., þ, TCBB Nov.-Dec. 2018 1783-1796

Amino acidsRF-NR: Random Forest Based Approach for Improved Classification ofNuclear Receptors. Ismail, H.D., þ, TCBB Nov.-Dec. 2018 1844-1852

Analytical modelsASSA-PBN: A Toolbox for Probabilistic Boolean Networks.Mizera, A., þ,TCBB July-Aug. 2018 1203-1216

Approximation algorithmsGenome Rearrangement with ILP. Hartmann, T., þ, TCBB Sept.-Oct. 20181585-1593

Approximation theoryAlgorithms for Pedigree Comparison. Chen, Z., þ, TCBB March-April2018 422-431DTL-RnB: Algorithms and Tools for Summarizing the Space of DTL Rec-onciliations.Ma, W., þ, TCBB March-April 2018 411-421Moment-Based Parameter Estimation for Stochastic Reaction Networks inEquilibrium. Backenk€ohler, M., þ, TCBB July-Aug. 2018 1180-1192Structural Target Controllability of Linear Networks. Czeizler, E., þ,TCBB July-Aug. 2018 1217-1228

ArraysA Simplified Description of Child Tables for Sequence Similarity Search.Frith, M.C., þ, TCBB Nov.-Dec. 2018 2067-2073

Artificial immune systemsConformational Sampling of a Biomolecular Rugged Energy Landscape.Rydzewski, J., þ, TCBB May -June 2018 732-739

Artificial neural networksRobust Gene Circuit Control Design for Time-Delayed Genetic RegulatoryNetworks Without SUM Regulatory Logic. Jiao, H., þ, TCBB Nov.-Dec.2018 2086-2093

Asymptotic stabilitySampled-Data Stabilization for Fuzzy Genetic Regulatory Networks withLeakage Delays. Ali, M.S., þ, TCBB Jan.-Feb. 2018 271-285

Atmospheric measurementsA Grouping Particle Swarm Optimizer with Personal-Best-Position Guidancefor Large ScaleOptimization.Guo,W.,þ, TCBBNov.-Dec. 2018 1904-1915

AttenuatorsComputational Models for Trapping Ebola Virus Using EngineeredBacteria.Martins, D.P., þ, TCBB Nov.-Dec. 2018 2017-2027Computational Models for Trapping Ebola Virus Using EngineeredBacteria.Martins, D.P., þ, TCBB Nov.-Dec. 2018 2017-2027

Automata theoryReduction of Qualitative Models of Biological Networks for TransientDynamics Analysis. Pauleve, L., TCBB July-Aug. 2018 1167-1179

B

Bayes methodsBayesian Multiresolution Variable Selection for Ultra-High DimensionalNeuroimaging Data. Zhao, Y., þ, TCBB March-April 2018 537-550

Classification of State Trajectories in Gene Regulatory Networks. Karba-layghareh, A., þ, TCBB Jan.-Feb. 2018 68-82Cortical Thinning and Cognitive Impairment in Parkinson’s Disease with-out Dementia. Zhang, L., þ, TCBB March-April 2018 570-580Deep Sequencing Data Analysis. Ghosh, B.K., þ, TCBB March-April 2018482-483Detecting Multivariate Gene Interactions in RNA-Seq Data Using OptimalBayesian Classification. Knight, J.M., þ, TCBB March-April 2018 484-493Predicting MicroRNA-Disease Associations Based on Improved Micro-RNA and Disease Similarities. Lan, W., þ, TCBB Nov.-Dec. 2018 1774-1782

Benchmark testingRF-NR: Random Forest Based Approach for Improved Classification ofNuclear Receptors. Ismail, H.D., þ, TCBB Nov.-Dec. 2018 1844-1852

Binomial distributionA Combined PLS and Negative Binomial Regression Model for InferringAssociation Networks from Next-Generation Sequencing Count Data.Pesonen, M., þ, TCBB May -June 2018 760-773

Bio-inspired computingSpecial Section on Swarm-Based Algorithms and Applications in Compu-tational Biology and Bioinformatics. Tan, Y., þ, TCBB Nov.-Dec. 20181863-1864Structure-Guided Protein Transition Modeling with a Probabilistic Road-map Algorithm.Maximova, T., þ, TCBB Nov.-Dec. 2018 1783-1796

BiochemistryAnalysis of the Genome Sequence and Prediction of B-Cell Epitopes of theEnvelope Protein of Middle East Respiratory Syndrome-Coronavirus. Xie,Q., þ, TCBB July-Aug. 2018 1344-1350Computing Minimum Reaction Modifications in a Boolean Metabolic Net-work. Tamura, T., þ, TCBB Nov.-Dec. 2018 1853-1862Continuous Petri Nets and microRNA Analysis in Melanoma. Russo, G.,þ,TCBB Sept.-Oct. 2018 1492-1499HEMEsPred: Structure-Based Ligand-Specific Heme Binding ResiduesPrediction by Using Fast-Adaptive Ensemble Learning Scheme. Zhang,J., þ, TCBB Jan.-Feb. 2018 147-156Identification and Analysis of Key Residues in Protein–RNA Complexes.Kulandaisamy, A., þ, TCBB Sept.-Oct. 2018 1436-1444Modeling Methylation Patterns with Long Read Sequencing Data. Meyer,K.N., þ, TCBB July-Aug. 2018 1379-1389Mutli-Features Prediction of Protein Translational Modification Sites. Bao,W., þ, TCBB Sept.-Oct. 2018 1453-1460Petri Net Siphon Analysis and Graph Theoretic Measures for IdentifyingCombination Therapies in Cancer. Behinaein, B., þ, TCBB Jan.-Feb.2018 231-243Sequence-Based Prediction of Putative Transcription Factor Binding Sitesin DNA Sequences of Any Length. Lee, W., þ, TCBB Sept.-Oct. 20181461-1469The Intrinsic Pepsin Resistance of Interleukin-8 Can Be Explained from aCombined Bioinformatical and Experimental Approach. Anders, G., þ,TCBB Jan.-Feb. 2018 300-308

Bioelectric phenomenaA Copula-Based Granger Causality Measure for the Analysis of NeuralSpike Train Data. Hu, M., þ, TCBB March-April 2018 562-569

Bioinformatics“Super Gene Set” Causal Relationship Discovery from Functional Geno-mics Data. Yue, Z., þ, TCBB Nov.-Dec. 2018 1991-1998A Bipartite Network and Resource Transfer-Based Approach to InferlncRNA-Environmental Factor Associations. Zhou, J., þ, TCBB May-June 2018 753-759A Comparative Study for Identifying the Chromosome-Wide SpatialClusters from High-Throughput Chromatin Conformation Capture Data.Li, X., þ, TCBB May -June 2018 774-787A Distributed Classifier for MicroRNA Target Prediction with ValidationThrough TCGA Expression Data. Ghoshal, A., þ, TCBB July-Aug. 20181037-1051A Graphical Model of Smoking-Induced Global Instability in Lung Cancer.Wang, Y., þ, TCBB Jan.-Feb. 2018 1-14A New Efficient Algorithm for the Frequent Gene Team Problem. Wang,B., TCBB March-April 2018 588-598A Novel Approach to Identify the miRNA-mRNA Causal Regulatory Mod-ules in Cancer. Luo, J., þ, TCBB Jan.-Feb. 2018 309-315A Review on Methods for Detecting SNP Interactions in High-DimensionalGenomic Data. Uppu, S., þ, TCBB March-April 2018 599-612A Self-Training Subspace Clustering Algorithm under Low-Rank Repre-sentation for Cancer Classification on Gene Expression Data. Xia, C., þ,TCBB July-Aug. 2018 1315-1324



A Study of Cell-Free DNA Fragmentation Pattern and Its Application inDNA Sample Type Classification. Chen, S., þ, TCBB Sept.-Oct. 20181718-1722ACID: Association Correction for Imbalanced Data in GWAS. Bao, F., þ,TCBB Jan.-Feb. 2018 316-322An Inference Attack on Genomic Data Using Kinship, Complex Correla-tions, and Phenotype Information. Deznabi, I., þ, TCBB July-Aug. 20181333-1343Analysis of the Genome Sequence and Prediction of B-Cell Epitopes of theEnvelope Protein of Middle East Respiratory Syndrome-Coronavirus. Xie,Q., þ, TCBB July-Aug. 2018 1344-1350Analyzing Differential Regulatory Networks Modulated by Continuous-State Genomic Features in Glioblastoma Multiforme. Chiu, Y., þ, TCBBNov.-Dec. 2018 1754-1764ANTENNA, a Multi-Rank, Multi-Layered Recommender System for Infer-ring Reliable Drug-Gene-Disease Associations: Repurposing Diazoxide asa Targeted Anti-Cancer Therapy. Wang, A., þ, TCBB Nov.-Dec. 20181960-1967Application of Genetic Programming (GP) Formalism for Building DiseasePredictive Models from Protein-Protein Interactions (PPI) Data. Vyas, R.,þ, TCBB Jan.-Feb. 2018 27-37Assessment of Semantic Similarity between Proteins Using InformationContent and Topological Properties of the Gene Ontology Graph. Dutta,P., þ, TCBB May -June 2018 839-849Autumn Algorithm—Computation of Hybridization Networks for RealisticPhylogenetic Trees. Huson, D.H., þ, TCBB March-April 2018 398-410Bijective Diameters of Gene Tree Parsimony Costs. G�orecki, P., þ, TCBBSept.-Oct. 2018 1723-1727Bioinformatic Workflow Extraction from Scientific Texts based on WordSense Disambiguation. Halioui, A., þ, TCBB Nov.-Dec. 2018 1979-1990BRANE Clust: Cluster-Assisted Gene Regulatory Network InferenceRefinement. Pirayre, A., þ, TCBB May -June 2018 850-860Co-Expression Network Approach to Studying the Effects of BotulinumNeurotoxin-A.Mukund, K., þ, TCBB Nov.-Dec. 2018 2009-2016Combining Supervised and Unsupervised Learning for Improved miRNATarget Prediction. Sedaghat, N., þ, TCBB Sept.-Oct. 2018 1594-1604Computing Minimum Reaction Modifications in a Boolean Metabolic Net-work. Tamura, T., þ, TCBB Nov.-Dec. 2018 1853-1862Constructing DNA Barcode Sets Based on Particle Swarm Optimization.Wang, B., þ, TCBB May -June 2018 999-1002Construction of Signaling Pathways with RNAi Data and Multiple Refer-ence Networks. Alim, M.A., þ, TCBB July-Aug. 2018 1079-1091Detecting Essential Proteins Based on Network Topology, Gene Expres-sion Data, and Gene Ontology Information. Zhang, W., þ, TCBB Jan.-Feb. 2018 109-116Detecting Multivariate Gene Interactions in RNA-Seq Data Using OptimalBayesian Classification. Knight, J.M., þ, TCBB March-April 2018 484-493Discovering Perturbation of Modular Structure in HIV Progression by Inte-grating Multiple Data Sources Through Non-Negative Matrix Factoriza-tion. Ray, S., þ, TCBB May -June 2018 869-877DNAWatermarking Using Codon Postfix Technique. Hamad, S., þ, TCBBSept.-Oct. 2018 1605-1610Editorial for Selected Papers of a Joint Conferences, Genome InformaticsWorkshop/International Conference on Bioinformatics (GIW/InCoB)2015. Kim, S., TCBB Nov.-Dec. 2018 1821Efficient Algorithms for Sequence Analysis with Entropic Profiles. Pizzi,C., þ, TCBB Jan.-Feb. 2018 117-128Encoding Data Using Biological Principles: The Multisample Variant For-mat for Phylogenomics and Population Genomics. Pease, J.B., þ, TCBBJuly-Aug. 2018 1231-1238Feature Selection for Optimized High-Dimensional Biomedical Data Usingan Improved Shuffled Frog Leaping Algorithm. Hu, B., þ, TCBB Nov.-Dec. 2018 1765-1773fmpRPMF: A Web Implementation for Protein Identification by RobustPeptide Mass Fingerprinting. Li, Y., þ, TCBB Sept.-Oct. 2018 1728-1731From Optimization to Mapping: An Evolutionary Algorithm for ProteinEnergy Landscapes. Sapin, E., þ, TCBB May -June 2018 719-731Gene Tree Construction and Correction Using SuperTree and Reconcilia-tion. Lafond, M., þ, TCBB Sept.-Oct. 2018 1560-1570Genome Rearrangement with ILP. Hartmann, T., þ, TCBB Sept.-Oct. 20181585-1593GPU-Based Point Cloud Superpositioning for Structural Comparisons ofProtein Binding Sites. Leinweber, M., þ, TCBB May -June 2018 740-752Great Lakes Bioinformatics Conference (GLBIO) 2015 Special SectionEditorial.Milenkovic, T., þ, TCBB July-Aug. 2018 1229-1230Guest Editorial.Murali, T.M., TCBB July-Aug. 2018 1036

Guest Editorial for Special Section on BIBM 2015. Tian, T., þ, TCBBNov.-Dec. 2018 1752-1753Guest Editorial for Special Section on the 12th International Conference onIntelligent Computing (ICIC). Huang, D., þ, TCBB Sept.-Oct. 2018 1433-1435Guest Editorial for Special Section on the Sixth National Conference onBioinformatics and System Biology of China. Fan, X., þ, TCBB July-Aug. 2018 1092Guest Editorial for the 14th Asia Pacific Bioinformatics Conference. Tang,J., þ, TCBB March-April 2018 396-397Guest Editorial for the 15th Asia Pacific Bioinformatics Conference.Wang,L., þ, TCBB Sept.-Oct. 2018 1513-1514hc-OTU: A Fast and Accurate Method for Clustering Operational Taxo-nomic Units Based on Homopolymer Compaction. Park, S., þ, TCBBMarch-April 2018 441-451HEMEsPred: Structure-Based Ligand-Specific Heme Binding ResiduesPrediction by Using Fast-Adaptive Ensemble Learning Scheme. Zhang,J., þ, TCBB Jan.-Feb. 2018 147-156IAS: Interaction Specific GO Term Associations for Predicting Protein-Pro-tein Interaction Networks. Yerneni, S.,þ, TCBB July-Aug. 2018 1247-1258Index-Based Network Aligner of Protein-Protein Interaction Networks.Elmsallati, A., þ, TCBB Jan.-Feb. 2018 330-336Inferring Gene-Species Assignments in the Presence of Horizontal GeneTransfer.Mykowiecka, A., þ, TCBB Sept.-Oct. 2018 1571-1578Inferring the Functions of Proteins from the Interrelationships betweenFunctional Categories. Taha, K., TCBB Jan.-Feb. 2018 157-167Inferring Unknown Biological Function by Integration of GO Annotationsand Gene Expression Data. Leale, G., þ, TCBB Jan.-Feb. 2018 168-180Integrating Imaging Genomic Data in the Quest for Biomarkers of Schizo-phrenia Disease. Deng, S., þ, TCBB Sept.-Oct. 2018 1480-1491Integrating Multiple Data Sources for Combinatorial Marker Discovery: AStudy in Tumorigenesis. Bandyopadhyay, S., þ, TCBB March-April 2018673-687Introducing a Stable Bootstrap Validation Framework for Reliable Geno-mic Signature Extraction. Chlis, N., þ, TCBB Jan.-Feb. 2018 181-190Investigating Correlation between Protein Sequence Similarity and Seman-tic Similarity Using Gene Ontology Annotations. Ikram, N., þ, TCBBMay -June 2018 905-912LMMO: A Large Margin Approach for Refining Regulatory Motifs. Zhu,L., þ, TCBB May -June 2018 913-925MeTDiff: A Novel Differential RNA Methylation Analysis for MeRIP-SeqData. Cui, X., þ, TCBB March-April 2018 526-534Modeling Methylation Patterns with Long Read Sequencing Data. Meyer,K.N., þ, TCBB July-Aug. 2018 1379-1389Multiple Network Alignment via MultiMAGNA++. Vijayan, V., þ, TCBBSept.-Oct. 2018 1669-1682Multiple-Swarm Ensembles: Improving the Predictive Power and Robust-ness of Predictive Models and Its Use in Computational Biology. Alves,P., þ, TCBB May -June 2018 926-933Multiscale and Multimodal Analysis for Computational Biology. Gao, X.,þ, TCBB Nov.-Dec. 2018 1951-1952NAHAL-Flex: A Numerical and Alphabetical Hinge Detection Algorithmfor Flexible Protein Structure Alignment. Fotoohifiroozabadi, S., þ,TCBB May -June 2018 934-943NGS-FC: A Next-Generation Sequencing Data Format Converter. Yu, C.,þ, TCBB Sept.-Oct. 2018 1683-1691Novelty Indicator for Enhanced Prioritization of Predicted Gene OntologyAnnotations. Chicco, D., þ, TCBB May -June 2018 954-965Optimal Block-Based Trimming for Next Generation Sequencing. Hedtke,I., þ, TCBB March-April 2018 364-376PerPAS: Topology-Based Single Sample Pathway Analysis Method. Liu,C., þ, TCBB May -June 2018 1022-1027Predicting the Absorption Potential of Chemical Compounds Through aDeep Learning Approach. Shin, M., þ, TCBB March-April 2018 432-440Prediction of Hot Regions in PPIs Based on Improved Local CommunityStructure Detecting. Lin, X., þ, TCBB Sept.-Oct. 2018 1470-1479PREMER: A Tool to Infer Biological Networks. Villaverde, A.F., þ, TCBBJuly-Aug. 2018 1193-1202Probabilistic Methods in Computational Neuroscience. Zhang, J., þ, TCBBMarch-April 2018 535-536Proteomic Evidence for In-Frame and Out-of-Frame Alternatively SplicedIsoforms in Human and Mouse. Ramalho, R.F., þ, TCBB July-Aug. 20181284-1289PyMut: A Web Tool for Overlapping Gene Loss-of-Function MutationDesign. Liu, K., þ, TCBB July-Aug. 2018 1107-1110Querying of Disparate Association and Interaction Data in BiomedicalApplications. Qiao, S., þ, TCBB July-Aug. 2018 1052-1065



Scaffolding of Ancient Contigs and Ancestral Reconstruction in a Phyloge-netic Framework. Luhmann, N., þ, TCBB Nov.-Dec. 2018 2094-2100Selected Papers of the First International Conference on Algorithms forComputational Biology (AlCoB 2014). Dediu, A., þ, TCBB March-April2018 350-351Sequence-Based Prediction of Putative Transcription Factor Binding Sitesin DNA Sequences of Any Length. Lee, W., þ, TCBB Sept.-Oct. 20181461-1469SparseNCA: Sparse Network Component Analysis for Recovering Tran-scription Factor Activities with Incomplete Prior Information. Noor, A.,þ, TCBB March-April 2018 387-395Species Tree Estimation Using ASTRAL: How Many Genes Are Enough?.Shekhar, S., þ, TCBB Sept.-Oct. 2018 1738-1747The Discovery of Mutated Driver Pathways in Cancer: Models and Algo-rithms. Zhang, J., þ, TCBB May -June 2018 988-998The Intrinsic Pepsin Resistance of Interleukin-8 Can Be Explained from aCombined Bioinformatical and Experimental Approach. Anders, G., þ,TCBB Jan.-Feb. 2018 300-308Towards Extracting Supporting Information About Predicted Protein-Pro-tein Interactions. Roth, A., þ, TCBB July-Aug. 2018 1239-1246Unified Deep Learning Architecture for Modeling Biology Sequence. Wu,H., þ, TCBB Sept.-Oct. 2018 1445-1452

Biological cellsGenome Rearrangement with ILP. Hartmann, T., þ, TCBB Sept.-Oct. 20181585-1593

Biological information theoryGrouped Gene Selection of Cancer via Adaptive Sparse Group Lasso Basedon Conditional Mutual Information. Li, J., þ, TCBB Nov.-Dec. 20182028-2038

Biological NMRThe Intrinsic Pepsin Resistance of Interleukin-8 Can Be Explained from aCombined Bioinformatical and Experimental Approach. Anders, G., þ,TCBB Jan.-Feb. 2018 300-308

Biological organsFuzzy-Rough Entropy Measure and Histogram Based Patient Selection formiRNARanking in Cancer.Pal, J.K.,þ, TCBBMarch-April 2018 659-672GSEH: ANovel Approach to Select Prostate Cancer-AssociatedGenes UsingGene Expression Heterogeneity.Kim, H.,þ, TCBB Jan.-Feb. 2018 129-146Identifying Condition-Specific Modules by Clustering Multiple Networks.Ma, X., þ, TCBB Sept.-Oct. 2018 1636-1648

Biological system modelingASSA-PBN: A Toolbox for Probabilistic Boolean Networks.Mizera, A., þ,TCBB July-Aug. 2018 1203-1216Computing Minimum Reaction Modifications in a Boolean Metabolic Net-work. Tamura, T., þ, TCBB Nov.-Dec. 2018 1853-1862Controllability Analysis and Control Synthesis for the Ribosome FlowModel. Zarai, Y., þ, TCBB July-Aug. 2018 1351-1364Identifying Gene Network Rewiring by Integrating Gene Expression andGene Network Data. Xu, T., þ, TCBB Nov.-Dec. 2018 2079-2085Improve Biomedical Information Retrieval Using Modified Learning toRank Methods. Xu, B., þ, TCBB Nov.-Dec. 2018 1797-1809

Biological systemsASSA-PBN: A Toolbox for Probabilistic Boolean Networks.Mizera, A., þ,TCBB July-Aug. 2018 1203-1216

Biological systems modelingGuest Editorial for Special Section on BIBM 2015. Tian, T., þ, TCBBNov.-Dec. 2018 1752-1753

Biological techniquesCodon Context Optimization in Synthetic Gene Design. Papamichail, D.,þ, TCBB March-April 2018 452-459Computational Prediction of Pathogenic Network Modules in Fusariumverticillioides. Kim, M., þ, TCBB March-April 2018 506-515Examining De Novo Transcriptome Assemblies via a Quality AssessmentPipeline. Ghaffari, N., þ, TCBB March-April 2018 494-505Mutli-Features Prediction of Protein Translational Modification Sites. Bao,W., þ, TCBB Sept.-Oct. 2018 1453-1460Optimal Block-Based Trimming for Next Generation Sequencing. Hedtke,I., þ, TCBB March-April 2018 364-376

Biological tissuesNucleosome Positioning of Intronless Genes in the Human Genome.Cheng, X., þ, TCBB July-Aug. 2018 1111-1121Proteomic Evidence for In-Frame and Out-of-Frame Alternatively SplicedIsoforms in Human and Mouse. Ramalho, R.F., þ, TCBB July-Aug. 20181284-1289

BiologyA GRASP-Based Heuristic for the Sorting by Length-Weighted InversionsProblem. Arruda, T.d.S., þ, TCBB March-April 2018 352-363

Application of Fractal Theory on Motifs Counting in Biological Networks.Joveini, M.B.Z., þ, TCBB March-April 2018 613-623Optimal Objective-Based Experimental Design for Uncertain DynamicalGene Networks with Experimental Error. Mohsenizadeh, D.N., þ, TCBBJan.-Feb. 2018 218-230Reduction of Qualitative Models of Biological Networks for TransientDynamics Analysis. Pauleve, L., TCBB July-Aug. 2018 1167-1179Sampled-Data Stabilization for Fuzzy Genetic Regulatory Networks withLeakage Delays. Ali, M.S., þ, TCBB Jan.-Feb. 2018 271-285

Biology computing3D Genome Reconstruction with ShRec3D+ and Hi-C Data. Li, J., þ,TCBB March-April 2018 460-468A Combined PLS and Negative Binomial Regression Model for InferringAssociation Networks from Next-Generation Sequencing Count Data.Pesonen, M., þ, TCBB May -June 2018 760-773A Comparative Study for Identifying the Chromosome-Wide Spatial Clus-ters from High-Throughput Chromatin Conformation Capture Data. Li,X., þ, TCBB May -June 2018 774-787A Memetic Algorithm for 3D Protein Structure Prediction Problem.Correa, L., þ, TCBB May -June 2018 690-704A Model-Based Tool for the Analysis and Design of Gene Regulatory Net-works. Ironi, L., þ, TCBB July-Aug. 2018 1301-1314A Sparse Regression Method for Group-Wise Feature Selection with FalseDiscovery Rate Control. Gossmann, A., þ, TCBB July-Aug. 2018 1066-1078Biological Event Trigger Identification with Noise Contrastive Estimation.Jiang, N., þ, TCBB Sept.-Oct. 2018 1549-1559Cell Population Tracking in a Honeycomb Structure Using an IMM FilterBased 3D Local Graph Matching Model. Liu, M., þ, TCBB Sept.-Oct.2018 1706-1717Classification of State Trajectories in Gene Regulatory Networks. Karba-layghareh, A., þ, TCBB Jan.-Feb. 2018 68-82Codon Context Optimization in Synthetic Gene Design. Papamichail, D.,þ, TCBB March-April 2018 452-459Combinatorics of Tandem Duplication Random Loss Mutations on CircularGenomes. Hartmann, T., þ, TCBB Jan.-Feb. 2018 83-95Complexity and Algorithms for Finding a Perfect Phylogeny from MixedTumor Samples. Hujdurovic, A., þ, TCBB Jan.-Feb. 2018 96-108Computational Prediction of Pathogenic Network Modules in Fusariumverticillioides. Kim, M., þ, TCBB March-April 2018 506-515Conformational Sampling of a Biomolecular Rugged Energy Landscape.Rydzewski, J., þ, TCBB May -June 2018 732-739Continuous Petri Nets and microRNA Analysis in Melanoma. Russo, G.,þ,TCBB Sept.-Oct. 2018 1492-1499Detecting Essential Proteins Based on Network Topology, Gene Expres-sion Data, and Gene Ontology Information. Zhang, W., þ, TCBB Jan.-Feb. 2018 109-116Discovering Gene Regulatory Elements Using Coverage-Based Heuristics.Al-Ouran, R., þ, TCBB July-Aug. 2018 1290-1300DTL-RnB: Algorithms and Tools for Summarizing the Space of DTL Rec-onciliations.Ma, W., þ, TCBB March-April 2018 411-421Dynamics in Epistasis Analysis. Awdeh, A., þ, TCBB May -June 2018 878-891Efficient Algorithms for Genomic Duplication Models. Paszek, J., þ,TCBB Sept.-Oct. 2018 1515-1524Efficient Quartet Representations of Trees and Applications to Supertreeand Summary Methods. Davidson, R., þ, TCBB May -June 2018 1010-1015Evolutionary Graph Clustering for Protein Complex Identification. He, T.,þ, TCBB May -June 2018 892-904Evolutionary Model for the Statistical Divergence of Paralogous andOrthologous Gene Pairs Generated by Whole Genome Duplication andSpeciation. Zhang, Y., þ, TCBB Sept.-Oct. 2018 1579-1584Gene Regulatory Network Inference from Perturbed Time-Series Expres-sion Data via Ordered Dynamical Expansion of Non-Steady State Actors.Zamanighomi, M., þ, TCBB July-Aug. 2018 1093-1106Gene Tree Construction and Correction Using SuperTree and Reconcilia-tion. Lafond, M., þ, TCBB Sept.-Oct. 2018 1560-1570Hardware Accelerator for the Multifractal Analysis of DNA Sequences.Duarte-Sanchez, J.E., þ, TCBB Sept.-Oct. 2018 1611-1624Identifying Condition-Specific Modules by Clustering Multiple Networks.Ma, X., þ, TCBB Sept.-Oct. 2018 1636-1648Incorporation of Solvent Effect into Multi-Objective Evolutionary Algo-rithm for Improved Protein Structure Prediction. Gao, S., þ, TCBB July-Aug. 2018 1365-1378Inferring Gene-Species Assignments in the Presence of Horizontal GeneTransfer.Mykowiecka, A., þ, TCBB Sept.-Oct. 2018 1571-1578



