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Bioinformatics Conference

International Conference on Bioinformatics and its Applications (ICBA’04)

December 16-19, 2004Nova Southeastern UniversityFort Lauderdale, Florida, USA

ICBA Poster | First Announcement | Second Announcement | Program Schedule | Abstracts

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1. Invited Talks 2. Contributed Talks 3. Poster Presentations

1. Invited Talks

IN SILICO CONSTRUCTION OF THE CARBON FIXATION PATHWAY INSYNECHOCOCCUS SP. WH8102

PHUONGAN DAM1,2, ZHENGCHANG SU1,2, VICTOR OLMAN1 AND YING XU1,2,3

[email protected], [email protected], [email protected] and [email protected] 1 Department of Biochemistry and Molecular Biology, University of Georgia at Athens, 2 Computational Biology Institute, Oak Ridge National Laboratory3 Correspondence: Ying Xu{[email protected]}

APPLICATIONS OF HYPER GENETIC CODE TO BIOINFORMATICS MIGUEL A. JIMENEZ-MONTAÑO Faculty of Physics & Artificial Intelligence, University of Veracruz , Sebastian Camacho # 5 Xalapa, Ver., 91000, [email protected]

MOLECULAR MAPPINGS: GROUP THEORY, CODING THEORY, AND THE EMERGENCE OF REPLICATIONDÓNALL A. MAC DÓNAILL Department of Chemistry, Trinity College Dublin 2, Republic of Ireland

SYMMETRY AND INFORMATION IN THE GENETIC CODETIDJANI NEGADI Physics Department, Faculty of Science, Oran University, Es-Sénia, 31100, Oran, Algeria

IN SILICO BIOLOGY: HAPLOTYPE INFERENCE, LINKAGE DISEQUILIBRIUM ANALYSIS, AND MICROARRAY-BASED GENE SELECTION TECHNIQUESTIANHUA NIUDivision of Preventive Medicine, Department of Medicine, Brigham and Women's Hospital Harvard Medical School, Boston, MA 02215, USA E-mail: [email protected]

SYMBOLIC CODING OF AMINO ACID AND NUCLEOTIDE PROPERTIES NIKOLA ŠTAMBUK *, PAŠKO KONJEVODA Rudjer Boškovi æ Institute, Bijeni è ka cesta 54, HR-10002 Zagreb, Croatia

http://polaris.nova.edu/MST/ICBA2004/html/speakers.html (1 of 18)9/21/2005 7:04:15 PM

http://polaris.nova.edu/MST/ICBA2004/pdfdocs/icbaposter.pdf

http://polaris.nova.edu/MST/ICBA2004/pdfdocs/firsticba.pdf

http://polaris.nova.edu/MST/ICBA2004/pdfdocs/secondicba.pdf

http://polaris.nova.edu/MST/ICBA2004/html/ICBAProg.htm

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[email protected]

NIKOLA GOTOVAC Department of Radiology, General Hospital Požega, Osje è ka bb, HR-34000 Požega, Croatia

FROM GENETIC CODE TO PROTEIN STRUCTURE PREDICTION: HOW NATURE FINDS A NEEDLE IN A HAYSTACK AND REMEMBERS ITROSEMARIE SWANSON Department of Biochemistry and Biophysics 2128 TAMU, Texas A&M University College Station, TX 77943-2128 [email protected]

MOLECULAR VERSUS ATOMIC INFORMATION LOGIC BEHIND THE GENETIC CODING CONTENTS CONSTRAINED BY TWO EVOLUTIONARY AXES AND THE FIBONACCI-PUCAS SEQUENCESCHI-MING YANG Neurochemistry and Physical Organic Chemistry LaboratoryNankai University, Tianjin, [email protected]

IDENTIFICATION OF CONTAMINANTS IN MALDI-TOF PROTEOMICS SPECTRA VIA DATA MINING CHIA-YU YEN Department of Computer Science and Engineering University of Colorado at Denver and Health Sciences Center Campus Box 109, Denver, CO 80217, USA

KRZYSZTOF J. CIOS Department of Computer Science and Engineering University of Colorado at Denver and Health Sciences Center Campus Box 109, Denver, CO 80217, USA

MARK W. DUNCAN Department of Pediatrics University of Colorado at Denver and Health Sciences Center MS 8119, Aurora, CO 80045,USA

2. Contributed Talks

COMPUTATIONAL EPIDEMIOLOGY: BAYESIAN DISEASE SURVEILLANCE KAJA ABBAS, ARMIN R. MIKLER, AMIR RAMEZANI, SHEENA MENEZES University of North Texas Denton, TX 76203, USA Email: {kaja, mikler}@cs.unt.edu, {ar0116, srm0034}@unt.edu

NON-EQUILIBRIUM FLUCTUATIONS IN A STOCHASTIC PLANKTON MODEL: PERIODICITY OF PHYTOPLANKTON BLOOMR. BHATTACHARYYA AND B. MUKHOPADHYAY Department of Applied Mathematics



University of Calcutta Kolkata - 700 009, India E-mail : [email protected]

