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Combinatorial libraries and drug design |
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A1 Pharmacophore Multiplets in Combinatorial Library Design: A Novel Approach to Generation and Storage Abrahamian, Edmond J.1, Clark, Robert D.2, Peter Fox, Inge Thøger Christensen, , Henning Thøgersen 1edmond@tripos.com, Tripos, Inc.; 2bclark@tripos.com, Tripos, Inc. Abstract |
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A2 The Docking Mesh Evaluator Roummel F. Marcia1, Julie C. Mitchell2, Susan D. Lindsey, J. Ben Rosen 1marcia@math.wisc.edu, UW-Madison; 2mitchell@math.wisc.edu, UW-Madison Abstract |
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A3 Using MEGA to Predict Molecular Bio-Activity Arun Qamra1, King-Shy Goh2, Edward Y. Chang 1arun@cs.ucsb.edu, Department of Computer Science, University of California Santa Barbara; 2kingshy@engineering.ucsb.edu, Department of Electrical and Computer Engineering, University of California Santa Barbara Abstract |
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A4 Structure-Based Design of HIV Entry Inhibitors Hepan Tan1, Jiang Zhu2, Wayne A. Hendrickson 1ht149@columbia.edu, Columbia University; 2jz2106@columbia.edu, Columbia University Abstract |
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A5 Shape Signatures, a New Approach to Computer-aided Ligand- and Receptor- Based Drug Design Lifeng Tian1, Randy J. Zauhar2 1lt0000@usip.edu, Univ of the Sciences in Philadephia; 2r.zauhar@usip.edu, Univ of the Sciences in Philadelphia Abstract |
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Complex systems and simulation |
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M1 A Full-length HIV-1 Integrase:Molecular Modeling and Molecular Dynamics Simulations Atchara Wijitkosoom1, Somsak Tonmunphean2, Vudhichai Parasuk, Supot Hannongbua, Thanh N. Truong 1i_am_atchara@hotmail.com, Department of Chemistry, Faculty of Science, Chulalongkorn University, Thailand; 2somsak.t@chula.ac.th, Department of Chemistry, Faculty of Science, Chulalongkorn University, Thailand Abstract |
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M2 Large-Scale Biopathway Modeling and Simulation Masao Nagasaki1, Atsushi Doi2, Kazuko Ueno, Eri Torikai, Hiroshi Matsuno, Satoru Miyano 1masao@ims.u-tokyo.ac.jp, University of Tokyo; 2atsushi@ib.sci.yamaguchi-u.ac.jp, Yamaguchi University Abstract |
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M5 Monte-Carlo Simulation of Metabolic Fluxes: Implications for Making Informative Experimental Measurements and Evaluating Systemic Impact of Enzymopathies Nathan D. Price1, Jan Schellenberger2, Bernhard O. Palsson 1nprice@ucsd.edu, UCSD; 2jschelle@ucsd.edu, UCSD Abstract |
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M6 Dynamic Pathway Modeling of Sphingolipid Metabolism Peter A. Henning1, Geoffrey Wang2, Alfred H. Merrill, and May D. Wang 1gtg841j@mail.gatech.edu, The Wallace H. Coulter Biomedical Engineering Department, Georgia Institute of Technology and Emory University; 2gte107k@mail.gatech.edu, School of Biology, Georgia Institute of Technology Abstract |
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Computational genetics |
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B1 Distributions of time to coalescence under stochastic population growths: application to MRCA dating Krzysztof A. Cyran1, Marek Kimmel2 1chrisc1@rice.edu, Stat Dept., Rice Univ. Houston TX, and Inst. of Comp. Sci., Silesian Univ. of Techn., Gliwice Poland; 2kimmel@rice.edu, Stat. Dept., Rice Univ. Houston TX Abstract |
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B10 Before SNP mapping: Data preprocessing by fixed length genomic sequence patterns Chia-Hao Ou1, Ming-Jing Hwang2 1ouch@gate.sinica.edu.tw, Institute of Biomedical Science, Academia Sinica; 2mjhwang@ibms.sinica.edu.tw, Institute of Biomedical Science, Academia Sinica Abstract |
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B11 Efficient method for Inferring Hierarchy of Clonal Complexes from Multi-Locus Sequence Types Wasinee Rungsarityotin1, Mark Achtman2, Homayoun Bagheri-Chaichian, Alexander Schliep 1rungsari@molgen.mpg.de, Max Planck Institute for Molecular Genetics; 2achtman@mpiib-berlin.mpg.de, Max Planck Institute for Infection Biology Abstract |
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B12 Description of Haplotypes and their Ancestry Structure from SNP Data Jonathan Sheffi1, Itsik Pe'er2, David Altshuler, Mark J. Daly 1jsheffi@broad.mit.edu, Broad Institute; 2peer@broad.mit.edu, Broad Institute Abstract |
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B13 FROM RESOURCE TO RESEARCH: MGI AND GO Mary E. Dolan1, Judy A. Blake2, Janan T. Eppig, Martin Ringwald, Carol J. Bult, Joel E. Richardson 1mdolan@informatics.jax.org, MGI, The Jackson Laboratory; 2, MGI, The Jackson Laboratory Abstract |
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B14 A Pattern Discovery-Based Method for Detecting Multi-Locus Genetic Association Zhong Li1, Aris Floratos2, David Wang, Andrea Califano 1zli@firstgenetic.net, First Genetic Trust, Inc.; 2afloratos@firstgenetic.net, First Genetic Trust, Inc Abstract |
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B15 Algebraic Statistical Genetics: Affected Sib-Pair Linkage Analysis Ingileif Hallgrimsdottir1 1ingileif@stat.berkeley.edu, UC Berkeley Abstract |
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B2 Knowledge-Driven Selection of SNP Markers for Genetic Association Studies of Complex Diseases Francisco De La Vega1, Hadar Isaac2 1delavefm@appliedbiosystems.com, Applied Biosystems; 2aviitzh@appliedbiosystems.com, Applied Biosystems Abstract |
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B3 Analysis of Sorting by Transpositions based on Algebraic Formalism Cleber Valgas Gomes Mira1, João Meidanis2 1cleber@ic.unicamp.br, Institute of Computing - State University of Campinas (UNICAMP); 2meidanis@scylla.com.br, Scylla Bioinformatics Abstract |
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B5 An Integrated Tool for Investigating Genetic Disorder-Relevant Tandem Repeats in Human Genome Feng-Mao Lin1, Ming-Yu Chen2, Hsien-Da Huang , Jorng-Tzong Horng 1meta@db.csie.ncu.edu.tw, Department of Computer Science and Information Engineering, National Central University; 2puenny@db.csie.ncu.edu.tw, Department of Computer Science and Information Engineering, National Central University Abstract |
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B6 Search Space Reduction via Clustering for Haplotype Reconstruction Jinghua Hu1, Weibo Gong2, Patrick A. Kelly 1jhu@ecs.umass.edu, Univ. of Massachusetts at Amherst; 2gong@ecs.umass.edu, Univ. of Massachusetts at Amherst Abstract |
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B7 Reconstructing Phylogenetic Trees from Dissimilarity Maps Dan Levy1, Francis E. Su2, Ruriko Yoshida 1levyd@math.berkeley.edu, University of California at Berkeley; 2su@math.hmc.edu, Harvey Mudd College Abstract |
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B8 Global optimization in QTL analysis Kajsa Ljungberg1, Sverker Holmgren2, Örjan Carlborg 1kajsa.ljungberg@it.uu.se, Uppsala University; 2sverker.holmgren@it.uu.se, Uppsala University Abstract |
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B9 The Portable Cray Bioinformatics Library James Long1 1jlong@arsc.edu, Arctic Region Supercomputing Center Abstract |
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Computational proteomics |
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C1 BOMP: a program to predict integral beta-barrel outer membrane proteins encoded within genomes of Gram-negative bacteria Frode S. Berven1, Kristian Flikka2, Harald B. Jensen, Ingvar Eidhammer 1frodeb@ii.uib.no, University of Bergen; 2flikka@ii.uib.no, Computational Biology Unit Abstract |
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C10 Tandem MS Analysis and An Emerging Genome: The Sea Urchin Sperm Plasma Membrane Proteome Anna T. Neill1, Terry Gaasterland2, John R. Yates III, Victor D. Vacquier 1aneill@ucsd.edu, SIO/UCSD; 2gaasterl@genomes.rockefeller.edu, The Rockefeller University Abstract |
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C11 Characterizing protein function by integrating interaction data and domain information Kinya Okada1, Md. Altaf-Ul-Amin2, Hirotada Mori , Shigehiko Kanaya , Kiyoshi Asai 1kinya-o@is.aist-nara.ac.jp, NAIST; 2amin-m@is.aist-nara.ac.jp, NAIST Abstract |