Influence Networks Compared with Reaction Networks: Semantics,Expressivity and Attractors. Fages, F., þ, TCBB July-Aug. 2018 1138-1151Local Traces: An Over-Approximation of the Behavior of the Proteins inRule-Based Models. Feret, J., þ, TCBB July-Aug. 2018 1124-1137Machine Learned Replacement of N-Labels for Basecalled Sequences inDNA Barcoding.Ma, E.Y.T., þ, TCBB Jan.-Feb. 2018 191-204MPIGeneNet: Parallel Calculation of Gene Co-Expression Networks onMulticore Clusters. Gonzalez-Dominguez, J., þ, TCBB Sept.-Oct. 20181732-1737Mutli-Features Prediction of Protein Translational Modification Sites. Bao,W., þ, TCBB Sept.-Oct. 2018 1453-1460Network-Regularized Sparse Logistic Regression Models for Clinical RiskPrediction and Biomarker Discovery. Min, W., þ, TCBB May -June 2018944-953NewGOA: Predicting New GO Annotations of Proteins by Bi-RandomWalks on a Hybrid Graph. Yu, G., þ, TCBB July-Aug. 2018 1390-1402NGS-FC: A Next-Generation Sequencing Data Format Converter. Yu, C.,þ, TCBB Sept.-Oct. 2018 1683-1691Nucleosome Positioning of Intronless Genes in the Human Genome.Cheng, X., þ, TCBB July-Aug. 2018 1111-1121Optimal Fault Detection and Diagnosis in Transcriptional Circuits UsingNext-Generation Sequencing. Bahadorinejad, A., þ, TCBB March-April2018 516-525Optimization of Gene Set Annotations Using Robust Trace-Norm Multi-task Learning. Liang, X., þ, TCBB May -June 2018 1016-1021Optimizing Phylogenetic Queries for Performance. Jamil, H.M., TCBBSept.-Oct. 2018 1692-1705Prediction of HIV Drug Resistance by Combining Sequence and StructuralProperties. Khalid, Z., þ, TCBB May -June 2018 966-973RAFP-Pred: Robust Prediction of Antifreeze Proteins Using LocalizedAnalysis of n-Peptide Compositions. Khan, S., þ, TCBB Jan.-Feb. 2018244-250Regularized Non-Negative Matrix Factorization for Identifying Differen-tially Expressed Genes and Clustering Samples: A Survey. Liu, J., þ,TCBB May -June 2018 974-987REPA: Applying Pathway Analysis to Genome-Wide Transcription FactorBinding Data. Patra, P., þ, TCBB July-Aug. 2018 1270-1283Reviving the Two-State Markov Chain Approach. Mizera, A., þ, TCBBSept.-Oct. 2018 1525-1537Simulating the Large-Scale Erosion of Genomic Privacy Over Time.Backes, M., þ, TCBB Sept.-Oct. 2018 1405-1412Species Tree Inference from Gene Splits by Unrooted STAR Methods. All-man, E.S., þ, TCBB Jan.-Feb. 2018 337-342Structural Class Classification of 3D Protein Structure Based on Multi-View 2D Images. Suryanto, C.H., þ, TCBB Jan.-Feb. 2018 286-299Structural Target Controllability of Linear Networks. Czeizler, E., þ,TCBB July-Aug. 2018 1217-1228

BiomassComputing Minimum Reaction Modifications in a Boolean Metabolic Net-work. Tamura, T., þ, TCBB Nov.-Dec. 2018 1853-1862

Biomedical imagingImmunological Approach for Full NURBS Reconstruction of OutlineCurves from Noisy Data Points in Medical Imaging. Iglesias, A., þ,TCBB Nov.-Dec. 2018 1929-1942SPF-CellTracker: Tracking Multiple Cells with Strongly-Correlated MovesUsing a Spatial Particle Filter. Hirose, O., þ, TCBB Nov.-Dec. 20181822-1831

Biomedical materialsEnumerating Substituted Benzene Isomers of Tree-Like Chemical Graphs.Li, J., þ, TCBB March-April 2018 633-646

Biomedical MRIBayesian Multiresolution Variable Selection for Ultra-High DimensionalNeuroimaging Data. Zhao, Y., þ, TCBB March-April 2018 537-550Classification of Alzheimer’s Disease Using Whole Brain HierarchicalNetwork. Liu, J., þ, TCBB March-April 2018 624-632Complex Network Measures in Autism Spectrum Disorders. Sato, J.R., þ,TCBB March-April 2018 581-587Cortical Thinning and Cognitive Impairment in Parkinson’s Disease with-out Dementia. Zhang, L., þ, TCBB March-April 2018 570-580Gender Identification of Human Brain Image with A Novel 3D Descriptor.Yuan, L., þ, TCBB March-April 2018 551-561Integrating Imaging Genomic Data in the Quest for Biomarkers of Schizo-phrenia Disease. Deng, S., þ, TCBB Sept.-Oct. 2018 1480-1491

BiomembranesComputational Models for Trapping Ebola Virus Using Engineered Bacte-ria.Martins, D.P., þ, TCBB Nov.-Dec. 2018 2017-2027

Biomolecular electronicsOptimal Fault Detection and Diagnosis in Transcriptional Circuits UsingNext-Generation Sequencing. Bahadorinejad, A., þ, TCBB March-April2018 516-525

BiotechnologyA Global Network Alignment Method Using Discrete Particle SwarmOptimization. Huang, J., þ, TCBB May -June 2018 705-718

Bipartite graphA Novel Computational Approach for Global Alignment for MultipleBiological Networks. Djeddi, W.E., þ, TCBB Nov.-Dec. 2018 2060-2066

BloodA Study of Cell-Free DNA Fragmentation Pattern and Its Application inDNA Sample Type Classification. Chen, S., þ, TCBB Sept.-Oct. 20181718-1722Algorithmic Mapping and Characterization of the Drug-Induced Pheno-typic-Response Space of Parasites Causing Schistosomiasis. Singh, R., þ,TCBB March-April 2018 469-481Computational Models for Trapping Ebola Virus Using Engineered Bacte-ria.Martins, D.P., þ, TCBB Nov.-Dec. 2018 2017-2027

BonesA Sparse Regression Method for Group-Wise Feature Selection with FalseDiscovery Rate Control. Gossmann, A., þ, TCBB July-Aug. 2018 1066-1078

Boolean algebraOptimal Fault Detection and Diagnosis in Transcriptional Circuits UsingNext-Generation Sequencing. Bahadorinejad, A., þ, TCBB March-April2018 516-525Reviving the Two-State Markov Chain Approach. Mizera, A., þ, TCBBSept.-Oct. 2018 1525-1537

Boolean functionsClassification of State Trajectories in Gene Regulatory Networks.Karbalayghareh, A., þ, TCBB Jan.-Feb. 2018 68-82Computing Minimum Reaction Modifications in a Boolean MetabolicNetwork. Tamura, T., þ, TCBB Nov.-Dec. 2018 1853-1862Reduction of Qualitative Models of Biological Networks for TransientDynamics Analysis. Pauleve, L., TCBB July-Aug. 2018 1167-1179

BotanyModeling the Geometry and Dynamics of the Endoplasmic ReticulumNetwork. Lin, C., þ, TCBB March-April 2018 377-386

Brain modelingA Copula-Based Granger Causality Measure for the Analysis of NeuralSpike Train Data. Hu, M., þ, TCBB March-April 2018 562-569Bayesian Multiresolution Variable Selection for Ultra-High DimensionalNeuroimaging Data. Zhao, Y., þ, TCBB March-April 2018 537-550Classification of Alzheimer’s Disease Using Whole Brain HierarchicalNetwork. Liu, J., þ, TCBB March-April 2018 624-632Complex Network Measures in Autism Spectrum Disorders. Sato, J.R., þ,TCBB March-April 2018 581-587Cortical Thinning and Cognitive Impairment in Parkinson’s Disease with-out Dementia. Zhang, L., þ, TCBB March-April 2018 570-580Gender Identification of Human Brain Image with A Novel 3D Descriptor.Yuan, L., þ, TCBB March-April 2018 551-561Probabilistic Methods in Computational Neuroscience. Zhang, J., þ, TCBBMarch-April 2018 535-536Proteomic Evidence for In-Frame and Out-of-Frame Alternatively SplicedIsoforms in Human and Mouse. Ramalho, R.F., þ, TCBB July-Aug. 20181284-1289

Breast cancerANTENNA, a Multi-Rank, Multi-Layered Recommender System for Infer-ring Reliable Drug-Gene-Disease Associations: Repurposing Diazoxide asa Targeted Anti-Cancer Therapy. Wang, A., þ, TCBB Nov.-Dec. 20181960-1967

C

CancerA Graphical Model of Smoking-Induced Global Instability in Lung Cancer.Wang, Y., þ, TCBB Jan.-Feb. 2018 1-14A Novel Approach to Identify the miRNA-mRNA Causal Regulatory Mod-ules in Cancer. Luo, J., þ, TCBB Jan.-Feb. 2018 309-315A Self-Training Subspace Clustering Algorithm under Low-Rank Repre-sentation for Cancer Classification on Gene Expression Data. Xia, C., þ,TCBB July-Aug. 2018 1315-1324ACID: Association Correction for Imbalanced Data in GWAS. Bao, F., þ,TCBB Jan.-Feb. 2018 316-322



Analyzing Differential Regulatory Networks Modulated by Continuous-State Genomic Features in Glioblastoma Multiforme. Chiu, Y., þ, TCBBNov.-Dec. 2018 1754-1764ANTENNA, a Multi-Rank, Multi-Layered Recommender System for Infer-ring Reliable Drug-Gene-Disease Associations: Repurposing Diazoxide asa Targeted Anti-Cancer Therapy. Wang, A., þ, TCBB Nov.-Dec. 20181960-1967Application of Genetic Programming (GP) Formalism for Building DiseasePredictive Models from Protein-Protein Interactions (PPI) Data. Vyas, R.,þ, TCBB Jan.-Feb. 2018 27-37Bi-level and Bi-objective p-Median Type Problems for Integrative Cluster-ing: Application to Analysis of Cancer Gene-Expression and Drug-Response Data. Ushakov, A.V., þ, TCBB Jan.-Feb. 2018 46-59Complexity and Algorithms for Finding a Perfect Phylogeny from MixedTumor Samples. Hujdurovic, A., þ, TCBB Jan.-Feb. 2018 96-108Construction of Signaling Pathways with RNAi Data and Multiple Refer-ence Networks. Alim, M.A., þ, TCBB July-Aug. 2018 1079-1091Continuous Petri Nets and microRNA Analysis in Melanoma. Russo, G.,þ,TCBB Sept.-Oct. 2018 1492-1499Extracting Stage-Specific and Dynamic Modules Through Analyzing Mul-tiple Networks Associated with Cancer Progression. Ma, X., þ, TCBBMarch-April 2018 647-658Fuzzy-Rough Entropy Measure and Histogram Based Patient Selection formiRNARanking in Cancer.Pal, J.K.,þ, TCBBMarch-April 2018 659-672Grouped Gene Selection of Cancer via Adaptive Sparse Group Lasso Basedon Conditional Mutual Information. Li, J., þ, TCBB Nov.-Dec. 20182028-2038GSEH: A Novel Approach to Select Prostate Cancer-Associated GenesUsing Gene Expression Heterogeneity. Kim, H., þ, TCBB Jan.-Feb. 2018129-146Identifying Condition-Specific Modules by Clustering Multiple Networks.Ma, X., þ, TCBB Sept.-Oct. 2018 1636-1648Identifying Gene Network Rewiring by Integrating Gene Expression andGene Network Data. Xu, T.,þ, TCBBNov.-Dec. 2018 2079-2085Influence Networks Compared with Reaction Networks: Semantics,Expressivity and Attractors.Fages, F.,þ, TCBB July-Aug. 2018 1138-1151Integrating Multiple Data Sources for Combinatorial Marker Discovery: AStudy in Tumorigenesis. Bandyopadhyay, S., þ, TCBB March-April 2018673-687Low Rank Subspace Clustering via Discrete Constraint and HypergraphRegularization for Tumor Molecular Pattern Discovery. Liu, J., þ, TCBBSept.-Oct. 2018 1500-1512Modeling Methylation Patterns with Long Read Sequencing Data. Meyer,K.N., þ, TCBB July-Aug. 2018 1379-1389Novel Consensus Gene Selection Criteria for Distributed GPU Partial LeastSquares-Based Gene Microarray Analysis in Diffused Large B Cell Lym-phoma (DLBCL) and Related Findings.Wu, H., þ, TCBB Nov.-Dec. 20182039-2052Optimal Fault Detection and Diagnosis in Transcriptional Circuits UsingNext-Generation Sequencing. Bahadorinejad, A., þ, TCBB March-April2018 516-525PerPAS: Topology-Based Single Sample Pathway Analysis Method. Liu,C., þ, TCBB May -June 2018 1022-1027Petri Net Siphon Analysis and Graph Theoretic Measures for IdentifyingCombination Therapies in Cancer. Behinaein, B., þ, TCBB Jan.-Feb.2018 231-243Predicting MicroRNA-Disease Associations Based on Improved Micro-RNA and Disease Similarities. Lan, W., þ, TCBB Nov.-Dec. 2018 1774-1782Predicting the Absorption Potential of Chemical Compounds Through aDeep Learning Approach. Shin, M., þ, TCBB March-April 2018 432-440The Discovery of Mutated Driver Pathways in Cancer: Models and Algo-rithms. Zhang, J., þ, TCBB May -June 2018 988-998

CardiologyProteomic Evidence for In-Frame and Out-of-Frame Alternatively SplicedIsoforms in Human and Mouse. Ramalho, R.F., þ, TCBB July-Aug. 20181284-1289

Cell motilityRandom Sets of Stadiums in Square and Collective Behavior of Bacteria.Czapla, R., TCBB Jan.-Feb. 2018 251-256

Cellular biophysicsA Bipartite Network and Resource Transfer-Based Approach to InferlncRNA-Environmental Factor Associations. Zhou, J., þ, TCBB May-June 2018 753-759A Comparative Study for Identifying the Chromosome-Wide Spatial Clus-ters from High-Throughput Chromatin Conformation Capture Data. Li,X., þ, TCBB May -June 2018 774-787

A Graphical Model of Smoking-Induced Global Instability in Lung Cancer.Wang, Y., þ, TCBB Jan.-Feb. 2018 1-14A Novel Approach to Identify the miRNA-mRNA Causal RegulatoryModules in Cancer. Luo, J., þ, TCBB Jan.-Feb. 2018 309-315An Organelle Correlation-Guided Feature Selection Approach for Classify-ing Multi-Label Subcellular Bio-Images. Shao, W., þ, TCBB May -June2018 828-838Analysis of the Genome Sequence and Prediction of B-Cell Epitopes of theEnvelope Protein of Middle East Respiratory Syndrome-Coronavirus. Xie,Q., þ, TCBB July-Aug. 2018 1344-1350Bi-level and Bi-objective p-Median Type Problems for Integrative Cluster-ing: Application to Analysis of Cancer Gene-Expression and Drug-Response Data. Ushakov, A.V., þ, TCBB Jan.-Feb. 2018 46-59BRANE Clust: Cluster-Assisted Gene Regulatory Network InferenceRefinement. Pirayre, A., þ, TCBB May -June 2018 850-860Calculating the Expected Time to Eradicate HIV-1 Using a Markov Chain.Viswanath, N.C., TCBB Jan.-Feb. 2018 60-67Cell Population Tracking in a Honeycomb Structure Using an IMM FilterBased 3D Local Graph Matching Model. Liu, M., þ, TCBB Sept.-Oct.2018 1706-1717Construction of Signaling Pathways with RNAi Data and Multiple Refer-ence Networks. Alim, M.A., þ, TCBB July-Aug. 2018 1079-1091Continuous Petri Nets and microRNA Analysis in Melanoma. Russo, G.,þ,TCBB Sept.-Oct. 2018 1492-1499Detecting Essential Proteins Based on Network Topology, Gene Expres-sion Data, and Gene Ontology Information. Zhang, W., þ, TCBB Jan.-Feb. 2018 109-116Influence Networks Compared with Reaction Networks: Semantics, Expres-sivity and Attractors. Fages, F.,þ, TCBB July-Aug. 2018 1138-1151Modeling Methylation Patterns with Long Read Sequencing Data. Meyer,K.N., þ, TCBB July-Aug. 2018 1379-1389Modeling the Geometry and Dynamics of the Endoplasmic Reticulum Net-work. Lin, C., þ, TCBB March-April 2018 377-386Nucleosome Positioning of Intronless Genes in the Human Genome.Cheng, X., þ, TCBB July-Aug. 2018 1111-1121PerPAS: Topology-Based Single Sample Pathway Analysis Method. Liu,C., þ, TCBB May -June 2018 1022-1027Predicting the Absorption Potential of Chemical Compounds Through aDeep Learning Approach. Shin, M., þ, TCBB March-April 2018 432-440Prediction of HIV Drug Resistance by Combining Sequence and StructuralProperties. Khalid, Z., þ, TCBB May -June 2018 966-973PREMER: A Tool to Infer Biological Networks. Villaverde, A.F., þ, TCBBJuly-Aug. 2018 1193-1202REPA: Applying Pathway Analysis to Genome-Wide Transcription FactorBinding Data. Patra, P., þ, TCBB July-Aug. 2018 1270-1283SparseNCA: Sparse Network Component Analysis for Recovering Tran-scription Factor Activities with Incomplete Prior Information. Noor, A.,þ, TCBB March-April 2018 387-395

ChaosFeature Selection for Optimized High-Dimensional Biomedical Data Usingan Improved Shuffled Frog Leaping Algorithm. Hu, B., þ, TCBB Nov.-Dec. 2018 1765-1773

Chemical reactionsOrganisation-Oriented Coarse Graining and Refinement of StochasticReaction Networks.Mu, C., þ, TCBB July-Aug. 2018 1152-1166

ChemicalsA Slice-based 13C-detected NMR Spin System Forming and ResonanceAssignment Method. Alazmi, M., þ, TCBB Nov.-Dec. 2018 1999-2008

Classification algorithmsFeature Selection for Optimized High-Dimensional Biomedical Data Usingan Improved Shuffled Frog Leaping Algorithm. Hu, B., þ, TCBB Nov.-Dec. 2018 1765-1773Grouped Gene Selection of Cancer via Adaptive Sparse Group Lasso Basedon Conditional Mutual Information. Li, J., þ, TCBB Nov.-Dec. 20182028-2038

Clustering algorithmsCo-Expression Network Approach to Studying the Effects of BotulinumNeurotoxin-A.Mukund, K., þ, TCBB Nov.-Dec. 2018 2009-2016Network Community Detection Based on the Physarum-Inspired Computa-tional Framework. Gao, C., þ, TCBB Nov.-Dec. 2018 1916-1928

Clustering methodsLow Rank Subspace Clustering via Discrete Constraint and HypergraphRegularization for Tumor Molecular Pattern Discovery. Liu, J., þ, TCBBSept.-Oct. 2018 1500-1512

CognitionClassification of Alzheimer’s Disease Using Whole Brain HierarchicalNetwork. Liu, J., þ, TCBB March-April 2018 624-632



Probabilistic Methods in Computational Neuroscience. Zhang, J., þ, TCBBMarch-April 2018 535-536

Collision avoidanceSwarm Robots Search for Multiple Targets Based on an Improved Group-ing Strategy. Tang, Q., þ, TCBB Nov.-Dec. 2018 1943-1950

Combinatorial mathematicsA GRASP-Based Heuristic for the Sorting by Length-Weighted InversionsProblem. Arruda, T.d.S., þ, TCBB March-April 2018 352-363Integrating Multiple Data Sources for Combinatorial Marker Discovery: AStudy in Tumorigenesis. Bandyopadhyay, S., þ, TCBB March-April 2018673-687

Complex networksApplication of Fractal Theory on Motifs Counting in Biological Networks.Joveini, M.B.Z., þ, TCBB March-April 2018 613-623Complex Network Measures in Autism Spectrum Disorders. Sato, J.R., þ,TCBB March-April 2018 581-587

CompoundsEffectively Identifying Compound-Protein Interactions by Learning from Posi-tive andUnlabeled Examples.Cheng, Z.,þ, TCBBNov.-Dec. 2018 1832-1843

Computational biologyAdvances in the Application and Development of Non-Linear Global Opti-mization Techniques in Computational Structural Biology. Handl, J., þ,TCBB May -June 2018 688-689Guest Editorial.Murali, T.M., TCBB July-Aug. 2018 1036Guest Editors’ Introduction to the Special Section on the 14th InternationalConference on Computational Methods in Systems Biology (CMSB2016). Bartocci, E., þ, TCBB July-Aug. 2018 1122-1123

Computational complexityA Global Network Alignment Method Using Discrete Particle Swarm Opti-mization. Huang, J., þ, TCBB May -June 2018 705-718A New Efficient Algorithm for the Frequent Gene Team Problem. Wang,B., TCBB March-April 2018 588-598Algorithms for Pedigree Comparison. Chen, Z., þ, TCBB March-April2018 422-431Algorithms for the Majority Rule (+) Consensus Tree and the FrequencyDifference Consensus Tree. Jansson, J., þ, TCBB Jan.-Feb. 2018 15-26Autumn Algorithm—Computation of Hybridization Networks for RealisticPhylogenetic Trees. Huson, D.H., þ, TCBB March-April 2018 398-410Complexity and Algorithms for Finding a Perfect Phylogeny from MixedTumor Samples. Hujdurovic, A., þ, TCBB Jan.-Feb. 2018 96-108DTL-RnB: Algorithms and Tools for Summarizing the Space of DTL Rec-onciliations.Ma, W., þ, TCBB March-April 2018 411-421Efficient Algorithms for Sequence Analysis with Entropic Profiles. Pizzi,C., þ, TCBB Jan.-Feb. 2018 117-128Gene Tree Construction and Correction Using SuperTree and Reconcilia-tion. Lafond, M., þ, TCBB Sept.-Oct. 2018 1560-1570Optimal Block-Based Trimming for Next Generation Sequencing. Hedtke,I., þ, TCBB March-April 2018 364-376SparseNCA: Sparse Network Component Analysis for Recovering Tran-scription Factor Activities with Incomplete Prior Information. Noor, A.,þ, TCBB March-April 2018 387-395Species Tree Estimation Using ASTRAL: How Many Genes Are Enough?.Shekhar, S., þ, TCBB Sept.-Oct. 2018 1738-1747Structural Target Controllability of Linear Networks. Czeizler, E., þ,TCBB July-Aug. 2018 1217-1228

Computational efficiencyNetwork Community Detection Based on the Physarum-Inspired Computa-tional Framework. Gao, C., þ, TCBB Nov.-Dec. 2018 1916-1928

Computational geometryModeling the Geometry and Dynamics of the Endoplasmic Reticulum Net-work. Lin, C., þ, TCBB March-April 2018 377-386

Computational linguisticsBiological Event Trigger Identification with Noise Contrastive Estimation.Jiang, N., þ, TCBB Sept.-Oct. 2018 1549-1559

Computational modelingA Novel Computational Approach for Global Alignment for Multiple Bio-logical Networks. Djeddi, W.E., þ, TCBB Nov.-Dec. 2018 2060-2066ASSA-PBN: A Toolbox for Probabilistic Boolean Networks.Mizera, A., þ,TCBB July-Aug. 2018 1203-1216Controllability Analysis and Control Synthesis for the Ribosome FlowModel. Zarai, Y., þ, TCBB July-Aug. 2018 1351-1364Deep Sequencing Data Analysis. Ghosh, B.K., þ, TCBB March-April 2018482-483Guest Editorial for Special Section on BIBM 2015. Tian, T., þ, TCBBNov.-Dec. 2018 1752-1753Improve Biomedical Information Retrieval Using Modified Learning toRank Methods. Xu, B., þ, TCBB Nov.-Dec. 2018 1797-1809

SPF-CellTracker: Tracking Multiple Cells with Strongly-Correlated MovesUsing a Spatial Particle Filter.Hirose, O.,þ, TCBBNov.-Dec. 2018 1822-1831Structure-Guided Protein Transition Modeling with a Probabilistic Road-map Algorithm.Maximova, T., þ, TCBB Nov.-Dec. 2018 1783-1796

Computed tomographyImproving Alzheimer’s Disease Classification by Combining MultipleMeasures. Liu, J., þ, TCBB Sept.-Oct. 2018 1649-1659

Computer graphicsA Graphical Model of Smoking-Induced Global Instability in Lung Cancer.Wang, Y., þ, TCBB Jan.-Feb. 2018 1-14

Concave programmingLMMO: A Large Margin Approach for Refining Regulatory Motifs. Zhu,L., þ, TCBB May -June 2018 913-925

Control designRobust Gene Circuit Control Design for Time-Delayed Genetic RegulatoryNetworks Without SUM Regulatory Logic. Jiao, H., þ, TCBB Nov.-Dec.2018 2086-2093

Control system synthesisSampled-Data Stabilization for Fuzzy Genetic Regulatory Networks withLeakage Delays. Ali, M.S., þ, TCBB Jan.-Feb. 2018 271-285

Control theoryAltering Indispensable Proteins in Controlling Directed Human ProteinInteraction Network. Zhang, X., TCBB Nov.-Dec. 2018 2074-2078

ControllabilityAltering Indispensable Proteins in Controlling Directed Human ProteinInteraction Network. Zhang, X., TCBB Nov.-Dec. 2018 2074-2078Controllability Analysis and Control Synthesis for the Ribosome FlowModel. Zarai, Y., þ, TCBB July-Aug. 2018 1351-1364Structural Target Controllability of Linear Networks. Czeizler, E., þ,TCBB July-Aug. 2018 1217-1228

ConvergenceCoevolutionary Structure-Redesigned-Based Bacterial Foraging Optimiza-tion. Niu, B., þ, TCBB Nov.-Dec. 2018 1865-1876

Convex programmingLMMO: A Large Margin Approach for Refining Regulatory Motifs. Zhu,L., þ, TCBB May -June 2018 913-925

CopyrightDNA Watermarking Using Codon Postfix Technique. Hamad, S., þ, TCBBSept.-Oct. 2018 1605-1610

CorrelationCo-Expression Network Approach to Studying the Effects of BotulinumNeurotoxin-A.Mukund, K., þ, TCBB Nov.-Dec. 2018 2009-2016Novel Consensus Gene Selection Criteria for Distributed GPU Partial LeastSquares-Based Gene Microarray Analysis in Diffused Large B Cell Lym-phoma (DLBCL) and Related Findings.Wu, H., þ, TCBB Nov.-Dec. 20182039-2052

Correlation coefficientAnalyzing Differential Regulatory Networks Modulated by Continuous-State Genomic Features in Glioblastoma Multiforme. Chiu, Y., þ, TCBBNov.-Dec. 2018 1754-1764

Cost functionLocal-Nearest-Neighbors-Based Feature Weighting for Gene Selection. An,S., þ, TCBB Sept.-Oct. 2018 1538-1548

Covariance matricesIdentifying Gene Network Rewiring by Integrating Gene Expression andGene Network Data. Xu, T., þ, TCBB Nov.-Dec. 2018 2079-2085

CryptographyImplementation and Evaluation of an Algorithm for Cryptographically Pri-vate Principal Component Analysis on Genomic Data. Bogdanov, D., þ,TCBB Sept.-Oct. 2018 1427-1432Protecting Privacy and Security of Genomic Data in i2b2 with Homomor-phic Encryption and Differential Privacy. Raisaro, J.L., þ, TCBB Sept.-Oct. 2018 1413-1426

Crystal structureAnalysis of the Genome Sequence and Prediction of B-Cell Epitopes of theEnvelope Protein of Middle East Respiratory Syndrome-Coronavirus. Xie,Q., þ, TCBB July-Aug. 2018 1344-1350Conformational Sampling of a Biomolecular Rugged Energy Landscape.Rydzewski, J., þ, TCBB May -June 2018 732-739

D

Data analysisA Combined PLS and Negative Binomial Regression Model for InferringAssociation Networks from Next-Generation Sequencing Count Data.Pesonen, M., þ, TCBB May -June 2018 760-773



A Copula-Based Granger Causality Measure for the Analysis of NeuralSpike Train Data. Hu, M., þ, TCBB March-April 2018 562-569A Framework for Identifying Genotypic Information from ClinicalRecords: Exploiting Integrated Ontology Structures to Transfer Annota-tions between ICD Codes and Gene Ontologies. Hashemikhabir, S., þ,TCBB July-Aug. 2018 1259-1269A Global Network Alignment Method Using Discrete Particle Swarm Opti-mization. Huang, J., þ, TCBB May -June 2018 705-718ANTENNA, a Multi-Rank, Multi-Layered Recommender System for Infer-ring Reliable Drug-Gene-Disease Associations: Repurposing Diazoxide asa Targeted Anti-Cancer Therapy. Wang, A., þ, TCBB Nov.-Dec. 20181960-1967Bi-level and Bi-objective p-Median Type Problems for Integrative Cluster-ing: Application to Analysis of Cancer Gene-Expression and Drug-Response Data. Ushakov, A.V., þ, TCBB Jan.-Feb. 2018 46-59Deep Sequencing Data Analysis. Ghosh, B.K., þ, TCBB March-April 2018482-483Detecting Multivariate Gene Interactions in RNA-Seq Data Using OptimalBayesian Classification. Knight, J.M., þ, TCBB March-April 2018 484-493Heavy-Tailed Noise Suppression and Derivative Wavelet Scalogram forDetecting DNA Copy Number Aberrations. Nguyen, N., þ, TCBB Sept.-Oct. 2018 1625-1635Local-Nearest-Neighbors-Based Feature Weighting for Gene Selection. An,S., þ, TCBB Sept.-Oct. 2018 1538-1548MeTDiff: A Novel Differential RNA Methylation Analysis for MeRIP-SeqData. Cui, X., þ, TCBB March-April 2018 526-534NGS-FC: A Next-Generation Sequencing Data Format Converter. Yu, C.,þ, TCBB Sept.-Oct. 2018 1683-1691Optimal Block-Based Trimming for Next Generation Sequencing. Hedtke,I., þ, TCBB March-April 2018 364-376Regularized Non-Negative Matrix Factorization for Identifying Differen-tially Expressed Genes and Clustering Samples: A Survey. Liu, J., þ,TCBB May -June 2018 974-987SparseNCA: Sparse Network Component Analysis for Recovering Tran-scription Factor Activities with Incomplete Prior Information. Noor, A.,þ, TCBB March-April 2018 387-395

Data encapsulationDNAWatermarking Using Codon Postfix Technique. Hamad, S., þ, TCBBSept.-Oct. 2018 1605-1610