FUZZY DECODING IN PROFILE HIDDEN MARKOV MODELS FOR PROTEIN FAMILY IDENTIFICATIONN.P. BIDARGADDI, M. CHETTY and J.KAMRUZZAMAN Gippsland School of Computing and Information Technology Monash University, Gippsland campus, Vic –3842, Australia Email: {niranjan.bidargaddi, madhu.chetty, joarder.kamruzzaman}@infotech.monash.edu.au

PREDICTING AND CHARACTERIZING METAL-BINDING SITES USING SUPPORT VECTOR MACHINESL. BOBADILLA AND F. NINO Intelligent Systems Laboratory Computer Engineering Department, National University of Colombia E-mail: [email protected] , [email protected]

G. NARASIMHAN School of Computer Science, Florida International University, Miami FL 33199, USA E-mail: [email protected]

USE OF EEG RECORDINGS AS VALID MEASURES OF KINESTHETIC AND VISUAL IMAGERY ABILITY J.G. CREMADES School of Human Performance and Leisure Sciences, Barry University, Miami Shores, FL 33161

M. TITO, M. ADJOUADI , AND A. BARRETO Electrical & Computer Engineering Department, Florida International University, Miami, FL 33174

MTMM-A MATLAB TOOLBOX FOR MACROMOLECULAR MODELINFENG CUI, TAUQIR BIBI, AND ZHIJUN WU Department Of Mathematics, Bio-informatics and Computational Biology Program, Laurence H. Baker Center for Bio-informatics and Statistical Biology, Iowa State University, Ames, IA 50014 USA E-mail: [email protected]

THE MERITS OF THE THIRD DIMENSION FOR VISUAL ANALYSIS OF MULTIPLE ANATOMY ONTOLOGIES ABA-SAH DADZIE †,1,2 , ALBERT BURGER 1,31. Department of Mathematical and Computer Sciences, Heriot-Watt UniversityRiccarton, Edinburgh EH14 4AS, Scotland [email protected], [email protected]

2. Ashesi University, No. 87, 3rd Norla Extension, North Labone, Accra, Ghana 3. MRC, HGU, Western General Hospital, Edinburgh EH4 2XU, Scotland



STABBING BALLS AND SIMPLIFYING PROTEINS O. DAESCU AND J. LUO Department of Computer Science, University of Texas at Dallas, Richardson, TX 75083, USA E-mail: {daescu, ljroger} @utdallas.edu

SCREENING POTENTIAL ALLELE-FREQUENCY DISEQUILIBRIUM IN DATA FROM AFFYMETRIX GENE EXPRESSION ARRAYS MANHONG DAI, YONGJIA WANG, ELZBIETA SLIWERSKA, MARGIT BURMEISTER, STANLEY J. WATSON, HUDA AKIL, FAN MENG † Microarray Laboratory, Mental Health Research Institute and Psychiatry Department, University of Michigan, 200 Zina Pitcher Place, Ann Arbor, MI 48109

STEP-WISE MUTATIONS OF MRNA SEQUENCES LEAD TO PROGRESSIVE CHANGES IN CALCULATED FOLDING FREE ENERGIES DAVID DIGBY and WILLIAM SEFFENS Clark Atlanta University Department of Biological Sciences 223 James P. Brawley Drive, S.W. Atlanta, GA 30134Emails: [email protected], [email protected]

THE APPLICATION OF SELF ORGANIZING MAPS FOR THE ANALYSES OF DNA SEQUENCESH. DOZONO, S. HARA, H. TOKUSHIMA AND Y. NOGUCHI Faculty of Science and Engineering Saga University 1-Honjyo Saga, 840-8502 JAPAN Email: [email protected] TEL.0952-28-8652 FAX.0952-28-8651

MICROARRAY NORMALIZATION USING PROPORTIONAL ABUNDANCESTEVEN A. ESCHRICH AND CRAIG A. BEAM Moffitt Cancer Center and Research Institute 12902 Magnolia DriveTampa, FL 33612, USA E-mail: {eschris,beamca}@moffitt.usf.edu

ALIGNING SEQUENCES WITH NON-AFFINE GAP PENALTY: PLAINS LGORITHM, A PRACTICAL IMPLEMENTATION, AND TS BIOLOGICAL APPLICATIONS IN COMPARATIVE GENOMICS Ofer Gill 1,4 , Yi Zhou 3 and Bud Mishra 1,2 1 Courant Institute of Mathematical Sciences, New York University 2 Department of Cell Biology, NYU School of Medicine 3Department of Biology, New York University 4 Corresponding Author: [email protected]; Phone: 212-998-3351

A DISTRIBUTED MULTIMEDIA DATABASE VISUALIZATION WITHIN AN IMMERSIVE ENVIRONMENT FOR BIOINFORMATICS P-E. GROS, N. FÉREY, J. HÉRISSON, R. GHERBI Bioinformatics team, LIMSI-CNRS, Université Paris-Sud BP 133, F-91403 Orsay Cedex, France{gros, ferey, herisson, gherbi}@limsi.fr

USING THE LENGTH CONSTRAINTS OF HELIX TO EVALUATE PROTEIN SECONDARY STRUCTURE PREDICTION FOR HELIX



Jing He, Yonggang Lu Department of Computer Science, New Mexico State UniversityLas Cruces, NM 88003 E-mail: {jinghe, ylu}@cs.nmsu.edu