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C12 THE ENCYCLOPEDIA OF LIFE: A NEW WEB RESOURCE FOR DOMAIN-BASED PROTEIN ANNOTATION DATA Greg Quinn1, Mark Miller2, Kim Baldridge, Ilya Shindyalov, Wilfred Li, Dmitry Pekurovsky, Robert W Byrnes, Kristine Briedis, Vicente Reyes, Adam Birnbaum, Coleman Mosley, Yohan Potier, Celine Amoreira , Julia Ponomarenko, Stella Veretnik ; Philip E. Bourne, 1quinn@sdsc.edu, San Diego Supercomputer Center; 2mmiller@sdsc.edu, San Diego Supercomputer Center Abstract |
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C13 Support Vector Machine approach to Active Sites Prediction using Local Sequence Information. Dariusz Plewczynski1, Leszek Rychlewski2, Adrian Tkacz 1darman@bioinfo.pl, BioInfoBank Institute; 2leszek@bioinfo.pl, BioInfoBank Institute Abstract |
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C14 Mechanisms for Antagonistic Regulation of AMPA and NMDA-D1 Receptor Complexes at Postsynaptic Sites Gabriele Scheler1, Johann Schumann2 1scheler@stanford.edu, ISLE; 2schumann@email.arc.nasa.gov, RIACS/NASA Abstract |
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C15 Do Sense-Antisense Proteins Really Interact? Ruchir R. Shah1, Todd J. Vision2, Alexander Tropsha 1ruchir@email.unc.edu, UNC-CH; 2tjv@biomass.bio.unc.edu, UNC-CH Abstract |
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C16 Predicting Co-Complexed Protein Pairs Using Genomic and Proteomic Data Integration Lan V. Zhang1, Sharyl L. Wong2, Oliver D. King and Frederick P. Roth 1lan_zhang@student.hms.harvard.edu, Harvard Medical School; 2sharyl_wong@student.hms.harvard.edu, Harvard Medical School Abstract |
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C17 Structal: A software for optimizing structural and sequence alignments Herve Seligmann1, Neeraja M. Krishnan2 1hselig1@lsu.edu, Louisiana State Univ.; 2nkrish2@lsu.edu, Louisiana State Univ. Abstract |
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C18 An alternative to the SEQUEST cross-correlation scoring algorit
hm for tandem spectra identification through database lookup: the Luck
measuring scoring function, and the probability of an unrelated spectra match model Tema Fridman1, Jane Razumovskaya2, Nathan VerBerkmoes, Greg Hurst and Ying Xu 1tfa@ornl.gov, UT/ORNL; 2rzw@ornl.gov, UT Abstract |
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C19 Cross-species Peptide Mass Fingerprinting Database Searching And Conserved-Domains Heming Xing1 1heming.xing@dds.criver.com, Charles River Proteomic Services Abstract |
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C2 Motif Finding and Multiple Alignment through Vector-Space Embedding of Protein Sequences Arnab Bhattacharya1, Tamer Kahveci2, Ambuj K. Singh 1arnab@cs.ucsb.edu, University of California, Santa Barbara; 2tamer@cs.ucsb.edu, University of California, Santa Barbara Abstract |
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C3 Long-Duration Molecular Dynamics Simulation on Constructed Nacrein Structure Frank Chang1, Samson Cheung2, Ming Wong, Cathy Bitler, Andrew Palma 1ftchang@changene.com, Changene Inc.; 2cheung@nas.arc.nasa.gov, NASA Advanced Supercomputing Division, Ames Research Center Abstract |
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C4 Gene Finding With Proteomic Data Kristen Dang1, Michael Giddings2, Edward Collins 1kamerath@email.unc.edu, University of North Carolina; 2giddings@unc.edu, University of North Carolina Abstract |
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C5 A Unified Representation of Multi-Protein Complex Data for Modeling Interaction Networks Chris Ding1, Xiaofeng He2, Richard F. Meraz, Stephen R. Holbrook 1chqding@lbl.gov, Lawrence Berkeley National Lab; 2xhe@lbl.gov, Lawrence Berkeley National Lab Abstract |
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C7 Which pathways cannot be reconstructed using protein phylogenetic profiles? Yohan Kim1, Shankar Subramaniam2 1ykim@ucsd.edu, Dept. of Chem.&Biochem., UCSD; 2shankar@sdsc.edu, Dept. of Bioeng., Chem.&Biochem., UCSD Abstract |
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C8 The Protein Mutant Resource: Visual and Statistical Analysis of Mutation with Implications for Homology Modeling Werner G. Krebs1, Philip E. Bourne2 1wkrebs@sdsc.edu, UCSD; 2bourne@sdsc.edu, UCSD Abstract |
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C9 OrthoMCL: application of a graph cluster algorithm to comparative genomics and genome annotation Li Li1, Christian J. Stoeckert2, David S. Roos 1lili4@sas.upenn.edu, Univerity of Pennsylvania; 2stoeckrt@pcbi.upenn.edu, University of Pennsylvania Abstract |
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Gene expression |
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D10 Stochastic Models Inspired by Hybridization Zhijin Wu1, Rafael Irizarry2, oligonucleotide arrays, expression measure, empirical Bayes 1zwu@jhsph.edu, Johns Hopkins University; 2rafa@jhu.edu, Johns Hopkins University Abstract |
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D12 ESTmapper: Efficiently Clustering EST Sequences Using Genome Maps Xue Wu1, Woei-Jyh (Adam) Lee2, Damayanti Gupta, Chau-Wen Tseng 1wu@cs.umd.edu, University of Maryland at College Park; 2adamlee@cs.umd.edu, University of Maryland at College Park Abstract |
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D2 GOMER: Predicting Gene Regulation by Modeling Binding Sites Joshua A. Granek1, Neil D. Clarke2 1jgranek@jhmi.edu, Johns Hopkins University, School of Medicine; 2nclarke@jhmi.edu, Johns Hopkins University, School of Medicine Abstract |
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D3 Discovery of Tumor-Specific Alternative Splicing Sites Fang Rong Hsu1, Chia Yang Cheng2 1frhsu@thmu.edu.tw, Department of Bioinformatics, Taichung Healthcare and Mangement University; 2std91242006@ms1.thmu.edu.tw, Department of Bioinformatics, Taichung Healthcare and Mangement University Abstract |
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D4 Adaptive evolution of E. coli on lactate leads to convergent, generalist phenotypes AndrewR. Joyce1, Stephen S. Fong2, Bernhard O. Palsson 1ajoyce@ucsd.edu, UCSD; 2ssfong@ucsd.edu, UCSD Abstract |
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D5 Principal Component Analysis combined with probabilistic analysis of Gene Ontology as applied to neuroblastoma gene expression data Alexei L. Krasnoselsky1, Jun Wei2, Sven Bilke, Quinrong Chen, Craig Whiteford and Javed Khan 1krasnosa@mail.nih.gov, National Cancer Institute, National Institutes of Health; 2weij@mail.nih.gov, National Cancer Institute, National Institutes of Health Abstract |
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D6 Discretization Methods for Expression Data Sonia Leach1 1sml@cs.brown.edu, Brown Univ and Univ of CO Abstract |
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D7 Suitability of Spherical SOM for Gene Expression Analysis Hirokazu Nishio1, Ken-nosuke Wada, Yoshiko Wada, Md. Altaf-Ul-Amin, Shigehiko Kanaya 1hiroka-n@is.aist-nara.ac.jp, NAIST Abstract |
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D8 In Silico Identification and Analysis of Tissue-Specific Genes using the Database of Human Expressed Sequence Tags Sheng-Ying Pao 1, Ming-Jing Hwang 2, Win-Li Lin 1r91548018@ntu.edu.tw, Institute of Biomedical Engineering, National Taiwan University College of Medicine; 2mjhwang@ibms.sinica.edu.tw, Institute of Biomedical Sciences, Academia Sinica Abstract |
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D9 Regulation of NF-kappaB responsive genes in a single cell Pawel Paszek1, Tomasz Lipniacki2, A. Brasier, B. Tian, B. Luxon, M. Kimmel 1ppaszek@rice.edu, Rice University; 2tomek@rice.edu, Rice University Abstract |
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Gene networks |
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E1 Improving Extreme Pathway Computations Steven L. Bell1, Bernhard O. Palsson2 1sbell@ucsd.edu, University of California, San Diego, Dept. of Bioengineering; 2bpalsson@bioeng.ucsd.edume, University of California, San Diego, Dept. of Bioengineering Abstract |
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E10 Linkage by context: Discovering functional linkages between proteins from their known interactions Insuk Lee1, Edward Marcotte2 1lee-micro@mail.utexas.edu, University of Texas; 2marcotte@icmb.utexas.edu, University of Texas Abstract |
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E11 Learning Context-sensitive Boolean Network from Steady-state Observations and Its Analysis Huai Li1, Jon Whitmore2, Edward Suh, Michael Bittner, Seungchan Kim 1hli@tgen.org, Translational Genomics Research Institute; 2jwhitmore@tgen.org, Translational Genomics Research Institute Abstract |