Data handlingA Sparse Regression Method for Group-Wise Feature Selection with FalseDiscovery Rate Control. Gossmann, A., þ, TCBB July-Aug. 2018 1066-1078Optimal Fault Detection and Diagnosis in Transcriptional Circuits UsingNext-Generation Sequencing. Bahadorinejad, A., þ, TCBB March-April2018 516-525

Data integrationIntegrating Multiple Data Sources for Combinatorial Marker Discovery: AStudy in Tumorigenesis. Bandyopadhyay, S., þ, TCBB March-April 2018673-687

Data miningA Review on Methods for Detecting SNP Interactions in High-DimensionalGenomic Data. Uppu, S., þ, TCBB March-April 2018 599-612A Two-Stage Biomedical Event Trigger Detection Method Integrating Fea-ture Selection and Word Embeddings. He, X., þ, TCBB July-Aug. 20181325-1332ACID: Association Correction for Imbalanced Data in GWAS. Bao, F., þ,TCBB Jan.-Feb. 2018 316-322ANTENNA, a Multi-Rank, Multi-Layered Recommender System for Infer-ring Reliable Drug-Gene-Disease Associations: Repurposing Diazoxide asa Targeted Anti-Cancer Therapy. Wang, A., þ, TCBB Nov.-Dec. 20181960-1967Attention Recognition in EEG-Based Affective Learning Research UsingCFS+KNN Algorithm. Hu, B., þ, TCBB Jan.-Feb. 2018 38-45Bioinformatic Workflow Extraction from Scientific Texts based on WordSense Disambiguation. Halioui, A., þ, TCBB Nov.-Dec. 2018 1979-1990Co-Expression Network Approach to Studying the Effects of BotulinumNeurotoxin-A.Mukund, K., þ, TCBB Nov.-Dec. 2018 2009-2016Discovering Gene Regulatory Elements Using Coverage-Based Heuristics.Al-Ouran, R., þ, TCBB July-Aug. 2018 1290-1300Integrating Multiple Data Sources for Combinatorial Marker Discovery: AStudy in Tumorigenesis. Bandyopadhyay, S., þ, TCBB March-April 2018673-687Multiple-Swarm Ensembles: Improving the Predictive Power and Robust-ness of Predictive Models and Its Use in Computational Biology. Alves,P., þ, TCBB May -June 2018 926-933

Multiscale and Multimodal Analysis for Computational Biology. Gao, X.,þ, TCBB Nov.-Dec. 2018 1951-1952Novelty Indicator for Enhanced Prioritization of Predicted Gene OntologyAnnotations. Chicco, D., þ, TCBB May -June 2018 954-965Regularized Non-Negative Matrix Factorization for Identifying Differen-tially Expressed Genes and Clustering Samples: A Survey. Liu, J., þ,TCBB May -June 2018 974-987Towards Extracting Supporting Information About Predicted Protein-Pro-tein Interactions. Roth, A., þ, TCBB July-Aug. 2018 1239-1246

Data modelsIdentifying Gene Network Rewiring by Integrating Gene Expression andGene Network Data. Xu, T., þ, TCBB Nov.-Dec. 2018 2079-2085Low Rank Subspace Clustering via Discrete Constraint and HypergraphRegularization for Tumor Molecular Pattern Discovery. Liu, J., þ, TCBBSept.-Oct. 2018 1500-1512Predicting Hospital Readmission via Cost-Sensitive Deep Learning. Wang,H., þ, TCBB Nov.-Dec. 2018 1968-1978Using Machine Learning to Improve the Prediction of Functional Outcomein Ischemic Stroke Patients. Monteiro, M., þ, TCBB Nov.-Dec. 20181953-1959

Data privacyAn Inference Attack on Genomic Data Using Kinship, Complex Correla-tions, and Phenotype Information. Deznabi, I., þ, TCBB July-Aug. 20181333-1343DNA Watermarking Using Codon Postfix Technique. Hamad, S., þ, TCBBSept.-Oct. 2018 1605-1610Implementation and Evaluation of an Algorithm for Cryptographically Pri-vate Principal Component Analysis on Genomic Data. Bogdanov, D., þ,TCBB Sept.-Oct. 2018 1427-1432Protecting Privacy and Security of Genomic Data in i2b2 with Homomor-phic Encryption and Differential Privacy. Raisaro, J.L., þ, TCBB Sept.-Oct. 2018 1413-1426Simulating the Large-Scale Erosion of Genomic Privacy Over Time.Backes, M., þ, TCBB Sept.-Oct. 2018 1405-1412

Data structuresEfficient Algorithms for Sequence Analysis with Entropic Profiles. Pizzi,C., þ, TCBB Jan.-Feb. 2018 117-128Encoding Data Using Biological Principles: The Multisample Variant For-mat for Phylogenomics and Population Genomics. Pease, J.B., þ, TCBBJuly-Aug. 2018 1231-1238NGS-FC: A Next-Generation Sequencing Data Format Converter. Yu, C.,þ, TCBB Sept.-Oct. 2018 1683-1691Sequence-Based Prediction of Putative Transcription Factor Binding Sitesin DNA Sequences of Any Length. Lee, W., þ, TCBB Sept.-Oct. 20181461-1469

Data visualizationAlgorithmic Mapping and Characterization of the Drug-Induced Pheno-typic-Response Space of Parasites Causing Schistosomiasis. Singh, R., þ,TCBB March-April 2018 469-481

Database management systemsOptimizing Phylogenetic Queries for Performance. Jamil, H.M., TCBBSept.-Oct. 2018 1692-1705

Decision treesAttention Recognition in EEG-Based Affective Learning Research UsingCFS+KNN Algorithm. Hu, B., þ, TCBB Jan.-Feb. 2018 38-45Comparison of Machine Learning Approaches for Prediction of AdvancedLiver Fibrosis in Chronic Hepatitis C Patients. Hashem, S., þ, TCBB May-June 2018 861-868

Deep learningPredicting Hospital Readmission via Cost-Sensitive Deep Learning. Wang,H., þ, TCBB Nov.-Dec. 2018 1968-1978

Delay effectsRobust Gene Circuit Control Design for Time-Delayed Genetic RegulatoryNetworks Without SUM Regulatory Logic. Jiao, H., þ, TCBB Nov.-Dec.2018 2086-2093

DelaysFilter Design with Adaptation to Time-Delay Parameters for Genetic Regu-latory Networks. Jiao, H., þ, TCBB Jan.-Feb. 2018 323-329Sampled-Data Stabilization for Fuzzy Genetic Regulatory Networks withLeakage Delays. Ali, M.S., þ, TCBB Jan.-Feb. 2018 271-285

DementiaImproving Alzheimer’s Disease Classification by Combining MultipleMeasures. Liu, J., þ, TCBB Sept.-Oct. 2018 1649-1659

Design of experimentsOptimal Objective-Based Experimental Design for Uncertain DynamicalGene Networks with Experimental Error. Mohsenizadeh, D.N., þ, TCBBJan.-Feb. 2018 218-230



Deterministic algorithmsAlgorithms for the Majority Rule (+) Consensus Tree and the FrequencyDifference Consensus Tree. Jansson, J., þ, TCBB Jan.-Feb. 2018 15-26

Differential equationsGene Regulatory Network Inference from Perturbed Time-Series Expres-sion Data via Ordered Dynamical Expansion of Non-Steady State Actors.Zamanighomi, M., þ, TCBB July-Aug. 2018 1093-1106Identifying Gene Network Rewiring by Integrating Gene Expression andGene Network Data. Xu, T., þ, TCBB Nov.-Dec. 2018 2079-2085

DiseasesA Bipartite Network and Resource Transfer-Based Approach to InferlncRNA-Environmental Factor Associations. Zhou, J., þ, TCBB May-June 2018 753-759A Framework for Identifying Genotypic Information from ClinicalRecords: Exploiting Integrated Ontology Structures to Transfer Annota-tions between ICD Codes and Gene Ontologies. Hashemikhabir, S., þ,TCBB July-Aug. 2018 1259-1269A Just-in-Time Learning Based Monitoring and Classification Method forHyper/Hypocalcemia Diagnosis. Peng, X., þ, TCBB May -June 2018 788-801A Review on Methods for Detecting SNP Interactions in High-DimensionalGenomic Data. Uppu, S., þ, TCBB March-April 2018 599-612A Spatial-Temporal Method to Detect Global Influenza Epidemics UsingHeterogeneous Data Collected from the Internet. Zhou, X., þ, TCBB May-June 2018 802-812ACID: Association Correction for Imbalanced Data in GWAS. Bao, F., þ,TCBB Jan.-Feb. 2018 316-322Algorithmic Mapping and Characterization of the Drug-Induced Pheno-typic-Response Space of Parasites Causing Schistosomiasis. Singh, R., þ,TCBB March-April 2018 469-481Algorithms for Pedigree Comparison. Chen, Z., þ, TCBB March-April2018 422-431Altering Indispensable Proteins in Controlling Directed Human ProteinInteraction Network. Zhang, X., TCBB Nov.-Dec. 2018 2074-2078Analysis of the Genome Sequence and Prediction of B-Cell Epitopes of theEnvelope Protein of Middle East Respiratory Syndrome-Coronavirus. Xie,Q., þ, TCBB July-Aug. 2018 1344-1350ANTENNA, a Multi-Rank, Multi-Layered Recommender System for Infer-ring Reliable Drug-Gene-Disease Associations: Repurposing Diazoxide asa Targeted Anti-Cancer Therapy. Wang, A., þ, TCBB Nov.-Dec. 20181960-1967Calculating the Expected Time to Eradicate HIV-1 Using a Markov Chain.Viswanath, N.C., TCBB Jan.-Feb. 2018 60-67Classification of Alzheimer’s Disease Using Whole Brain HierarchicalNetwork. Liu, J., þ, TCBB March-April 2018 624-632Classification of State Trajectories in Gene Regulatory Networks. Karba-layghareh, A., þ, TCBB Jan.-Feb. 2018 68-82Combining Supervised and Unsupervised Learning for Improved miRNATarget Prediction. Sedaghat, N., þ, TCBB Sept.-Oct. 2018 1594-1604Comparison of Machine Learning Approaches for Prediction of AdvancedLiver Fibrosis in Chronic Hepatitis C Patients. Hashem, S., þ, TCBB May-June 2018 861-868Complex Network Measures in Autism Spectrum Disorders. Sato, J.R., þ,TCBB March-April 2018 581-587Cortical Thinning and Cognitive Impairment in Parkinson’s Disease with-out Dementia. Zhang, L., þ, TCBB March-April 2018 570-580Discovering Perturbation of Modular Structure in HIV Progression by Inte-grating Multiple Data Sources Through Non-Negative Matrix Factoriza-tion. Ray, S., þ, TCBB May -June 2018 869-877Extracting Stage-Specific and Dynamic Modules Through Analyzing Mul-tiple Networks Associated with Cancer Progression. Ma, X., þ, TCBBMarch-April 2018 647-658From Optimization to Mapping: An Evolutionary Algorithm for ProteinEnergy Landscapes. Sapin, E., þ, TCBB May -June 2018 719-731GSEH: A Novel Approach to Select Prostate Cancer-Associated GenesUsing Gene Expression Heterogeneity. Kim, H., þ, TCBB Jan.-Feb. 2018129-146Hardware Accelerator for the Multifractal Analysis of DNA Sequences.Duarte-Sanchez, J.E., þ, TCBB Sept.-Oct. 2018 1611-1624Heavy-Tailed Noise Suppression and Derivative Wavelet Scalogram forDetecting DNA Copy Number Aberrations. Nguyen, N., þ, TCBB Sept.-Oct. 2018 1625-1635HEMEsPred: Structure-Based Ligand-Specific Heme Binding ResiduesPrediction by Using Fast-Adaptive Ensemble Learning Scheme. Zhang,J., þ, TCBB Jan.-Feb. 2018 147-156Identifying Condition-Specific Modules by Clustering Multiple Networks.Ma, X., þ, TCBB Sept.-Oct. 2018 1636-1648

Integrating Imaging Genomic Data in the Quest for Biomarkers of Schizo-phrenia Disease. Deng, S., þ, TCBB Sept.-Oct. 2018 1480-1491Predicting MicroRNA-Disease Associations Based on Improved Micro-RNA and Disease Similarities. Lan, W., þ, TCBB Nov.-Dec. 2018 1774-1782Prediction of HIV Drug Resistance by Combining Sequence and StructuralProperties. Khalid, Z., þ, TCBB May -June 2018 966-973Sparse Pathway-Induced Dynamic Network Biomarker Discovery for EarlyWarning Signal Detection in Complex Diseases. Torshizi, A.D., þ, TCBBMay -June 2018 1028-1034Structural Target Controllability of Linear Networks. Czeizler, E., þ,TCBB July-Aug. 2018 1217-1228

Distance learningAttention Recognition in EEG-Based Affective Learning Research UsingCFS+KNN Algorithm. Hu, B., þ, TCBB Jan.-Feb. 2018 38-45

DNAA GRASP-Based Heuristic for the Sorting by Length-Weighted InversionsProblem. Arruda, T.d.S., þ, TCBB March-April 2018 352-363A Review on Methods for Detecting SNP Interactions in High-DimensionalGenomic Data. Uppu, S., þ, TCBB March-April 2018 599-612A Simplified Description of Child Tables for Sequence Similarity Search.Frith, M.C., þ, TCBB Nov.-Dec. 2018 2067-2073A Sparse Regression Method for Group-Wise Feature Selection with FalseDiscovery Rate Control.Gossmann, A.,þ, TCBB July-Aug. 2018 1066-1078A Study of Cell-Free DNA Fragmentation Pattern and Its Application inDNA Sample Type Classification. Chen, S., þ, TCBB Sept.-Oct. 20181718-1722Advances in the Application and Development of Non-Linear Global Opti-mization Techniques in Computational Structural Biology. Handl, J., þ,TCBB May -June 2018 688-689Codon Context Optimization in Synthetic Gene Design. Papamichail, D.,þ, TCBB March-April 2018 452-459Constructing DNA Barcode Sets Based on Particle Swarm Optimization.Wang, B., þ, TCBB May -June 2018 999-1002DiscMLA: An Efficient Discriminative Motif Learning Algorithm over High-Throughput Datasets. Zhang, H.,þ, TCBBNov.-Dec. 2018 1810-1820Discovering Gene Regulatory Elements Using Coverage-Based Heuristics.Al-Ouran, R., þ, TCBB July-Aug. 2018 1290-1300DNA Assembly with De Bruijn Graphs Using an FPGA Platform. Poirier,C., þ, TCBB May -June 2018 1003-1009DNA Watermarking Using Codon Postfix Technique. Hamad, S., þ, TCBBSept.-Oct. 2018 1605-1610Efficient Algorithms for Sequence Analysis with Entropic Profiles. Pizzi,C., þ, TCBB Jan.-Feb. 2018 117-128Genome Rearrangement with ILP. Hartmann, T., þ, TCBB Sept.-Oct. 20181585-1593Hardware Accelerator for the Multifractal Analysis of DNA Sequences.Duarte-Sanchez, J.E., þ, TCBB Sept.-Oct. 2018 1611-1624Heavy-Tailed Noise Suppression and Derivative Wavelet Scalogram forDetecting DNA Copy Number Aberrations. Nguyen, N., þ, TCBB Sept.-Oct. 2018 1625-1635Inferring Gene-Species Assignments in the Presence of Horizontal GeneTransfer.Mykowiecka, A., þ, TCBB Sept.-Oct. 2018 1571-1578Influence Networks Compared with Reaction Networks: Semantics, Expres-sivity and Attractors. Fages, F.,þ, TCBB July-Aug. 2018 1138-1151Integrating Imaging Genomic Data in the Quest for Biomarkers of Schizo-phrenia Disease. Deng, S., þ, TCBB Sept.-Oct. 2018 1480-1491Introducing a Stable Bootstrap Validation Framework for Reliable Geno-mic Signature Extraction. Chlis, N., þ, TCBB Jan.-Feb. 2018 181-190Machine Learned Replacement of N-Labels for Basecalled Sequences inDNA Barcoding.Ma, E.Y.T., þ, TCBB Jan.-Feb. 2018 191-204Modeling Methylation Patterns with Long Read Sequencing Data. Meyer,K.N., þ, TCBB July-Aug. 2018 1379-1389Nucleosome Positioning of Intronless Genes in the Human Genome.Cheng, X., þ, TCBB July-Aug. 2018 1111-1121Scaffolding of Ancient Contigs and Ancestral Reconstruction in a Phyloge-netic Framework. Luhmann, N., þ, TCBB Nov.-Dec. 2018 2094-2100Sequence-Based Prediction of Putative Transcription Factor Binding Sitesin DNA Sequences of Any Length. Lee, W., þ, TCBB Sept.-Oct. 20181461-1469Simulating the Large-Scale Erosion of Genomic Privacy Over Time.Backes, M., þ, TCBB Sept.-Oct. 2018 1405-1412

Drug deliveryANTENNA, a Multi-Rank, Multi-Layered Recommender System for Infer-ring Reliable Drug-Gene-Disease Associations: Repurposing Diazoxide asa Targeted Anti-Cancer Therapy. Wang, A., þ, TCBB Nov.-Dec. 20181960-1967



DrugsAlgorithmic Mapping and Characterization of the Drug-Induced Pheno-typic-Response Space of Parasites Causing Schistosomiasis. Singh, R., þ,TCBB March-April 2018 469-481Altering Indispensable Proteins in Controlling Directed Human ProteinInteraction Network. Zhang, X., TCBB Nov.-Dec. 2018 2074-2078Bi-level and Bi-objective p-Median Type Problems for Integrative Cluster-ing: Application to Analysis of Cancer Gene-Expression and Drug-Response Data. Ushakov, A.V., þ, TCBB Jan.-Feb. 2018 46-59Continuous Petri Nets and microRNA Analysis in Melanoma. Russo, G.,þ,TCBB Sept.-Oct. 2018 1492-1499Effectively Identifying Compound-Protein Interactions by Learning fromPositive and Unlabeled Examples. Cheng, Z., þ, TCBB Nov.-Dec. 20181832-1843Enumerating Substituted Benzene Isomers of Tree-Like Chemical Graphs.Li, J., þ, TCBB March-April 2018 633-646HEMEsPred: Structure-Based Ligand-Specific Heme Binding ResiduesPrediction by Using Fast-Adaptive Ensemble Learning Scheme. Zhang,J., þ, TCBB Jan.-Feb. 2018 147-156PerPAS: Topology-Based Single Sample Pathway Analysis Method. Liu,C., þ, TCBB May -June 2018 1022-1027Petri Net Siphon Analysis and Graph Theoretic Measures for IdentifyingCombination Therapies in Cancer. Behinaein, B., þ, TCBB Jan.-Feb.2018 231-243Predicting the Absorption Potential of Chemical Compounds Through aDeep Learning Approach. Shin, M., þ, TCBB March-April 2018 432-440Prediction of HIV Drug Resistance by Combining Sequence and StructuralProperties. Khalid, Z., þ, TCBB May -June 2018 966-973

Dynamic programmingAlgorithms for Pedigree Comparison. Chen, Z., þ, TCBB March-April2018 422-431Enumerating Substituted Benzene Isomers of Tree-Like Chemical Graphs.Li, J., þ, TCBB March-April 2018 633-646Gene Tree Construction and Correction Using SuperTree and Reconcilia-tion. Lafond, M., þ, TCBB Sept.-Oct. 2018 1560-1570NAHAL-Flex: A Numerical and Alphabetical Hinge Detection Algorithmfor Flexible Protein Structure Alignment. Fotoohifiroozabadi, S., þ,TCBB May -June 2018 934-943

E

ElectroencephalographyAttention Recognition in EEG-Based Affective Learning Research UsingCFS+KNN Algorithm. Hu, B., þ, TCBB Jan.-Feb. 2018 38-45

Electronic data interchangeNGS-FC: A Next-Generation Sequencing Data Format Converter. Yu, C.,þ, TCBB Sept.-Oct. 2018 1683-1691

Electronic health recordsA Framework for Identifying Genotypic Information from ClinicalRecords: Exploiting Integrated Ontology Structures to Transfer Annota-tions between ICD Codes and Gene Ontologies. Hashemikhabir, S., þ,TCBB July-Aug. 2018 1259-1269Protecting Privacy and Security of Genomic Data in i2b2 with Homomor-phic Encryption and Differential Privacy. Raisaro, J.L., þ, TCBB Sept.-Oct. 2018 1413-1426

Electronic medical recordsPredicting Hospital Readmission via Cost-Sensitive Deep Learning. Wang,H., þ, TCBB Nov.-Dec. 2018 1968-1978

EncodingEncoding Data Using Biological Principles: The Multisample Variant For-mat for Phylogenomics and Population Genomics. Pease, J.B., þ, TCBBJuly-Aug. 2018 1231-1238

EntropyComplex Network Measures in Autism Spectrum Disorders. Sato, J.R., þ,TCBB March-April 2018 581-587Efficient Algorithms for Sequence Analysis with Entropic Profiles. Pizzi,C., þ, TCBB Jan.-Feb. 2018 117-128Fuzzy-Rough Entropy Measure and Histogram Based Patient Selection formiRNA Ranking in Cancer. Pal, J.K., þ, TCBB March-April 2018 659-672Grouped Gene Selection of Cancer via Adaptive Sparse Group Lasso Basedon Conditional Mutual Information. Li, J., þ, TCBB Nov.-Dec. 20182028-2038PREMER: A Tool to Infer Biological Networks. Villaverde, A.F., þ, TCBBJuly-Aug. 2018 1193-1202

EnzymesContinuous Petri Nets and microRNA Analysis in Melanoma. Russo, G.,þ,TCBB Sept.-Oct. 2018 1492-1499Identification and Analysis of Key Residues in Protein–RNA Complexes.Kulandaisamy, A., þ, TCBB Sept.-Oct. 2018 1436-1444Prediction of HIV Drug Resistance by Combining Sequence and StructuralProperties. Khalid, Z., þ, TCBB May -June 2018 966-973

EpidemicsA Spatial-Temporal Method to Detect Global Influenza Epidemics UsingHeterogeneous Data Collected from the Internet. Zhou, X., þ, TCBB May-June 2018 802-812

ErosionSimulating the Large-Scale Erosion of Genomic Privacy Over Time.Backes, M., þ, TCBB Sept.-Oct. 2018 1405-1412

Evolution (biological)Bijective Diameters of Gene Tree Parsimony Costs. G�orecki, P., þ, TCBBSept.-Oct. 2018 1723-1727DTL-RnB: Algorithms and Tools for Summarizing the Space of DTL Rec-onciliations.Ma, W., þ, TCBB March-April 2018 411-421Efficient Quartet Representations of Trees and Applications to Supertreeand Summary Methods. Davidson, R., þ, TCBB May -June 2018 1010-1015Inferring Gene-Species Assignments in the Presence of Horizontal GeneTransfer.Mykowiecka, A., þ, TCBB Sept.-Oct. 2018 1571-1578Nonbinary Tree-Based Phylogenetic Networks. Jetten, L., þ, TCBB Jan.-Feb. 2018 205-217Species Tree Estimation Using ASTRAL: How Many Genes Are Enough?.Shekhar, S., þ, TCBB Sept.-Oct. 2018 1738-1747Species Tree Inference from Gene Splits by Unrooted STAR Methods. All-man, E.S., þ, TCBB Jan.-Feb. 2018 337-342Tanglegrams: A Reduction Tool for Mathematical Phylogenetics. Matsen,F.A., þ, TCBB Jan.-Feb. 2018 343-349

Evolutionary computationA GRASP-Based Heuristic for the Sorting by Length-Weighted InversionsProblem. Arruda, T.d.S., þ, TCBB March-April 2018 352-363A Memetic Algorithm for 3D Protein Structure Prediction Problem.Correa, L., þ, TCBB May -June 2018 690-704Coevolutionary Structure-Redesigned-Based Bacterial Foraging Optimiza-tion. Niu, B., þ, TCBB Nov.-Dec. 2018 1865-1876Environment Sensitivity-Based Cooperative Co-Evolutionary Algorithmsfor Dynamic Multi-Objective Optimization. Xu, B., þ, TCBB Nov.-Dec.2018 1877-1890From Optimization to Mapping: An Evolutionary Algorithm for ProteinEnergy Landscapes. Sapin, E., þ, TCBB May -June 2018 719-731GPU-Based Point Cloud Superpositioning for Structural Comparisons ofProtein Binding Sites. Leinweber, M., þ, TCBB May -June 2018 740-752Incorporation of Solvent Effect into Multi-Objective Evolutionary Algo-rithm for Improved Protein Structure Prediction. Gao, S., þ, TCBB July-Aug. 2018 1365-1378Special Section on Swarm-Based Algorithms and Applications in Compu-tational Biology and Bioinformatics. Tan, Y., þ, TCBB Nov.-Dec. 20181863-1864

F

Fault detectionDeep Sequencing Data Analysis. Ghosh, B.K., þ, TCBB March-April 2018482-483

Fault diagnosisOptimal Fault Detection and Diagnosis in Transcriptional Circuits UsingNext-Generation Sequencing. Bahadorinejad, A., þ, TCBB March-April2018 516-525

Feature extractionA Self-Training Subspace Clustering Algorithm under Low-Rank Repre-sentation for Cancer Classification on Gene Expression Data. Xia, C., þ,TCBB July-Aug. 2018 1315-1324A Two-Stage Biomedical Event Trigger Detection Method Integrating Fea-ture Selection and Word Embeddings. He, X., þ, TCBB July-Aug. 20181325-1332An Organelle Correlation-Guided Feature Selection Approach for Classify-ing Multi-Label Subcellular Bio-Images. Shao, W., þ, TCBB May -June2018 828-838Classification of Alzheimer’s Disease Using Whole Brain HierarchicalNetwork. Liu, J., þ, TCBB March-April 2018 624-632



Combining Supervised and Unsupervised Learning for Improved miRNATarget Prediction. Sedaghat, N., þ, TCBB Sept.-Oct. 2018 1594-1604Improving Alzheimer’s Disease Classification by Combining MultipleMeasures. Liu, J., þ, TCBB Sept.-Oct. 2018 1649-1659Predicting Hospital Readmission via Cost-Sensitive Deep Learning. Wang,H., þ, TCBB Nov.-Dec. 2018 1968-1978Region Growing for Segmenting Green Microalgae Images. Borges, V.R.P., þ, TCBB Jan.-Feb. 2018 257-270RF-NR: Random Forest Based Approach for Improved Classification ofNuclear Receptors. Ismail, H.D., þ, TCBB Nov.-Dec. 2018 1844-1852

Feature selectionA Sparse Regression Method for Group-Wise Feature Selection with FalseDiscovery Rate Control. Gossmann, A., þ, TCBB July-Aug. 2018 1066-1078An Organelle Correlation-Guided Feature Selection Approach for Classify-ing Multi-Label Subcellular Bio-Images. Shao, W., þ, TCBB May -June2018 828-838Integrating Imaging Genomic Data in the Quest for Biomarkers of Schizo-phrenia Disease. Deng, S., þ, TCBB Sept.-Oct. 2018 1480-1491Introducing a Stable Bootstrap Validation Framework for Reliable Geno-mic Signature Extraction. Chlis, N., þ, TCBB Jan.-Feb. 2018 181-190Mutli-Features Prediction of Protein Translational Modification Sites. Bao,W., þ, TCBB Sept.-Oct. 2018 1453-1460Prediction of Hot Regions in PPIs Based on Improved Local CommunityStructure Detecting. Lin, X., þ, TCBB Sept.-Oct. 2018 1470-1479

FeedbackComputing Minimum Reaction Modifications in a Boolean Metabolic Net-work. Tamura, T., þ, TCBB Nov.-Dec. 2018 1853-1862

Field programmable gate arraysDNA Assembly with De Bruijn Graphs Using an FPGA Platform. Poirier,C., þ, TCBB May -June 2018 1003-1009Hardware Accelerator for the Multifractal Analysis of DNA Sequences.Duarte-Sanchez, J.E., þ, TCBB Sept.-Oct. 2018 1611-1624

Filtering theoryCell Population Tracking in a Honeycomb Structure Using an IMM FilterBased 3D Local Graph Matching Model. Liu, M., þ, TCBB Sept.-Oct.2018 1706-1717

FractalsApplication of Fractal Theory on Motifs Counting in Biological Networks.Joveini, M.B.Z., þ, TCBB March-April 2018 613-623Hardware Accelerator for the Multifractal Analysis of DNA Sequences.Duarte-Sanchez, J.E., þ, TCBB Sept.-Oct. 2018 1611-1624

Fuzzy controlSampled-Data Stabilization for Fuzzy Genetic Regulatory Networks withLeakage Delays. Ali, M.S., þ, TCBB Jan.-Feb. 2018 271-285

Fuzzy set theoryAssessment of Semantic Similarity between Proteins Using InformationContent and Topological Properties of the Gene Ontology Graph. Dutta,P., þ, TCBB May -June 2018 839-849Fuzzy-Rough Entropy Measure and Histogram Based Patient Selection formiRNA Ranking in Cancer. Pal, J.K., þ, TCBB March-April 2018 659-672