A DODECAHEDRON-BASED MODEL OF SPATIAL REPRESENTATION OF THE CANONICAL SET OF AMINO ACIDSV.A. KARASEV, V.V. LUCHININSt.-Petersburg State Electrotechnical UniversitPopov Str. 5, St.-Petersburg, 197376 RussiaE-Mail: [email protected]

V.E. StefanovDepartment Of Biochemistry, St.Petersburg State UniversityUniversitetskaya Nab. 7/9, St.-Petersburg, 199034 Russia

EMERGING PATTERN BASED SUBSPACE CLUSTERING OF MICROARRAY GENE EXPRESSION DATA USING MIXTURE MODELS YOUNG BUN KIM, JUNG HUN OH, and JEAN GAO Department of Computer Science and Engineering, The University of TexasArlington, TX 76019, USA E-mail:{ kim, joh, gao}@cse.uta.edu

AN ALGORITHM FOR FINDING SIMILARITIES IN PROTEIN ACTIVE SITESK. KUPAS AND A. ULTSCH Data Bionics Research Group University of Marburg, D-35032 Marburg, GermanyE-mail: [email protected]@informatik.uni-marburg.de

G. KLEBEInstitute of Pharmaceutical ChemistryUniversity of Marburg, D-35032 Marburg, Germany, E-mail: [email protected]

GAUSSIAN KERNEL WIDTH GENERATOR FOR SUPPORT VECTOR CLUSTERING Sei-Hyung Lee, Karen Daniels Department of Computer Science, University of Massachusetts Lowell One University Avenue, Lowell, MA 01854 USA phone: +1-978-934-3631, fax: +1-978-934-3551 Email: {slee, kdaniels}@cs.uml.edu

PARALLEL TEMPERING IN ROSETTA PRACTICE YAOHANG LI Department of Computer Science North Carolina A&T State University Greensboro, NC 27411, USA email: [email protected]

CHARLIE E. M. STRAUSS Computer Science and Mathematics Division Los Alamos National Laboratory Los Alamos, NM 87545, USA email: [email protected]

ANDREY GORIN



Computer Science and Mathematics Division Oak Ridge National Laboratory Oak Ridge, TN 37831, USA email: [email protected]

SERUM PROTEOMIC PATTERN ANALYSIS FOR EARLY CANCER DETECTION YING LIU Georgia Institute of Technology College of Computing Atlanta, GA 30322, USA

A LINEAR SOLUTION FOR HAPLOTYPE PERFECT PHYLOGENY PROBLEM YUNKAI LIU Lane Department of Computer Sciences and Electronic Engineering P. O. Box 6109 West Virginia University Morgantown, WV 26506 Email: liuyk [email protected]

CUN-QUAN ZHANG Department of Mathematics P. O. Box 6310 West Virginia University Morgantown, WV 26506 Email: [email protected]

APPLICATIONS OF DATA MINING IN EPITOPE PREDICTION Tom Milledge Florida International University School of Computer Science Miami, FL 33199 [email protected]

Gaolin Zheng Florida International University School of Computer Science Miami, FL [email protected]

Giri Narasimhan Florida International University School of Computer Science Miami, FL [email protected]

LOCALIZATION OF BRAIN ACTIVATION THROUGH INTEGRATION OF OPTICAL TOPOGRAPHY AND MAGNETIC RESONANCE IMAGING MICHEL MOURAD, M.S.C.E, MALEK ADJOUADI, Ph.D., AND ILKER YAYLALI, Ph.D., M.D. Department of Electrical & Computer Engineering, Florida International University, 10555 W. Flagler Street, Miami FL [email protected], [email protected]

Department of Neurology, Miami Children’s Hospital, 3100 S.W. 62nd AvenueMiami, Fl 33155, [email protected]



THERMODYNAMIC FEASIBILITY OF METABOLIC NETWORKSR. NIGAM Department of Physics, Stanford University, Stanford, CA 94305, USA E-mail: [email protected]

S. LIANG NASA Advanced Supercomuting Division NASA Ames Research Center, Moffett Field, CA, 94035, USA E-mail: [email protected]

A TWO-WAY SEARCHING ALGORITHM FOR DE NOVO PEPTIDE SEQUENCING VIA TANDEM MASS SPECTROMETRY

JUNG HUN OH, YOUNG BUN KIM, and JEAN GAO Department of Computer Science and Engineering The University of Texas, Arlington, TX 76019, USA E-mail : {joh, kim,gao}@cse.uta.edu

THE ROLE OF FEATURE REDUNDANCY IN TUMOR CLASSIFICATION CHIA HUEY OOI, MADHU CHETTY, IQBAL GONDAL School of Computing and Information Technology Monash University, CHURCHILL 3842 Victoria, Australia [email protected]