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E12 Stochastic regulation of NF-kappaB pathway Tomasz Lipniacki1, Pawel Paszek2, A. Brasier, B Luxon, M. Kimmel 1tomek@rice.edu, Rice University; 2ppaszek@rice.edu, Rice University Abstract |
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E13 Probabilistic Representation of Gene Regulatory Networks Linyong Mao1, Haluk Resat2 1linyong.mao@pnl.gov , Pacific Northwest National Laboratory; 2haluk.resat@pnl.gov, Pacific Northwest National Laboratory Abstract |
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E14 Non-exclusive Gene Groupings using SVD: A Critical Approach Subashini Ramalingam1, Rajagopalan Srinivasan2, Jonnalagadda Sudhakar 1eng02122@nus.edu.sg, National University of Singapore; 2chergs@nus.edu.sg, National University of Singapore Abstract |
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E15 Vector PathBlazer 1.0: A New Pathway Analysis And Visualization Tool Feodor Tereshchenko1, Valeriy Reshetnikov2, Artur Karpov, David Pot 1feodor@informaxinc.com, Invitrogen; 2resh@informaxinc.com, Invitrogen Abstract |
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E16 Simulation mammalian molecular circadian oscillators by dynamic gene network Yanhong Tong1, Hava Sieglemann2, NA 1ytong@cs.umass.edu, University of Massachusetts at Amherst; 2hava@cs.umass.edu, University of Massachusetts at Amherst Abstract |
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E18 The EcoTFs Web Site: Escherichia Coli Transcription Factors and Signals William S. Hlavacek1, Michael L. Blinov2, Michael A. Savageau, Michael E. Wall 1wish@lanl.gov, Los Alamos National Laboratory; 2mblinov@lanl.gov, Los Alamos National Laboratory Abstract |
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E19 Discovering Activated Regulatory Networks
in the DNA Damage Response Pathways of Yeast Chris Workman1, Scott McCuine2, Ryan Kelley, Trey Ideker 1cworkman@bioeng.ucsd.edu, UCSD; 2scott@bioeng.ucsd.edu, UCSD Abstract |
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E2 Analysis of Heterogeneous Regulation in Biological Networks. Irit Gat-Viks1, Amos Tanay2, Ron Shamir 1iritg@post.tau.ac.il, Tel-Aviv University; 2amos@post.tau.ac.il, Tel-Aviv University Abstract |
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E20 Parallel Data Mining of Bayesian Networks from Gene Expression Data Longde Yin1, Chun-Hsi Huang2, Sanguthevar Rajasekaran 1yin@engr.uconn.edu, Dept of Computer Science, University of Connecticut; 2 huang@engr.uconn.edu, Dept of Computer Science, University of Connecticut Abstract |
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E21 Discovery of Gene-Regulation Pathways in Mouse Asbestos Using Background Knowledge Changwon Yoo1, Mark Pershouse2, Elizabeth Putnam 1cwyoo@cs.umt.edu, University of Montana; 2markp@selway.umt.edu, University of Montana Abstract |
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E22 On Some Choices in Bayesian Network Learning for Reconstructing Regulatory Networks Xuesong Lu1, Xing Wang2, Ying Huang, Wei Hu, Yanda Li, Xuegong Zhang 1lxs97@mails.tsinghua.edu.cn, Tsinghua University; 2xwang@mail.eecis.udel.edu, University of Deleware Abstract |
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E23 PathBLAST Silpa Suthram1, Taylor Sittler2, Trey Ideker 1ssuthram@ucsd.edu, UCSD; 2tsittler@be-research.ucsd.edu, UCSD Abstract |
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E24 Learning kernels from biological networks by maximizing entropy Koji Tsuda1, William Stafford Noble2 1koji.tsuda@tuebingen.mpg.de, Max Planck Institute for Biological Cybernetics; 2noble@gs.washington.edu, University of Washington Abstract |
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E3 CAMP - a computational system for Comparative Analysis of Metabolic Pathways Chun-Yu Chen1, Chuan-Hsiung Chang2 1cyc@gel.ym.edu.tw, Bioinformatics Program, Institute of Health Informatics and Decision Making, National Yang-Ming University; 2cchang@ym.edu.tw, Institute of Bioinformatics, National Yang-Ming University Abstract |
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E4 Converting KEGG pathway database to SBML Akira Funahashi1, Akiya Jouraku2, Hiroaki Kitano 1funa@symbio.jst.go.jp, ERATO-SORST Kitano Symbiotic Systems Project, JST, Japan; 2jouraku@am.ics.keio.ac.jp, Graduate School of Science and Technology, Keio University, Japan. Abstract |
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E6 An Integrated Platform to Construct Transcriptional Network from Gene Expression Data Tao-Wei Huang1, Hwa-Sheng Chiu2, Ming-Hong Lin, Han-Yu Chuang, Chi-Ying F. Huang, Cheng-Yan Kao 1d90016@csie.ntu.edu.tw, Department of Computer Science and Information Engineering, National Taiwan University; 2r91031@csie.ntu.edu.tw, Department of Computer Science and Information Engineering, National Taiwan University Abstract |
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E7 Path Finding and Topology Correction in Biological Networks Ryan Kelley1, Astrid Haugen2, Bennet Van Houten, Trey Ideker 1rmkelley@ucsd.edu, Department of Bioinformatics, UCSD; 2haugen@niehs.nih.gov, Laboratory of Molecular Genetics, NIEHS Abstract |
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E8 Predicting cis-Regulatory Elements and Regulatory Networks Stefan Kirov1, Bing Zhang2, Denise Schmoyer, Oakley Crawford, Jay Snoddy 1skirov@utk.edu, UT/ORNL; 2bhzang@utk.edu, UT/ORNL Abstract |
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E9 Towards Automated Explanation of Gene-Gene Relationships Waclaw Kusnierczyk1, Agnar Aamodt2, Astrid Lægreid 1waku@idi.ntnu.no, NTNU; 2agnar@idi.ntnu.no, NTNU Abstract |
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Genomics |
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F1 Phylogeny of Tumor Progression from CGH Data Sven Bilke1, Qingrong Chen2, Javed Khan 1bilkes@mail.nih.gov, NIH; 2chenqi@mail.nih.gov, NIH Abstract |
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F10 Combinatorial chemistry discriminating analysis of complex microbial systems with restricted site tags (RST) Alexey Kutsenko1, Veronika Zabarovska2, Lev Petrenko, Tore Midtvedt, Ingemar Ernberg, Eugene R. Zabarovsky 1Alexey.Kutsenko@mtc.ki.se, Microbiology and Tumor Biology Center, Karolinska Institute; 2verzab@ki.se, Microbiology and Tumor Biology Center, Karolinska Institute Abstract |
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F11 Aligning Optical Maps Yu-Chi Liu1, Michael S. Waterman2, Anton Valouev, Lei Li, Yu Zhang, Yi Yang, Jong-Hyun Kim, David C. Schwartz 1ycliu@usc.edu, Program of Molecular and Computational Biology, University of Southern California; 2msw@usc.edu, Program of Molecular and Computational Biology, University of Southern California Abstract |
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F12 Unsupervised Learning of Biological Sequences and Its Applications in Genomic DNA Sequence Annotation Jing Liu1, L. Ridgway Scott2, John Goldsmith 1jliu@cs.uchicago.edu, University of Chicago; 2ridg@cs.uchicago.edu, University of Chicago Abstract |
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F13 Characterization of Retroid Agents in the Human Genome: An Automated Approach Marcella A. McClure1, Rochelle A. Clinton2, Hugh S. Richardson, Vijay A. Raghavan, Crystal M. Hepp, Brad A. Crowther, Angela K. Olsen, Eric F. Donaldson, Aaron R. Juntunen 1mars@parvati.msu.montana.edu, Montana State University; 2rochelle@parvati.msu.montana.edu, Montana State University Abstract |
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F14 MGAW : a Microbial Genome Annotation Workbench under Web-based Analysis Interface Hwajung Seo1, Hyeweon Nam2, Daesang Lee , Hongseok Tae, Kiejung Park 1hjseo@smallsoft.co.kr , SmallSoft Co., Ltd.; 2hwnam@smallsoft.co.kr , SmallSoft Co., Ltd. Abstract |
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F15 A Bioinformatics Approach Toward Identification of Genes involved in Hematopoiesis and Leukemia Twyla T. Pohar1, Hao Sun2, Sandya Liyanarachchi, S. James S. Stapleton, Ramana V. Davuluri 1pohar-2@medctr.osu.edu, The Ohio State University; 2sun.143@osu.edu, The Ohio State University Abstract |
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F16 The complete genome sequence of Rickettsia typhi and comparison with other rickettsial genomes Xiang Qin1, Michael P. McLeod2, Sandor E. Karpathy, Jason Gioia , Sarah K. Highlander, George E. Fox, Thomas Z. McNeill, Huaiyang Jiang, Donna Muzny, Leni S. Jacob, Alicia C. Hawes, Erica Sodergren, Anita G. Amin, Rachel Gill, Jennifer Hume, Maggie Morgan, Guangwei Fan, Richard A. Gibbs, Chao Hong, Xue-jie Yu, David H. Walker, George M. Weinstock 1xiangq@bcm.tmc.edu, Baylor College of Medicine, Human Genome Sequencing Center; 2mmcleod@bcm.tmc.edu, Baylor College of Medicine, Human Genome Sequencing Center Abstract |