G

Gaussian distributionHeavy-Tailed Noise Suppression and Derivative Wavelet Scalogram forDetecting DNA Copy Number Aberrations. Nguyen, N., þ, TCBB Sept.-Oct. 2018 1625-1635

Gaussian noiseHeavy-Tailed Noise Suppression and Derivative Wavelet Scalogram forDetecting DNA Copy Number Aberrations. Nguyen, N., þ, TCBB Sept.-Oct. 2018 1625-1635

Gene expression“Super Gene Set” Causal Relationship Discovery from Functional Geno-mics Data. Yue, Z., þ, TCBB Nov.-Dec. 2018 1991-1998A Bi-Objective RNN Model to Reconstruct Gene Regulatory Network: AModified Multi-Objective Simulated Annealing Approach. Biswas, S., þ,TCBB Nov.-Dec. 2018 2053-2059Correction to “Detecting Essential Proteins Based on Network Topology,Gene Expression Data, and Gene Ontology Information”. Zhang, W., þ,TCBB May -June 2018 1035DiscMLA: An Efficient Discriminative Motif Learning Algorithm overHigh-Throughput Datasets. Zhang, H., þ, TCBB Nov.-Dec. 2018 1810-1820

Identifying Gene Network Rewiring by Integrating Gene Expression andGene Network Data. Xu, T., þ, TCBB Nov.-Dec. 2018 2079-2085Local-Nearest-Neighbors-Based Feature Weighting for Gene Selection. An,S., þ, TCBB Sept.-Oct. 2018 1538-1548Low Rank Subspace Clustering via Discrete Constraint and HypergraphRegularization for Tumor Molecular Pattern Discovery. Liu, J., þ, TCBBSept.-Oct. 2018 1500-1512Novel Consensus Gene Selection Criteria for Distributed GPU Partial LeastSquares-Based Gene Microarray Analysis in Diffused Large B Cell Lym-phoma (DLBCL) and Related Findings.Wu, H., þ, TCBB Nov.-Dec. 20182039-2052

Genetic algorithmsApplication of Genetic Programming (GP) Formalism for Building DiseasePredictive Models from Protein-Protein Interactions (PPI) Data. Vyas, R.,þ, TCBB Jan.-Feb. 2018 27-37Comparison of Machine Learning Approaches for Prediction of AdvancedLiver Fibrosis in Chronic Hepatitis C Patients. Hashem, S., þ, TCBB May-June 2018 861-868Feature Selection for Optimized High-Dimensional Biomedical Data Usingan Improved Shuffled Frog Leaping Algorithm. Hu, B., þ, TCBB Nov.-Dec. 2018 1765-1773NAHAL-Flex: A Numerical and Alphabetical Hinge Detection Algorithmfor Flexible Protein Structure Alignment. Fotoohifiroozabadi, S., þ,TCBB May -June 2018 934-943Network Community Detection Based on the Physarum-Inspired Computa-tional Framework. Gao, C., þ, TCBB Nov.-Dec. 2018 1916-1928

Genetics3D Genome Reconstruction with ShRec3D+ and Hi-C Data. Li, J., þ,TCBB March-April 2018 460-468A Bi-Objective RNN Model to Reconstruct Gene Regulatory Network: AModified Multi-Objective Simulated Annealing Approach. Biswas, S., þ,TCBB Nov.-Dec. 2018 2053-2059A Bipartite Network and Resource Transfer-Based Approach to InferlncRNA-Environmental Factor Associations. Zhou, J., þ, TCBB May-June 2018 753-759A Comparative Study for Identifying the Chromosome-Wide Spatial Clus-ters from High-Throughput Chromatin Conformation Capture Data. Li,X., þ, TCBB May -June 2018 774-787A Framework for Identifying Genotypic Information from ClinicalRecords: Exploiting Integrated Ontology Structures to Transfer Annota-tions between ICD Codes and Gene Ontologies. Hashemikhabir, S., þ,TCBB July-Aug. 2018 1259-1269A Graphical Model of Smoking-Induced Global Instability in Lung Cancer.Wang, Y., þ, TCBB Jan.-Feb. 2018 1-14A GRASP-Based Heuristic for the Sorting by Length-Weighted InversionsProblem. Arruda, T.d.S., þ, TCBB March-April 2018 352-363A Model-Based Tool for the Analysis and Design of Gene Regulatory Net-works. Ironi, L., þ, TCBB July-Aug. 2018 1301-1314A New Efficient Algorithm for the Frequent Gene Team Problem. Wang,B., TCBB March-April 2018 588-598A Novel Approach to Identify the miRNA-mRNA Causal Regulatory Mod-ules in Cancer. Luo, J., þ, TCBB Jan.-Feb. 2018 309-315A Novel Computational Approach for Global Alignment for Multiple Bio-logical Networks. Djeddi, W.E., þ, TCBB Nov.-Dec. 2018 2060-2066A Review on Methods for Detecting SNP Interactions in High-DimensionalGenomic Data. Uppu, S., þ, TCBB March-April 2018 599-612A Self-Training Subspace Clustering Algorithm under Low-Rank Repre-sentation for Cancer Classification on Gene Expression Data. Xia, C., þ,TCBB July-Aug. 2018 1315-1324A Simplified Description of Child Tables for Sequence Similarity Search.Frith, M.C., þ, TCBB Nov.-Dec. 2018 2067-2073A Sparse Regression Method for Group-Wise Feature Selection with FalseDiscovery Rate Control.Gossmann, A.,þ, TCBB July-Aug. 2018 1066-1078ACID: Association Correction for Imbalanced Data in GWAS. Bao, F., þ,TCBB Jan.-Feb. 2018 316-322Aggregation for Computing Multi-Modal Stationary Distributions in 1-DGene Regulatory Networks. Avcu, N., þ, TCBB May -June 2018 813-827Algorithmic Mapping and Characterization of the Drug-Induced Pheno-typic-Response Space of Parasites Causing Schistosomiasis. Singh, R., þ,TCBB March-April 2018 469-481Algorithms for Pedigree Comparison. Chen, Z., þ, TCBB March-April2018 422-431An Inference Attack on Genomic Data Using Kinship, Complex Correlations,and Phenotype Information.Deznabi, I.,þ, TCBB July-Aug. 2018 1333-1343Analysis of the Genome Sequence and Prediction of B-Cell Epitopes of theEnvelope Protein of Middle East Respiratory Syndrome-Coronavirus. Xie,Q., þ, TCBB July-Aug. 2018 1344-1350



Analyzing Differential Regulatory Networks Modulated by Continuous-State Genomic Features in Glioblastoma Multiforme. Chiu, Y., þ, TCBBNov.-Dec. 2018 1754-1764Assessment of Semantic Similarity between Proteins Using InformationContent and Topological Properties of the Gene Ontology Graph. Dutta,P., þ, TCBB May -June 2018 839-849Autumn Algorithm—Computation of Hybridization Networks for RealisticPhylogenetic Trees. Huson, D.H., þ, TCBB March-April 2018 398-410Bi-level and Bi-objective p-Median Type Problems for Integrative Cluster-ing: Application to Analysis of Cancer Gene-Expression and Drug-Response Data. Ushakov, A.V., þ, TCBB Jan.-Feb. 2018 46-59Bijective Diameters of Gene Tree Parsimony Costs. G�orecki, P., þ, TCBBSept.-Oct. 2018 1723-1727BRANE Clust: Cluster-Assisted Gene Regulatory Network InferenceRefinement. Pirayre, A., þ, TCBB May -June 2018 850-860Cell Population Tracking in a Honeycomb Structure Using an IMM FilterBased 3D Local Graph Matching Model. Liu, M., þ, TCBB Sept.-Oct.2018 1706-1717Classification of State Trajectories in Gene Regulatory Networks. Karba-layghareh, A., þ, TCBB Jan.-Feb. 2018 68-82Codon Context Optimization in Synthetic Gene Design. Papamichail, D.,þ, TCBB March-April 2018 452-459Combining Supervised and Unsupervised Learning for Improved miRNATarget Prediction. Sedaghat, N., þ, TCBB Sept.-Oct. 2018 1594-1604Computational Prediction of Pathogenic Network Modules in Fusariumverticillioides. Kim, M., þ, TCBB March-April 2018 506-515Construction of Signaling Pathways with RNAi Data and Multiple Refer-ence Networks. Alim, M.A., þ, TCBB July-Aug. 2018 1079-1091Continuous Petri Nets and microRNA Analysis in Melanoma. Russo, G.,þ,TCBB Sept.-Oct. 2018 1492-1499Detecting Essential Proteins Based on Network Topology, Gene Expres-sion Data, and Gene Ontology Information. Zhang, W., þ, TCBB Jan.-Feb. 2018 109-116Detecting Multivariate Gene Interactions in RNA-Seq Data Using OptimalBayesian Classification. Knight, J.M., þ, TCBB March-April 2018 484-493Discovering Gene Regulatory Elements Using Coverage-Based Heuristics.Al-Ouran, R., þ, TCBB July-Aug. 2018 1290-1300DNAWatermarking Using Codon Postfix Technique. Hamad, S., þ, TCBBSept.-Oct. 2018 1605-1610DTL-RnB: Algorithms and Tools for Summarizing the Space of DTL Rec-onciliations.Ma, W., þ, TCBB March-April 2018 411-421Dynamics in Epistasis Analysis. Awdeh, A., þ, TCBB May -June 2018 878-891Efficient Quartet Representations of Trees and Applications to Supertree andSummaryMethods.Davidson, R.,þ, TCBBMay -June 2018 1010-1015Encoding Data Using Biological Principles: The Multisample Variant For-mat for Phylogenomics and Population Genomics. Pease, J.B., þ, TCBBJuly-Aug. 2018 1231-1238Evolutionary Graph Clustering for Protein Complex Identification. He, T.,þ, TCBB May -June 2018 892-904Evolutionary Model for the Statistical Divergence of Paralogous andOrthologous Gene Pairs Generated by Whole Genome Duplication andSpeciation. Zhang, Y., þ, TCBB Sept.-Oct. 2018 1579-1584Examining De Novo Transcriptome Assemblies via a Quality AssessmentPipeline. Ghaffari, N., þ, TCBB March-April 2018 494-505Extracting Stage-Specific and Dynamic Modules Through Analyzing Mul-tiple Networks Associated with Cancer Progression. Ma, X., þ, TCBBMarch-April 2018 647-658Filter Design with Adaptation to Time-Delay Parameters for Genetic Regu-latory Networks. Jiao, H., þ, TCBB Jan.-Feb. 2018 323-329Fuzzy-Rough Entropy Measure and Histogram Based Patient Selection formiRNA Ranking in Cancer. Pal, J.K., þ, TCBB March-April 2018 659-672Gene Regulatory Network Inference from Perturbed Time-Series Expres-sion Data via Ordered Dynamical Expansion of Non-Steady State Actors.Zamanighomi, M., þ, TCBB July-Aug. 2018 1093-1106Gene Tree Construction and Correction Using SuperTree and Reconcilia-tion. Lafond, M., þ, TCBB Sept.-Oct. 2018 1560-1570Grouped Gene Selection of Cancer via Adaptive Sparse Group Lasso Basedon Conditional Mutual Information. Li, J., þ, TCBB Nov.-Dec. 20182028-2038GSEH: A Novel Approach to Select Prostate Cancer-Associated GenesUsing Gene Expression Heterogeneity. Kim, H., þ, TCBB Jan.-Feb. 2018129-146Hardware Accelerator for the Multifractal Analysis of DNA Sequences.Duarte-Sanchez, J.E., þ, TCBB Sept.-Oct. 2018 1611-1624

hc-OTU: A Fast and Accurate Method for Clustering Operational Taxo-nomic Units Based on Homopolymer Compaction. Park, S., þ, TCBBMarch-April 2018 441-451Identifying Condition-Specific Modules by Clustering Multiple Networks.Ma, X., þ, TCBB Sept.-Oct. 2018 1636-1648Identifying Gene Network Rewiring by Integrating Gene Expression andGene Network Data. Xu, T., þ, TCBB Nov.-Dec. 2018 2079-2085Implementation and Evaluation of an Algorithm for Cryptographically Pri-vate Principal Component Analysis on Genomic Data. Bogdanov, D., þ,TCBB Sept.-Oct. 2018 1427-1432Inferring Gene-Species Assignments in the Presence of Horizontal GeneTransfer.Mykowiecka, A., þ, TCBB Sept.-Oct. 2018 1571-1578Inferring Unknown Biological Function by Integration of GO Annotationsand Gene Expression Data. Leale, G., þ, TCBB Jan.-Feb. 2018 168-180Influence Networks Compared with Reaction Networks: Semantics,Expressivity and Attractors. Fages, F., þ, TCBB July-Aug. 2018 1138-1151Integrating Imaging Genomic Data in the Quest for Biomarkers of Schizo-phrenia Disease. Deng, S., þ, TCBB Sept.-Oct. 2018 1480-1491Integrating Multiple Data Sources for Combinatorial Marker Discovery: AStudy in Tumorigenesis. Bandyopadhyay, S., þ, TCBB March-April 2018673-687Introducing a Stable Bootstrap Validation Framework for Reliable Geno-mic Signature Extraction. Chlis, N., þ, TCBB Jan.-Feb. 2018 181-190Investigating Correlation between Protein Sequence Similarity and Seman-tic Similarity Using Gene Ontology Annotations. Ikram, N., þ, TCBBMay -June 2018 905-912Machine Learned Replacement of N-Labels for Basecalled Sequences inDNA Barcoding.Ma, E.Y.T., þ, TCBB Jan.-Feb. 2018 191-204MeTDiff: A Novel Differential RNA Methylation Analysis for MeRIP-SeqData. Cui, X., þ, TCBB March-April 2018 526-534Modeling Methylation Patterns with Long Read Sequencing Data. Meyer,K.N., þ, TCBB July-Aug. 2018 1379-1389MPIGeneNet: Parallel Calculation of Gene Co-Expression Networks onMulticore Clusters. Gonzalez-Dominguez, J., þ, TCBB Sept.-Oct. 20181732-1737Network-Regularized Sparse Logistic Regression Models for Clinical RiskPrediction and Biomarker Discovery. Min, W., þ, TCBB May -June 2018944-953NewGOA: Predicting New GO Annotations of Proteins by Bi-RandomWalks on a Hybrid Graph. Yu, G., þ, TCBB July-Aug. 2018 1390-1402Nonbinary Tree-Based Phylogenetic Networks. Jetten, L., þ, TCBB Jan.-Feb. 2018 205-217Novel Consensus Gene Selection Criteria for Distributed GPU Partial LeastSquares-Based Gene Microarray Analysis in Diffused Large B Cell Lym-phoma (DLBCL) and Related Findings.Wu, H., þ, TCBB Nov.-Dec. 20182039-2052Novelty Indicator for Enhanced Prioritization of Predicted Gene OntologyAnnotations. Chicco, D., þ, TCBB May -June 2018 954-965Nucleosome Positioning of Intronless Genes in the Human Genome.Cheng, X., þ, TCBB July-Aug. 2018 1111-1121Optimization of Gene Set Annotations Using Robust Trace-Norm Multi-task Learning. Liang, X., þ, TCBB May -June 2018 1016-1021Optimizing Phylogenetic Queries for Performance. Jamil, H.M., TCBBSept.-Oct. 2018 1692-1705PerPAS: Topology-Based Single Sample Pathway Analysis Method. Liu,C., þ, TCBB May -June 2018 1022-1027Prediction of HIV Drug Resistance by Combining Sequence and StructuralProperties. Khalid, Z., þ, TCBB May -June 2018 966-973Protecting Privacy and Security of Genomic Data in i2b2 with Homomor-phic Encryption and Differential Privacy. Raisaro, J.L., þ, TCBB Sept.-Oct. 2018 1413-1426Proteomic Evidence for In-Frame and Out-of-Frame Alternatively SplicedIsoforms in Human and Mouse. Ramalho, R.F., þ, TCBB July-Aug. 20181284-1289PyMut: A Web Tool for Overlapping Gene Loss-of-Function MutationDesign. Liu, K., þ, TCBB July-Aug. 2018 1107-1110Reduction of Qualitative Models of Biological Networks for TransientDynamics Analysis. Pauleve, L., TCBB July-Aug. 2018 1167-1179Regularized Non-Negative Matrix Factorization for Identifying Differen-tially Expressed Genes and Clustering Samples: A Survey. Liu, J., þ,TCBB May -June 2018 974-987REPA: Applying Pathway Analysis to Genome-Wide Transcription FactorBinding Data. Patra, P., þ, TCBB July-Aug. 2018 1270-1283Robust Gene Circuit Control Design for Time-Delayed Genetic RegulatoryNetworks Without SUM Regulatory Logic. Jiao, H., þ, TCBB Nov.-Dec.2018 2086-2093



Sampled-Data Stabilization for Fuzzy Genetic Regulatory Networks withLeakage Delays. Ali, M.S., þ, TCBB Jan.-Feb. 2018 271-285Sequence-Based Prediction of Putative Transcription Factor Binding Sitesin DNA Sequences of Any Length. Lee, W., þ, TCBB Sept.-Oct. 20181461-1469Sparse Pathway-Induced Dynamic Network Biomarker Discovery for EarlyWarning Signal Detection in Complex Diseases. Torshizi, A.D., þ, TCBBMay -June 2018 1028-1034SparseNCA: Sparse Network Component Analysis for Recovering Tran-scription Factor Activities with Incomplete Prior Information. Noor, A.,þ, TCBB March-April 2018 387-395Species Tree Estimation Using ASTRAL: How Many Genes Are Enough?.Shekhar, S., þ, TCBB Sept.-Oct. 2018 1738-1747Species Tree Inference from Gene Splits by Unrooted STAR Methods. All-man, E.S., þ, TCBB Jan.-Feb. 2018 337-342Tanglegrams: A Reduction Tool for Mathematical Phylogenetics. Matsen,F.A., þ, TCBB Jan.-Feb. 2018 343-349The Discovery of Mutated Driver Pathways in Cancer: Models and Algo-rithms. Zhang, J., þ, TCBB May -June 2018 988-998

Genomics“Super Gene Set” Causal Relationship Discovery from Functional Geno-mics Data. Yue, Z., þ, TCBB Nov.-Dec. 2018 1991-19983D Genome Reconstruction with ShRec3D+ and Hi-C Data. Li, J., þ,TCBB March-April 2018 460-468A Bipartite Network and Resource Transfer-Based Approach to InferlncRNA-Environmental Factor Associations. Zhou, J., þ, TCBB May-June 2018 753-759A Combined PLS and Negative Binomial Regression Model for InferringAssociation Networks from Next-Generation Sequencing Count Data.Pesonen, M., þ, TCBB May -June 2018 760-773A Comparative Study for Identifying the Chromosome-Wide Spatial Clus-ters from High-Throughput Chromatin Conformation Capture Data. Li,X., þ, TCBB May -June 2018 774-787A Framework for Identifying Genotypic Information from ClinicalRecords: Exploiting Integrated Ontology Structures to Transfer Annota-tions between ICD Codes and Gene Ontologies. Hashemikhabir, S., þ,TCBB July-Aug. 2018 1259-1269A GRASP-Based Heuristic for the Sorting by Length-Weighted InversionsProblem. Arruda, T.d.S., þ, TCBB March-April 2018 352-363A New Efficient Algorithm for the Frequent Gene Team Problem. Wang,B., TCBB March-April 2018 588-598A Novel Approach to Identify the miRNA-mRNA Causal Regulatory Mod-ules in Cancer. Luo, J., þ, TCBB Jan.-Feb. 2018 309-315A Review on Methods for Detecting SNP Interactions in High-DimensionalGenomic Data. Uppu, S., þ, TCBB March-April 2018 599-612A Simplified Description of Child Tables for Sequence Similarity Search.Frith, M.C., þ, TCBB Nov.-Dec. 2018 2067-2073A Sparse Regression Method for Group-Wise Feature Selection with FalseDiscovery Rate Control.Gossmann, A.,þ, TCBB July-Aug. 2018 1066-1078A Study of Cell-Free DNA Fragmentation Pattern and Its Application inDNA Sample Type Classification. Chen, S., þ, TCBB Sept.-Oct. 20181718-1722ACID: Association Correction for Imbalanced Data in GWAS. Bao, F., þ,TCBB Jan.-Feb. 2018 316-322An Inference Attack on Genomic Data Using Kinship, Complex Correla-tions, and Phenotype Information. Deznabi, I., þ, TCBB July-Aug. 20181333-1343Analysis of the Genome Sequence and Prediction of B-Cell Epitopes of theEnvelope Protein of Middle East Respiratory Syndrome-Coronavirus. Xie,Q., þ, TCBB July-Aug. 2018 1344-1350Analyzing Differential Regulatory Networks Modulated by Continuous-State Genomic Features in Glioblastoma Multiforme. Chiu, Y., þ, TCBBNov.-Dec. 2018 1754-1764ANTENNA, a Multi-Rank, Multi-Layered Recommender System for Infer-ring Reliable Drug-Gene-Disease Associations: Repurposing Diazoxide asa Targeted Anti-Cancer Therapy. Wang, A., þ, TCBB Nov.-Dec. 20181960-1967Bijective Diameters of Gene Tree Parsimony Costs. G�orecki, P., þ, TCBBSept.-Oct. 2018 1723-1727BRANE Clust: Cluster-Assisted Gene Regulatory Network InferenceRefinement. Pirayre, A., þ, TCBB May -June 2018 850-860Combinatorics of Tandem Duplication Random Loss Mutations on CircularGenomes. Hartmann, T., þ, TCBB Jan.-Feb. 2018 83-95Continuous Petri Nets and microRNA Analysis in Melanoma. Russo, G.,þ,TCBB Sept.-Oct. 2018 1492-1499Detecting Multivariate Gene Interactions in RNA-Seq Data Using OptimalBayesian Classification.Knight, J.M.,þ, TCBBMarch-April 2018 484-493

Discovering Gene Regulatory Elements Using Coverage-Based Heuristics.Al-Ouran, R., þ, TCBB July-Aug. 2018 1290-1300DNA Assembly with De Bruijn Graphs Using an FPGA Platform. Poirier,C., þ, TCBB May -June 2018 1003-1009Editorial for Selected Papers of a Joint Conferences, Genome InformaticsWorkshop/International Conference on Bioinformatics (GIW/InCoB)2015. Kim, S., TCBB Nov.-Dec. 2018 1821Efficient Algorithms for Genomic Duplication Models. Paszek, J., þ,TCBB Sept.-Oct. 2018 1515-1524Efficient Algorithms for Sequence Analysis with Entropic Profiles. Pizzi,C., þ, TCBB Jan.-Feb. 2018 117-128Encoding Data Using Biological Principles: The Multisample Variant For-mat for Phylogenomics and Population Genomics. Pease, J.B., þ, TCBBJuly-Aug. 2018 1231-1238Evolutionary Model for the Statistical Divergence of Paralogous andOrthologous Gene Pairs Generated by Whole Genome Duplication andSpeciation. Zhang, Y., þ, TCBB Sept.-Oct. 2018 1579-1584Examining De Novo Transcriptome Assemblies via a Quality AssessmentPipeline. Ghaffari, N., þ, TCBB March-April 2018 494-505Extracting Stage-Specific and Dynamic Modules Through Analyzing Mul-tiple Networks Associated with Cancer Progression. Ma, X., þ, TCBBMarch-April 2018 647-658Genome Rearrangement with ILP. Hartmann, T., þ, TCBB Sept.-Oct. 20181585-1593GenoPri’16: International Workshop on Genome Privacy and Security.Ayday, E., þ, TCBB Sept.-Oct. 2018 1403-1404Guest Editorial for Special Section on BIBM 2015. Tian, T., þ, TCBBNov.-Dec. 2018 1752-1753hc-OTU: A Fast and Accurate Method for Clustering Operational Taxo-nomic Units Based on Homopolymer Compaction. Park, S., þ, TCBBMarch-April 2018 441-451Heavy-Tailed Noise Suppression and Derivative Wavelet Scalogram forDetecting DNA Copy Number Aberrations. Nguyen, N., þ, TCBB Sept.-Oct. 2018 1625-1635Implementation and Evaluation of an Algorithm for Cryptographically Pri-vate Principal Component Analysis on Genomic Data. Bogdanov, D., þ,TCBB Sept.-Oct. 2018 1427-1432Improve Biomedical Information Retrieval Using Modified Learning toRank Methods. Xu, B., þ, TCBB Nov.-Dec. 2018 1797-1809Incorporation of Solvent Effect into Multi-Objective Evolutionary Algo-rithm for Improved Protein Structure Prediction. Gao, S., þ, TCBB July-Aug. 2018 1365-1378Inferring Gene-Species Assignments in the Presence of Horizontal GeneTransfer.Mykowiecka, A., þ, TCBB Sept.-Oct. 2018 1571-1578Inferring Unknown Biological Function by Integration of GO Annotationsand Gene Expression Data. Leale, G., þ, TCBB Jan.-Feb. 2018 168-180Integrating Imaging Genomic Data in the Quest for Biomarkers of Schizo-phrenia Disease. Deng, S., þ, TCBB Sept.-Oct. 2018 1480-1491Introducing a Stable Bootstrap Validation Framework for Reliable Geno-mic Signature Extraction. Chlis, N., þ, TCBB Jan.-Feb. 2018 181-190Machine Learned Replacement of N-Labels for Basecalled Sequences inDNA Barcoding.Ma, E.Y.T., þ, TCBB Jan.-Feb. 2018 191-204Modeling Methylation Patterns with Long Read Sequencing Data. Meyer,K.N., þ, TCBB July-Aug. 2018 1379-1389Multiple Network Alignment via MultiMAGNA++. Vijayan, V., þ, TCBBSept.-Oct. 2018 1669-1682NewGOA: Predicting New GO Annotations of Proteins by Bi-RandomWalks on a Hybrid Graph. Yu, G., þ, TCBB July-Aug. 2018 1390-1402Novelty Indicator for Enhanced Prioritization of Predicted Gene OntologyAnnotations. Chicco, D., þ, TCBB May -June 2018 954-965Nucleosome Positioning of Intronless Genes in the Human Genome.Cheng, X., þ, TCBB July-Aug. 2018 1111-1121Optimal Block-Based Trimming for Next Generation Sequencing. Hedtke,I., þ, TCBB March-April 2018 364-376Protecting Privacy and Security of Genomic Data in i2b2 with Homomor-phic Encryption and Differential Privacy. Raisaro, J.L., þ, TCBB Sept.-Oct. 2018 1413-1426PyMut: A Web Tool for Overlapping Gene Loss-of-Function MutationDesign. Liu, K., þ, TCBB July-Aug. 2018 1107-1110REPA: Applying Pathway Analysis to Genome-Wide Transcription FactorBinding Data. Patra, P., þ, TCBB July-Aug. 2018 1270-1283Scaffolding of Ancient Contigs and Ancestral Reconstruction in a Phyloge-netic Framework. Luhmann, N., þ, TCBB Nov.-Dec. 2018 2094-2100Simulating the Large-Scale Erosion of Genomic Privacy Over Time.Backes, M., þ, TCBB Sept.-Oct. 2018 1405-1412Species Tree Estimation Using ASTRAL: How Many Genes Are Enough?.Shekhar, S., þ, TCBB Sept.-Oct. 2018 1738-1747



Species Tree Inference from Gene Splits by Unrooted STAR Methods. All-man, E.S., þ, TCBB Jan.-Feb. 2018 337-342The Discovery of Mutated Driver Pathways in Cancer: Models and Algo-rithms. Zhang, J., þ, TCBB May -June 2018 988-998

Graph coloringComplexity and Algorithms for Finding a Perfect Phylogeny from MixedTumor Samples. Hujdurovic, A., þ, TCBB Jan.-Feb. 2018 96-108

Graph theory3D Genome Reconstruction with ShRec3D+ and Hi-C Data. Li, J., þ,TCBB March-April 2018 460-468A Global Network Alignment Method Using Discrete Particle Swarm Opti-mization. Huang, J., þ, TCBB May -June 2018 705-718Algorithmic Mapping and Characterization of the Drug-Induced Pheno-typic-Response Space of Parasites Causing Schistosomiasis. Singh, R., þ,TCBB March-April 2018 469-481Algorithms for Pedigree Comparison. Chen, Z., þ, TCBB March-April2018 422-431Application of Fractal Theory on Motifs Counting in Biological Networks.Joveini, M.B.Z., þ, TCBB March-April 2018 613-623Assessment of Semantic Similarity between Proteins Using InformationContent and Topological Properties of the Gene Ontology Graph. Dutta,P., þ, TCBB May -June 2018 839-849BRANE Clust: Cluster-Assisted Gene Regulatory Network InferenceRefinement. Pirayre, A., þ, TCBB May -June 2018 850-860Cell Population Tracking in a Honeycomb Structure Using an IMM FilterBased 3D Local Graph Matching Model. Liu, M., þ, TCBB Sept.-Oct.2018 1706-1717DNA Assembly with De Bruijn Graphs Using an FPGA Platform. Poirier,C., þ, TCBB May -June 2018 1003-1009Evolutionary Graph Clustering for Protein Complex Identification. He, T.,þ, TCBB May -June 2018 892-904Index-Based Network Aligner of Protein-Protein Interaction Networks.Elmsallati, A., þ, TCBB Jan.-Feb. 2018 330-336Modeling the Geometry and Dynamics of the Endoplasmic Reticulum Net-work. Lin, C., þ, TCBB March-April 2018 377-386NewGOA: Predicting New GO Annotations of Proteins by Bi-RandomWalks on a Hybrid Graph. Yu, G., þ, TCBB July-Aug. 2018 1390-1402Nonbinary Tree-Based Phylogenetic Networks. Jetten, L., þ, TCBB Jan.-Feb. 2018 205-217Optimizing Phylogenetic Queries for Performance. Jamil, H.M., TCBBSept.-Oct. 2018 1692-1705Petri Net Siphon Analysis and Graph Theoretic Measures for IdentifyingCombination Therapies in Cancer. Behinaein, B., þ, TCBB Jan.-Feb.2018 231-243Sparse Pathway-Induced Dynamic Network Biomarker Discovery for EarlyWarning Signal Detection in Complex Diseases. Torshizi, A.D., þ, TCBBMay -June 2018 1028-1034Structural Target Controllability of Linear Networks. Czeizler, E., þ,TCBB July-Aug. 2018 1217-1228