CLUSTERING OF EUKARYOTIC ORTHOLOGS BASED ON SEQUENCE AND DOMAIN SIMILARITIES USING THE MARKOV GRAPH-FLOW ALGORITHM HATICE GULCIN OZER 1 , JINGCHUN CHEN 2,3,4 , FA ZHANG 2,3,4,5,6 , BO YUAN 1,2,3,4,* Program in Biophysics 1 , Departments of Biomedical Informatics 2 , and Pharmacology 3 , Program in Pharmacogenomics 4 , The Ohio State University, Columbus OH 43210; Institute of Computing Technology 5 , Graduate School 6 , The Chinese Academe of Sciences, Beijing, China 100080

MODULAR NEURAL NETWORKS AND THEIR APPLICATION IN EXON PREDICTION YOULIAN PAN Institute for Information Technology, National Research Council Canada 1200 Montreal Road, M-50, Ottawa, Ontario, K1A 0R6 Canada [email protected]

CHRISTOPH W. SENSEN Faculty of Medicine, Department of Biochemistry and Molecular BiologyUniversity of Calgary, 3330 Hospital Drive N.W., Calgary, Alberta, T2N 4N1 Canada

RAPID DRUG TARGET IDENTIFICATION IN MICROBIAL GENOMES – AN IN SILICO APPROACH WITH SPECIAL REFERENCE TO SALMONELLA SPECIES KISHORE R. SAKHARKAR AND CHANDRA VERMA BioInformatics Institute, Matrix, 30 Biopolis StreetSingaporeE-mail: [email protected], [email protected]

MEENA KISHORE SAKHARKAR Nanyang Center for Supercomputing and Visualization, School of Mechanical and



Production Engineering, Nanyang Technological University, Singapore E-mail: [email protected]

CHOW T.K., VINCENT Human Genome Laboratory,Department of Microbiology, Faculty of Medicine, National University of Singapore, Kent RidgeSingapore E-mail: [email protected]

AN ALGORITHM FOR DETERMINING GLYCAN STRUCTURES FROM MS/MS SPECTRAB. SHAN, K. ZHANG AND B. MA Department of Computer Science University of Western Ontario, London, ON N6A 5B7, CanadaE-mail: bxshan, kzhang, [email protected]

C. ZHANG AND G. LAJOIE Department of Biochemistry University of Western Ontario, London, ON N6A 5C1, CanadaE-mail: czhang04, [email protected]

A COLLIMATOR NEURAL NETWORK MODEL FOR THE CLASSIFICATION OF GENETIC DATA MUHAMMAD SHOAIB .B. SEHGAL GSCIT, MONASH UniversityChurchill, Victoria 3842, Australia E-mail: [email protected]

IQBAL GONDAL GSCIT, MONASH UniversityChurchill, Victoria 3842, Australia, E-mail: [email protected]

LAURENCE DOOLEYGSCIT, MONASH UniversityChurchill, Victoria 3842, Australia, E-mail: [email protected]

COUNTING AND ENUMERATION OF SELF-ASSEMBLY PATHWAYS FOR SYMMETRIC MACROMOLECULAR STRUCTURES MEERA SITHARAM CISE dept., University of Florida Gainesville, FL 32611Email: [email protected]

MIKLOS BONA Department of Mathematics University of Florida, Gainesville, FL 32611. Email: [email protected]

TRAINING SET DESIGN FOR PATTERN DISCOVERY WITH APPLICATIONS TO PROTEIN MOTIF DETECTION



Yanli Sun 1, Zhengyue Deng 1 , Kalai Mathee 2 , and Giri Narasimhan 1 1 Bioinformatics Research Group (BioRG), School of Computer ScienceFlorida International University, Miami, FL2 Department of Biological SciencesFlorida International University, Miami, FL

ANALYSING PATTERNS OF TRIPEPTIDES USING STATISTICAL APPROACH AND NEURAL NETWORK PARADIGMRAISA SZABO, MATTEW HE, ERICK BURNHAM, JESSICA JURANI Nova Southeastern University, Ft. Lauderdale, Florida 33314 [email protected], [email protected]

GENE DEFINITION IN DIFFERENT DATABASES AND ITS IMPLICATION IN MICROARRAY DATA INTERPRETATION PINGLANG WANG, MANHONG DAI, ROBERT THOMPSONSTANLEY J. WATSON AND FAN MENG † Mental Health Research Institute and Department of Psychiatry, University of MichiganAnn Arbor, Michigan 48109, USA

EXPLORING IMPORTANT ISSUES IN THE IMPLEMENTATION OF GENE SET ENRICHMENT ANALYSIS YONGJIA WANG, STANLEY J. WATSON, FAN MENG † Mental Health Research Institute and Psychiatry Department University of Michigan, Ann Arbor, MI 48109, USA

GENE SELECTION BY WEIGHTED FISHER CRITERION FOR MULTICLASS PREDICTION JIANHUA XUAN 1 , YIBIN DONG 1,5† 1 Dept. of Electrical Engineering and Computer ScienceThe Catholic University of America, Washington, DC 20064, USA

JAVED KHAN 2 , ROBERT CLARKE 3 , ERIC HOFFMAN 4 2 Dept. of Pediatric Oncology, National Cancer Institute, Gaithersburg, MD 20877, USA 3 Lombardi Cancer Center, Georgetown University, Washington, DC 20007, USA 4 Research Center for Genetic Medicine, Children's National Medical Center Washington, DC 20010, USA