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F17 Providing an automatically derived high quality immunoglobulin V gene sequence database Ida Retter1, Werner Muller2 1ida.retter@gbf.de, German Research Centre for Biotechnology; 2wmueller@gbf.de, German Research Centre for Biotechnology Abstract |
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F18 The role of pre-mRNA secondary structure in splicing of Saccharomyces cerevisiae Sanja Rogic1, Holger H. Hoos2, B.F. Francis Ouellette, Alan K. Mackworth 1rogic@cs.ubc.ca, Department of Computer Science, UBC; 2hoos@cs.ubc.ca, Department of Computer Science, UBC Abstract |
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F19 e2g - A Web-Based Tool for Efficiently Aligning Genomic Sequence to EST and cDNA data Alexander Sczyrba1, Jan Krueger2, Robert Giegerich 1asczyrba@techfak.uni-bielefeld.de, Bielefeld University; 2jkrueger@techfak.uni-bielefeld.de, Bielefeld University Abstract |
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F2 Human transcript clustering Ronghua Chen1, Archie Russell2, Guoya Li, Nicholas Tsinoremas, Guy Cavet 1ronghua_chen@merck.com, Rosetta Inpharmatics, Merck &Co. Inc.; 2archie_russell@merck.com, Rosetta Inpharmatics, Merck &Co. Inc. Abstract |
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F20 LinkageView: a powerful graphical tool for integrating statistical data with the Ensembl Genome Browser Judith E. Stenger 1, HongXu2, Carol Haynes, Jeffery M. Vance, Margaret Pericak-Vance, and Elizabeth R. Hauser. 1jstenger@chg.duhs.duke.edu, Duke University Medical Center; 2hxu@chg.duhs.duke.edu, Duke University Medical Center Abstract |
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F21 HMM-based System for Identification of Related Gene/Protein Names L. Yeganova1, L. Smith2, W. J. Wilbur 1yeganova@ncbi.nlm.nih.gov, NIH; 2lsmith@ncbi.nlm.nih.gov, NIH Abstract |
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F23 A New Tool for Enumerative Combinatorics? James Nulton1, Ben Felts2, J. Mahaffy, M. Breitbart, B. Rodriguez Brito, D. Bangor, F. Rohwer, and P. Salamon 1jnulton@mail.sdsu.edu, San Diego State University; 2ben.felts@conexant.com, San Diego State University Abstract |
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F3 Massively Parallel DNA Sequencing using Single Molecule Array Technology Anthony J. Cox1 1anthony.cox@solexa.com, Solexa Limited Abstract |
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F4 Clann: Software for phylogenomic investigation and analysis of horizontal gene transfer using supertrees Christopher Creevey1, James McInerney2 1chris.creevey@may.ie, National University of Ireland, Maynooth; 2chris.creevey@may.ie, National University of Ireland, Maynooth Abstract |
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F5 Monte Carlo Estimation and Graphical Analysis of Likelihood Landscapes (of the Population Structure of Shotgun Libraries) Ben Felts1, James Nulton2, Joe Mahaffy, Peter Salamon, Forest Rohwer, Mya Breitbart, Beltran Rodriguez Brito, David Bangor 1bfelts@myth.sdsu.edu, Department of Mathematical Sciences, San Diego State University; 2jnulton@mail.sdsu.edu, Department of Mathematical Sciences, San Diego State University Abstract |
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F6 Using local alignment to discern haplotypes from optical maps Steve Goldstein1, Susan Reslewic2, Scott Kohn, David C. Schwartz 1steveg@lmcg.wisc.edu, University of Wisconsin-Madison; 2susan@lmcg.wisc.edu, University of Wisconsin-Madison Abstract |
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F7 Bayesian Inference of Protein Function Using Homology, Pathway, and Operon Data Michelle L. Green1, Peter D. Karp2 1green@ai.sri.com, Bioinformatics Research Group, SRI International; 2pkarp@ai.sri.com, Bioinformatics Research Group, SRI International Abstract |
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F8 A Novel Method to speed up Multiple-Use PCR Primer Design Yu-Cheng Huang1, Huai-Kuang Tsai2, Han-Yu Chuang, Chun-Fan Chang, Cheng-Yan Kao 1r91021@csie.ntu.edu.tw, Bioinfo Lab., Computer Science and Information Engineering Department, National Taiwan University; 2d7526010@csie.ntu.edu.tw, Bioinfo Lab., Computer Science and Information Engineering Department, National Taiwan University Abstract |
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F9 Building a Laboratory Information Management System for FP-TDI Genotyping Research Daniel C. Koboldt1, Pui-Yan Kwok2, Raymond D. Miller 1dkoboldt@psts.wustl.edu, Washington University School of Medicine; 2kwok@cvrimail.ucsf.edu, University of California, San Francisco Abstract |
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Methods |
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N1 Evaluation of a New Algorithm for Keyword-Based Functional Clustering of Genes Ying Liu1, Brian J. Ciliax2, Alex Pivoshenko, Jorge Civera, Venu Dasigi , Ashwin Ram, Ray Dingledine, Shamkant B. Navathe 1yingliu@cc.gatech.edu, Georgia Institute of Technology; 2bciliax@emory.edu, Emory University Medical School Abstract |
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N10 Motif Preservation in Biochemical Pathways Zachary Saul1, Vladimir Filkov2 1saul@cs.ucdavis.edu, UC Davis; 2filkov@cs.ucdavis.edu, UC Davis Abstract |
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N2 A web-based approach to bio-informatics tool integration using MVC design pattern Sean Huang1, Lang-Yang Ch'ang2, Wen-Chang Lin , Chung-Shyan Liu 1g9177029@cycu.edu.tw , Chung Yuan C. University; 2 lychang@ibms.sinica.edu.tw, Academia Sinica Abstract |
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N3 Computational analysis of homologous chromosome pairing in fission yeast Mineo Morohashi1, Ding Da-Qiao2, Ayumu Yamamoto, Yasushi Hiraoka, Shuichi Onami, Hiroaki Kitano 1moro@symbio.jst.go.jp, ERATO-SORST Kitano Symbiotic Systems Project, JST; 2ding@crl.go.jp, CREST Research Project, Kansai Advanced Research Center, Communications Research Laboratory Abstract |
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N4 Primary Human Hepatocytes – A Suitable Tool in Systems Biology Runge, D.1, Koczan, D.2, Haase, D., Christoph, H., Lorenz, P., Kohlschein, P., Schuff-Werner, P., Glocker, M.O., Thiesen, H.-J. 1dieter.j.runge@web.de, Institute of Immunology; 2dirk.koczan@med.uni-rostock.de, Institute of Immunology Abstract |
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N5 GO trees: Predicting GO associations from protein domain composition using decision trees Boris Hayete1, Jadwiga Bienkowska2 1theboris@bu.edu, Boston University; 2jadwiga.bienkowska@serono.com, Serono Reproductive Biology Institute Abstract |
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N6 Development of an Integrated LIMS for Microarray Facility Center Jianchang Ning1 1ning@dbi.udel.edu, University of Delaware Abstract |
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N7 Cooperative Biomedical Knowledge Inference Chun-Hsi Huang1, Sanguthevar Rajasekaran2, Longde Yin 1huang@cse.uconn.edu, Uniuversity of Connecticut; 2rajase@cse.uconn.edu, University of Connecticut Abstract |
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N8 A property-based model for lung cancer diagnosis Alma Barranco-Mendoza1, Deryck R. Persaud2, Veronica Dahl 1abm@cs.sfu.ca, School of Computing Sc., Simon Fraser University; 2deryck@infogenetica.com, Infogenetica Bioinformatics Abstract |
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Microarray design and data analysis |
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G1 A Latent Process Decomposition Model for Interpreting cDNA Microarray Datasets Simon Rogers1, Mark Girolami2, Colin Campbell 1Simon.Rogers@bris.ac.uk, Bristol University; 2girolami@dcs.gla.ac.uk, Glasgow University Abstract |
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G10 Genome-wide statistical analysis of gene coexpression: application to GATA transcription factors in Arabidopsis thaliana Chih-hung Jen1, David Robert Westhead2 1bmbcj@bmb.leeds.ac.uk, Bioinformatics Research group, School of Biochemistry and Molecular Biology, University of Leeds; 2D.R.Westhead@leeds.ac.uk, Bioinformatics Research group, School of Biochemistry and Molecular Biology, University of Leeds Abstract |
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G11 Using the Human Genome as a Framework for Sequence Clustering and Microarray Design Barbara Lin1, Tim Burcham2 1blin@diadexus.com, diaDexus, Inc; 2tburcham@diadexus.com, diaDexus, Inc Abstract |
