ISBRA 2019alan.cs.gsu.edu/isbra19/sites/default/files/isbra-2019... · 2019-05-10 · Message from the Program Chairs On behalf of the Program Committee, we would like to welcome

ISBRA 201915th International Symposiumon Bioinformatics Researchand Applications

June 3–6, 2019

Technical University of CataloniaBarcelona, Spain

http://alan.cs.gsu.edu/isbra19/

About the Technical University ofCatalonia

The Technical University of Catalonia (UPC) is a public institution of Higher Education andResearch, specialized in the areas of Architecture, Engineering, Science and Technology. TheUPC has a wide spread presence in Catalonia, with nine campuses located in Barcelona andnearby towns. The campuses are accessible, well connected by public transport and equippedwith the necessary facilities and services to contribute to learning, research and universitylife.

Founded in 1968 by grouping together existing state technical schools of Architecture andEngineering in Barcelona, which date back from the mid-19th century, it gained universitystatus in 1971. The UPC today has a student population of over 30,000, with more than3,000 teaching and research staff and about 2,000 administrative and service staff. There are64 bachelor’s degrees, 68 master’s degrees, and 46 doctoral programs offered by 20 schools.Further, there are 50 international double-degree agreements with 30 universities, and about3,000 students in international mobility programs. Research teams generate e60 million inannual funding, with a total budget of about e300 million.

About the Department of ComputerScience

The Department of Computer Science was created in 1987 and is one of the largest depart-ments at the UPC. It has about 90 full-time faculty and 50 Ph.D. students. The Departmentis responsible for teaching and research in several disciplines related to the foundations ofcomputing and their applications.

The core of the teaching activities is concentrated in the undergraduate and master’s programsof the Barcelona School of Informatics, but the Department is also teaching at several otherUPC schools. The Department is coordinating two Ph.D. programs: Computing and ArtificialIntelligence.

The research activities of the Department are organized in different research groups, coveringvarious Computer Science disciplines. It has an active presence in the main conferences of thefield and an intense participation in public and industrial projects, as well as in the creation ofspin-off companies.

Message from the General Chairs

We are delighted to welcome you to the 15th International Symposium on BioinformaticsResearch and Applications (ISBRA 2019) being held on the campus of Technical Universityof Catalonia in Barcelona. We are honored to serve the international community by bringingtogether scholars, scientists, and students from academia, laboratories, and industry to thispremier meeting.

We would like to thank Program Chairs Zhipeng Cai, Pavel Skums, and Min Li for puttingtogether a terrific technical program. We thank the program committee and reviewers for theirhard work, and also thank all authors who submitted papers and abstracts for their contribu-tions. We believe that you will enjoy all contributed and keynote talks this week!

We are grateful to Mıriam Hernandez and Ana Ibanez from the Technical University of Cat-alonia for help in coordinating ISBRA 2019. We also thank the Publications Chairs OlgaGlebova, Mingon Kang, and Fa Zhang and Webmasters Filipp Rondel and Sergey Knyazevfor their efforts in publicizing the symposium.

We would like to recognize Technical University of Catalonia for hosting ISBRA 2019. Wewould like to thank Carme Casas and Xavier Masso for their help in making these venuesavailable for symposium presentations and on-campus housing of participants. Last but notleast, we would like to thank our sponsors: the National Science Foundation, the Departmentof Computer Science of the Technical University of Catalonia, and the Department of Com-puter Science of Georgia State University. Thanks to their generous support we have beenable to award travel fellowships to graduate students and post-doctoral scholars from USAand abroad.

We hope you will have a wonderful time at the symposium and enjoy the beautiful Barcelona.

Gabriel Valiente, Technical University of Barcelona, SpainAlexander Zelikovsky, Georgia State University, USA

Message from the Program Chairs

On behalf of the Program Committee, we would like to welcome you to the proceedings ofthe 15th edition of the International Symposium on Bioinformatics Research and Applica-tions (ISBRA 2019), held in Barcelona, Spain, June 3–6, 2019. The symposium provides aforum for the exchange of ideas and results among researchers, developers, and practitionersworking on all aspects of bioinformatics and computational biology and their applications.This year we received 95 submissions in response to the call for extended abstracts. The Pro-gram Committee decided to accept 22 of them for full publication in the proceedings and oralpresentation at the symposium. We also accepted 23 for oral presentation. Furthermore, wereceived 20 submissions in response to the call for short abstracts.