YUE WANG 5 5 Dept. of Electrical and Computer EngineeringVirginia Polytechnic Institute and State UniversityAlexandria, VA 22314, USA

SEQUENTIAL BIFURCATION APPROACH TO LEARNING PROTEIN FUNCTIONAL CLASSES MARY QU YANG, OKAN K. ERSOY Purdue University, School of Electrical and Computer Engineering West Lafayette, Indiana, 47907-2035 USA

JACK Y. YANG Indiana University School of Medicine, Center for Bioinformatics Indianapolis, Indiana 46202, USA

QUERYING A DATABASE OF REGULATORY ELEMENTS Chengyong Yang & Erliang Zeng BioRG, School of Computer Science



Florida International University Miami FL 33199, USA{cyang01, ezeng001}@cs.fiu.edu

Kalai Mathee Department of Biological Sciences Florida International University Miami FL 33199, USA

Giri Narasimhan BioRG, School of Computer Science Florida International University Miami FL 33199, [email protected]

IMPROVING MULTIPLE WHOLE GENOME ALIGNMENT BY CONSIDERING REARRANGEMENT JINGYI YANG AND JITENDER S. DEOGUN Department of Computer Science and Engineering, University of Nebraska-LincolnLincoln, NE, 68588-0115, USA E-mail: jyang f deogun g @cse.unl.edu

A FILTERING APPROACH TO SPLICE SITE PREDICTIONS IN HUMAN GENESKIHOON YOON, STEPHEN KWEK University of Texas at San Antonio Department of Computer Science 6900 North Loop 1604 West, San Antonio, Texas 78249, USA E-mail: kyoon, [email protected]

THE CONSTRUCTION OF STRUCTURAL TEMPLATES FOR THE MODELING OF CONSERVED PROTEIN DOMAINS FA ZHANG 1,2,3,4,5 , JINGCHUN CHEN 1,2,3 , ZHIYONG LIU 4 , BO YUAN 1,2,3,* Departments of 1 Biomedical Informatics, and 2 Pharmacology, 3 Program in Pharmacogenomics, The Ohio State University, Columbus OH 43210, USA; 4 Institute of Computing Technology, 5 Graduate School, The Chinese Academe of Sciences, Beijing, China 100080

ANALYSIS OF THE EFFECTS OF RECOMBINANT HUMAN ERYTHROPOIETIN (EPO) ON MURINE BONE MARROW POPULATIONS USING MIXTURE MODELING TECHNIQUES GAOLIN ZHENG 1,3 , RENOLD CAPOCASALE 2 , BERNARD AMEGADZIE 1 , PETER J. BUGELSKI 2 , JIN LU 1*1 Departments of Molecular Discovery Technologies, 2 Toxicology and Investigative Pharmacology, Centocor, Inc, Radnor, PA 19087, USA3 School of Computer Science, Florida International UniversityMiami, FL 33199, USA

DISCOVERY OF LOCAL PROTEIN SEQUENCE MOTIFS USING IMPROVED K-MEANS CLUSTERING TECHNIQUE * WEI ZHONG Computer Science Department, Georgia State University Atlanta, GA 30303-4110, USA



GULSAH ALTUN Computer Science Department, Georgia State University Atlanta, GA 30303-4110, USA

ROBERT HARRISON Computer Science and Biology Departments, Georgia State University Atlanta, GA 30303-4110, USA

PHANG C. TAI Biology Department, Georgia State University Atlanta, GA 30303-4110, USA

YI PAN Computer Science Department, Georgia State University Atlanta, GA 30303-4110, USA

3. Posters (Part I)

Temporal Analysis of Infectious Diseases: InfluenzaKaja Abbas, Armin R. Mikler, Robert GattiComputational Epidemiology Research Lab, Department of Computer Science & Engineering University of North Texas, Denton, TX 76203, USA Email: {kaja, mikler} @cs.unt.edu, [email protected]

Biclustering noisy gene expression data Ahsan Abdullah, Amir Hussain, Andrzej Ordys Center for Agro-Informatics Research National Univ. of Computer & Emerging Sciences FAST Tower, Rohtas Road, G-9/4, Islamabad, Pakistan Email: [email protected]

Department of Computing Science & Mathematics University of Stirling, Stirling FK9 4LA Scotland, UK Email: [email protected]

Department of Electronic & Electrical EngineeringUniversity of Strathclyde, Glasgow UKEmail: [email protected]

DNA sequence and histone affinity Ivan V. Baji † and Peter Luykx ‡ † Department of Electrical and Computer Engineering ‡ Department of Biology University of Miami, Coral Gables, FL 33 24, USA [email protected], [email protected]

Using MinPD to study within-host HIV evolution Patricia Buendia & Giri Narasimhan Bioinformatics Research Group (BioRG) School of Computer Science Florida International University



Miami, FL 33199

Improvement of Affymetrix Genechip data analysis accuracy using a bioinformatics and model-based approach Li Chen, Wing Cheong Wong and He Yang* Bioinformatics Institute, 30 Biopolis Street, Matrix #07-01, Singapore 138671 Email: [email protected]