Graphics processing unitsGPU-Based Point Cloud Superpositioning for Structural Comparisons ofProtein Binding Sites. Leinweber, M., þ, TCBB May -June 2018 740-752Novel Consensus Gene Selection Criteria for Distributed GPU Partial LeastSquares-Based Gene Microarray Analysis in Diffused Large B Cell Lym-phoma (DLBCL) and Related Findings.Wu, H., þ, TCBB Nov.-Dec. 20182039-2052

Greedy algorithmsA GRASP-Based Heuristic for the Sorting by Length-Weighted InversionsProblem. Arruda, T.d.S., þ, TCBB March-April 2018 352-363Discovering Gene Regulatory Elements Using Coverage-Based Heuristics.Al-Ouran, R., þ, TCBB July-Aug. 2018 1290-1300Structural Target Controllability of Linear Networks. Czeizler, E., þ,TCBB July-Aug. 2018 1217-1228

Group theoryTanglegrams: A Reduction Tool for Mathematical Phylogenetics. Matsen,F.A., þ, TCBB Jan.-Feb. 2018 343-349

GynecologyModeling Methylation Patterns with Long Read Sequencing Data. Meyer,K.N., þ, TCBB July-Aug. 2018 1379-1389

H

Hamming distanceDiscMLA: An Efficient Discriminative Motif Learning Algorithm over High-Throughput Datasets. Zhang, H.,þ, TCBBNov.-Dec. 2018 1810-1820

Heuristic algorithmsAnalyzing Differential Regulatory Networks Modulated by Continuous-State Genomic Features in Glioblastoma Multiforme. Chiu, Y., þ, TCBBNov.-Dec. 2018 1754-1764Coevolutionary Structure-Redesigned-Based Bacterial Foraging Optimiza-tion. Niu, B., þ, TCBB Nov.-Dec. 2018 1865-1876Environment Sensitivity-Based Cooperative Co-Evolutionary Algorithmsfor Dynamic Multi-Objective Optimization. Xu, B., þ, TCBB Nov.-Dec.2018 1877-1890Network Community Detection Based on the Physarum-Inspired Computa-tional Framework. Gao, C., þ, TCBB Nov.-Dec. 2018 1916-1928Scaffolding of Ancient Contigs and Ancestral Reconstruction in a Phyloge-netic Framework. Luhmann, N., þ, TCBB Nov.-Dec. 2018 2094-2100Structure-Guided Protein Transition Modeling with a Probabilistic Road-map Algorithm.Maximova, T., þ, TCBB Nov.-Dec. 2018 1783-1796

Heuristic programmingCodon Context Optimization in Synthetic Gene Design. Papamichail, D.,þ, TCBB March-April 2018 452-459Optimal Block-Based Trimming for Next Generation Sequencing. Hedtke,I., þ, TCBB March-April 2018 364-376

Hidden Markov modelsA Spatial-Temporal Method to Detect Global Influenza Epidemics UsingHeterogeneous Data Collected from the Internet. Zhou, X., þ, TCBB May-June 2018 802-812

Honeycomb structuresCell Population Tracking in a Honeycomb Structure Using an IMM FilterBased 3D Local Graph Matching Model. Liu, M., þ, TCBB Sept.-Oct.2018 1706-1717

HospitalsPredicting Hospital Readmission via Cost-Sensitive Deep Learning. Wang,H., þ, TCBB Nov.-Dec. 2018 1968-1978Using Machine Learning to Improve the Prediction of Functional Outcomein Ischemic Stroke Patients. Monteiro, M., þ, TCBB Nov.-Dec. 20181953-1959

HydrophobicityIdentification and Analysis of Key Residues in Protein–RNA Complexes.Kulandaisamy, A., þ, TCBB Sept.-Oct. 2018 1436-1444

I

IEEE publishing2018 Reviewers List*. TCBB Sept.-Oct. 2018 1748-1751

Intelligent systemsGuest Editorial for Special Section on the 12th International Conference onIntelligent Computing (ICIC). Huang, D., þ, TCBB Sept.-Oct. 2018 1433-1435

Image classificationAn Organelle Correlation-Guided Feature Selection Approach for Classify-ing Multi-Label Subcellular Bio-Images. Shao, W., þ, TCBB May -June2018 828-838Classification of Alzheimer’s Disease Using Whole Brain HierarchicalNetwork. Liu, J., þ, TCBB March-April 2018 624-632Gender Identification of Human Brain Image with A Novel 3D Descriptor.Yuan, L., þ, TCBB March-April 2018 551-561Structural Class Classification of 3D Protein Structure Based on Multi-View 2D Images. Suryanto, C.H., þ, TCBB Jan.-Feb. 2018 286-299

Image matchingCell Population Tracking in a Honeycomb Structure Using an IMM FilterBased 3D Local Graph Matching Model. Liu, M., þ, TCBB Sept.-Oct.2018 1706-1717

Image reconstructionImmunological Approach for Full NURBS Reconstruction of OutlineCurves from Noisy Data Points in Medical Imaging. Iglesias, A., þ,TCBB Nov.-Dec. 2018 1929-1942

Image representationAlgorithmic Mapping and Characterization of the Drug-Induced Pheno-typic-Response Space of Parasites Causing Schistosomiasis. Singh, R., þ,TCBB March-April 2018 469-481

Image resolutionBayesian Multiresolution Variable Selection for Ultra-High DimensionalNeuroimaging Data. Zhao, Y., þ, TCBB March-April 2018 537-550

Image segmentationCell Population Tracking in a Honeycomb Structure Using an IMM FilterBased 3D Local Graph Matching Model. Liu, M., þ, TCBB Sept.-Oct.2018 1706-1717



Region Growing for Segmenting Green Microalgae Images. Borges, V.R.P., þ, TCBB Jan.-Feb. 2018 257-270

Independent component analysisA Just-in-Time Learning Based Monitoring and Classification Method forHyper/Hypocalcemia Diagnosis. Peng, X.,þ, TCBBMay -June 2018 788-801

IndexingA Simplified Description of Child Tables for Sequence Similarity Search.Frith, M.C., þ, TCBB Nov.-Dec. 2018 2067-2073Index-Based Network Aligner of Protein-Protein Interaction Networks.Elmsallati, A., þ, TCBB Jan.-Feb. 2018 330-336

Inference mechanismsAn Inference Attack on Genomic Data Using Kinship, Complex Correla-tions, and Phenotype Information. Deznabi, I., þ, TCBB July-Aug. 20181333-1343BRANE Clust: Cluster-Assisted Gene Regulatory Network InferenceRefinement. Pirayre, A., þ, TCBB May -June 2018 850-860Efficient Quartet Representations of Trees and Applications to Supertree andSummaryMethods.Davidson, R.,þ, TCBBMay -June 2018 1010-1015Inferring Gene-Species Assignments in the Presence of Horizontal GeneTransfer.Mykowiecka, A., þ, TCBB Sept.-Oct. 2018 1571-1578SparseNCA: Sparse Network Component Analysis for Recovering Tran-scription Factor Activities with Incomplete Prior Information. Noor, A.,þ, TCBB March-April 2018 387-395Species Tree Inference from Gene Splits by Unrooted STAR Methods. All-man, E.S., þ, TCBB Jan.-Feb. 2018 337-342

InformaticsEditorial for Selected Papers of a Joint Conferences, Genome InformaticsWorkshop/International Conference on Bioinformatics (GIW/InCoB)2015. Kim, S., TCBB Nov.-Dec. 2018 1821Guest Editorial for Special Section on BIBM 2015. Tian, T., þ, TCBBNov.-Dec. 2018 1752-1753Multiscale and Multimodal Analysis for Computational Biology. Gao, X.,þ, TCBB Nov.-Dec. 2018 1951-1952

Information retrievalImprove Biomedical Information Retrieval Using Modified Learning toRank Methods. Xu, B., þ, TCBB Nov.-Dec. 2018 1797-1809Inferring the Functions of Proteins from the Interrelationships betweenFunctional Categories. Taha, K., TCBB Jan.-Feb. 2018 157-167Towards Extracting Supporting Information About Predicted Protein-Pro-tein Interactions. Roth, A., þ, TCBB July-Aug. 2018 1239-1246

Information theoryEfficient Algorithms for Sequence Analysis with Entropic Profiles. Pizzi,C., þ, TCBB Jan.-Feb. 2018 117-128

Integrated circuit modelingRobust Gene Circuit Control Design for Time-Delayed Genetic RegulatoryNetworks Without SUM Regulatory Logic. Jiao, H., þ, TCBB Nov.-Dec.2018 2086-2093

InternetA Spatial-Temporal Method to Detect Global Influenza Epidemics UsingHeterogeneous Data Collected from the Internet. Zhou, X., þ, TCBB May-June 2018 802-812PyMut: A Web Tool for Overlapping Gene Loss-of-Function MutationDesign. Liu, K., þ, TCBB July-Aug. 2018 1107-1110

IsomerismEnumerating Substituted Benzene Isomers of Tree-Like Chemical Graphs.Li, J., þ, TCBB March-April 2018 633-646

Iterative methodsA GRASP-Based Heuristic for the Sorting by Length-Weighted InversionsProblem. Arruda, T.d.S., þ, TCBB March-April 2018 352-363LMMO: A Large Margin Approach for Refining Regulatory Motifs. Zhu,L., þ, TCBB May -June 2018 913-925SparseNCA: Sparse Network Component Analysis for Recovering Tran-scription Factor Activities with Incomplete Prior Information. Noor, A.,þ, TCBB March-April 2018 387-395

J

JavaNGS-FC: A Next-Generation Sequencing Data Format Converter. Yu, C.,þ, TCBB Sept.-Oct. 2018 1683-1691

K

Kalman filtersOptimal Fault Detection and Diagnosis in Transcriptional Circuits Using Next-Generation Sequencing.Bahadorinejad, A.,þ,TCBBMarch-April 2018 516-525

KidneyProteomic Evidence for In-Frame and Out-of-Frame Alternatively SplicedIsoforms in Human and Mouse. Ramalho, R.F., þ, TCBB July-Aug. 20181284-1289

Knowledge discoveryMultiscale and Multimodal Analysis for Computational Biology. Gao, X.,þ, TCBB Nov.-Dec. 2018 1951-1952

L

Lab-on-a-chipSparse Pathway-Induced Dynamic Network Biomarker Discovery for EarlyWarning Signal Detection in Complex Diseases. Torshizi, A.D., þ, TCBBMay -June 2018 1028-1034

LabelingImprove Biomedical Information Retrieval Using Modified Learning toRank Methods. Xu, B., þ, TCBB Nov.-Dec. 2018 1797-1809Scaffolding of Ancient Contigs and Ancestral Reconstruction in a Phyloge-netic Framework. Luhmann, N., þ, TCBB Nov.-Dec. 2018 2094-2100

Large-scale systemsA Grouping Particle Swarm Optimizer with Personal-Best-Position Guid-ance for Large Scale Optimization. Guo, W., þ, TCBB Nov.-Dec. 20181904-1915

Learning (artificial intelligence)A Distributed Classifier for MicroRNA Target Prediction with ValidationThrough TCGA Expression Data. Ghoshal, A., þ, TCBB July-Aug. 20181037-1051A Just-in-Time Learning Based Monitoring and Classification Method forHyper/Hypocalcemia Diagnosis. Peng, X., þ, TCBB May -June 2018 788-801A Review on Methods for Detecting SNP Interactions in High-DimensionalGenomic Data. Uppu, S., þ, TCBB March-April 2018 599-612A Self-Training Subspace Clustering Algorithm under Low-Rank Repre-sentation for Cancer Classification on Gene Expression Data. Xia, C., þ,TCBB July-Aug. 2018 1315-1324ACID: Association Correction for Imbalanced Data in GWAS. Bao, F., þ,TCBB Jan.-Feb. 2018 316-322Attention Recognition in EEG-Based Affective Learning Research UsingCFS+KNN Algorithm. Hu, B., þ, TCBB Jan.-Feb. 2018 38-45Biological Event Trigger Identification with Noise Contrastive Estimation.Jiang, N., þ, TCBB Sept.-Oct. 2018 1549-1559Classification of Alzheimer’s Disease Using Whole Brain HierarchicalNetwork. Liu, J., þ, TCBB March-April 2018 624-632Comparison of Machine Learning Approaches for Prediction of AdvancedLiver Fibrosis in Chronic Hepatitis C Patients. Hashem, S., þ, TCBB May-June 2018 861-868HEMEsPred: Structure-Based Ligand-Specific Heme Binding ResiduesPrediction by Using Fast-Adaptive Ensemble Learning Scheme. Zhang,J., þ, TCBB Jan.-Feb. 2018 147-156Introducing a Stable Bootstrap Validation Framework for Reliable Geno-mic Signature Extraction. Chlis, N., þ, TCBB Jan.-Feb. 2018 181-190LMMO: A Large Margin Approach for Refining Regulatory Motifs. Zhu,L., þ, TCBB May -June 2018 913-925Machine Learned Replacement of N-Labels for Basecalled Sequences inDNA Barcoding.Ma, E.Y.T., þ, TCBB Jan.-Feb. 2018 191-204Multiple-Swarm Ensembles: Improving the Predictive Power and Robust-ness of Predictive Models and Its Use in Computational Biology. Alves,P., þ, TCBB May -June 2018 926-933Optimization of Gene Set Annotations Using Robust Trace-Norm Multi-task Learning. Liang, X., þ, TCBB May -June 2018 1016-1021Predicting the Absorption Potential of Chemical Compounds Through aDeep Learning Approach. Shin, M., þ, TCBB March-April 2018 432-440RAFP-Pred: Robust Prediction of Antifreeze Proteins Using LocalizedAnalysis of n-Peptide Compositions. Khan, S., þ, TCBB Jan.-Feb. 2018244-250Regularized Non-Negative Matrix Factorization for Identifying Differen-tially Expressed Genes and Clustering Samples: A Survey. Liu, J., þ,TCBB May -June 2018 974-987Reviving the Two-State Markov Chain Approach. Mizera, A., þ, TCBBSept.-Oct. 2018 1525-1537Structural Class Classification of 3D Protein Structure Based on Multi-View 2D Images. Suryanto, C.H., þ, TCBB Jan.-Feb. 2018 286-299Towards Extracting Supporting Information About Predicted Protein-Pro-tein Interactions. Roth, A., þ, TCBB July-Aug. 2018 1239-1246



Unified Deep Learning Architecture for Modeling Biology Sequence. Wu,H., þ, TCBB Sept.-Oct. 2018 1445-1452

Learning systemsCoevolutionary Structure-Redesigned-Based Bacterial Foraging Optimiza-tion. Niu, B., þ, TCBB Nov.-Dec. 2018 1865-1876Effectively Identifying Compound-Protein Interactions by Learning fromPositive and Unlabeled Examples. Cheng, Z., þ, TCBB Nov.-Dec. 20181832-1843Using Machine Learning to Improve the Prediction of Functional Outcomein Ischemic Stroke Patients. Monteiro, M., þ, TCBB Nov.-Dec. 20181953-1959

Least squares approximationsA Combined PLS and Negative Binomial Regression Model for InferringAssociation Networks from Next-Generation Sequencing Count Data.Pesonen, M., þ, TCBB May -June 2018 760-773

Least squares methodsNovel Consensus Gene Selection Criteria for Distributed GPU Partial LeastSquares-Based Gene Microarray Analysis in Diffused Large B Cell Lym-phoma (DLBCL) and Related Findings.Wu, H., þ, TCBB Nov.-Dec. 20182039-2052

Linear matrix inequalitiesSampled-Data Stabilization for Fuzzy Genetic Regulatory Networks withLeakage Delays. Ali, M.S., þ, TCBB Jan.-Feb. 2018 271-285

Linear programmingA Bi-Objective RNN Model to Reconstruct Gene Regulatory Network: AModified Multi-Objective Simulated Annealing Approach. Biswas, S., þ,TCBB Nov.-Dec. 2018 2053-2059Computing Minimum Reaction Modifications in a Boolean Metabolic Net-work. Tamura, T., þ, TCBB Nov.-Dec. 2018 1853-1862Network Community Detection Based on the Physarum-Inspired Computa-tional Framework. Gao, C., þ, TCBB Nov.-Dec. 2018 1916-1928

LiverComparison of Machine Learning Approaches for Prediction of AdvancedLiver Fibrosis in Chronic Hepatitis C Patients. Hashem, S., þ, TCBB May-June 2018 861-868Proteomic Evidence for In-Frame and Out-of-Frame Alternatively SplicedIsoforms in Human and Mouse. Ramalho, R.F., þ, TCBB July-Aug. 20181284-1289

LogisticsLocal-Nearest-Neighbors-Based Feature Weighting for Gene Selection. An,S., þ, TCBB Sept.-Oct. 2018 1538-1548

LungA Graphical Model of Smoking-Induced Global Instability in Lung Cancer.Wang, Y., þ, TCBB Jan.-Feb. 2018 1-14Influence of Airway Secretion on Airflow Dynamics of Mechanical Venti-lated Respiratory System. Ren, S., þ, TCBB Sept.-Oct. 2018 1660-1668Proteomic Evidence for In-Frame and Out-of-Frame Alternatively SplicedIsoforms in Human and Mouse. Ramalho, R.F., þ, TCBB July-Aug. 20181284-1289

Lyapunov methodsFilter Design with Adaptation to Time-Delay Parameters for Genetic Regu-latory Networks. Jiao, H., þ, TCBB Jan.-Feb. 2018 323-329Robust Gene Circuit Control Design for Time-Delayed Genetic RegulatoryNetworks Without SUM Regulatory Logic. Jiao, H., þ, TCBB Nov.-Dec.2018 2086-2093Sampled-Data Stabilization for Fuzzy Genetic Regulatory Networks withLeakage Delays. Ali, M.S., þ, TCBB Jan.-Feb. 2018 271-285

M

Machine learningANTENNA, a Multi-Rank, Multi-Layered Recommender System for Infer-ring Reliable Drug-Gene-Disease Associations: Repurposing Diazoxide asa Targeted Anti-Cancer Therapy. Wang, A., þ, TCBB Nov.-Dec. 20181960-1967Coevolutionary Structure-Redesigned-Based Bacterial Foraging Optimiza-tion. Niu, B., þ, TCBB Nov.-Dec. 2018 1865-1876Deep Sequencing Data Analysis. Ghosh, B.K., þ, TCBB March-April 2018482-483Effectively Identifying Compound-Protein Interactions by Learning fromPositive and Unlabeled Examples. Cheng, Z., þ, TCBB Nov.-Dec. 20181832-1843Feature Selection for Optimized High-Dimensional Biomedical Data Usingan Improved Shuffled Frog Leaping Algorithm. Hu, B., þ, TCBB Nov.-Dec. 2018 1765-1773

Guest Editorial for Special Section on the 12th International Conference onIntelligent Computing (ICIC). Huang, D., þ, TCBB Sept.-Oct. 2018 1433-1435Improve Biomedical Information Retrieval Using Modified Learning toRank Methods. Xu, B., þ, TCBB Nov.-Dec. 2018 1797-1809Multiscale and Multimodal Analysis for Computational Biology. Gao, X.,þ, TCBB Nov.-Dec. 2018 1951-1952Predicting Hospital Readmission via Cost-Sensitive Deep Learning. Wang,H., þ, TCBB Nov.-Dec. 2018 1968-1978Predicting Hospital Readmission via Cost-Sensitive Deep Learning. Wang,H., þ, TCBB Nov.-Dec. 2018 1968-1978Using Machine Learning to Improve the Prediction of Functional Outcomein Ischemic Stroke Patients. Monteiro, M., þ, TCBB Nov.-Dec. 20181953-1959

MacromoleculesAnalysis of the Genome Sequence and Prediction of B-Cell Epitopes of theEnvelope Protein of Middle East Respiratory Syndrome-Coronavirus. Xie,Q., þ, TCBB July-Aug. 2018 1344-1350

Magnetic resonance imagingImmunological Approach for Full NURBS Reconstruction of OutlineCurves from Noisy Data Points in Medical Imaging. Iglesias, A., þ,TCBB Nov.-Dec. 2018 1929-1942Improving Alzheimer’s Disease Classification by Combining MultipleMeasures. Liu, J., þ, TCBB Sept.-Oct. 2018 1649-1659

Maintenance engineeringA Grouping Particle Swarm Optimizer with Personal-Best-Position Guid-ance for Large Scale Optimization. Guo, W., þ, TCBB Nov.-Dec. 20181904-1915

ManifoldsLow Rank Subspace Clustering via Discrete Constraint and HypergraphRegularization for Tumor Molecular Pattern Discovery. Liu, J., þ, TCBBSept.-Oct. 2018 1500-1512

Markov processesAggregation for Computing Multi-Modal Stationary Distributions in 1-DGene Regulatory Networks. Avcu, N., þ, TCBB May -June 2018 813-827An Inference Attack on Genomic Data Using Kinship, Complex Correla-tions, and Phenotype Information. Deznabi, I., þ, TCBB July-Aug. 20181333-1343Bayesian Multiresolution Variable Selection for Ultra-High DimensionalNeuroimaging Data. Zhao, Y., þ, TCBB March-April 2018 537-550Calculating the Expected Time to Eradicate HIV-1 Using a Markov Chain.Viswanath, N.C., TCBB Jan.-Feb. 2018 60-67Detecting Multivariate Gene Interactions in RNA-Seq Data Using OptimalBayesian Classification.Knight, J.M.,þ, TCBBMarch-April 2018 484-493Network Community Detection Based on the Physarum-Inspired Computa-tional Framework. Gao, C., þ, TCBB Nov.-Dec. 2018 1916-1928Organisation-Oriented Coarse Graining and Refinement of StochasticReaction Networks.Mu, C., þ, TCBB July-Aug. 2018 1152-1166Reviving the Two-State Markov Chain Approach. Mizera, A., þ, TCBBSept.-Oct. 2018 1525-1537SPF-CellTracker: Tracking Multiple Cells with Strongly-Correlated MovesUsing a Spatial Particle Filter. Hirose, O., þ, TCBB Nov.-Dec. 20181822-1831SPF-CellTracker: Tracking Multiple Cells with Strongly-Correlated MovesUsing a Spatial Particle Filter. Hirose, O., þ, TCBB Nov.-Dec. 20181822-1831

Mass spectraProteomic Evidence for In-Frame and Out-of-Frame Alternatively SplicedIsoforms in Human and Mouse. Ramalho, R.F., þ, TCBB July-Aug. 20181284-1289

Master equationAggregation for Computing Multi-Modal Stationary Distributions in 1-DGene Regulatory Networks. Avcu, N., þ, TCBB May -June 2018 813-827Organisation-Oriented Coarse Graining and Refinement of StochasticReaction Networks.Mu, C., þ, TCBB July-Aug. 2018 1152-1166

Mathematical modelASSA-PBN: A Toolbox for Probabilistic Boolean Networks.Mizera, A.,þ,TCBB July-Aug. 2018 1203-1216Computing Minimum Reaction Modifications in a Boolean Metabolic Net-work. Tamura, T., þ, TCBB Nov.-Dec. 2018 1853-1862

MathematicsCorrection to “Detecting Essential Proteins Based on Network Topology,Gene Expression Data, and Gene Ontology Information”. Zhang, W., þ,TCBB May -June 2018 1035

Matrix algebraBRANE Clust: Cluster-Assisted Gene Regulatory Network InferenceRefinement. Pirayre, A., þ, TCBB May -June 2018 850-860



Complexity and Algorithms for Finding a Perfect Phylogeny from MixedTumor Samples. Hujdurovic, A., þ, TCBB Jan.-Feb. 2018 96-108Network-Regularized Sparse Logistic Regression Models for Clinical RiskPrediction and Biomarker Discovery. Min, W., þ, TCBB May -June 2018944-953Sparse Pathway-Induced Dynamic Network Biomarker Discovery for EarlyWarning Signal Detection in Complex Diseases. Torshizi, A.D., þ, TCBBMay -June 2018 1028-1034SparseNCA: Sparse Network Component Analysis for Recovering Tran-scription Factor Activities with Incomplete Prior Information. Noor, A.,þ, TCBB March-April 2018 387-395

Matrix decompositionA Comparative Study for Identifying the Chromosome-Wide Spatial Clus-ters from High-Throughput Chromatin Conformation Capture Data. Li,X., þ, TCBB May -June 2018 774-787Discovering Perturbation of Modular Structure in HIV Progression by Inte-grating Multiple Data Sources Through Non-Negative Matrix Factoriza-tion. Ray, S., þ, TCBB May -June 2018 869-877Regularized Non-Negative Matrix Factorization for Identifying Differen-tially Expressed Genes and Clustering Samples: A Survey. Liu, J., þ,TCBB May -June 2018 974-987

Maximum likelihood estimationApplication of Fractal Theory on Motifs Counting in Biological Networks.Joveini, M.B.Z., þ, TCBB March-April 2018 613-623Evolutionary Model for the Statistical Divergence of Paralogous andOrthologous Gene Pairs Generated by Whole Genome Duplication andSpeciation. Zhang, Y., þ, TCBB Sept.-Oct. 2018 1579-1584

Mean square error methodsA Memetic Algorithm for 3D Protein Structure Prediction Problem.Correa, L., þ, TCBB May -June 2018 690-704Application of Genetic Programming (GP) Formalism for Building DiseasePredictive Models from Protein-Protein Interactions (PPI) Data. Vyas, R.,þ, TCBB Jan.-Feb. 2018 27-37

MechatronicsCorrection to “Detecting Essential Proteins Based on Network Topology,Gene Expression Data, and Gene Ontology Information”. Zhang, W., þ,TCBB May -June 2018 1035

Medical computingA Framework for Identifying Genotypic Information from ClinicalRecords: Exploiting Integrated Ontology Structures to Transfer Annota-tions between ICD Codes and Gene Ontologies. Hashemikhabir, S., þ,TCBB July-Aug. 2018 1259-1269A Spatial-Temporal Method to Detect Global Influenza Epidemics UsingHeterogeneous Data Collected from the Internet. Zhou, X., þ, TCBB May-June 2018 802-812Analysis of the Genome Sequence and Prediction of B-Cell Epitopes of theEnvelope Protein of Middle East Respiratory Syndrome-Coronavirus. Xie,Q., þ, TCBB July-Aug. 2018 1344-1350Application of Genetic Programming (GP) Formalism for Building DiseasePredictive Models from Protein-Protein Interactions (PPI) Data. Vyas, R.,þ, TCBB Jan.-Feb. 2018 27-37Bi-level and Bi-objective p-Median Type Problems for Integrative Cluster-ing: Application to Analysis of Cancer Gene-Expression and Drug-Response Data. Ushakov, A.V., þ, TCBB Jan.-Feb. 2018 46-59Extracting Stage-Specific and Dynamic Modules Through Analyzing Mul-tiple Networks Associated with Cancer Progression. Ma, X., þ, TCBBMarch-April 2018 647-658Fuzzy-Rough Entropy Measure and Histogram Based Patient Selection formiRNA Ranking in Cancer. Pal, J.K., þ, TCBB March-April 2018 659-672PerPAS: Topology-Based Single Sample Pathway Analysis Method. Liu,C., þ, TCBB May -June 2018 1022-1027Petri Net Siphon Analysis and Graph Theoretic Measures for IdentifyingCombination Therapies in Cancer. Behinaein, B., þ, TCBB Jan.-Feb.2018 231-243Prediction of HIV Drug Resistance by Combining Sequence and StructuralProperties. Khalid, Z., þ, TCBB May -June 2018 966-973The Discovery of Mutated Driver Pathways in Cancer: Models and Algo-rithms. Zhang, J., þ, TCBB May -June 2018 988-998

Medical diagnostic computingA Just-in-Time Learning Based Monitoring and Classification Method forHyper/Hypocalcemia Diagnosis. Peng, X., þ, TCBB May -June 2018 788-801Comparison of Machine Learning Approaches for Prediction of AdvancedLiver Fibrosis in Chronic Hepatitis C Patients. Hashem, S., þ, TCBB May-June 2018 861-868