The technical program invited keynote talks were given by Prof. Niko Beerenwinkel fromETH Zurich, Prof. Roderic Guigo from the Centre for Genomic Regulation, and Prof. Mar-tin Vingron from the Max Planck Institute for Molecular Genetics. We would like to thankthe Program Committee members and the additional reviewers for volunteering their time toreview and discuss symposium papers. We would like to extend special thanks to the Steer-ing and General Chairs of the symposium for their leadership, and to the Publicity and LocalChairs for their hard work in making ISBRA 2019 a successful event. Last but not least, wewould like to thank all authors for presenting their work at the symposium.

Zhipeng Cai, Georgia State UniversityPavel Skums, Georgia State UniversityMin Li, Central South University

Keynote Speakers

Niko Beerenwinkel

Associate Professor, Computational Biology,ETH Zurich

Roderic Guigo

Director, Bioinformatics Program, Centre forGenomic Regulation, Barcelona

Martin Vingron

Director, Max Planck Institute for MolecularGenetics, Head of Computational MolecularBiology Department

Symposium Organizers

Steering Committee

Yi Pan (Georgia State University, USA), ChairDan Gusfield (University of California, Davis, USA)Ion Mandoiu (University of Connecticut, USA)Marie-France Sagot (INRIA, France)Ying Xu (University of Georgia, USA)Aidong Zhang (University of Virginia, USA)

General Chairs

Gabriel Valiente (Technical University of Catalonia, Spain)Alexander Zelikovsky (Georgia State University, USA)

Local Chair

Gabriel Valiente (Technical University of Catalonia, Spain)

Program Chairs

Zhipeng Cai (Georgia State University, USA)Pavel Skums (Georgia State University, USA)Min Li (Central South University, China)

Publicity Chairs

Olga Glebova (Georgia State University, USA)Mingon Kang (Kennesaw State University, USA)Fa Zhang (Chinese Academy of Science, China)

Webmasters

Filipp Rondel (Georgia State University, USA)Sergey Knyazev (Georgia State University, USA)

Program Committee Members

Kamal Al Nasr (Tennessee State University)Max Alekseyev (George Washington Univer-sity)Nikita Alexeev (ITMO University)Mukul S. Bansal (University of Connecticut)Paola Bonizzoni (Universita di Milano-Bicocca)Zhipeng Cai (Georgia State University)Hongmin Cai (South China University ofTechnology)Xing Chen (Chinese Academy of Sciences)Xuefeng Cui (Tsinghua University)Ovidiu Daescu (Univ. of Texas at Dallas)Lei Deng (Central South University)Pufeng Du (Tianjin University)Oliver Eulenstein (Iowa State University)Xin Gao (King Abdullah University of Sci-ence and Technology)Xuan Guo (University of North Texas)Olga Glebova (Georgia State University)Zengyou He (Dalian University of Technol-ogy)Steffen Heber (North Carolina State Univ.)Jinling Huang (East Carolina University)Mingon Kang (Kennesaw State University)Wooyoung Kim (University of Washington)Danny Krizanc (Wesleyan University)Xiujuan Lei (Shaanxi Normal University)Shuai-Cheng Li (City University of HongKong)Yaohang Li (Old Dominion University)Jing Li (Case Western Reserve University)Min Li (Central South University)Xiaowen Liu (Indiana University)Bingqiang Liu (Shandong University)Ion Mandoiu (University of Connecticut)Igor Mandric (University of California, LosAngeles)Serghei Mangul (University of California, LosAngeles)

Fenglou Mao (National Institute of Health)Yuri Orlovich (Belarusian State Univ.)Andrei Paun (University of Bucharest)Nadia Pisanti (Universita di Pisa)Yuri Porozov (ITMO University)Russell Schwartz (Carnegie Mellon Univer-sity)Joao Setubal (University of Sao Paulo)Yi Shi (Shanghai Jiaotong University)Xinghua Shi (University of North Carolina atCharlotte)Dong Si (University of Washington)Pavel Skums (Georgia State University)Ileana Streinu (University of MassachusettsAmherst)Emily Su (Taipei Medical University)Shiwei Sun (Chinese Academy of Sciences)Sing-Hoi Sze (Texas A&M University)Weitian Tong (Georgia Southern University)Gabriel Valiente (Technical University of Cat-alonia)Jianxin Wang (Central South University)Li-San Wang (University of Pennsylvania)Guohua Wang (Harbin Institute of Technol-ogy)Seth Weinberg (Virginia Commonwealth Uni-versity)Yubao Wu (Georgia State University)Fangxiang Wu (University of Saskatchewan)Yufeng Wu (University of Connecticut)Zeng Xiangxiang (Xiamen University)Guoxian Yu (Southwest University)Ning Yu (Georgia State University)Alex Zelikovsky (Georgia State University)Le Zhang (Southwest University)Xuegong Zhang (Tsinghua University)Xing-Ming Zhao (Tongji University)Leming Zhou (University of Pittsburgh)Shuigeng Zhou (Fudan University)Quan Zou (Tianjin University)