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G12 Programs for the Inference and Analysis of Gene Influence Networks Gary Livingston1, Liwu Hao2, Guangyi Li, Xiao Li 1gary@cs.uml.edu, University of Massachusets Lowell; 2lhao@cs.uml.edu, University of Massachusetts Lowell Abstract |
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G13 Analysis of Microarray Time Course Data Tanya Logvinenko1, David Schoenfeld, Douglas Hayden 1tlogvinenko@partners.org, MGH Abstract |
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G14 GOArray: Interpreting microarrays with GODB Michael V Osier1, David Tuck2, Kevin P. White, Christopher E. Mason, Hongyu Zhao, Kei-Hoi Cheung 1michael.osier@yale.edu, Yale University; 2david.tuck@yale.edu, Yale University Abstract |
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G15 SVM Model Selection for Microarray Classification David A. Peterson1 1petersod@cs.colostate.edu, Department of Computer Science Abstract |
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G16 Stability Analysis of Gene Expression Data Pickl, Stefan1, Wuenschiers2, Gebert, Laetsch, Radde, Veroff, Wünschiers 1pickl@zpr.uni-koeln.de, UNM; 2robbe.wunschiers@uni-koeln.de Abstract |
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G17 Non-Unique Probe Selection by Matrix Condition Optimization Sven Rahmann1, Tobias Müller2, Martin Vingron 1Sven.Rahmann@molgen.mpg.de, {Max Planck Institute for Molecular Genetics; 2Tobias.Mueller@biozentrum.uni-wuerzburg.de, Biozentrum, Universität Würzburg Abstract |
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G18 Incorporation of Target RNA Secondary Structure Parameter into Synthetic Oligomer Probe Design Vladyslava G. Ratushna1, Jennifer W. Weller2, Cynthia J. Gibas 1vratushn@vt.edu, Virginia Polytechnic Institute and State University; 2jweller@gmu.edu, George Mason University Abstract |
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G19 Identification of Transcribed Differentiating Genes in Brucella abortus, B.melitensis and B.suis Vladyslava G. Ratushna1, David M. Sturgill2, Sheela Ramamoorthy, Sherry A. Poff, Nammalwar Sriranganathan, Stephen M. Boyle, Cynthia J. Gibas 1vratushn@vt.edu, Virginia Polytechnic Institute and State University; 2dsturgil@vt.edu, Virginia Polytechnic Institute and State University Abstract |
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G20 MeSH Key Terms for Validation and Annotation of Gene Expression Clusters Andreas Rechtsteiner1, Luis M Rocha2 1andreas@lanl.gov, CCS-3, Los Alamos National Laboratory; 2rocha@lanl.gov, CCS-3, Los Alamos National Laboratory Abstract |
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G21 Evaluation of Statistical Methods for cDNA Microarray Differential Expression Analysis Wei Sha1, Keying Ye2, Pedro Mendes 1wsha@vt.edu, Virginia Bioinformatics Institute, Virginia Polytechnic Institute and State University; 2keying@vt.edu, Dept. of Statistics, Virginia Polytechnic Institute and State University Abstract |
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G22 How Noisy are DNA Microarray Data? Suman Sundaresh1, She-pin Hung2, G. Wesley Hatfield, Pierre Baldi 1suman@uci.edu, University of California, Irvine; 2shung@uci.edu, University of California, Irvine Abstract |
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G23 Identification of transcriptional programs along defined stages of human carcinogenesis Yuval Tabach1, Michael Milyavsky2, Zuk O, Shats I, Erez N, Tang X, Goldfinger N, Ginsberg D, Pilpel T, Domany E, Rotter V 1yuval.tabach@weizmann.ac.il, Weizmann; 2, Weizmann Abstract |
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G24 Tight clustering: a method for extracting stable and tight patterns in expression profiles George C. Tseng1, Wing H. Wong2 1ctseng@pitt.edu, University of Pittsburgh; 2wwong@hsph.harvard.edu, Harvard University Abstract |
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G25 A Method for 3D visualization of Microarray Data L. G. Volkert1, M. Tamboli2, P. Siddula, J. I. Maletic 1volkert@cs.kent.edu, Department of Computer Science, Kent State University; 2mtamboli@cs.kent.edu, Department of Computer Science, Kent State University Abstract |
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G26 A Robust, Noise-Insensitive Variable Selection Algorithm for Molecular Profiling Data Michael Wagner1, Zhongming Yang2 1mwagner@cchmc.org, Cincinnati Children's Hospital Research Foundation; 2zhongming.yang@cchmc.org, Cincinnati Children's Hospital Research Foundation Abstract |
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G27 Finding biclusters in gene expression data by random projection Stefano Lonardi1, Wojciech Szpankowski2, Qiaofeng Yang 1stelo@cs.ucr.edu, University of California, Riverside; 2spa@cs.purdue.edu, Purdue Univeristy Abstract |
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G28 gMap: extracting and interactively visualizing nonlinear relationships of genes from expression Chaolin Zhang1, Yanda Li2, Xuegong Zhang 1zcl98@mails.tsinghua.edu.cn, Tsinghua University; 2daulyd@tsinghua.edu.cn, Tsinghua University Abstract |
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G29 Efficient Selection of Unique and Popular Oligos for Large EST Databases JIE ZHENG1, TIMOTHY J. CLOSE2, TAO JIANG, STEFANO LONARDI 1ZJIE@CS.UCR.EDU, UC, RIVERSIDE; 2TIMOTHY@UCR.EDU, UC, RIVERSIDE Abstract |
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G3 Discovering Statistically Significant Clusters by Using Genetic Algorithms in Gene Expression Data Hwa-Sheng Chiu1, Han-Yu Chuang2, Huai-Kuang Tsai, Tao-Wei Huang, Cheng-Yan Kao 1r91031@csie.ntu.edu.tw, Dept of CSIE, NTU; 2r90002@csie.ntu.edu.tw, Dept of CSIE, NTU Abstract |
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G30 Gene Co-regulation vs. Co-expression Ya Zhang1, Hongyuan Zha2, James Z. Wang3, Chao-Hsien Chu4 1yzz100@psu.edu, PSU; 2zha@cse.psu.edu, PSU; 3jwang@ist.psu.edu; 4chu@ist.psu.edu Abstract |
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G31 Deconvolution of cDNA Microarray Images and Significance Testing for Gene Expression Levels Hye Young Kim1, Min Jung Kim2, Yong Sung Lee, Young Seek Lee, Tae Sung Park, Ki Woong Kim, and Jin Hyuk Kim 1hykim121@hanyang.ac.kr, Hanyang University; 2midung@hanyang.ac.kr, Hanyang University Abstract |
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G32 A New HMM-based Clustering Technique for the Analysis of Gene Expression Time Series Data Yujing Zeng1, Javier Garcia-Frias2 1zeng@ee.udel.edu, University of Delaware; 2jgarcia@ee.udel.edu, University of Delaware Abstract |
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G33 A Novel HMM-based Cluster Validity Index for Gene Expression Time-Course Data Yujing Zeng1, Javier Garcia-Frias2 1zeng@ee.udel.edu, University of Delaware; 2jgarcia@ee.udel.edu, University of Delaware Abstract |
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G34 Clustering of Time-Course Gene Expression Data Ya Zhang1, Hongyuan Zha2, James Z. Wang3, Chao-Hsien Chu4 1yzz100@psu.edu, PSU; 2zha@cse.psu.edu, PSU; 3jwang@ist.psu.edu; 4chu@ist.psu.edu Abstract |
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G35 Improving temporal gene expression profiles with probabilistic modes. Marta Milo1, Neil Lawrence2, M.C. Holley, M. Rattray and M. Niranjan 1M.Milo@sheffield.ac.uk, University of Sheffield, UK; 2neil@dcs.shef.ac.uk, University of Sheffield,UK Abstract |
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G4 J-Express - an integrated tool for processing and analyzing microarray gene expression data Bjarte Dysvik1, Kjell Petersen, Inge Jonassen, Trond Hellem Bø, Kristin Sandereid 1bjarted@ii.ui.no, Institutt for informatikk, University of Bergen Abstract |
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G5 Sorting Points Into Neighborhoods (SPIN): a novel data organization and visualization tool Ilan Tsafrir1, Liat Ein-Dor2, Dafna Tsafrir, Or Zuk and Eytan Domany 1Ilan.tsafrir@weizmann.ac.il, Department of Complex Systems, Weizmann Institute of Science, Rehovot 76100, Israel; 2liat.ein-dor@weizmann.ac.il, Department of Complex Systems, Weizmann Institute of Science, Rehovot 76100, Israel Abstract |
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G6 Reproducibility, Variance Stabilization, and Normalization in CodeLink Data with Application to Cancer in Rats Sue Geller1, David M. Rocke2, Danh Nguyen, Raymond Carroll 1geller@math.tamu.edu, Texas A&M University; 2dmrocke@ucdavis.edu, University of California, Davis Abstract |
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G7 ChipQC: Microarray Artifact Visualization Tool Peter A. Henning1, Paul K. Tan2, Tung Yu Chu, David A. Stiles, David Wheeler, Pushkar Mukewar, Margaret C. Cam, and May D. Wang 1gtg841j@mail.gatech.edu, The Wallace H. Coulter Biomedical Engineering Department, Georgia Tech and Emory University; 2MaggieC@intra.niddk.nih.gov, University of Hawaii, NIDDK Abstract |