Medical disordersBayesian Multiresolution Variable Selection for Ultra-High DimensionalNeuroimaging Data. Zhao, Y., þ, TCBB March-April 2018 537-550Complex Network Measures in Autism Spectrum Disorders. Sato, J.R., þ,TCBB March-April 2018 581-587Cortical Thinning and Cognitive Impairment in Parkinson’s Disease with-out Dementia. Zhang, L., þ, TCBB March-April 2018 570-580

Medical image processingAlgorithmic Mapping and Characterization of the Drug-Induced Pheno-typic-Response Space of Parasites Causing Schistosomiasis. Singh, R., þ,TCBB March-April 2018 469-481An Organelle Correlation-Guided Feature Selection Approach for Classify-ing Multi-Label Subcellular Bio-Images. Shao, W., þ, TCBB May -June2018 828-838Bayesian Multiresolution Variable Selection for Ultra-High DimensionalNeuroimaging Data. Zhao, Y., þ, TCBB March-April 2018 537-550Classification of Alzheimer’s Disease Using Whole Brain HierarchicalNetwork. Liu, J., þ, TCBB March-April 2018 624-632Complex Network Measures in Autism Spectrum Disorders. Sato, J.R., þ,TCBB March-April 2018 581-587Cortical Thinning and Cognitive Impairment in Parkinson’s Disease with-out Dementia. Zhang, L., þ, TCBB March-April 2018 570-580Gender Identification of Human Brain Image with A Novel 3D Descriptor.Yuan, L., þ, TCBB March-April 2018 551-561Integrating Imaging Genomic Data in the Quest for Biomarkers of Schizo-phrenia Disease. Deng, S., þ, TCBB Sept.-Oct. 2018 1480-1491

Medical information systemsA Two-Stage Biomedical Event Trigger Detection Method Integrating Fea-ture Selection and Word Embeddings. He, X., þ, TCBB July-Aug. 20181325-1332Comparison of Machine Learning Approaches for Prediction of AdvancedLiver Fibrosis in Chronic Hepatitis C Patients. Hashem, S., þ, TCBB May-June 2018 861-868

Medical signal detectionA Copula-Based Granger Causality Measure for the Analysis of NeuralSpike Train Data. Hu, M., þ, TCBB March-April 2018 562-569Sparse Pathway-Induced Dynamic Network Biomarker Discovery for EarlyWarning Signal Detection in Complex Diseases. Torshizi, A.D., þ, TCBBMay -June 2018 1028-1034

MeetingsEditorial for Selected Papers of a Joint Conferences, Genome InformaticsWorkshop/International Conference on Bioinformatics (GIW/InCoB)2015. Kim, S., TCBB Nov.-Dec. 2018 1821GenoPri’16: International Workshop on Genome Privacy and Security.Ayday, E., þ, TCBB Sept.-Oct. 2018 1403-1404Great Lakes Bioinformatics Conference (GLBIO) 2015 Special SectionEditorial.Milenkovic, T., þ, TCBB July-Aug. 2018 1229-1230Guest Editorial.Murali, T.M., TCBB July-Aug. 2018 1036Guest Editorial for Special Section on BIBM 2015. Tian, T., þ, TCBBNov.-Dec. 2018 1752-1753Guest Editorial for Special Section on the 12th International Conference onIntelligent Computing (ICIC). Huang, D., þ, TCBB Sept.-Oct. 2018 1433-1435Guest Editorial for Special Section on the Sixth National Conference onBioinformatics and System Biology of China. Fan, X., þ, TCBB July-Aug. 2018 1092Guest Editorial for the 14th Asia Pacific Bioinformatics Conference. Tang,J., þ, TCBB March-April 2018 396-397Guest Editorial for the 15th Asia Pacific Bioinformatics Conference.Wang,L., þ, TCBB Sept.-Oct. 2018 1513-1514Guest Editors’ Introduction to the Special Section on the 14th InternationalConference on Computational Methods in Systems Biology (CMSB2016). Bartocci, E., þ, TCBB July-Aug. 2018 1122-1123Multiscale and Multimodal Analysis for Computational Biology. Gao, X.,þ, TCBB Nov.-Dec. 2018 1951-1952Special Section on Swarm-Based Algorithms and Applications in Compu-tational Biology and Bioinformatics. Tan, Y., þ, TCBB Nov.-Dec. 20181863-1864

MemeticsAdvances in the Application and Development of Non-Linear Global Opti-mization Techniques in Computational Structural Biology. Handl, J., þ,TCBB May -June 2018 688-689

Message passingAn Inference Attack on Genomic Data Using Kinship, Complex Correla-tions, and Phenotype Information. Deznabi, I., þ, TCBB July-Aug. 20181333-1343



MetadataBioinformatic Workflow Extraction from Scientific Texts based on WordSense Disambiguation. Halioui, A., þ, TCBB Nov.-Dec. 2018 1979-1990Encoding Data Using Biological Principles: The Multisample Variant For-mat for Phylogenomics and Population Genomics. Pease, J.B., þ, TCBBJuly-Aug. 2018 1231-1238

MicrofluidicsComputational Models for Trapping Ebola Virus Using Engineered Bacte-ria.Martins, D.P., þ, TCBB Nov.-Dec. 2018 2017-2027

MicroorganismsA New Efficient Algorithm for the Frequent Gene Team Problem. Wang,B., TCBB March-April 2018 588-598A Spatial-Temporal Method to Detect Global Influenza Epidemics UsingHeterogeneous Data Collected from the Internet. Zhou, X., þ, TCBB May-June 2018 802-812Algorithmic Mapping and Characterization of the Drug-Induced Pheno-typic-Response Space of Parasites Causing Schistosomiasis. Singh, R., þ,TCBB March-April 2018 469-481Analysis of the Genome Sequence and Prediction of B-Cell Epitopes of theEnvelope Protein of Middle East Respiratory Syndrome-Coronavirus. Xie,Q., þ, TCBB July-Aug. 2018 1344-1350Coevolutionary Structure-Redesigned-Based Bacterial Foraging Optimiza-tion. Niu, B., þ, TCBB Nov.-Dec. 2018 1865-1876Computational Models for Trapping Ebola Virus Using Engineered Bacte-ria.Martins, D.P., þ, TCBB Nov.-Dec. 2018 2017-2027Computational Prediction of Pathogenic Network Modules in Fusariumverticillioides. Kim, M., þ, TCBB March-April 2018 506-515Discovering Perturbation of Modular Structure in HIV Progression by Inte-grating Multiple Data Sources Through Non-Negative Matrix Factoriza-tion. Ray, S., þ, TCBB May -June 2018 869-877Inferring Gene-Species Assignments in the Presence of Horizontal GeneTransfer.Mykowiecka, A., þ, TCBB Sept.-Oct. 2018 1571-1578Prediction of HIV Drug Resistance by Combining Sequence and StructuralProperties. Khalid, Z., þ, TCBB May -June 2018 966-973Random Sets of Stadiums in Square and Collective Behavior of Bacteria.Czapla, R., TCBB Jan.-Feb. 2018 251-256Region Growing for Segmenting Green Microalgae Images. Borges, V.R.P., þ, TCBB Jan.-Feb. 2018 257-270

Microprocessor chipsMPIGeneNet: Parallel Calculation of Gene Co-Expression Networks onMulticore Clusters. Gonzalez-Dominguez, J., þ, TCBB Sept.-Oct. 20181732-1737

MinimizationConformational Sampling of a Biomolecular Rugged Energy Landscape.Rydzewski, J., þ, TCBB May -June 2018 732-739

ModulationAnalyzing Differential Regulatory Networks Modulated by Continuous-State Genomic Features in Glioblastoma Multiforme. Chiu, Y., þ, TCBBNov.-Dec. 2018 1754-1764

Molecular biophysics3D Genome Reconstruction with ShRec3D+ and Hi-C Data. Li, J., þ,TCBB March-April 2018 460-468A Bipartite Network and Resource Transfer-Based Approach to InferlncRNA-Environmental Factor Associations. Zhou, J., þ, TCBB May-June 2018 753-759A Comparative Study for Identifying the Chromosome-Wide Spatial Clus-ters from High-Throughput Chromatin Conformation Capture Data. Li,X., þ, TCBB May -June 2018 774-787A Global Network Alignment Method Using Discrete Particle Swarm Opti-mization. Huang, J., þ, TCBB May -June 2018 705-718A Graphical Model of Smoking-Induced Global Instability in Lung Cancer.Wang, Y., þ, TCBB Jan.-Feb. 2018 1-14A Memetic Algorithm for 3D Protein Structure Prediction Problem.Correa, L., þ, TCBB May -June 2018 690-704A Novel Approach to Identify the miRNA-mRNA Causal Regulatory Mod-ules in Cancer. Luo, J., þ, TCBB Jan.-Feb. 2018 309-315A Review on Methods for Detecting SNP Interactions in High-DimensionalGenomic Data. Uppu, S., þ, TCBB March-April 2018 599-612ACID: Association Correction for Imbalanced Data in GWAS. Bao, F., þ,TCBB Jan.-Feb. 2018 316-322An Organelle Correlation-Guided Feature Selection Approach for Classify-ing Multi-Label Subcellular Bio-Images. Shao, W., þ, TCBB May -June2018 828-838Analysis of the Genome Sequence and Prediction of B-Cell Epitopes of theEnvelope Protein of Middle East Respiratory Syndrome-Coronavirus. Xie,Q., þ, TCBB July-Aug. 2018 1344-1350

Application of Genetic Programming (GP) Formalism for Building DiseasePredictive Models from Protein-Protein Interactions (PPI) Data. Vyas, R.,þ, TCBB Jan.-Feb. 2018 27-37Assessment of Semantic Similarity between Proteins Using InformationContent and Topological Properties of the Gene Ontology Graph. Dutta,P., þ, TCBB May -June 2018 839-849Codon Context Optimization in Synthetic Gene Design. Papamichail, D.,þ, TCBB March-April 2018 452-459Computational Prediction of Pathogenic Network Modules in Fusariumverticillioides. Kim, M., þ, TCBB March-April 2018 506-515Conformational Sampling of a Biomolecular Rugged Energy Landscape.Rydzewski, J., þ, TCBB May -June 2018 732-739Construction of Signaling Pathways with RNAi Data and Multiple Refer-ence Networks. Alim, M.A., þ, TCBB July-Aug. 2018 1079-1091Continuous Petri Nets and microRNA Analysis in Melanoma. Russo, G.,þ,TCBB Sept.-Oct. 2018 1492-1499Detecting Essential Proteins Based on Network Topology, Gene Expres-sion Data, and Gene Ontology Information. Zhang, W., þ, TCBB Jan.-Feb. 2018 109-116Detecting Multivariate Gene Interactions in RNA-Seq Data Using OptimalBayesian Classification. Knight, J.M., þ, TCBB March-April 2018 484-493Discovering Gene Regulatory Elements Using Coverage-Based Heuristics.Al-Ouran, R., þ, TCBB July-Aug. 2018 1290-1300Discovering Perturbation of Modular Structure in HIV Progression by Inte-grating Multiple Data Sources Through Non-Negative Matrix Factoriza-tion. Ray, S., þ, TCBB May -June 2018 869-877Efficient Algorithms for Sequence Analysis with Entropic Profiles. Pizzi,C., þ, TCBB Jan.-Feb. 2018 117-128Encoding Data Using Biological Principles: The Multisample Variant For-mat for Phylogenomics and Population Genomics. Pease, J.B., þ, TCBBJuly-Aug. 2018 1231-1238Evolutionary Graph Clustering for Protein Complex Identification. He, T.,þ, TCBB May -June 2018 892-904Examining De Novo Transcriptome Assemblies via a Quality AssessmentPipeline. Ghaffari, N., þ, TCBB March-April 2018 494-505fmpRPMF: A Web Implementation for Protein Identification by RobustPeptide Mass Fingerprinting. Li, Y., þ, TCBB Sept.-Oct. 2018 1728-1731From Optimization to Mapping: An Evolutionary Algorithm for ProteinEnergy Landscapes. Sapin, E., þ, TCBB May -June 2018 719-731Fuzzy-Rough Entropy Measure and Histogram Based Patient Selection formiRNA Ranking in Cancer. Pal, J.K., þ, TCBB March-April 2018 659-672Gene Regulatory Network Inference from Perturbed Time-Series Expres-sion Data via Ordered Dynamical Expansion of Non-Steady State Actors.Zamanighomi, M., þ, TCBB July-Aug. 2018 1093-1106GPU-Based Point Cloud Superpositioning for Structural Comparisons ofProtein Binding Sites. Leinweber, M., þ, TCBB May -June 2018 740-752Hardware Accelerator for the Multifractal Analysis of DNA Sequences.Duarte-Sanchez, J.E., þ, TCBB Sept.-Oct. 2018 1611-1624HEMEsPred: Structure-Based Ligand-Specific Heme Binding ResiduesPrediction by Using Fast-Adaptive Ensemble Learning Scheme. Zhang,J., þ, TCBB Jan.-Feb. 2018 147-156IAS: Interaction Specific GO Term Associations for Predicting Protein-Protein Interaction Networks. Yerneni, S., þ, TCBB July-Aug. 2018 1247-1258Identification and Analysis of Key Residues in Protein–RNA Complexes.Kulandaisamy, A., þ, TCBB Sept.-Oct. 2018 1436-1444Identifying Condition-Specific Modules by Clustering Multiple Networks.Ma, X., þ, TCBB Sept.-Oct. 2018 1636-1648Incorporation of Solvent Effect into Multi-Objective Evolutionary Algo-rithm for Improved Protein Structure Prediction. Gao, S., þ, TCBB July-Aug. 2018 1365-1378Index-Based Network Aligner of Protein-Protein Interaction Networks.Elmsallati, A., þ, TCBB Jan.-Feb. 2018 330-336Inferring Gene-Species Assignments in the Presence of Horizontal GeneTransfer.Mykowiecka, A., þ, TCBB Sept.-Oct. 2018 1571-1578Machine Learned Replacement of N-Labels for Basecalled Sequences inDNA Barcoding.Ma, E.Y.T., þ, TCBB Jan.-Feb. 2018 191-204MeTDiff: A Novel Differential RNA Methylation Analysis for MeRIP-SeqData. Cui, X., þ, TCBB March-April 2018 526-534Modeling Methylation Patterns with Long Read Sequencing Data. Meyer,K.N., þ, TCBB July-Aug. 2018 1379-1389Multiple Network Alignment via MultiMAGNA++. Vijayan, V., þ, TCBBSept.-Oct. 2018 1669-1682Mutli-Features Prediction of Protein Translational Modification Sites. Bao,W., þ, TCBB Sept.-Oct. 2018 1453-1460



NAHAL-Flex: A Numerical and Alphabetical Hinge Detection Algorithmfor Flexible Protein Structure Alignment. Fotoohifiroozabadi, S., þ,TCBB May -June 2018 934-943NewGOA: Predicting New GO Annotations of Proteins by Bi-RandomWalks on a Hybrid Graph. Yu, G., þ, TCBB July-Aug. 2018 1390-1402Nucleosome Positioning of Intronless Genes in the Human Genome.Cheng, X., þ, TCBB July-Aug. 2018 1111-1121Petri Net Siphon Analysis and Graph Theoretic Measures for IdentifyingCombination Therapies in Cancer. Behinaein, B., þ, TCBB Jan.-Feb.2018 231-243Prediction of HIV Drug Resistance by Combining Sequence and StructuralProperties. Khalid, Z., þ, TCBB May -June 2018 966-973Prediction of Hot Regions in PPIs Based on Improved Local CommunityStructure Detecting. Lin, X., þ, TCBB Sept.-Oct. 2018 1470-1479Proteomic Evidence for In-Frame and Out-of-Frame Alternatively SplicedIsoforms in Human and Mouse. Ramalho, R.F., þ, TCBB July-Aug. 20181284-1289PyMut: A Web Tool for Overlapping Gene Loss-of-Function MutationDesign. Liu, K., þ, TCBB July-Aug. 2018 1107-1110Querying of Disparate Association and Interaction Data in BiomedicalApplications. Qiao, S., þ, TCBB July-Aug. 2018 1052-1065REPA: Applying Pathway Analysis to Genome-Wide Transcription FactorBinding Data. Patra, P., þ, TCBB July-Aug. 2018 1270-1283Sequence-Based Prediction of Putative Transcription Factor Binding Sitesin DNA Sequences of Any Length. Lee, W., þ, TCBB Sept.-Oct. 20181461-1469Structural Class Classification of 3D Protein Structure Based on Multi-View 2D Images. Suryanto, C.H., þ, TCBB Jan.-Feb. 2018 286-299Structural Target Controllability of Linear Networks. Czeizler, E., þ,TCBB July-Aug. 2018 1217-1228The Intrinsic Pepsin Resistance of Interleukin-8 Can Be Explained from aCombined Bioinformatical and Experimental Approach. Anders, G., þ,TCBB Jan.-Feb. 2018 300-308Unified Deep Learning Architecture for Modeling Biology Sequence. Wu,H., þ, TCBB Sept.-Oct. 2018 1445-1452

Molecular configurationsA Bipartite Network and Resource Transfer-Based Approach to InferlncRNA-Environmental Factor Associations. Zhou, J., þ, TCBB May-June 2018 753-759A Comparative Study for Identifying the Chromosome-Wide Spatial Clus-ters from High-Throughput Chromatin Conformation Capture Data. Li,X., þ, TCBB May -June 2018 774-787Codon Context Optimization in Synthetic Gene Design. Papamichail, D.,þ, TCBB March-April 2018 452-459Conformational Sampling of a Biomolecular Rugged Energy Landscape.Rydzewski, J., þ, TCBB May -June 2018 732-739From Optimization to Mapping: An Evolutionary Algorithm for ProteinEnergy Landscapes. Sapin, E., þ, TCBB May -June 2018 719-731GPU-Based Point Cloud Superpositioning for Structural Comparisons ofProtein Binding Sites. Leinweber, M., þ, TCBB May -June 2018 740-752HEMEsPred: Structure-Based Ligand-Specific Heme Binding ResiduesPrediction by Using Fast-Adaptive Ensemble Learning Scheme. Zhang,J., þ, TCBB Jan.-Feb. 2018 147-156Identification and Analysis of Key Residues in Protein–RNA Complexes.Kulandaisamy, A., þ, TCBB Sept.-Oct. 2018 1436-1444Incorporation of Solvent Effect into Multi-Objective Evolutionary Algo-rithm for Improved Protein Structure Prediction. Gao, S., þ, TCBB July-Aug. 2018 1365-1378MeTDiff: A Novel Differential RNA Methylation Analysis for MeRIP-SeqData. Cui, X., þ, TCBB March-April 2018 526-534Modeling Methylation Patterns with Long Read Sequencing Data. Meyer,K.N., þ, TCBB July-Aug. 2018 1379-1389Mutli-Features Prediction of Protein Translational Modification Sites. Bao,W., þ, TCBB Sept.-Oct. 2018 1453-1460NAHAL-Flex: A Numerical and Alphabetical Hinge Detection Algorithmfor Flexible Protein Structure Alignment. Fotoohifiroozabadi, S., þ,TCBB May -June 2018 934-943Petri Net Siphon Analysis and Graph Theoretic Measures for IdentifyingCombination Therapies in Cancer. Behinaein, B., þ, TCBB Jan.-Feb.2018 231-243Prediction of HIV Drug Resistance by Combining Sequence and StructuralProperties. Khalid, Z., þ, TCBB May -June 2018 966-973Proteomic Evidence for In-Frame and Out-of-Frame Alternatively SplicedIsoforms in Human and Mouse. Ramalho, R.F., þ, TCBB July-Aug. 20181284-1289PyMut: A Web Tool for Overlapping Gene Loss-of-Function MutationDesign. Liu, K., þ, TCBB July-Aug. 2018 1107-1110

Sequence-Based Prediction of Putative Transcription Factor Binding Sitesin DNA Sequences of Any Length. Lee, W., þ, TCBB Sept.-Oct. 20181461-1469Structural Class Classification of 3D Protein Structure Based on Multi-View 2D Images. Suryanto, C.H., þ, TCBB Jan.-Feb. 2018 286-299The Intrinsic Pepsin Resistance of Interleukin-8 Can Be Explained from aCombined Bioinformatical and Experimental Approach. Anders, G., þ,TCBB Jan.-Feb. 2018 300-308

Monte Carlo methodsA Sparse Regression Method for Group-Wise Feature Selection with FalseDiscovery Rate Control. Gossmann, A., þ, TCBB July-Aug. 2018 1066-1078Bayesian Multiresolution Variable Selection for Ultra-High DimensionalNeuroimaging Data. Zhao, Y., þ, TCBB March-April 2018 537-550Detecting Multivariate Gene Interactions in RNA-Seq Data Using OptimalBayesian Classification. Knight, J.M., þ, TCBB March-April 2018 484-493Inferring Gene-Species Assignments in the Presence of Horizontal GeneTransfer.Mykowiecka, A., þ, TCBB Sept.-Oct. 2018 1571-1578

Multilayer perceptronsBiological Event Trigger Identification with Noise Contrastive Estimation.Jiang, N., þ, TCBB Sept.-Oct. 2018 1549-1559

Multiprocessing systemsMPIGeneNet: Parallel Calculation of Gene Co-Expression Networks onMulticore Clusters. Gonzalez-Dominguez, J., þ, TCBB Sept.-Oct. 20181732-1737

MusclesCo-Expression Network Approach to Studying the Effects of BotulinumNeurotoxin-A.Mukund, K., þ, TCBB Nov.-Dec. 2018 2009-2016

Mutual informationGrouped Gene Selection of Cancer via Adaptive Sparse Group Lasso Basedon Conditional Mutual Information. Li, J., þ, TCBB Nov.-Dec. 20182028-2038

N

Natural language processingBiological Event Trigger Identification with Noise Contrastive Estimation.Jiang, N., þ, TCBB Sept.-Oct. 2018 1549-1559

Nearest neighbor methodsFeature Selection for Optimized High-Dimensional Biomedical Data Usingan Improved Shuffled Frog Leaping Algorithm. Hu, B., þ, TCBB Nov.-Dec. 2018 1765-1773

Network analyzersIdentifying Gene Network Rewiring by Integrating Gene Expression andGene Network Data. Xu, T., þ, TCBB Nov.-Dec. 2018 2079-2085

Network theory (graphs)Application of Fractal Theory on Motifs Counting in Biological Networks.Joveini, M.B.Z., þ, TCBB March-April 2018 613-623Autumn Algorithm—Computation of Hybridization Networks for RealisticPhylogenetic Trees. Huson, D.H., þ, TCBB March-April 2018 398-410Index-Based Network Aligner of Protein-Protein Interaction Networks.Elmsallati, A., þ, TCBB Jan.-Feb. 2018 330-336Modeling the Geometry and Dynamics of the Endoplasmic Reticulum Net-work. Lin, C., þ, TCBB March-April 2018 377-386Optimal Objective-Based Experimental Design for Uncertain DynamicalGene Networks with Experimental Error. Mohsenizadeh, D.N., þ, TCBBJan.-Feb. 2018 218-230Structural Target Controllability of Linear Networks. Czeizler, E., þ,TCBB July-Aug. 2018 1217-1228

Network topologyA Novel Computational Approach for Global Alignment for Multiple Bio-logical Networks. Djeddi, W.E., þ, TCBB Nov.-Dec. 2018 2060-2066Correction to “Detecting Essential Proteins Based on Network Topology,Gene Expression Data, and Gene Ontology Information”. Zhang, W., þ,TCBB May -June 2018 1035Detecting Essential Proteins Based on Network Topology, Gene Expres-sion Data, and Gene Ontology Information. Zhang, W., þ, TCBB Jan.-Feb. 2018 109-116

Neural networksMutli-Features Prediction of Protein Translational Modification Sites. Bao,W., þ, TCBB Sept.-Oct. 2018 1453-1460Predicting the Absorption Potential of Chemical Compounds Through aDeep Learning Approach. Shin, M., þ, TCBB March-April 2018 432-440



NeuronsSPF-CellTracker: Tracking Multiple Cells with Strongly-Correlated MovesUsing a Spatial Particle Filter. Hirose, O., þ, TCBB Nov.-Dec. 20181822-1831

NeurophysiologyA Copula-Based Granger Causality Measure for the Analysis of NeuralSpike Train Data. Hu, M., þ, TCBB March-April 2018 562-569Bayesian Multiresolution Variable Selection for Ultra-High DimensionalNeuroimaging Data. Zhao, Y., þ, TCBB March-April 2018 537-550Classification of Alzheimer’s Disease Using Whole Brain HierarchicalNetwork. Liu, J., þ, TCBB March-April 2018 624-632Complex Network Measures in Autism Spectrum Disorders. Sato, J.R., þ,TCBB March-April 2018 581-587Cortical Thinning and Cognitive Impairment in Parkinson’s Disease with-out Dementia. Zhang, L., þ, TCBB March-April 2018 570-580Gender Identification of Human Brain Image with A Novel 3D Descriptor.Yuan, L., þ, TCBB March-April 2018 551-561Probabilistic Methods in Computational Neuroscience. Zhang, J., þ, TCBBMarch-April 2018 535-536

Nuclear magnetic resonanceA Slice-based 13C-detected NMR Spin System Forming and ResonanceAssignment Method. Alazmi, M., þ, TCBB Nov.-Dec. 2018 1999-2008

O

Object trackingCell Population Tracking in a Honeycomb Structure Using an IMM FilterBased 3D Local Graph Matching Model. Liu, M., þ, TCBB Sept.-Oct.2018 1706-1717

OntologiesA Comparative Study for Identifying the Chromosome-Wide Spatial Clus-ters from High-Throughput Chromatin Conformation Capture Data. Li,X., þ, TCBB May -June 2018 774-787A Framework for Identifying Genotypic Information from ClinicalRecords: Exploiting Integrated Ontology Structures to Transfer Annota-tions between ICD Codes and Gene Ontologies. Hashemikhabir, S., þ,TCBB July-Aug. 2018 1259-1269A Novel Computational Approach for Global Alignment for Multiple Bio-logical Networks. Djeddi, W.E., þ, TCBB Nov.-Dec. 2018 2060-2066Assessment of Semantic Similarity between Proteins Using InformationContent and Topological Properties of the Gene Ontology Graph. Dutta,P., þ, TCBB May -June 2018 839-849Bioinformatic Workflow Extraction from Scientific Texts based on WordSense Disambiguation. Halioui, A., þ, TCBB Nov.-Dec. 2018 1979-1990Correction to “Detecting Essential Proteins Based on Network Topology,Gene Expression Data, and Gene Ontology Information”. Zhang, W., þ,TCBB May -June 2018 1035Detecting Essential Proteins Based on Network Topology, Gene Expres-sion Data, and Gene Ontology Information. Zhang, W., þ, TCBB Jan.-Feb. 2018 109-116Discovering Perturbation of Modular Structure in HIV Progression by Inte-grating Multiple Data Sources Through Non-Negative Matrix Factoriza-tion. Ray, S., þ, TCBB May -June 2018 869-877Evolutionary Graph Clustering for Protein Complex Identification. He, T.,þ, TCBB May -June 2018 892-904IAS: Interaction Specific GO Term Associations for Predicting Protein-Protein Interaction Networks. Yerneni, S., þ, TCBB July-Aug. 2018 1247-1258Investigating Correlation between Protein Sequence Similarity and Seman-tic Similarity Using Gene Ontology Annotations. Ikram, N., þ, TCBBMay -June 2018 905-912NewGOA: Predicting New GO Annotations of Proteins by Bi-RandomWalks on a Hybrid Graph. Yu, G., þ, TCBB July-Aug. 2018 1390-1402Novelty Indicator for Enhanced Prioritization of Predicted Gene OntologyAnnotations. Chicco, D., þ, TCBB May -June 2018 954-965Predicting MicroRNA-Disease Associations Based on Improved Micro-RNA and Disease Similarities. Lan, W., þ, TCBB Nov.-Dec. 2018 1774-1782

Open systemsNGS-FC: A Next-Generation Sequencing Data Format Converter. Yu, C.,þ, TCBB Sept.-Oct. 2018 1683-1691

OptimizationA Comparative Study for Identifying the Chromosome-Wide Spatial Clus-ters from High-Throughput Chromatin Conformation Capture Data. Li,X., þ, TCBB May -June 2018 774-787

A GRASP-Based Heuristic for the Sorting by Length-Weighted InversionsProblem. Arruda, T.d.S., þ, TCBB March-April 2018 352-363A Grouping Particle Swarm Optimizer with Personal-Best-Position Guid-ance for Large Scale Optimization. Guo, W., þ, TCBB Nov.-Dec. 20181904-1915Coevolutionary Structure-Redesigned-Based Bacterial Foraging Optimiza-tion. Niu, B., þ, TCBB Nov.-Dec. 2018 1865-1876DTL-RnB: Algorithms and Tools for Summarizing the Space of DTL Rec-onciliations.Ma, W., þ, TCBB March-April 2018 411-421Environment Sensitivity-Based Cooperative Co-Evolutionary Algorithmsfor Dynamic Multi-Objective Optimization. Xu, B., þ, TCBB Nov.-Dec.2018 1877-1890Feature Selection for Optimized High-Dimensional Biomedical Data Usingan Improved Shuffled Frog Leaping Algorithm. Hu, B., þ, TCBB Nov.-Dec. 2018 1765-1773From Optimization to Mapping: An Evolutionary Algorithm for ProteinEnergy Landscapes. Sapin, E., þ, TCBB May -June 2018 719-731GPU-Based Point Cloud Superpositioning for Structural Comparisons ofProtein Binding Sites. Leinweber, M., þ, TCBB May -June 2018 740-752Modeling the Geometry and Dynamics of the Endoplasmic Reticulum Net-work. Lin, C., þ, TCBB March-April 2018 377-386Multiple Network Alignment via MultiMAGNA++. Vijayan, V., þ, TCBBSept.-Oct. 2018 1669-1682Optimal Block-Based Trimming for Next Generation Sequencing. Hedtke,I., þ, TCBB March-April 2018 364-376Optimizing Phylogenetic Queries for Performance. Jamil, H.M., TCBBSept.-Oct. 2018 1692-1705Sparse Pathway-Induced Dynamic Network Biomarker Discovery for EarlyWarning Signal Detection in Complex Diseases. Torshizi, A.D., þ, TCBBMay -June 2018 1028-1034