Composition-based Modifications of Scoring Matrices Improve Pairwise Comparisons of Low-complexity Sequences Juan Coronado 1 ,Oliver Attie 1 ,Susan Epstein 2 ,Wei-Gang Qiu 1 ,Peter N. Lipke 11 Department of Biological Sciences an Center for Gene Structure and Function,Hunter College of City University of New York, New York 10021,USA 2 Department of Computer Science, Hunter College of City University of New York, 10021,USA

Immersive Exploration by Visualization of Factual and Textual Genomic Data Nicolas FEREY, Pierre-Emmanuel GROS, Joan HERISSON and Rachid GHERBI LIMSI-CNRS, Université Paris-Sud XI, BP 133, 91403 Orsay CEDEX, France {ferey, gros, herisson, gherbi}@limsi.fr

Functional Clustering Of Biological Sequences Using Sequence Information And Expression ProfilesZoee Gokhale 1 , Jingchun Chen 2 , Hatice Ozer 1 , Fa Zhang 2 , Junshui Ma 3 Daolong Wang 5 , Mario, Lauria 4 , and Bo Yuan 2,* Biophysics Program, College of Biological Sciences 1 , Departments of Biomedical Informatics, and Pharmacology, College of Medicine and Public Health 2 , Ohio Supercomputing Center 3 , Department of Computer Science and Engineering, College of Engineering 4 , the Ohio State University, Columbus, Ohio; Siteman Cancer Center, Washington University 5 , St. Louis, Missouri

Improved Folding Algorithms In The Hp Model Xiaoxu Han, Jun Ni, Xiaoqian Jiang Applied Mathematical and Computational Science, Department of Computer Science The University of Iowa, Iowa City, IA 52242, USA {xihan, jni, xjia}@cs.uiowa.edu

4 novel genes and the repertoire of SLC6 transporters in human and mouse Pär J.Höglund, Helgi B.Sc iöt 1 and Robert Fredriksson Department of Neuro cience,Upp ala Univer ity,BMC,Box 593, 751 24,Uppsala, Sweden

Model Driven Approach for Capturing and Exchanging Data in BioinformaticsX.K. Hu, J. Zhou, D. Martin, X. Wang, H. Garton, J. Wang, T. Saxton, G. Robinson Xtensible Solutions Inc. PO Box 372969, Satellite Beach, FL 32937 Email: [email protected]

Data and Information: Effect of Bioinformatics on Traditional Biology Donald E. Johnson Azusa Pacific University [email protected]

Pathway Comparison Using the NCI Thesaurus Bruce Kapron & Samuel Leung Department of Computer Science, University of Victoria, BC, Canada



Email: {bmkapron, samuelc}@cs.uvic.ca

An Intron Analysis Website is Needed Sawsan Khuri The Dr. John T. Macdonald Foundation Center for Medical GeneticsUniversity of Miami School of Medicine, Florida, USAEmail [email protected]

Amino Acid Composition and Folding of the Monosaccharide Binding Sites of Enzymic ProteinsKhuri S. * , Nassif H., Al-Ali Merheby H., Khalaf K., Khachfe H., and Keyrouz W. Computational Sciences and Bioinformatics Unit (HAM, HK) and the Departments of Computer Science (HN, WK), and Mechanical Engineering (KK), American University of Beirut, Lebanon; * The Dr. John T. Macdonald Foundation Center for Medical Genetics, University of Miami School of Medicine, Florida, USACorresponding author email : [email protected]

An Effective Visual-Based Classifier And Its Application On Sea Urchin Data Danyu Liu, Alan P. Sprague Department of Computer & Info. Sci, University of Alabama at Birmingham 153 Campbell Hall, 1300 Univ. Blvd Birmingham AL 35294-1170, USA E-mail: { liudy,sprague}@cis.uab.edu

AELE W CUNNINGHAM Department of BiologyUniversity of Alabama at Birmingham 374 Campbell Hall, 1300 Univ. Blvd Birmingham AL 35294-1170, USA [email protected]

An Integrated System for Immunoglobulin Sequence Analyses Jin Lu, Andy Hackett, Bernard Amegadzie, Ray Sweet Dept of Molecular Discovery Technologies, Centocor, Inc. (A Johnson and Johnson Company) 145 King of Prussia Rd. Radnor PA 19087

A Potential Link Between Atherogenic LDL and Inflammation: Insights from Protein Structure Studies Hassan Al-Ali Merheby 1 , Diana Azzam 2 , Sawsan Khuri 3 and Hassan Khachfe 1,2 1 Computational Sciences and Bioinformatics Unit and 2 Department of PhysiologyFaculty of Medicine, American University of Beirut, Beirut, Lebanon. 3 The Dr. John T. Macdonald Foundation Center for Medical GeneticsUniversity of Miami School of Medicine, Florida, USACorresponding author email [email protected]

Protein Structure Prediction using a combination of Ab Initio and knowledge-based techniques Gaurav Porwal*, Deepak K. Singh, S.D. Babu, Hemant Nanavati, Santosh Noronha Department of Chemical Engineering, Indian Institute of Technology BombayMumbai 400076, Maharashta, INDIA. Email: [email protected]