Sponsors

Technical University of Catalonia Georgia State University National Science Foundation

Department of Department of

Computer Science Computer Science

ISBRA 2019 Program

Monday, June 3rd, 2019

7:00pm-9:00pm

ReceptionGardens of the Torre Girona estate

Jordi Girona, 3108034 Barcelona

Tuesday, June 4th, 2019

9:00am-10:00am

Plenary SessionRoom: Aula MasterChair: Pavel Skums

Session 1: Keynote TalkPredicting enhancers from chromatin marksMartin Vingron, Max Planck Institute for Molecular Genetics

10:00am-10:20am

Coffee BreakRoom: Sala Polivalent

10:20am-12:20pm

Parallel SessionsRoom: Aula Master Room: Sala Agora

Session 2A:Machine Learning 1Chair: Ion Mandoiu

Session 2B:Protein-Protein InteractionsChair: Gabriel Valiente

10:20am-10:45am

DeepFrag-k: A fragment-baseddeep learning approach forprotein fold recognition, WessamElhefnawy, Yaohang Li

Improving identification ofessential proteins by a novelensemble method, Wei Dai, Xia Li,Wei Peng, Junrong Song,Jiancheng Zhong, Jianxin Wang

10:45am-11:10am

A machine learning algorithm forgenotyping the mixture datasetconsidering copy number variant,Tian Zheng, Xuanping Zhang,Zhongmeng Zhao, Xiao Xiao,Jiayin Wang

Automated hub-protein detectionvia a new fused similarity measure-based multi-objective clusteringframework, Sudipta Acharya, CuiLaizhong, Pan Yi

11:10am-11:35am

Machine and deep learning-basedaugmentation of small RNA dataexpression data profiles, JelenaFiosina, Maksims Fiosins

AligNet: Alignment of protein-protein interaction networks,Ricardo Alberich, Adria Alcala,Merce Llabres, Francesc Rossello,Gabriel Valiente

11:35am-12:00pm

DeepiRNA: Predicting transposon-derived piRNAs with deep learning,Wen Zhang, Jiangtao Song, FengLiu

Identifying human essential genesby network embedding protein-protein interaction network, WeiDai, Qi Chang, Wei Peng,Jiancheng Zhong

12:00pm-12:20pm

PU-Caller: Sensitive somatic variantcalling using positive-unlabeledlearning, Elham Sherafat, IonMandoiu

Alignment of biological networks byinteger linear programming: Virus-host protein-protein interactionnetworks, Merce Llabres, GabrielRiera, Francesc Rossello, GabrielValiente

12:20pm-2:00pm

Lunch BreakRestaurant: Unity Sodexo

2:00pm-3:35pm


Session 3A:Machine Learning 2Chair: Heta Desai

Session 3B:Phylogeny 1Chair: Sagi Snir

2:00pm-2:25pm

Iterative sure independent rankingand screening for drug responseprediction, Yufang Qin, Biao An,Qianwen Zhang, Yun Fang, MingChen

Simultaneous multi-domain-multi-gene reconciliation under thedomain-gene-species reconciliationmodel, Lei Li, Mukul S. Bansal

2:25pm-2:50pm

Gene and pathway-based deepneural network for multi-omicsdata integration to predict cancersurvival outcomes, Jie Hao,Mohammad Masum, Jung Hun Oh,Mingon Kang

Greedy partition distance understochastic models: Analytic results,Sagi Snir

2:50pm-3:15pm

On tower and checkerboard neuralnetwork architectures for geneexpression inference, Vladimır Kunc,Jiri Klema

Computing a consensus phylogenyvia leaf removal, Zhi-Zhong Chen,Shohei Ueta, Jingyu Li, LushengWang

3:15pm-3:35pm

16S ribosomal gene classificationusing recurrent neural networkmodels, Heta Desai, AnujaParameshwaran, Michael Weeks,Rajshekhar Sunderraman

Spanning trees with extremals-metric and their applications inmolecular epidemiology, YuryOrlovich, Volker Kaibel, KirillKukharenko, Pavel Skums

3:35pm-3:55pm


3:55pm-5:05pm


Session 4A:Sequence AnalysisChair: Fa Zhang

Session 4B:PrivacyChair: Pavel Skums

3:55pm-4:20pm

Paired-end small RNA sequencingreveals a possible overestimation inisomiR sequence repertoirepreviously reported fromconventional single read dataanalysis, Antonio Luna de Haro,Raquel Pluvinet, Jose FranciscoSanchez Herrero, Lauro Sumoy