Organic compoundsEnumerating Substituted Benzene Isomers of Tree-Like Chemical Graphs.Li, J., þ, TCBB March-April 2018 633-646

P

Parallel processingAutumn Algorithm—Computation of Hybridization Networks for RealisticPhylogenetic Trees. Huson, D.H., þ, TCBB March-April 2018 398-410MPIGeneNet: Parallel Calculation of Gene Co-Expression Networks onMulticore Clusters. Gonzalez-Dominguez, J., þ, TCBB Sept.-Oct. 20181732-1737PREMER: A Tool to Infer Biological Networks. Villaverde, A.F., þ, TCBBJuly-Aug. 2018 1193-1202

Parameter estimationMoment-Based Parameter Estimation for Stochastic Reaction Networks inEquilibrium. Backenk€ohler, M., þ, TCBB July-Aug. 2018 1180-1192

Pareto optimizationBi-level and Bi-objective p-Median Type Problems for Integrative Cluster-ing: Application to Analysis of Cancer Gene-Expression and Drug-Response Data. Ushakov, A.V., þ, TCBB Jan.-Feb. 2018 46-59

Particle swarm optimizationA Global Network Alignment Method Using Discrete Particle Swarm Opti-mization. Huang, J., þ, TCBB May -June 2018 705-718A Grouping Particle Swarm Optimizer with Personal-Best-Position Guid-ance for Large Scale Optimization. Guo, W., þ, TCBB Nov.-Dec. 20181904-1915Advances in the Application and Development of Non-Linear Global Opti-mization Techniques in Computational Structural Biology. Handl, J., þ,TCBB May -June 2018 688-689Comparison of Machine Learning Approaches for Prediction of AdvancedLiver Fibrosis in Chronic Hepatitis C Patients. Hashem, S., þ, TCBB May-June 2018 861-868Constructing DNA Barcode Sets Based on Particle Swarm Optimization.Wang, B., þ, TCBB May -June 2018 999-1002Environment Sensitivity-Based Cooperative Co-Evolutionary Algorithmsfor Dynamic Multi-Objective Optimization. Xu, B., þ, TCBB Nov.-Dec.2018 1877-1890Feature Selection for Optimized High-Dimensional Biomedical Data Usingan Improved Shuffled Frog Leaping Algorithm. Hu, B., þ, TCBB Nov.-Dec. 2018 1765-1773Multiple-Swarm Ensembles: Improving the Predictive Power and Robust-ness of Predictive Models and Its Use in Computational Biology. Alves,P., þ, TCBB May -June 2018 926-933



Robust Dynamic Multi-Objective Vehicle Routing Optimization Method.Guo, Y., þ, TCBB Nov.-Dec. 2018 1891-1903Special Section on Swarm-Based Algorithms and Applications in Compu-tational Biology and Bioinformatics. Tan, Y., þ, TCBB Nov.-Dec. 20181863-1864Swarm Robots Search for Multiple Targets Based on an Improved Group-ing Strategy. Tang, Q., þ, TCBB Nov.-Dec. 2018 1943-1950

Partitioning algorithmsUsing Machine Learning to Improve the Prediction of Functional Outcomein Ischemic Stroke Patients. Monteiro, M., þ, TCBB Nov.-Dec. 20181953-1959

Patient diagnosisClassification of State Trajectories in Gene Regulatory Networks. Karba-layghareh, A., þ, TCBB Jan.-Feb. 2018 68-82Comparison of Machine Learning Approaches for Prediction of AdvancedLiver Fibrosis in Chronic Hepatitis C Patients. Hashem, S., þ, TCBB May-June 2018 861-868Extracting Stage-Specific and Dynamic Modules Through Analyzing Mul-tiple Networks Associated with Cancer Progression. Ma, X., þ, TCBBMarch-April 2018 647-658

Patient monitoringA Just-in-Time Learning Based Monitoring and Classification Method forHyper/Hypocalcemia Diagnosis. Peng, X., þ, TCBB May -June 2018 788-801

Patient treatmentClassification of State Trajectories in Gene Regulatory Networks. Karba-layghareh, A., þ, TCBB Jan.-Feb. 2018 68-82Continuous Petri Nets and microRNA Analysis in Melanoma. Russo, G.,þ,TCBB Sept.-Oct. 2018 1492-1499Extracting Stage-Specific and Dynamic Modules Through Analyzing Mul-tiple Networks Associated with Cancer Progression. Ma, X., þ, TCBBMarch-April 2018 647-658Influence of Airway Secretion on Airflow Dynamics of Mechanical Venti-lated Respiratory System. Ren, S., þ, TCBB Sept.-Oct. 2018 1660-1668PerPAS: Topology-Based Single Sample Pathway Analysis Method. Liu,C., þ, TCBB May -June 2018 1022-1027Petri Net Siphon Analysis and Graph Theoretic Measures for IdentifyingCombination Therapies in Cancer. Behinaein, B., þ, TCBB Jan.-Feb.2018 231-243Prediction of HIV Drug Resistance by Combining Sequence and StructuralProperties. Khalid, Z., þ, TCBB May -June 2018 966-973

Pattern classificationA Distributed Classifier for MicroRNA Target Prediction with ValidationThrough TCGA Expression Data. Ghoshal, A., þ, TCBB July-Aug. 20181037-1051A Just-in-Time Learning Based Monitoring and Classification Method forHyper/Hypocalcemia Diagnosis. Peng, X., þ, TCBB May -June 2018 788-801A Self-Training Subspace Clustering Algorithm under Low-Rank Repre-sentation for Cancer Classification on Gene Expression Data. Xia, C., þ,TCBB July-Aug. 2018 1315-1324Application of Genetic Programming (GP) Formalism for Building DiseasePredictive Models from Protein-Protein Interactions (PPI) Data. Vyas, R.,þ, TCBB Jan.-Feb. 2018 27-37Classification of State Trajectories in Gene Regulatory Networks. Karba-layghareh, A., þ, TCBB Jan.-Feb. 2018 68-82Combining Supervised and Unsupervised Learning for Improved miRNATarget Prediction. Sedaghat, N., þ, TCBB Sept.-Oct. 2018 1594-1604Comparison of Machine Learning Approaches for Prediction of AdvancedLiver Fibrosis in Chronic Hepatitis C Patients. Hashem, S., þ, TCBB May-June 2018 861-868Detecting Multivariate Gene Interactions in RNA-Seq Data Using OptimalBayesian Classification. Knight, J.M., þ, TCBB March-April 2018 484-493HEMEsPred: Structure-Based Ligand-Specific Heme Binding ResiduesPrediction by Using Fast-Adaptive Ensemble Learning Scheme. Zhang,J., þ, TCBB Jan.-Feb. 2018 147-156Inferring the Functions of Proteins from the Interrelationships betweenFunctional Categories. Taha, K., TCBB Jan.-Feb. 2018 157-167Introducing a Stable Bootstrap Validation Framework for Reliable Geno-mic Signature Extraction. Chlis, N., þ, TCBB Jan.-Feb. 2018 181-190Mutli-Features Prediction of Protein Translational Modification Sites. Bao,W., þ, TCBB Sept.-Oct. 2018 1453-1460Optimization of Gene Set Annotations Using Robust Trace-Norm Multi-task Learning. Liang, X., þ, TCBB May -June 2018 1016-1021Predicting the Absorption Potential of Chemical Compounds Through aDeep Learning Approach. Shin, M., þ, TCBB March-April 2018 432-440

Prediction of Hot Regions in PPIs Based on Improved Local CommunityStructure Detecting. Lin, X., þ, TCBB Sept.-Oct. 2018 1470-1479RAFP-Pred: Robust Prediction of Antifreeze Proteins Using LocalizedAnalysis of n-Peptide Compositions. Khan, S., þ, TCBB Jan.-Feb. 2018244-250

Pattern clusteringA Novel Approach to Identify the miRNA-mRNA Causal Regulatory Mod-ules in Cancer. Luo, J., þ, TCBB Jan.-Feb. 2018 309-315A Self-Training Subspace Clustering Algorithm under Low-Rank Repre-sentation for Cancer Classification on Gene Expression Data. Xia, C., þ,TCBB July-Aug. 2018 1315-1324Assessment of Semantic Similarity between Proteins Using InformationContent and Topological Properties of the Gene Ontology Graph. Dutta,P., þ, TCBB May -June 2018 839-849Bi-level and Bi-objective p-Median Type Problems for Integrative Cluster-ing: Application to Analysis of Cancer Gene-Expression and Drug-Response Data. Ushakov, A.V., þ, TCBB Jan.-Feb. 2018 46-59Complex Network Measures in Autism Spectrum Disorders. Sato, J.R., þ,TCBB March-April 2018 581-587Discovering Perturbation of Modular Structure in HIV Progression by Inte-grating Multiple Data Sources Through Non-Negative Matrix Factoriza-tion. Ray, S., þ, TCBB May -June 2018 869-877Efficient Algorithms for Genomic Duplication Models. Paszek, J., þ,TCBB Sept.-Oct. 2018 1515-1524Evolutionary Graph Clustering for Protein Complex Identification. He, T.,þ, TCBB May -June 2018 892-904hc-OTU: A Fast and Accurate Method for Clustering Operational Taxo-nomic Units Based on Homopolymer Compaction. Park, S., þ, TCBBMarch-April 2018 441-451Identifying Condition-Specific Modules by Clustering Multiple Networks.Ma, X., þ, TCBB Sept.-Oct. 2018 1636-1648Inferring Unknown Biological Function by Integration of GO Annota-tions and Gene Expression Data. Leale, G., þ, TCBB Jan.-Feb. 2018168-180Integrating Multiple Data Sources for Combinatorial Marker Discovery: AStudy in Tumorigenesis. Bandyopadhyay, S., þ, TCBB March-April 2018673-687Prediction of Hot Regions in PPIs Based on Improved Local CommunityStructure Detecting. Lin, X., þ, TCBB Sept.-Oct. 2018 1470-1479

PermeabilityPredicting the Absorption Potential of Chemical Compounds Through aDeep Learning Approach. Shin, M., þ, TCBB March-April 2018 432-440

Petri netsContinuous Petri Nets and microRNA Analysis in Melanoma. Russo, G.,þ,TCBB Sept.-Oct. 2018 1492-1499Petri Net Siphon Analysis and Graph Theoretic Measures for IdentifyingCombination Therapies in Cancer. Behinaein, B., þ, TCBB Jan.-Feb.2018 231-243Reduction of Qualitative Models of Biological Networks for TransientDynamics Analysis. Pauleve, L., TCBB July-Aug. 2018 1167-1179

PhylogenyBioinformatic Workflow Extraction from Scientific Texts based on WordSense Disambiguation. Halioui, A., þ, TCBB Nov.-Dec. 2018 1979-1990Scaffolding of Ancient Contigs and Ancestral Reconstruction in a Phyloge-netic Framework. Luhmann, N., þ, TCBB Nov.-Dec. 2018 2094-2100

Physiological modelsA Just-in-Time Learning Based Monitoring and Classification Method forHyper/Hypocalcemia Diagnosis. Peng, X., þ, TCBB May -June 2018 788-801

PlasmasA Study of Cell-Free DNA Fragmentation Pattern and Its Application inDNA Sample Type Classification. Chen, S., þ, TCBB Sept.-Oct. 20181718-1722

PneumodynamicsInfluence of Airway Secretion on Airflow Dynamics of Mechanical Venti-lated Respiratory System. Ren, S., þ, TCBB Sept.-Oct. 2018 1660-1668

PolymorphismA Review on Methods for Detecting SNP Interactions in High-DimensionalGenomic Data. Uppu, S., þ, TCBB March-April 2018 599-612Integrating Imaging Genomic Data in the Quest for Biomarkers of Schizo-phrenia Disease. Deng, S., þ, TCBB Sept.-Oct. 2018 1480-1491

PolynomialsOptimal Block-Based Trimming for Next Generation Sequencing. Hedtke,I., þ, TCBB March-April 2018 364-376

Potential energy functionsConformational Sampling of a Biomolecular Rugged Energy Landscape.Rydzewski, J., þ, TCBB May -June 2018 732-739



Potential energy surfacesConformational Sampling of a Biomolecular Rugged Energy Landscape.Rydzewski, J., þ, TCBB May -June 2018 732-739

Power measurementDiscMLA: An Efficient Discriminative Motif Learning Algorithm overHigh-Throughput Datasets. Zhang, H., þ, TCBB Nov.-Dec. 2018 1810-1820

Prediction algorithmsEnvironment Sensitivity-Based Cooperative Co-Evolutionary Algorithmsfor Dynamic Multi-Objective Optimization. Xu, B., þ, TCBB Nov.-Dec.2018 1877-1890Predicting Hospital Readmission via Cost-Sensitive Deep Learning. Wang,H., þ, TCBB Nov.-Dec. 2018 1968-1978

Prediction theoryCombining Supervised and Unsupervised Learning for Improved miRNATarget Prediction. Sedaghat, N., þ, TCBB Sept.-Oct. 2018 1594-1604

Predictive methodsANTENNA, a Multi-Rank, Multi-Layered Recommender System for Infer-ring Reliable Drug-Gene-Disease Associations: Repurposing Diazoxide asa Targeted Anti-Cancer Therapy. Wang, A., þ, TCBB Nov.-Dec. 20181960-1967Using Machine Learning to Improve the Prediction of Functional Outcomein Ischemic Stroke Patients. Monteiro, M., þ, TCBB Nov.-Dec. 20181953-1959

Principal component analysisAlgorithmic Mapping and Characterization of the Drug-Induced Pheno-typic-Response Space of Parasites Causing Schistosomiasis. Singh, R., þ,TCBB March-April 2018 469-481Implementation and Evaluation of an Algorithm for Cryptographically Pri-vate Principal Component Analysis on Genomic Data. Bogdanov, D., þ,TCBB Sept.-Oct. 2018 1427-1432

PrivacyGenoPri’16: International Workshop on Genome Privacy and Security.Ayday, E., þ, TCBB Sept.-Oct. 2018 1403-1404

Probabilistic logicA Memetic Algorithm for 3D Protein Structure Prediction Problem.Correa, L., þ, TCBB May -June 2018 690-704A Model-Based Tool for the Analysis and Design of Gene RegulatoryNetworks. Ironi, L., þ, TCBB July-Aug. 2018 1301-1314Aggregation for Computing Multi-Modal Stationary Distributions in 1-DGene Regulatory Networks. Avcu, N., þ, TCBB May -June 2018 813-827Heavy-Tailed Noise Suppression and Derivative Wavelet Scalogram forDetecting DNA Copy Number Aberrations. Nguyen, N., þ, TCBB Sept.-Oct. 2018 1625-1635Local-Nearest-Neighbors-Based Feature Weighting for Gene Selection. An,S., þ, TCBB Sept.-Oct. 2018 1538-1548Moment-Based Parameter Estimation for Stochastic Reaction Networks inEquilibrium. Backenk€ohler, M., þ, TCBB July-Aug. 2018 1180-1192Probabilistic Methods in Computational Neuroscience. Zhang, J., þ, TCBBMarch-April 2018 535-536Reviving the Two-State Markov Chain Approach. Mizera, A., þ, TCBBSept.-Oct. 2018 1525-1537Simulating the Large-Scale Erosion of Genomic Privacy Over Time.Backes, M., þ, TCBB Sept.-Oct. 2018 1405-1412Species Tree Estimation Using ASTRAL: How Many Genes Are Enough?.Shekhar, S., þ, TCBB Sept.-Oct. 2018 1738-1747

ProductionControllability Analysis and Control Synthesis for the Ribosome FlowModel. Zarai, Y., þ, TCBB July-Aug. 2018 1351-1364

Prognostics and health managementUsing Machine Learning to Improve the Prediction of Functional Outcomein Ischemic Stroke Patients. Monteiro, M., þ, TCBB Nov.-Dec. 20181953-1959

Protein engineeringControllability Analysis and Control Synthesis for the Ribosome FlowModel. Zarai, Y., þ, TCBB July-Aug. 2018 1351-1364

Protein sequenceA Simplified Description of Child Tables for Sequence Similarity Search.Frith, M.C., þ, TCBB Nov.-Dec. 2018 2067-2073RF-NR: Random Forest Based Approach for Improved Classification ofNuclear Receptors. Ismail, H.D., þ, TCBB Nov.-Dec. 2018 1844-1852

ProteinsA Bipartite Network and Resource Transfer-Based Approach to InferlncRNA-Environmental Factor Associations. Zhou, J., þ, TCBB May-June 2018 753-759A Global Network Alignment Method Using Discrete Particle Swarm Opti-mization. Huang, J., þ, TCBB May -June 2018 705-718

A Graphical Model of Smoking-Induced Global Instability in Lung Cancer.Wang, Y., þ, TCBB Jan.-Feb. 2018 1-14A Memetic Algorithm for 3D Protein Structure Prediction Problem.Correa, L., þ, TCBB May -June 2018 690-704A Novel Computational Approach for Global Alignment for Multiple Bio-logical Networks. Djeddi, W.E., þ, TCBB Nov.-Dec. 2018 2060-2066A Slice-based 13C-detected NMR Spin System Forming and ResonanceAssignment Method. Alazmi, M., þ, TCBB Nov.-Dec. 2018 1999-2008Altering Indispensable Proteins in Controlling Directed Human ProteinInteraction Network. Zhang, X., TCBB Nov.-Dec. 2018 2074-2078An Organelle Correlation-Guided Feature Selection Approach for Classify-ing Multi-Label Subcellular Bio-Images. Shao, W., þ, TCBB May -June2018 828-838Analysis of the Genome Sequence and Prediction of B-Cell Epitopes of theEnvelope Protein of Middle East Respiratory Syndrome-Coronavirus. Xie,Q., þ, TCBB July-Aug. 2018 1344-1350Application of Genetic Programming (GP) Formalism for Building DiseasePredictive Models from Protein-Protein Interactions (PPI) Data. Vyas, R.,þ, TCBB Jan.-Feb. 2018 27-37Assessment of Semantic Similarity between Proteins Using InformationContent and Topological Properties of the Gene Ontology Graph. Dutta,P., þ, TCBB May -June 2018 839-849Co-Expression Network Approach to Studying the Effects of BotulinumNeurotoxin-A.Mukund, K., þ, TCBB Nov.-Dec. 2018 2009-2016Codon Context Optimization in Synthetic Gene Design. Papamichail, D.,þ, TCBB March-April 2018 452-459Computational Models for Trapping Ebola Virus Using Engineered Bacte-ria.Martins, D.P., þ, TCBB Nov.-Dec. 2018 2017-2027Conformational Sampling of a Biomolecular Rugged Energy Landscape.Rydzewski, J., þ, TCBB May -June 2018 732-739Construction of Signaling Pathways with RNAi Data and Multiple Refer-ence Networks. Alim, M.A., þ, TCBB July-Aug. 2018 1079-1091Controllability Analysis and Control Synthesis for the Ribosome FlowModel. Zarai, Y., þ, TCBB July-Aug. 2018 1351-1364Correction to “Detecting Essential Proteins Based on Network Topology,Gene Expression Data, and Gene Ontology Information”. Zhang, W., þ,TCBB May -June 2018 1035Detecting Essential Proteins Based on Network Topology, Gene Expres-sion Data, and Gene Ontology Information. Zhang, W., þ, TCBB Jan.-Feb. 2018 109-116Discovering Perturbation of Modular Structure in HIV Progression by Inte-grating Multiple Data Sources Through Non-Negative Matrix Factoriza-tion. Ray, S., þ, TCBB May -June 2018 869-877Effectively Identifying Compound-Protein Interactions by Learning fromPositive and Unlabeled Examples. Cheng, Z., þ, TCBB Nov.-Dec. 20181832-1843Encoding Data Using Biological Principles: The Multisample Variant For-mat for Phylogenomics and Population Genomics. Pease, J.B., þ, TCBBJuly-Aug. 2018 1231-1238Evolutionary Graph Clustering for Protein Complex Identification. He, T.,þ, TCBB May -June 2018 892-904fmpRPMF: A Web Implementation for Protein Identification by RobustPeptide Mass Fingerprinting. Li, Y., þ, TCBB Sept.-Oct. 2018 1728-1731From Optimization to Mapping: An Evolutionary Algorithm for ProteinEnergy Landscapes. Sapin, E., þ, TCBB May -June 2018 719-731Gene Regulatory Network Inference from Perturbed Time-Series Expres-sion Data via Ordered Dynamical Expansion of Non-Steady State Actors.Zamanighomi, M., þ, TCBB July-Aug. 2018 1093-1106GPU-Based Point Cloud Superpositioning for Structural Comparisons ofProtein Binding Sites. Leinweber, M., þ, TCBB May -June 2018 740-752HEMEsPred: Structure-Based Ligand-Specific Heme Binding ResiduesPrediction by Using Fast-Adaptive Ensemble Learning Scheme. Zhang,J., þ, TCBB Jan.-Feb. 2018 147-156IAS: Interaction Specific GO Term Associations for Predicting Protein-Protein Interaction Networks. Yerneni, S., þ, TCBB July-Aug. 2018 1247-1258Incorporation of Solvent Effect into Multi-Objective Evolutionary Algo-rithm for Improved Protein Structure Prediction. Gao, S., þ, TCBB July-Aug. 2018 1365-1378Index-Based Network Aligner of Protein-Protein Interaction Networks.Elmsallati, A., þ, TCBB Jan.-Feb. 2018 330-336Inferring the Functions of Proteins from the Interrelationships betweenFunctional Categories. Taha, K., TCBB Jan.-Feb. 2018 157-167Investigating Correlation between Protein Sequence Similarity and Seman-tic Similarity Using Gene Ontology Annotations. Ikram, N., þ, TCBBMay -June 2018 905-912



Local Traces: An Over-Approximation of the Behavior of the Proteins inRule-Based Models. Feret, J., þ, TCBB July-Aug. 2018 1124-1137Machine Learned Replacement of N-Labels for Basecalled Sequences inDNA Barcoding.Ma, E.Y.T., þ, TCBB Jan.-Feb. 2018 191-204Mutli-Features Prediction of Protein Translational Modification Sites. Bao,W., þ, TCBB Sept.-Oct. 2018 1453-1460NAHAL-Flex: A Numerical and Alphabetical Hinge Detection Algorithmfor Flexible Protein Structure Alignment. Fotoohifiroozabadi, S., þ,TCBB May -June 2018 934-943NewGOA: Predicting New GO Annotations of Proteins by Bi-RandomWalks on a Hybrid Graph. Yu, G., þ, TCBB July-Aug. 2018 1390-1402Novelty Indicator for Enhanced Prioritization of Predicted Gene OntologyAnnotations. Chicco, D., þ, TCBB May -June 2018 954-965Petri Net Siphon Analysis and Graph Theoretic Measures for IdentifyingCombination Therapies in Cancer. Behinaein, B., þ, TCBB Jan.-Feb.2018 231-243Prediction of Hot Regions in PPIs Based on Improved Local CommunityStructure Detecting. Lin, X., þ, TCBB Sept.-Oct. 2018 1470-1479Proteomic Evidence for In-Frame and Out-of-Frame Alternatively SplicedIsoforms in Human and Mouse. Ramalho, R.F., þ, TCBB July-Aug. 20181284-1289RAFP-Pred: Robust Prediction of Antifreeze Proteins Using LocalizedAnalysis of n-Peptide Compositions. Khan, S., þ, TCBB Jan.-Feb. 2018244-250Sequence-Based Prediction of Putative Transcription Factor Binding Sitesin DNA Sequences of Any Length. Lee, W., þ, TCBB Sept.-Oct. 20181461-1469Structural Class Classification of 3D Protein Structure Based on Multi-View 2D Images. Suryanto, C.H., þ, TCBB Jan.-Feb. 2018 286-299Structure-Guided Protein Transition Modeling with a ProbabilisticRoadmap Algorithm.Maximova, T., þ, TCBB Nov.-Dec. 2018 1783-1796The Intrinsic Pepsin Resistance of Interleukin-8 Can Be Explained from aCombined Bioinformatical and Experimental Approach. Anders, G., þ,TCBB Jan.-Feb. 2018 300-308Towards Extracting Supporting Information About Predicted Protein-Pro-tein Interactions. Roth, A., þ, TCBB July-Aug. 2018 1239-1246Unified Deep Learning Architecture for Modeling Biology Sequence. Wu,H., þ, TCBB Sept.-Oct. 2018 1445-1452

ProteomicsfmpRPMF: A Web Implementation for Protein Identification by RobustPeptide Mass Fingerprinting. Li, Y., þ, TCBB Sept.-Oct. 2018 1728-1731Proteomic Evidence for In-Frame and Out-of-Frame Alternatively SplicedIsoforms in Human and Mouse. Ramalho, R.F., þ, TCBB July-Aug. 20181284-1289

Public domain softwareAutumn Algorithm—Computation of Hybridization Networks for RealisticPhylogenetic Trees. Huson, D.H., þ, TCBB March-April 2018 398-410PREMER: A Tool to Infer Biological Networks. Villaverde, A.F., þ, TCBBJuly-Aug. 2018 1193-1202

Pulse width modulationDiscMLA: An Efficient Discriminative Motif Learning Algorithm over High-Throughput Datasets. Zhang, H.,þ, TCBBNov.-Dec. 2018 1810-1820

Q

Query languagesOptimizing Phylogenetic Queries for Performance. Jamil, H.M., TCBBSept.-Oct. 2018 1692-1705

Query processingOptimizing Phylogenetic Queries for Performance. Jamil, H.M., TCBBSept.-Oct. 2018 1692-1705Querying of Disparate Association and Interaction Data in BiomedicalApplications. Qiao, S., þ, TCBB July-Aug. 2018 1052-1065

R

Random processesA Grouping Particle Swarm Optimizer with Personal-Best-PositionGuidance for Large Scale Optimization. Guo, W., þ, TCBB Nov.-Dec.2018 1904-1915Inferring the Functions of Proteins from the Interrelationships betweenFunctional Categories. Taha, K., TCBB Jan.-Feb. 2018 157-167NewGOA: Predicting New GO Annotations of Proteins by Bi-RandomWalks on a Hybrid Graph. Yu, G., þ, TCBB July-Aug. 2018 1390-1402

Random Sets of Stadiums in Square and Collective Behavior of Bacteria.Czapla, R., TCBB Jan.-Feb. 2018 251-256SPF-CellTracker: Tracking Multiple Cells with Strongly-Correlated MovesUsing a Spatial Particle Filter. Hirose, O., þ, TCBB Nov.-Dec. 20181822-1831

Randomized algorithmsA GRASP-Based Heuristic for the Sorting by Length-Weighted InversionsProblem. Arruda, T.d.S., þ, TCBB March-April 2018 352-363

Ranking (statistics)Improve Biomedical Information Retrieval Using Modified Learning toRank Methods. Xu, B., þ, TCBB Nov.-Dec. 2018 1797-1809

Reachability analysisReduction of Qualitative Models of Biological Networks for TransientDynamics Analysis. Pauleve, L., TCBB July-Aug. 2018 1167-1179

Reaction rate constantsMoment-Based Parameter Estimation for Stochastic Reaction Networks inEquilibrium. Backenk€ohler, M., þ, TCBB July-Aug. 2018 1180-1192

Real-time systemsCo-Expression Network Approach to Studying the Effects of BotulinumNeurotoxin-A.Mukund, K., þ, TCBB Nov.-Dec. 2018 2009-2016

Receptor (biochemistry)Computational Models for Trapping Ebola Virus Using Engineered Bacte-ria.Martins, D.P., þ, TCBB Nov.-Dec. 2018 2017-2027

ReceptorsRF-NR: Random Forest Based Approach for Improved Classification ofNuclear Receptors. Ismail, H.D., þ, TCBB Nov.-Dec. 2018 1844-1852

Recurrent neural networksA Bi-Objective RNN Model to Reconstruct Gene Regulatory Network: AModified Multi-Objective Simulated Annealing Approach. Biswas, S., þ,TCBB Nov.-Dec. 2018 2053-2059Unified Deep Learning Architecture for Modeling Biology Sequence. Wu,H., þ, TCBB Sept.-Oct. 2018 1445-1452