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G8 A Database Aiding Probe Design System for Virus Identification Feng-Mao Lin1, Pak-Leong Chan2, Yu-Chung Chang , Hsien-Da Huang , Jorng-Tzong Horng 1meta@db.csie.ncu.edu.tw, Department of Computer Science and Information Engineering, National Central University; 2leong@db.csie.ncu.edu.tw, Department of Computer Science and Information Engineering, National Central University Abstract |
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G9 Quickly Choosing Choice SNPs for Chips Earl Hubbell1, Teresa Webster2, Hajime Matsuzake 1hubbell_earl@affymetrix.com, Affymetrix,Inc.; 2webster_teresa@affymetrix.com, Affymetrix,Inc Abstract |
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Molecular evolution |
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H1 Approximating geodesic tree distance Nina Amenta1, Matthew Godwin2, Katherine St. John 1amenta@cs.ucdavis.edu, UC Davis; 2mjgodwin@ucdavis.edu, UC Davis Abstract |
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H10 Alu Clustering in the Human Genome: Origins and Consequences Hackenberg Michael1, Oliver José2 1genmol@ugr.es, Universidad de Granada; 2oliver@ugr.es, Universidad de Granada Abstract |
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H11 Pruned PDM Method for Detecting Recombination Dirk Husmeier1 1dirk@bioss.ac.uk, Biomathematics & Statistics Scotland Abstract |
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H12 Phylogenetic analyses detect site-specific perturbations in asymmetric mutation gradients in primate mitochondria Neeraja M. Krishnan1, Hervé Seligmann2, Sameer Z. Raina, David D. Pollock 1nkrish2@lsu.edu, Louisiana State Univ.; 2hselig1@lsu.edu, Louisiana State Univ. Abstract |
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H13 Length distributions of exons and introns imply the evolutionary constraints for exon/intron length Yiyu Jia1, Yan Zhang2, Chee Keong Kwoh1, Vivek Gopalan2 1yyjia@pmail.ntu.edu.sg, Bioinformatics Research Centre, Nanyang Technological University Singapore; 2yzBirc@pmail.ntu.edu.sg, Bioinformatics Research Centre, Nanyang Technological University Singapore Abstract |
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H14 Evaluating Indels as Phylogenetic Markers for the Prokaryotes Timothy G. Lilburn1, Yufeng Wang2 1tlilburn@atcc.org, American Type Culture Collection; 2ywang@utsa.edu, University of Texas at an Antonio Abstract |
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H15 A triplet approach to approximations of evolutionary trees Eva-Marta Lundell1, Andrzej Lingas2, Jesper Jansson 1Eva-Marta.Lundell@cs.lth.se, Department of Computer Science, Lund University, Sweden; 2Andrzej.Lingas@cs.lth.se, Department of Computer Science, Lund University, Sweden Abstract |
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H16 Dual Multiple Change Point Model Leads to More Accurate Recombination Detection Vladimir N. Minin1, Karin S. Dorman2, Marc A. Suchard 1vminin@ucla.edu, UCLA, Department of Biomathematics; 2kdorman@iastate.edu, Iowa State University, Department of Statistics Abstract |
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H17 Internal Gene Duplication Patterns in Transmembrane Protein Evolution Hironori Mitsuke1, Keisuke Noto2, Masafumi Arai, Toshio Shimizu 1mitsuke@si.hirosaki-u.ac.jp, Hirosaki University; 2gs0214@si.hirosaki-u.ac.jp, Hirosaki University Abstract |
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H18 A liberal Supertree approach to test the Ecdysozoa hypothesis Gayle K. Philip1, James O. McInerney2, Christopher J. Creevey 1gayle.k.philip@may.ie, NUI, Maynooth; 2james.o.mcinerney@may.ie, NUI, Maynooth Abstract |
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H19 Joint Bayesian Estimation of Alignment and Phylogeny Benjamin D. Redelings1, Marc A. Suchard2 1bredelin@ucla.edu, UCLA; 2msuchard@ucla.edu, UCLA Abstract |
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H2 Identification of interacting sites in protein families Vijayalakshmi Chelliah1, Simon Lovell2, Tom L Blundell 1viji@cryst.bioc.cam.ac.uk, University of Cambridge; 2lovell@bioinf.man.ac.uk, University of Manchester Abstract |
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H20 Conservation Patterns of Human Phosphorylation Sites Keith Robison1 1robison@mpi.com, Millennium Pharmaceuticals Abstract |
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H21 Protein Structure and Evolutionary History Determine Sequence Space Topology Shaknnovich1, delisi2, Deeds, E, Shakhnovich E, I. 1borya@acs.bu.edu, BU; 2delisi@bu.edu, BU Abstract |
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H22 Minimal Convex Recoloring of Phylogenetic Trees Shlomo Moran1, Sagi Snir2 1moran@cs.technion.ac.il, Technion, Israel; 2ssagi@cs.technion.ac.il, Technion Israel Abstract |
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H23 Evolutionary Study of Amino Acid Substitution Patterns Associated with Accelerated Evolution in Endosymbiotic Bacteria Jun-ichi Takeda1, Takeshi Itoh2, Tadashi Imanishi, Takashi Gojobori 1jtakeda@jbirc.aist.go.jp, JBIRC; 2taitoh@jbirc.aist.go.jp, JBIRC Abstract |
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H24 Genome comparison allowing complex rearrangements Mariel Vazquez1, Dan Levy2, Rainer Sachs 1mariel@math.berkeley.edu, Math Dept, UC Berkeley; 2levyd@math.berkeley.edu, Math Dept, UC Berkeley Abstract |
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H25 A Naïve Bayesian Classifier for Rapid Assignment of rRNA Sequences into the New Bacterial Taxonomy Qiong Wang1, James R. Cole2, George M. Garrity, James M. Tiedje 1wangqion@msu.edu, Michigan State University; 2colej@msu.edu, Michigan State University Abstract |
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H26 Amino Acid Coevolution in COI Zhengyuan Wang1, David Pollock2 1zwang3@lsu.edu, LSU; 2dpollock@lsu.edu, LSU Abstract |
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H27 A Markovian model of genome evolution: distribution of paralogs Jerzy Tiuryn1, Damian Wojtowicz2 1tiuryn@mimuw.edu.pl, Warsaw University; 2dami@mimuw.edu.pl, Warsaw University Abstract |
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H28 Retention of functionality in protein recombinants Yanlong O. Xu1, Randall W. Hall2, Richard A. Goldstein, David D. Pollock 1yxu3@lsu.edu, Dept. of Chemistry; 2rhall@lsu.edu, Dept of Chemistry Abstract |
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H29 Fitting nonreversible substitution processes to multiple alignments Von Bing Yap1 1vonbing@math.berkeley.edu, University of California Abstract |
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H3 Streamlining the Conserved Domain Database: A Taxonomic Approach Praveen Frazer Cherukuri1, Aron Marchler-Bauer2, Lewis Y. Geer, Stephen H. Bryant 1cherukur@ncbi.nlm.nih.gov, NCBI, NIH / Boston University; 2bauer@ncbi.nlm.nih.gov, NCBI, NIH Abstract |
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H30 A web of Prokaryotic Life Stefan R. Henz1, Daniel H. Huson2, Alexander Auch, Vincent Moulton, Stephan C. Schuster 1stefan.henz@tuebingen.mpg.de, MPI Developmental Biology Tuebingen; 2huson@informatik.uni-tuebingen.de, Center for Bioinformatics Tuebingen Abstract |
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H4 Heterogeneous Maximum Likelihood Methods for the Detection of Adaptive Evolution Jennifer M. Commins1, Dr. Peter Foster2, Dr. James O. McInerney 1jennifer.commins@may.ie, NUI Maynooth; 2p.foster@nhm.ac.uk, Natural History Museum, London Abstract |
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H5 Homogeneous Phylogenetic Models: Invariants and Parametric Inference Nicholas Eriksson1 1eriksson@math.berkeley.edu, UC Berkeley Abstract |
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H6 Structural RNA has lower folding energy than
random RNA of the same dinucleotide frequency Peter Clote1, Fabrizio Ferre2, Evangelos Kranakis, Danny Krizanc 1clote@bc.edu, Boston College; 2ferref@bc.edu, Boston College Abstract |
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H7 Convergent evolution of domain architectures Julian Gough1 1gough@supfam.org, RIKEN genome sciences centre Abstract |
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H8 Extracting the phylogenetic signal from Mutual Information estimates Rodrigo Gouveia-Oliveira1, Anders Gorm Pedersen2 1rodrigo@cbs.dtu.dk, Center for Biological Sequence Analysis (CBS) - BioCentrum - DTU; 2gorm@cbs.dtu.dk, Center for Biological Sequence Analysis (CBS) - BioCentrum - DTU Abstract |