Detecting illicit drug ads in GooglePlus, Fengpan Zhao, Pavel Skums,Alex Zelikovsky, Eric L. Sevigny,Monica Haavisto Swahn, Sheryl M.Strasser, Yubao Wu

4:20pm-4:45pm

Analysis of codon usage patterns incitrus based on coding sequencedata, Zenan Shen, Zhimeng Gan, FaZhang, Xinyao Yi, Xiaohua Wan,Jinzhi Zhang

Differentially private genomic datapublishing, Zaobo He, Jianqiang Li

4:45pm-5:05pm

CleanBreak: Complex genomicstructural variant discovery in high-throughput sequencing data,Matthew Hayes, Derrick Mullins

Identifying relatives (almost)privately, Benny Chor, OritMoskovich, Benny Pinkas

Wednesday, June 5th, 2019

9:00am-10:10am


Session 5A:Protein StructureChair: Tun-Wen Pai

Session 5B:Comparative GenomicsChair: Alex Zelikovsky

9:00am-9:25am

PSLDoc3: A high-throughputprotein function prediction by thenovel k-nearest neighbor and votingalgorithms, Yi-Wei Liu, Tz-Wei Hsu,Che-Yu Chang, Wen-Hung Liao,Jia-Ming Chang

Using earth mover’s distancebetween k-mers for viral outbreakinvestigations, Andrii Melnyk,Sergey Knyazev, Yury Khudyakov,Leonid Bunimovich, FredrikVannberg, Pavel Skums, AlexZelikovsky

9:25am-9:50am

Conformational epitope matchingand prediction based on proteinsurface spiral features, Tun-Wen Pai

Iterative spaced seed hashing:Closing the gap between spacedseed hashing and k-mer hashing,Enrico Petrucci, Laurent Noe,Cinzia Pizzi, Matteo Comin

9:50am-10:10am

TLC SDSB: A two-layer structuredclassifier for identifying single-strandedand double-stranded DNA-bindingproteins from protein sequence, JingHu, Filip Keri

Toward a dynamic threshold forquality-score distortion in reference-based alignment, Ana Hernandez,Marco Mattavelli, Claudio Alberti

10:10am-10:30am


10:30am-12:30pm


Session 6A:NetworksChair: Merce Llabres

Session 6B:Structural AnalysisChair: Nikita Alexeev

10:30am-10:55am

Model revision of booleanregulatory networks at stable state,Filipe Gouveia, Ines Lynce, PedroT. Monteiro

The review of bioinformatics toolfor 3D plant genomics research,Xiangyu Yang, Jingtian Zhao,Zhenghao Li, Pengcao Li, Le Zhang

10:55am-11:20am

Constructing cancer patient-specificand group-specific gene networkswith multi-omics data, Wook Lee,Kyungsook Han

Maximum stacking base pairs:Hardness and approximation bynonlinear LP-rounding, Lixin Liu,Haitao Jiang, Peiqing Liu, BinhaiZhu, Daming Zhu

11:20am-11:45am

Flexible comparative genomics ofprokaryotic transcriptionalregulatory networks, Sefa Kilic,Miquel Sanchez-Osuna, AntonioCollado-Padilla, Jordi Barbe, IvanErill

Graph transformations, semigroups,and isotopic labeling, Jakob LykkeAndersen, Daniel Merkle, PeterSeverin Rasmussen

11:45am-12:10am

IDNDDI: An integrated drugsimilarity network method forpredicting drug-drug interactions,Cheng Yan, Guihua Duan, YayanZhang, Fangxiang Wu, Yi Pan,Jianxin Wang

A robustness analysis of dynamicboolean models of cellular circuits,Roded Sharan, Ariel Bruner

12:10am-12:30am

Comparison of parameterestimation methods in the presenceof overdispersion: An infectiousdisease based simulation study,Kimberlyn Roosa, Ruiyan Luo,Gerardo Chowell

Evolutionary switches structuraltransition states explored withminimalist coarse grained models,Francesco Delfino, Yuri Porozov,Eugene Stepanov, Gaik Tamazian,Valentina Tozzini

12:30pm-2:00pm


2:00pm-3:00pm

Plenary SessionRoom: Aula MasterChair: Alex Zelikovsky

Session 7: Keynote TalkLearning tumor phylogenies from single-cell dataNiko Beerenwinkel, ETH Zurich