Regression analysisA Combined PLS and Negative Binomial Regression Model for InferringAssociation Networks from Next-Generation Sequencing Count Data.Pesonen, M., þ, TCBB May -June 2018 760-773A Distributed Classifier for MicroRNA Target Prediction with ValidationThrough TCGA Expression Data. Ghoshal, A., þ, TCBB July-Aug. 20181037-1051A Sparse Regression Method for Group-Wise Feature Selection with FalseDiscovery Rate Control. Gossmann, A., þ, TCBB July-Aug. 2018 1066-1078Application of Genetic Programming (GP) Formalism for Building DiseasePredictive Models from Protein-Protein Interactions (PPI) Data. Vyas, R.,þ, TCBB Jan.-Feb. 2018 27-37Bayesian Multiresolution Variable Selection for Ultra-High DimensionalNeuroimaging Data. Zhao, Y., þ, TCBB March-April 2018 537-550Comparison of Machine Learning Approaches for Prediction of AdvancedLiver Fibrosis in Chronic Hepatitis C Patients. Hashem, S., þ, TCBB May-June 2018 861-868Network-Regularized Sparse Logistic Regression Models for Clinical RiskPrediction and Biomarker Discovery. Min, W., þ, TCBB May -June 2018944-953

Reverse engineeringPREMER: A Tool to Infer Biological Networks. Villaverde, A.F., þ, TCBBJuly-Aug. 2018 1193-1202

RNAA Bipartite Network and Resource Transfer-Based Approach to InferlncRNA-Environmental Factor Associations. Zhou, J., þ, TCBB May-June 2018 753-759A Distributed Classifier for MicroRNA Target Prediction with ValidationThrough TCGA Expression Data. Ghoshal, A., þ, TCBB July-Aug. 20181037-1051A Novel Approach to Identify the miRNA-mRNA Causal Regulatory Mod-ules in Cancer. Luo, J., þ, TCBB Jan.-Feb. 2018 309-315Algorithmic Mapping and Characterization of the Drug-Induced Pheno-typic-Response Space of Parasites Causing Schistosomiasis. Singh, R., þ,TCBB March-April 2018 469-481Analyzing Differential Regulatory Networks Modulated by Continuous-State Genomic Features in Glioblastoma Multiforme. Chiu, Y., þ, TCBBNov.-Dec. 2018 1754-1764Codon Context Optimization in Synthetic Gene Design. Papamichail, D.,þ, TCBB March-April 2018 452-459Combining Supervised and Unsupervised Learning for Improved miRNATarget Prediction. Sedaghat, N., þ, TCBB Sept.-Oct. 2018 1594-1604Computational Prediction of Pathogenic Network Modules in Fusariumverticillioides. Kim, M., þ, TCBB March-April 2018 506-515



Construction of Signaling Pathways with RNAi Data and Multiple Refer-ence Networks. Alim, M.A., þ, TCBB July-Aug. 2018 1079-1091Continuous Petri Nets and microRNA Analysis in Melanoma. Russo, G.,þ,TCBB Sept.-Oct. 2018 1492-1499Detecting Multivariate Gene Interactions in RNA-Seq Data Using OptimalBayesian Classification. Knight, J.M., þ, TCBB March-April 2018 484-493Discovering Gene Regulatory Elements Using Coverage-Based Heuristics.Al-Ouran, R., þ, TCBB July-Aug. 2018 1290-1300Fuzzy-Rough Entropy Measure and Histogram Based Patient Selection formiRNA Ranking in Cancer. Pal, J.K., þ, TCBB March-April 2018 659-672Gene Regulatory Network Inference from Perturbed Time-Series Expres-sion Data via Ordered Dynamical Expansion of Non-Steady State Actors.Zamanighomi, M., þ, TCBB July-Aug. 2018 1093-1106hc-OTU: A Fast and Accurate Method for Clustering Operational Taxo-nomic Units Based on Homopolymer Compaction. Park, S., þ, TCBBMarch-April 2018 441-451Identification and Analysis of Key Residues in Protein–RNA Complexes.Kulandaisamy, A., þ, TCBB Sept.-Oct. 2018 1436-1444MeTDiff: A Novel Differential RNA Methylation Analysis for MeRIP-SeqData. Cui, X., þ, TCBB March-April 2018 526-534Nucleosome Positioning of Intronless Genes in the Human Genome.Cheng, X., þ, TCBB July-Aug. 2018 1111-1121Predicting MicroRNA-Disease Associations Based on Improved Micro-RNA and Disease Similarities. Lan, W., þ, TCBB Nov.-Dec. 2018 1774-1782Proteomic Evidence for In-Frame and Out-of-Frame Alternatively SplicedIsoforms in Human and Mouse. Ramalho, R.F., þ, TCBB July-Aug. 20181284-1289Sequence-Based Prediction of Putative Transcription Factor Binding Sitesin DNA Sequences of Any Length. Lee, W., þ, TCBB Sept.-Oct. 20181461-1469

Robot kinematicsSwarm Robots Search for Multiple Targets Based on an Improved Group-ing Strategy. Tang, Q., þ, TCBB Nov.-Dec. 2018 1943-1950

Robot motionStructure-Guided Protein Transition Modeling with a Probabilistic Road-map Algorithm.Maximova, T., þ, TCBB Nov.-Dec. 2018 1783-1796

Robot sensing systemsSwarm Robots Search for Multiple Targets Based on an Improved Group-ing Strategy. Tang, Q., þ, TCBB Nov.-Dec. 2018 1943-1950

Robust controlRobust Dynamic Multi-Objective Vehicle Routing Optimization Method.Guo, Y., þ, TCBB Nov.-Dec. 2018 1891-1903

Rough set theoryFuzzy-Rough Entropy Measure and Histogram Based Patient Selection formiRNARanking in Cancer.Pal, J.K.,þ, TCBBMarch-April 2018 659-672

S

Sampled data systemsSampled-Data Stabilization for Fuzzy Genetic Regulatory Networks withLeakage Delays. Ali, M.S., þ, TCBB Jan.-Feb. 2018 271-285

Sampling methodsMoment-Based Parameter Estimation for Stochastic Reaction Networks inEquilibrium. Backenk€ohler, M., þ, TCBB July-Aug. 2018 1180-1192

Search problemsA Global Network Alignment Method Using Discrete Particle SwarmOptimization. Huang, J., þ, TCBB May -June 2018 705-718A GRASP-Based Heuristic for the Sorting by Length-Weighted InversionsProblem. Arruda, T.d.S., þ, TCBB March-April 2018 352-363A Memetic Algorithm for 3D Protein Structure Prediction Problem.Correa, L., þ, TCBB May -June 2018 690-704From Optimization to Mapping: An Evolutionary Algorithm for ProteinEnergy Landscapes. Sapin, E., þ, TCBB May -June 2018 719-731Swarm Robots Search for Multiple Targets Based on an Improved Group-ing Strategy. Tang, Q., þ, TCBB Nov.-Dec. 2018 1943-1950

SecurityGenoPri’16: International Workshop on Genome Privacy and Security.Ayday, E., þ, TCBB Sept.-Oct. 2018 1403-1404

Self-organizing feature mapsLow Rank Subspace Clustering via Discrete Constraint and HypergraphRegularization for Tumor Molecular Pattern Discovery. Liu, J., þ, TCBBSept.-Oct. 2018 1500-1512

SemanticsBioinformatic Workflow Extraction from Scientific Texts based on WordSense Disambiguation. Halioui, A., þ, TCBB Nov.-Dec. 2018 1979-1990Predicting MicroRNA-Disease Associations Based on Improved Micro-RNA and Disease Similarities. Lan, W., þ, TCBB Nov.-Dec. 2018 1774-1782Towards Extracting Supporting Information About Predicted Protein-Pro-tein Interactions. Roth, A., þ, TCBB July-Aug. 2018 1239-1246

Sensitivity analysisComparison of Machine Learning Approaches for Prediction of AdvancedLiver Fibrosis in Chronic Hepatitis C Patients. Hashem, S., þ, TCBB May-June 2018 861-868

Sequential analysisA Study of Cell-Free DNA Fragmentation Pattern and Its Application inDNA Sample Type Classification. Chen, S., þ, TCBB Sept.-Oct. 20181718-1722Deep Sequencing Data Analysis. Ghosh, B.K., þ, TCBB March-April 2018482-483Scaffolding of Ancient Contigs and Ancestral Reconstruction in a Phyloge-netic Framework. Luhmann, N., þ, TCBB Nov.-Dec. 2018 2094-2100

Set theoryAlgorithms for the Majority Rule (+) Consensus Tree and the FrequencyDifference Consensus Tree. Jansson, J., þ, TCBB Jan.-Feb. 2018 15-26Random Sets of Stadiums in Square and Collective Behavior of Bacteria.Czapla, R., TCBB Jan.-Feb. 2018 251-256

Signal denoisingHeavy-Tailed Noise Suppression and Derivative Wavelet Scalogram forDetecting DNA Copy Number Aberrations. Nguyen, N., þ, TCBB Sept.-Oct. 2018 1625-1635

Signal processingDeep Sequencing Data Analysis. Ghosh, B.K., þ, TCBB March-April 2018482-483

Simulated annealingA Bi-Objective RNN Model to Reconstruct Gene Regulatory Network:A Modified Multi-Objective Simulated Annealing Approach. Biswas, S.,þ, TCBB Nov.-Dec. 2018 2053-2059A Memetic Algorithm for 3D Protein Structure Prediction Problem.Correa, L., þ, TCBB May -June 2018 690-704

Smoothing methodsA Slice-based 13C-detected NMR Spin System Forming and ResonanceAssignment Method. Alazmi, M., þ, TCBB Nov.-Dec. 2018 1999-2008

Software toolsDTL-RnB: Algorithms and Tools for Summarizing the Space of DTL Rec-onciliations.Ma, W., þ, TCBB March-April 2018 411-421PREMER: A Tool to Infer Biological Networks. Villaverde, A.F., þ, TCBBJuly-Aug. 2018 1193-1202

Solvent effectsIncorporation of Solvent Effect into Multi-Objective Evolutionary Algo-rithm for Improved Protein Structure Prediction. Gao, S., þ, TCBB July-Aug. 2018 1365-1378

SortingA GRASP-Based Heuristic for the Sorting by Length-Weighted InversionsProblem. Arruda, T.d.S., þ, TCBB March-April 2018 352-363Genome Rearrangement with ILP. Hartmann, T., þ, TCBB Sept.-Oct. 20181585-1593

Sparse matricesA Sparse Regression Method for Group-Wise Feature Selection with FalseDiscovery Rate Control.Gossmann, A.,þ, TCBB July-Aug. 2018 1066-1078

Special issues and sectionsAdvances in the Application and Development of Non-Linear GlobalOptimization Techniques in Computational Structural Biology. Handl, J.,þ, TCBB May -June 2018 688-689Deep Sequencing Data Analysis. Ghosh, B.K., þ, TCBB March-April 2018482-483Editorial for Selected Papers of a Joint Conferences, Genome InformaticsWorkshop/International Conference on Bioinformatics (GIW/InCoB)2015. Kim, S., TCBB Nov.-Dec. 2018 1821GenoPri’16: International Workshop on Genome Privacy and Security.Ayday, E., þ, TCBB Sept.-Oct. 2018 1403-1404Great Lakes Bioinformatics Conference (GLBIO) 2015 Special SectionEditorial.Milenkovic, T., þ, TCBB July-Aug. 2018 1229-1230Guest Editorial.Murali, T.M., TCBB July-Aug. 2018 1036Guest Editorial for Special Section on BIBM 2015. Tian, T., þ, TCBBNov.-Dec. 2018 1752-1753Guest Editorial for Special Section on the 12th International Conference onIntelligent Computing (ICIC). Huang, D., þ, TCBB Sept.-Oct. 2018 1433-1435



Guest Editorial for Special Section on the Sixth National Conference onBioinformatics and System Biology of China. Fan, X., þ, TCBB July-Aug. 2018 1092Guest Editorial for the 14th Asia Pacific Bioinformatics Conference. Tang,J., þ, TCBB March-April 2018 396-397Guest Editorial for the 15th Asia Pacific Bioinformatics Conference.Wang,L., þ, TCBB Sept.-Oct. 2018 1513-1514Guest Editors’ Introduction to the Special Section on the 14th InternationalConference on Computational Methods in Systems Biology (CMSB2016). Bartocci, E., þ, TCBB July-Aug. 2018 1122-1123Multiscale and Multimodal Analysis for Computational Biology. Gao, X.,þ, TCBB Nov.-Dec. 2018 1951-1952Special Section on Swarm-Based Algorithms and Applications in Compu-tational Biology and Bioinformatics. Tan, Y., þ, TCBB Nov.-Dec. 20181863-1864

SpectroscopyA Slice-based 13C-detected NMR Spin System Forming and ResonanceAssignment Method. Alazmi, M., þ, TCBB Nov.-Dec. 2018 1999-2008

Splines (mathematics)Immunological Approach for Full NURBS Reconstruction of OutlineCurves from Noisy Data Points in Medical Imaging. Iglesias, A., þ,TCBB Nov.-Dec. 2018 1929-1942

Stability analysisAltering Indispensable Proteins in Controlling Directed Human ProteinInteraction Network. Zhang, X., TCBB Nov.-Dec. 2018 2074-2078Robust Gene Circuit Control Design for Time-Delayed Genetic RegulatoryNetworks Without SUM Regulatory Logic. Jiao, H., þ, TCBB Nov.-Dec.2018 2086-2093

State estimationOptimal Fault Detection and Diagnosis in Transcriptional Circuits UsingNext-Generation Sequencing. Bahadorinejad, A., þ, TCBB March-April2018 516-525

Statistical analysisA Copula-Based Granger Causality Measure for the Analysis of NeuralSpike Train Data. Hu, M., þ, TCBB March-April 2018 562-569Detecting Multivariate Gene Interactions in RNA-Seq Data Using OptimalBayesian Classification. Knight, J.M., þ, TCBB March-April 2018 484-493Mutli-Features Prediction of Protein Translational Modification Sites. Bao,W., þ, TCBB Sept.-Oct. 2018 1453-1460Protecting Privacy and Security of Genomic Data in i2b2 with Homomor-phic Encryption and Differential Privacy. Raisaro, J.L., þ, TCBB Sept.-Oct. 2018 1413-1426Reviving the Two-State Markov Chain Approach. Mizera, A., þ, TCBBSept.-Oct. 2018 1525-1537Species Tree Inference from Gene Splits by Unrooted STAR Methods. All-man, E.S., þ, TCBB Jan.-Feb. 2018 337-342

Statistical distributionsRandom Sets of Stadiums in Square and Collective Behavior of Bacteria.Czapla, R., TCBB Jan.-Feb. 2018 251-256Region Growing for Segmenting Green Microalgae Images. Borges, V.R.P., þ, TCBB Jan.-Feb. 2018 257-270

Statistical testingA Grouping Particle Swarm Optimizer with Personal-Best-Position Guid-ance for Large Scale Optimization. Guo, W., þ, TCBB Nov.-Dec. 20181904-1915Detecting Multivariate Gene Interactions in RNA-Seq Data Using OptimalBayesian Classification. Knight, J.M., þ, TCBB March-April 2018 484-493Introducing a Stable Bootstrap Validation Framework for Reliable Geno-mic Signature Extraction. Chlis, N., þ, TCBB Jan.-Feb. 2018 181-190

Steady-stateASSA-PBN: A Toolbox for Probabilistic Boolean Networks.Mizera, A., þ,TCBB July-Aug. 2018 1203-1216

Stochastic processesA Model-Based Tool for the Analysis and Design of Gene Regulatory Net-works. Ironi, L., þ, TCBB July-Aug. 2018 1301-1314Aggregation for Computing Multi-Modal Stationary Distributions in 1-DGene Regulatory Networks. Avcu, N., þ, TCBB May -June 2018 813-827Gene Regulatory Network Inference from Perturbed Time-Series Expres-sion Data via Ordered Dynamical Expansion of Non-Steady State Actors.Zamanighomi, M., þ, TCBB July-Aug. 2018 1093-1106Moment-Based Parameter Estimation for Stochastic Reaction Networks inEquilibrium. Backenk€ohler, M., þ, TCBB July-Aug. 2018 1180-1192Optimal Fault Detection and Diagnosis in Transcriptional Circuits UsingNext-Generation Sequencing. Bahadorinejad, A., þ, TCBB March-April2018 516-525

Organisation-Oriented Coarse Graining and Refinement of StochasticReaction Networks.Mu, C., þ, TCBB July-Aug. 2018 1152-1166

String matchingEfficient Algorithms for Sequence Analysis with Entropic Profiles. Pizzi,C., þ, TCBB Jan.-Feb. 2018 117-128

Stroke (medical condition)Using Machine Learning to Improve the Prediction of Functional Outcomein Ischemic Stroke Patients. Monteiro, M., þ, TCBB Nov.-Dec. 20181953-1959

Supervised learningPredicting MicroRNA-Disease Associations Based on Improved MicroRNAandDisease Similarities. Lan, W.,þ, TCBBNov.-Dec. 2018 1774-1782

Support vector machinesA Distributed Classifier for MicroRNA Target Prediction with ValidationThrough TCGA Expression Data. Ghoshal, A., þ, TCBB July-Aug. 20181037-1051Combining Supervised and Unsupervised Learning for Improved miRNATarget Prediction. Sedaghat, N., þ, TCBB Sept.-Oct. 2018 1594-1604Effectively Identifying Compound-Protein Interactions by Learning fromPositive and Unlabeled Examples. Cheng, Z., þ, TCBB Nov.-Dec. 20181832-1843fmpRPMF: A Web Implementation for Protein Identification by RobustPeptide Mass Fingerprinting. Li, Y., þ, TCBB Sept.-Oct. 2018 1728-1731Fuzzy-Rough Entropy Measure and Histogram Based Patient Selection formiRNARanking in Cancer. Pal, J.K.,þ, TCBBMarch-April 2018 659-672Mutli-Features Prediction of Protein Translational Modification Sites. Bao,W., þ, TCBB Sept.-Oct. 2018 1453-1460Prediction of HIV Drug Resistance by Combining Sequence and StructuralProperties. Khalid, Z., þ, TCBB May -June 2018 966-973Prediction of Hot Regions in PPIs Based on Improved Local CommunityStructure Detecting. Lin, X., þ, TCBB Sept.-Oct. 2018 1470-1479

Surface reconstructionImmunological Approach for Full NURBS Reconstruction of OutlineCurves from Noisy Data Points in Medical Imaging. Iglesias, A., þ,TCBB Nov.-Dec. 2018 1929-1942Improving Alzheimer’s Disease Classification by Combining MultipleMeasures. Liu, J., þ, TCBB Sept.-Oct. 2018 1649-1659

Surface topographyImmunological Approach for Full NURBS Reconstruction of OutlineCurves from Noisy Data Points in Medical Imaging. Iglesias, A., þ,TCBB Nov.-Dec. 2018 1929-1942

Surface treatmentComputational Models for Trapping Ebola Virus Using Engineered Bacte-ria.Martins, D.P., þ, TCBB Nov.-Dec. 2018 2017-2027

SurveillanceA Spatial-Temporal Method to Detect Global Influenza Epidemics UsingHeterogeneous Data Collected from the Internet. Zhou, X., þ, TCBB May-June 2018 802-812

SuspensionsRandom Sets of Stadiums in Square and Collective Behavior of Bacteria.Czapla, R., TCBB Jan.-Feb. 2018 251-256

System-on-chipHardware Accelerator for the Multifractal Analysis of DNA Sequences.Duarte-Sanchez, J.E., þ, TCBB Sept.-Oct. 2018 1611-1624

Systems biology“Super Gene Set” Causal Relationship Discovery from Functional Geno-mics Data. Yue, Z., þ, TCBB Nov.-Dec. 2018 1991-1998

Systems engineering and theoryDeep Sequencing Data Analysis. Ghosh, B.K., þ, TCBB March-April 2018482-483

T

Target trackingCell Population Tracking in a Honeycomb Structure Using an IMM FilterBased 3D Local Graph Matching Model. Liu, M., þ, TCBB Sept.-Oct.2018 1706-1717SPF-CellTracker: Tracking Multiple Cells with Strongly-Correlated MovesUsing a Spatial Particle Filter. Hirose, O., þ, TCBB Nov.-Dec. 20181822-1831

Task analysisA Simplified Description of Child Tables for Sequence Similarity Search.Frith, M.C., þ, TCBB Nov.-Dec. 2018 2067-2073Bioinformatic Workflow Extraction from Scientific Texts based on WordSense Disambiguation. Halioui, A., þ, TCBB Nov.-Dec. 2018 1979-1990



Text analysisA Two-Stage Biomedical Event Trigger Detection Method Integrating FeatureSelection andWord Embeddings.He, X.,þ, TCBB July-Aug. 2018 1325-1332Biological Event Trigger Identification with Noise Contrastive Estimation.Jiang, N., þ, TCBB Sept.-Oct. 2018 1549-1559Inferring the Functions of Proteins from the Interrelationships betweenFunctional Categories. Taha, K., TCBB Jan.-Feb. 2018 157-167Towards Extracting Supporting Information About Predicted Protein-Protein Interactions. Roth, A., þ, TCBB July-Aug. 2018 1239-1246

Text miningImprove Biomedical Information Retrieval Using Modified Learning toRank Methods. Xu, B., þ, TCBB Nov.-Dec. 2018 1797-1809

Three-dimensional displaysA Slice-based 13C-detected NMR Spin System Forming and ResonanceAssignment Method. Alazmi, M., þ, TCBB Nov.-Dec. 2018 1999-2008

Time seriesA Copula-Based Granger Causality Measure for the Analysis of NeuralSpike Train Data. Hu, M., þ, TCBB March-April 2018 562-569Gene Regulatory Network Inference from Perturbed Time-Series Expres-sion Data via Ordered Dynamical Expansion of Non-Steady State Actors.Zamanighomi, M., þ, TCBB July-Aug. 2018 1093-1106Optimal Fault Detection and Diagnosis in Transcriptional Circuits UsingNext-Generation Sequencing. Bahadorinejad, A., þ, TCBB March-April2018 516-525

Time series analysisPredicting Hospital Readmission via Cost-Sensitive Deep Learning. Wang,H., þ, TCBB Nov.-Dec. 2018 1968-1978

TrackingCell Population Tracking in a Honeycomb Structure Using an IMM FilterBased 3D Local Graph Matching Model. Liu, M., þ, TCBB Sept.-Oct.2018 1706-1717

Training dataEffectively Identifying Compound-Protein Interactions by Learning from Posi-tive andUnlabeled Examples.Cheng, Z.,þ, TCBBNov.-Dec. 2018 1832-1843

TransformsGenome Rearrangement with ILP. Hartmann, T., þ, TCBB Sept.-Oct. 20181585-1593

Transient analysisReduction of Qualitative Models of Biological Networks for TransientDynamics Analysis. Pauleve, L., TCBB July-Aug. 2018 1167-1179

Tree data structuresEfficient Algorithms for Sequence Analysis with Entropic Profiles. Pizzi,C., þ, TCBB Jan.-Feb. 2018 117-128

Trees (mathematics)A Framework for Identifying Genotypic Information from ClinicalRecords: Exploiting Integrated Ontology Structures to Transfer Annota-tions between ICD Codes and Gene Ontologies. Hashemikhabir, S., þ,TCBB July-Aug. 2018 1259-1269A GRASP-Based Heuristic for the Sorting by Length-Weighted InversionsProblem. Arruda, T.d.S., þ, TCBB March-April 2018 352-363Algorithms for the Majority Rule (+) Consensus Tree and the FrequencyDifference Consensus Tree. Jansson, J., þ, TCBB Jan.-Feb. 2018 15-26Autumn Algorithm—Computation of Hybridization Networks for RealisticPhylogenetic Trees. Huson, D.H., þ, TCBB March-April 2018 398-410Bijective Diameters of Gene Tree Parsimony Costs. G�orecki, P., þ, TCBBSept.-Oct. 2018 1723-1727DTL-RnB: Algorithms and Tools for Summarizing the Space of DTL Rec-onciliations.Ma, W., þ, TCBB March-April 2018 411-421Efficient Algorithms for Genomic Duplication Models. Paszek, J., þ,TCBB Sept.-Oct. 2018 1515-1524Efficient Algorithms for Sequence Analysis with Entropic Profiles. Pizzi,C., þ, TCBB Jan.-Feb. 2018 117-128Efficient Quartet Representations of Trees and Applications to Supertree andSummaryMethods.Davidson, R.,þ, TCBBMay -June 2018 1010-1015Enumerating Substituted Benzene Isomers of Tree-Like Chemical Graphs.Li, J., þ, TCBB March-April 2018 633-646Gene Tree Construction and Correction Using SuperTree and Reconcilia-tion. Lafond, M., þ, TCBB Sept.-Oct. 2018 1560-1570hc-OTU: A Fast and Accurate Method for Clustering Operational Taxo-nomic Units Based on Homopolymer Compaction. Park, S., þ, TCBBMarch-April 2018 441-451Inferring Gene-Species Assignments in the Presence of Horizontal GeneTransfer.Mykowiecka, A., þ, TCBB Sept.-Oct. 2018 1571-1578Integrating Imaging Genomic Data in the Quest for Biomarkers of Schizo-phrenia Disease. Deng, S., þ, TCBB Sept.-Oct. 2018 1480-1491Nonbinary Tree-Based Phylogenetic Networks. Jetten, L., þ, TCBB Jan.-Feb. 2018 205-217

Species Tree Estimation Using ASTRAL: How Many Genes Are Enough?.Shekhar, S., þ, TCBB Sept.-Oct. 2018 1738-1747Species Tree Inference from Gene Splits by Unrooted STAR Methods.Allman, E.S., þ, TCBB Jan.-Feb. 2018 337-342Tanglegrams: A Reduction Tool for Mathematical Phylogenetics. Matsen,F.A., þ, TCBB Jan.-Feb. 2018 343-349

TumorsA Graphical Model of Smoking-Induced Global Instability in Lung Cancer.Wang, Y., þ, TCBB Jan.-Feb. 2018 1-14A Study of Cell-Free DNA Fragmentation Pattern and Its Application inDNA Sample Type Classification. Chen, S., þ, TCBB Sept.-Oct. 20181718-1722Bi-level and Bi-objective p-Median Type Problems for Integrative Cluster-ing: Application to Analysis of Cancer Gene-Expression and Drug-Response Data. Ushakov, A.V., þ, TCBB Jan.-Feb. 2018 46-59Complexity and Algorithms for Finding a Perfect Phylogeny from MixedTumor Samples. Hujdurovic, A., þ, TCBB Jan.-Feb. 2018 96-108Continuous Petri Nets and microRNA Analysis in Melanoma. Russo, G.,þ,TCBB Sept.-Oct. 2018 1492-1499Integrating Multiple Data Sources for Combinatorial Marker Discovery: AStudy in Tumorigenesis. Bandyopadhyay, S., þ, TCBB March-April 2018673-687Low Rank Subspace Clustering via Discrete Constraint and HypergraphRegularization for Tumor Molecular Pattern Discovery. Liu, J., þ, TCBBSept.-Oct. 2018 1500-1512

U

Uncertain systemsFilter Design with Adaptation to Time-Delay Parameters for Genetic Regu-latory Networks. Jiao, H., þ, TCBB Jan.-Feb. 2018 323-329

Unsupervised learningCombining Supervised and Unsupervised Learning for Improved miRNATarget Prediction. Sedaghat, N., þ, TCBB Sept.-Oct. 2018 1594-1604

V

Vehicle dynamicsRobust Dynamic Multi-Objective Vehicle Routing Optimization Method.Guo, Y., þ, TCBB Nov.-Dec. 2018 1891-1903

Vehicle routingRobust Dynamic Multi-Objective Vehicle Routing Optimization Method.Guo, Y., þ, TCBB Nov.-Dec. 2018 1891-1903

VentilationInfluence of Airway Secretion on Airflow Dynamics of Mechanical Venti-lated Respiratory System. Ren, S., þ, TCBB Sept.-Oct. 2018 1660-1668

Viruses (medical)Computational Models for Trapping Ebola Virus Using Engineered Bacte-ria.Martins, D.P., þ, TCBB Nov.-Dec. 2018 2017-2027

ViscosityInfluence of Airway Secretion on Airflow Dynamics of Mechanical Venti-lated Respiratory System. Ren, S., þ, TCBB Sept.-Oct. 2018 1660-1668Random Sets of Stadiums in Square and Collective Behavior of Bacteria.Czapla, R., TCBB Jan.-Feb. 2018 251-256

Visual languagesOptimizing Phylogenetic Queries forPerformance. Jamil, H.M., TCBBSept.-Oct. 2018 1692-1705

W

WatermarkingDNA Watermarking Using Codon PostfixTechnique. Hamad, S., þ, TCBBSept.-Oct. 2018 1605-1610

Wavelet transformsHeavy-Tailed Noise Suppression andDerivative Wavelet Scalogram forDetecting DNA Copy Number Aberrations. Nguyen, N., þ, TCBB Sept.-Oct. 2018 1625-1635

Z

ZoologyExamining De Novo Transcriptome Assembliesvia a Quality AssessmentPipeline. Ghaffari, N., þ, TCBB March-April 2018 494-505



Documents

2018 Index IEEE/ACM Transactions on Computational Biology ... · IEEE/ACM Transactions on Computational Biology and Bioinformatics Vol. 15 This index covers all technical items—papers,