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H9 Optimal, Efficient Reconstruction of Root-Unknown Phylogenetic Networks with Constrained Recombination Dan Gusfield1 1gusfield@cs.ucdavis.edu, CS, UC Davis Abstract |
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Molecular sequence analysis |
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I1 Using HMMs to Identify the Druggable Proteome Joanne I Adamkewicz1, R. Glenn Hammonds2 1jadamkew@exelixis.com, Exelixis, Inc.; 2rghammonds@earthlink.net, Exelixis, Inc. Abstract |
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I12 Exact Algorithms for Motif Extraction Paul Horton1, Wataru Fujibuchi2 1horton-p@aist.go.jp, Computational Biology Research Center, AIST, Japan; 2fujibuchi-wataru@aist.go.jp, Computational Biology Research Center, AIST, Japan Abstract |
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I13 An improved method of finding over-represented sequence motifs in sets of DNA sequences. Tadashi Imanishi1, Hiroki Hokari2, Motohiko Tanino, Jun-ichi Takeda, Taichiro Sugisaki, Shin Nurimoto 1imanishi@jbirc.aist.go.jp, BIRC, AIST; 2hhokari@jbirc.aist.go.jp, Mitsui Knowledge Industry, Co., Ltd. Abstract |
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I14 Exact algorithm for discovery of consensus sequences among multiple sequences Chul Hyun Joo1, Hwisun Lee2, Jinho Lee, Heuiran Lee, Yoo Kyum Kim 1chjoo@amc.seoul.kr, Department of Microbiology, University of Ulsan College of Medicine; 2hwisun@amc.seoul.kr, Department of Microbiology, University of Ulsan College of Medicine Abstract |
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I15 GAME: Genome Alignment by Match Extension Jeong-Hyeon Choi1, Hwan-Gue Cho2, Sun Kim 1jeochoi@indiana.edu, Pusan National University; 2hgcho@pusan.ac.kr, Pusan National University Abstract |
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I16 Cumulative Local Cross-Correlation – an Algorithm for the Decomposition of Sequence Patterns Simon Kogan1 1skogan@research.haifa.ac.il, Institute of Evolution, University of Haifa, Israel Abstract |
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I17 Predicting the modular domain architecture of a protein Gulriz Kurban1 1gulriz@cs.uchicago.edu, The University of Chicago Abstract |
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I18 A web-based tool for the identification of conformationally flexible segments in protein sequences. Igor Kuznetsov1, Byron Gerlach2, S. Rackovsky 1igor@ku.edu, University of Kansas; 2gerlach@mail.ku.edu, University of Kansas Abstract |
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I19 In silico Analysis of LASS1 (LAG1 Longevity Assurance homology 1) and Related Orthologs Using Target Identification Software Tools Darryl Leon1, Scott Markel2 1darryl.leon@lionbioscience.com, LION bioscience; 2scott.markel@lionbioscience.com, LION bioscience Abstract |
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I2 Phylogenetic Relationship of Sessile Barnacles Based on Mitochondrial DNA Rowshan Ara Begum1, Toshiyuki Yamaguchi2, Shugo Watabe 1rowshanbegum@hotmail.com, Department of Aquatic Bioscience, Graduate School of Agricultural and Life Sciences, The University of Tokyo; 2tyamaguc@msi.biglobe.ne.jp, Marine Biosystems Research Center, Chiba University Abstract |
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I20 Novel Gene Discovery with Sequence Profile Comparison Weizhong Li1, Lukasz Jaroszewski2, Adam Godzik 1wli@quorex.com, Quorex Pharmaceuticals; 2lukasz@sdsc.edu, San Diego Supercomputer Center Abstract |
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I21 Clustering protein sequences with a novel metric transformed from sequence similarity scores and sequence alignments with neural networks Qicheng Ma1, N. R. Nirmala2, Gung-wei Chirn, Richard Cai 1qicheng.ma@pharma.novartis.com, Novartis Institute of Biomedical Research Inc; 2nanguneri.nirmala@pharma.novartis.com, Novartis Institute of Biomedical Research Inc Abstract |
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I23 A tool for constructing EST splice graphs and consensus sequence assembly Ketil Malde1, Eivind Coward2, Inge Jonassen 1ketil@ii.uib.no, University of Bergen; 2coward@ii.uib.no, University of Bergen Abstract |
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I24 Evolutionary Analysis of Enzymatic Functions Elizabeth Marland Glass1, Tanuja Bompada2, Jason C. Ting, Barnett GlickFeld, Natalia Maltsev 1marland@mcs.anl.gov, Argonne National Laboratory; 2tanuja@mcs.anl.gov, Argonne National Laboratory Abstract |
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I25 Molecular characterisation of a versatile peroxidase from a novel Bjerkandera strain. Patrícia R. Moreira1, C. Duez2, A. Antunes , E. Almeida-Vara, F. Xavier Malcata, & J. Cardoso Duarte 1pmoreira@mail.esb.ucp.pt, Escola Superior de Biotecnologia, Universidade Católica Portuguesa; 2, Centre d’Ingénierie des Protéines, Université de Liège Abstract |
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I27 Primer Designer for Site-Directed Mutagenesis Alexey Novoradovsky1, Vivian Zhang2, Madhushree Ghosh, Holly Hogrefe, William Detrich, Joseph A. Sorge, Terry Gaasterland 1anovorad@san.rr.com, Center For Marine Genomics, SIO, UCSD; 2Vivian_Zhang@stratagene.com, Stratagene Abstract |
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I28 PLOC: Analysis of features for protein’s subcellular localization prediction Keun-Joon Park1, Paul Horton2 1park-kj@aist.go.jp, CBRC, AIST; 2horton-p@aist.go.jp, CBRC, AIST Abstract |
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I29 An Evolutionary Computation Approach for Detecting Repetitions in Biosequences Adam Adamopoulos1, Katerina Perdikuri2 1adam@med.duth.gr, Laboratory of Medical Physics, Department of Medicine, Democritus University of Thrace, Alexandroupolis, Greece; 2perdikur@ceid.upatras.gr, Research Academic Computer Technology Institute, Patras, Greece Abstract |
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I31 Euclidean Distance Measure of Markov Models for Genome Comparison Without Alignment Tuan Pham1 1t.pham@griffith.edu.au, Griffith University Abstract |
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I32 HMMERHEAD - Accelerating HMM Searches On Large Databases Elon Portugaly1, Matan Ninio2 1elonp-recomb04@cs.huji.ac.il, The Hebrew University of Jerusalem; 2ninio@recomb04.cs.huji.ninio.org, The Hebrew University of Jerusalem Abstract |
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I33 Understanding RNA Pseudoknotted Structures Anne Condon1, Beth Davy2, Baharak Rastegari, Shelly Zhao, Finbarr Tarrant 1condon@cs.ubc.ca, Department of Computer Science, UBC; 2bdavy@cs.ubc.ca, Department of Computer Science, UBC Abstract |
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I35 ELXR: A Resource For Rapid Exon-Directed Sequence Analysis Jeoffrey J. Schageman1, Alexander Pertsemlidis2 1jeff.schageman@utsouthwestern.edu, Howard Hughes Medical Institute; 2alexander.pertsemlidis@utsouthwestern.edu, UT Southwestern Medical Center Abstract |
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I37 Effect of alternative splicing on structure and function of mouse transcription factors. Bahar Taneri1, Ben Snyder2, Terry Gaasterland 1bahar@genomes.rockefeller.edu, The Rockefeller University; 2ben@genomes.rockefeller.edu, The Rockefeller University Abstract |
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I38 A Novel Approach for Efficient Query of Single Nucleotide Variations in DNA Databases Hsiao Ping Lee1, Yin Te Tsai2, Ching Hua Shih, Tzu Fang Sheu, Chuan Yi Tang 1shopping@cs.nthu.edu.tw, National Tsing-Hua University; 2yttsai@pu.edu.tw, Providence University Abstract |
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I39 Predicting Regulatory Motif based on Multiple Genome Sequences Ting Wang1, Gary D. Stormo2 1twang@ural.wustl.edu, Washington University; 2stormo@ural.wustl.edu, Washington University Abstract |
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I4 Resequencing the Human Genome using Short Sequence Fragments Anthony J. Cox1, Clive G. Brown2, Lisa J. Davies 1anthony.cox@solexa.com, Solexa Limited; 2clive.brown@solexa.com, Solexa Limited Abstract |
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I41 Predictive Classification Jialu Zhang1, Francoise Seillier-Moiseiwitsch2 1jzhang8@math.umbc.edu, Department of Mathematics and Statistics, University of Maryland Baltimore County; 2seillier@math.umbc.edu, Bioinformatics Research Center, University of Maryland Baltimore County Abstract |