3:00pm-3:20pm


3:20pm-4:55pm


Session 8A:Phylogeny 2Chair: Oliver Eulenstein

Session 8B:EpigenomicsChair: Ion Mandoiu

3:20pm-3:45pm

The cluster affinity distance forphylogenies, Jucheol Moon, OliverEulenstein

PeakPass: Automating ChIP-Seqblacklist creation, CharlesWimberley, Steffen Heber

3:45pm-4:10pm

An alignment-free heuristic for fastsequence comparisons withapplications to phylogenyreconstruction, Jodh Pannu, SaharHooshmand, Sriram P.Chockalingam, Sharma V.Thankachan, Srinivas Aluru

A novel neoantigen discoveryapproach based on chromatin highorder conformation, Yi Shi,Mingxuan Zhang, Luming Meng,Xianbin Su, Xueying Shang,Qingjiao Li, Mengna Lin, Xin Zou,Qing Luo, Yangyang Zhai, KunyanHe, Lan Wang, Cong Chen,Xiaofang Cui, Na Wang, Jian He,Yaoliang Yu, Yanting Wu, LintaiDa, Weidong Cai, Ze-Guang Han

4:10pm-4:35pm

Unifying gene duplication, loss, andcoalescence on phylogeneticnetworks, Peng Du, Huw Ogilvie,Luay Nakhleh

MADA: A web service for analysingDNA methylation array data, XinyuHu, Li Tang, Linconghua Wang,Fangxiang Wu, Min Li

4:35pm-4:55pm

Reconstruction of fitness landscapesof intra-host viral populations usingNGS data, Viachaslau Tsyvina,Yury Khudyakov, Pavel Skums

ZCMM: A novel algorithm ofZ-curve based and position weightmatrix for nucleosome positioning,Ying Cui, Jianzhong Li

7:00pm-9:00pm

BanquetEl Principal del Eixample

Provenca, 286–28808008 Barcelona

Thursday, June 6th, 2019

9:00am-10:00am

Plenary SessionRoom: Aula MasterChair: Gabriel Valiente

Session 9: Keynote TalkThe molecular anatomy of the human bodyRoderic Guigo, Centre for Genomic Regulation, Barcelona

10:00am-10:20am


10:20am-12:45pm


Session 10A:Image AnalysisChair: Fa Zhang

Session 10B:ClusteringChair: Yuri Porozov

10:20am-10:45am

Identification of early mild cognitiveimpairment using multi-modal dataand graph convolutional networks,Guanxin Tan, Jin Liu, Wei Lan,Jianxin Wang

Markov chain Monte Carlo foractive module identificationproblem, Nikita Alexeev, JavlonIsomurodov, Gennady Korotkevich,Alexey Sergushichev

10:45am-11:10am

Anomaly detection of pedestriantrajectory based on adaptivedensity clustering, Aiguo Chen,Jiacheng Luo, Ling Tian, HaotianRao

Sorting by reversals, transpositions,and indels on both gene order andintergenic sizes, Klairton LimaBrito, Geraldine Jean, GuillaumeFertin, Andre Rodrigues Oliveira,Ulisses Dias, Zanoni Dias

11:10am-11:35am

Compressed sensing improvedreconstruction-reprojectionalgorithm for electron tomography,Lun Li, Renmin Han, Zhiyong Liu,Fa Zhang

Using DenseFly algorithm for cellsearching on massive scRNA-seqdatasets, Yixin Chen, Sijie Chen,Xuegong Zhang

11:35am-12:00pm

DM-SIRT: A distribute methodfor multi-tilt reconstruction inelectron tomography, Zihao Wang,Jingrong Zhang, Xintong Liu,Zhiyong Liu, Xiaohua Wan, FaZhang

A multi-view clustering method formicrobiome analysis by symmetricnonnegative matrix factorizationwith Hessian regularization,Yuanyuan Ma

12:00pm-12:25pm

A multi-label classification modelfor full slice brain computerisedtomography image, Guanghui Fu,Jianqiang Li, Yan Pei

MDAPlatform: A component-basedplatform for constructing andassessing miRNA-diseaseassociations prediction method,Yayan Zhang, Cheng Yan, HaolunYi, Jianxin Wang

12:25pm-12:45pm

An attention-based framework formicroaneurysms detection onFundus images, Lizong Zhang, YingLi, Guiduo Duan, Guangchun Luo,Ling Tian

Unveiling deeper relationshipsamong circulating virus sequences:Using a shared change searchmethod, Kun Zhao

12:45pm-2:00pm


ISBRA 2019 Map

Reception

Symposium

Documents

ISBRA 2019alan.cs.gsu.edu/isbra19/sites/default/files/isbra-2019... · 2019-05-10 · Message from the Program Chairs On behalf of the Program Committee, we would like to welcome