Protein Function Analyzer: A tool to infer protein functions



using sequence and structure information Ganesh Rajagopalan 1 and Li-Wei Hung 2 1 Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA|2 Biological and Quantum Physics Group, Physics Division, Los Alamos National Laboratory, Los Alamos, NM, USA

A new approach to automatically detecting grids in DNA microarray images Luis Rueday and Vidya Vidyadharany School of Computer Science, University of Windsor401 Sunset Ave., Windsor, ON, N9B 3P4, CanadaE-mail: [email protected]

Can Ends Justify the Means: To Fuse or Note to Fuse Meena K. Sakharkar, Yu Yiting and Pandjassarame Kangueane

Understanding cellular differentiation using parallel, multi-cellular pathway modeling Richard L. Schiek, Elebeoba E. MayComputational Sciences & Computational Biology Sandia National Laboratories, P.O. Box 5800 MS 0316 Albuquerque, NM, 87185-0316, [email protected]

BioRel: A novel way to detect "structured relationship" between functions and structures in proteins by mutual training of existing taxonomies Vivek Sehgal1, Kshitiz Gupta,1 ; 2 ; 3, K.V.Venkatesh 2 ; 3 ; 41. Department of Comptuer Science and Engineering, IIT Bombay, India 2. School of Biosciences and Bioengineering, IIT Bombay, India 3. Department of Chemical Engineering, IIT Bombay, India 4. Department of Chemical Engineering, University of Delaware, Newark

PHYSICS OF CARCINOGENIC BEHAVIOUR Tapas Kumar Sinha Computer Centre, Bijni Complex North Eastern Hill University, Shillong, 793 003 India

Incremental Estimation of Gaussian Mixture Models for Online Data Stream Clustering Mingzhou Song Department of Computer Science Queens College and Graduate Center City University of New York Flushing, NY 11367 [email protected]

Hongbin Wang Ph.D. Program in Computer Science Graduate Center City University of New York New York, NY 10016 [email protected]

Modeling, Simulation, Visualization, and Animation of the Fundamental DNA Operations Using the Programming Language Easel VOJISLAV STOJKOVIC, GRACE STEELE, and CHRISTEL HYOUSSEU Morgan State University, Baltimore, MD 21251



[email protected], [email protected]@hotmail.com

Human Biotin Carboxylases: Motif Analysis and Putative Minimal Functional Regions Required for Enzymatic Activity *K.V. Venkatachalam, Rishi Kumar†, Josh Fields† *Corresponding Author: Department of Biochemistry, College of Medical Sciences, †Health Profession Division, Nova Southeastern University, Ft. Lauderdale, FL 33328-2018 E-mail: [email protected]

Enzymes that Uses Vitamin B12 (Cobalamin) Coenzymes: The Putative Cobalamin Binding Motif’s. K.V. Venkatachalam Department of Biochemistry, College of Medical SciencesHealth Profession Division, Nova Southeastern UniversityFt. Lauderdale, FL 33328-2018 E-mail: [email protected]

Using Fuzzy Set Principles to Account for Imprecision in the Discovery of New Knowledge in Drug Analysis Giovanni Vincenti 1 Robert J. Hammell II 2 Department of Computer and Information Sciences Towson University Towson, MD 21204 {gvince1, rhammell}@towson.edu

Exploring Biomedical Literature Using Batch Sequence Id Weijian Xuan, Stanley J. Watson, and Fan Meng * Mental Health Research Institute and Department of Psychiatry University of Michigan, Ann Arbor, Michigan 48109 Contact: [email protected]

Biclustering using Adaptive Self-Organizing Maps Chengyong Yang, Yong Wang, Giri Narasimhan School of Computer Science Florida International University Miami FL 33199, USA {cyang01, giri}@cs.fiu.edu

Ranking of Enzyme-Substrate Specificity Determining Residue Clusters Gong-Xin Yu ¶ , Byung-Hoon Park ¶ , Praveen Chandramohan, Rajesh Munavalli, Al Geist, and Nagiza F. Samatova * Computational Biology Institute, Oak Ridge National Laboratory ¥ Corresponding Authors: {yug, samatovan}@ornl.gov ¶

Signatures of Gene Sequences Revealed by Mining the UniGene Affiliation Network Jiexin Zhang, Li Zhang and Kevin R. Coombes 1 Department of Biostatistics, U.T. M.D. Anderson Cancer Center 1515 Holcombe Blvd,Box 447, Houston, TX 77030-4009, USA

3. Posters (Part II)

Using Short Memory Markov Models To Detect Regulatory Elements



Irina Abnizova, Mark Robinson, Alistair G. Rust , Maria Schilstra, Chrystopher L. Nehaniv And Rene Te Boekhorst BSU MRC Cambridge

Bible and Genetics Tatiana A. Baeva Independent Scholar

Self-similar solutions of diffusion model of genome ecolution F. Barezovskaya and G. Karev Howard University and National Institutes of Health

SEQOPTICS Yonghui Chen, Kevin Reilly, Alan Sprague University Of Alabama At Birmingham

A Hidden Markov Model For Gene Function Prediction From Sequential Expression Data Xutao Deng, Huimin Geng, Hesham Ali University Of Nebraska At Omaha

ploring Augmented Microarray Data Using Immersive Visualization N. Férey, P-E. Gros, J. Hérisson, R. Gherbi LIMSI/CNRS

A Neural Network Based Approach For Assessing Feasibility Of Arbitrary Contact Maps Nitin Gupta, Nitin Mangal Indian Institute Of Technology, Kanpur

Protein Sequence Similarity Detection Based On Spectral Similarity Score (SSS) As Used In Music Database Retrieval SystemsKshitiz Gupta, K.V. Venkatesh, S. Ramakumar Indian Institute Of Technology, BombayIndian Insitute Of Science, Bangalore

Signal Peptide Prediction On DNA Sequences With Artificial Neural Networks Artemis Hatzigeorgiou & Martin Reczko University Of Pennsylvania

The Statistics Of DNA Words Of Eucaryotes Heli Hiisila And Ella Bingham Helsinki University Of Technology

Identifying Patterns In Data By Latent Path Models Donald D. Hua, Dechang Chen, And Zhenqiu Liu The George Washington UniversityUniformed Services University Of The Health SciencesThe Ohio State University

Finding Reversals In DNA Kathleen M. Kaplan, D.Sc., And John J. Kaplan, Ph.D., J.D. Howard University And United States Air Force



Comparison And Analysis Of Neural Network And Support Vector Machine Approaches To Biodata MiningKeivan Kianmehr, Hongchao Zhang, Konstantin Nikolov, Tansel Özyer, And Reda Alhajj University Of Calgary

Prediction Of Distinct RNA Stem-Loop Structures In Genomic Sequences Shu-Yun Le, Jih-H. Chen And Jacob V. Maizel, Jr. Lab. Of Experimental And Computational Biology, CCR, NCI, NIH

SWAT Yifeng Li And Hesham H. Ali University Of Nebraska At Omaha Face Registration And Recognition Using 3D Profiles And Contours Chao Li And Armando Barreto Florida International University

Identification Of Ligands For Orphan G-Protein Coupled Receptor Ling Li Nova Southeastern University

Bioinformatics Analysis Of Antisense Activity And Target RNA Structure Li Liao, Zhongwei Li University Of Delaware, Florida Atlantic University

Discovering Highly Differentiative Gene Groups From Microarray Gene Expression Data Shihong Mao, Guozhu Dong Wright State University

Kullback-Leibler Divergence Of Hidden Markov Models For DNA Sequence Comparison T.D. Pham And D.I. Crane Griffith University, Australia

Analyzing Reliability Of Independent Component Analysis Using Bacillus Subtilis T. Pompey, C. Williams, J. Kim, W. Alexander North Carolina A&T State University

Natural Language Pattern Extractions From Bioinformatics Data Manas Ranjan Pradhan,Rashmi Karn,Amruta Samal, Rajshree Dash Teqnium Global Soft Services

Hintikka-Like Games And The Design Cycle For Biological Hypotheses Stephen Racunas Pennsylvania State University

A Computational Cognitive Model For Bioinformatics Knowledge Discovery Jorge Reyes-Spindola, Olga A. Kuchar, Michel Benaroch Pacific Northwest National Laboratory

Knowledge Base Triage In A Clinical Setting Tod Sedbrook University Of Northern Colorado



Secondary Structure Sequence Alignment For Improving Detection Of Homologous ProteinsL. Gwenn Volkert & Deborah A. Stoffer Kent State University

Probabilistic Prediction Of Structural And Functional Classes Of Proteins By Mutual Training Of Existing Taxonomies In SCOP And PROSITEVivek Sehgal, Kshitiz Gupta, K.V.Venkatesh IIT Bombay, University Of Delaware, Newark

Independent And Principle Component Analysis Of The Global Stress Response Of Bacillus SubtilisC.M. Williams1, W.E. Alexander1, Ph.D, T.L. Pompey North Carolina State University, North Carolina A&T State University

Inferring Large Gene Regulatory Networks From Gene Expression Data Fangxiang Wu University Of Saskatchewan

Music And Bioinformatics Igor Yevin And Alexander Koblyakov Russian Academy Of Sciences

A Rule-Based Voting Algorithm For High-Throughput Protein Functional Annotation Gong-Xin Yu Oak Ridge National Lab

Instrumentation For Automatic Monitoring Of Affective State In Human-Computer InteractionJing Zhai And Armando B. Barreto Florida International University

Identification Of Haplotype Tagging Snps Using Genotype Data On Chromosome 5q31 From A Crohn's Disease Susceptibility LocusGao Zhang University Of North Carolina At Charlotte

Making Physical Interaction Out Of Statistics Of Protein Yaoqi Zhou University At Buffalo

Nova Southeastern University3301 College Avenue, Fort Lauderdale, Florida 33314

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Home | Department of Mathematics | West Virginia Universitycqzhang/Publication-files/my-paper/... · 2005. 9. 22. · University of Marburg, D-35032 Marburg, Germany E-mail: [email protected]