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I42 An Eulerian Path Approach to Local Multiple Alignment of DNA Sequences Yu Zhang1, Michael S. Waterman2 1yuzhang@usc.edu, USC; 2msw@usc.edu, USC Abstract |
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I43 FastR: Fast database search tool for structured RNA Vineet Bafna1, Shaojie Zhang2 1vbafna@cs.ucsd.edu, University of California at San Diego; 2shzhang@cs.ucsd.edu, University of California at San Diego Abstract |
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I44 Transcription unit organization of prokaryotes Gabriel Moreno-Hagelsieb1, Warren F. Lamboy2 1gm94@cornell.edu, USDA-ARS; 2wfl1@cornell.edu, USDA-ARS Abstract |
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I45 Performance Comparison of Multiple Sequence Alignment Programs Using Nonparametric Statistics Conrad Shyu1, Luke Sheneman2, James A. Foster 1shyu4751@uidaho.edu, University of Idaho; 2shen0614@uidaho.edu, University of Idaho Abstract |
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I46 Searching Bioinformatic Sequence Databases using UM-BLAST -- A Wrapper for High Performance BLASTs Xue Wu1, Chau-Wen Tseng2 1wu@cs.umd.edu, University of Maryland at College Park; 2tseng@cs.umd.edu, University of Maryland at College Park Abstract |
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I47 FastGroup II: A web-based bioinformatics platform for analyses of large 16S rDNA libraries Yanan Yu1, Pat McNairnie2, Forest Rohwer 1yyu@rohan.sdsu.edu, San Diego State University; 2acrum@cox.net, San Diego State University Abstract |
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I48 Paradigms for Computational Nucleic Acid Design Robert M. Dirks1, Milo Lin2, Erik Winfree, Niles A. Pierce 1dirks@caltech.edu, Caltech; 2miloiq@caltech.edu, Caltech Abstract |
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I49 Modeling Phage Species Abundance David I Bangor1, Beltran Rodriguez Brito2, Peter Salamon, James Nulton, Ben Felts, Joe Mahaffy, Mya Breitbart, Forest Rohwer 1heimdalle@yahoo.com, San Diego State University; 2brodrigu@rohan.sdsu.edu, San Diego State University Abstract |
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I5 Detecting correlated amino acid substitutions using Bayesian phylogenetic techniques Matthew W. Dimmic1, Melissa J. Todd2, Carlos D. Bustamante, Rasmus Nielsen 1mdimmic@umich.edu, Cornell University; 2melissa@mail.bscb.cornell.edu, Cornell University Abstract |
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I51 Cyber Infrastructure for Phylogenetic Research Fran Berman1, Bernard Moret2, Satish Rao, David Swofford, Tandy Warnow 1berman@cs.ucsd.edu, UCSD/SDSC; 2moret@cs.unm.edu, Univeristy of New Mexico Abstract |
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I6 Scientific Workflows for High Resolution Genetic Sequence Analysis Luke Ulrich1, Elizabeth Marland Glass2, Mark D'Souza, Praveen Chandramohan, Natalia Maltsev 1ulrich@mcs.anl.gov, Argonne National Laboratory; 2marland@mcs.anl.gov, Argonne National Laboratory Abstract |
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I7 Anchors: Pre-Classification and its Effects on Hidden Markov Models Jeremy Fisher1, Alan Sprague2 1fisherje@cis.uab.edu, University of Alabama at Birmingham; 2sprague@cis.uab.edu, University of Alabama at Birmingham Abstract |
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I8 Genome Organization Analysis Tool Aaron Kaluszka1, Cynthia Gibas2 1megabyte@vt.edu, Virginia Tech; 2cgibas@vt.edu, Virginia Tech Abstract |
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I9 Computing the Global Similarity of two Strings with a Vector Algorithm Sylvie Hamel1 1hamelsyl@iro.umontreal.ca, Université de Montréal Abstract |
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Protein structure |
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J1 Cross-Link Analysis and Experiment Planning for Elucidation of Protein Structure Xiaoduan Ye1, Janusz M. Bujnicki2, Alan M. Friedman, Chris Bailey-Kellogg 1ye@cs.purdue.edu, Purdue CS; 2iamb@genesilico.pl, International Institute of Molecular and Cell Biology Abstract |
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J10 Modelling and Simulation Studies of the Intracellular Domains of the Inwardly Rectifying K+ Channels Shozeb Haider1, Frances Ashcroft2, Mark S P Sansom 1shozeb@biop.ox.ac.uk, Dept. of Biochemistry, The University of Oxford; 2frances.ashcroft@physiol.ox.ac.uk, Dept. of Physiology, The University of Oxford Abstract |
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J11 Hybrid Probabilistic Roadmap and Monte Carlo Methods for Biomolecule Confomrational Changes Li Han1 1lhan@clarku.edu, Clark University Abstract |
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J12 A Physical Scoring Function Based on the AMBER Force Field and the Poisson-Boltzmann Implicit Solvent for Protein Structure Prediction Mengjuei Hsieh1, Ray Luo2 1mengjueh@uci.edu, Department of Molecular Biology and Biochemistry, University of California Irvine; 2rluo@uci.edu, Department of Molecular Biology and Biochemistry, University of California Irvine Abstract |
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J13 Mining Spatial Motifs from Protein Graph Databases Jun Huan1, wei wang2, Deepak Bandyopadhyay, Jack Snoeyink, Jan Prins, Alexander Tropsha 1huan@cs.unc.edu, UNC; 2weiwang@cs.unc.edu, UNC Abstract |
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J14 Molecular dynamics simulation of branch migration in RuvA tetramer - Holliday junction DNA complex Hisashi Ishida1, Nobuhiro Go2 1ishida@apr.jaeri.go.jp, Japan Atomic Energy Institute; 2go@apr.jaeri.go.jp, Japan Atomic Energy Institute Abstract |
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J15 Flexible Docking of Peptides to MHC Joo Chuan Tong1, Shoba Ranganathan2, Tin Wee Tan 1victor@bic.nus.edu.sg, National University of Singapore; 2shoba@bic.nus.edu.sg, National University of Singapore Abstract |
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J16 Protein Families Classification using Support Vector Machine Tong Joo Chuan1, Kong Lesheng2, Joo Chuan Tong , Khar Heng Choo, Teck Kwong Lee, Soon Heng Tan, Tin Wee Tan, Shoba Ranganathan 1victor@bic.nus.edu.sg, National University of Singapore; 2lesheng@bic.nus.edu.sg, National University of Singapore Abstract |
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J17 Combining structure and function information in a local alignment search tool for sequence-sequence comparison. Maricel Kann1, Paul Thiessen2, Anna Panchenko, Alejandro Schaffer, Stephen F. Altschul and Stephen H. Bryant 1kann@mail.nih.gov, Computational Biology Branch, National Center for Biotechnology Information, National Institutes of Health.; 2thiessen@ncbi.nlm.nih.gov, Computational Biology Branch, National Center for Biotechnology Information, National Institutes of Health. Abstract |
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J18 Native and non-native oligopeptide fragments biased to alpha-helical formation Gelena Kilosanidze1, Alexey Kutsenko2 1Gelena.Kilosanidze@mtc.ki.se, Microbiology and Tumor Biology Center, Karolinska Institute; 2Alexey.Kutsenko@mtc.ki.se, Microbiology and Tumor Biology Center, Karolinska Institute Abstract |
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J19 Web-based Prediction of Membrane Spanning b-strands in Outer Membrane Proteins M. Michael Gromiha1, Shandar Ahmad2, Makiko Suwa 1michael-gromiha@aist.go.jp, CBRC, AIST, Tokyo, Japan; 2, KIT, Iizuka, Japan Abstract |
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J2 Analyzing protein structure using almost-Delaunay tetrahedra Deepak Bandyopadhyay1, Jack Snoeyink2, Alexander Tropsha 1debug@cs.unc.edu, Dept. of Computer Science, UNC Chapel Hill; 2snoeyink@cs.unc.edu, Dept. of Computer Science, UNC Chapel Hill Abstract |
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J20 Computational Studies of Thioredoxin Superfamily Efrosini Moutevelis1, Jim Warwicker2 1E.Moutevelis@postgrad.umist.ac.uk, UMIST; 2j.warwicker@umist.ac.uk, UMIST Abstract |
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J21 Bounding a Protein's Free Energy in Lattice Models Via Linear Programming Robert Carr1, William E. Hart2, Alantha Newman 1rdcarr@cs.sandia.gov, Sandia; 2wehart@cs.sandia.gov, Sandia Abstract |
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J22 Protein Structure Alignment by Principle Component Analysis Sung-Hee Park1, Soo-Jun Park2, Seon-Hee Park 1sunghee@etri.re.kr, ETRI; 2psj@etri.re.kr, ETRI Abstract |
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J23 Protein Fold Recognition Using an Optimal Structure-Discriminative Amino Acid Index J. B. Rosen1, R. H. Leary2, P. Jambeck, C. X. Wu 1jbrosen@cs.ucsd.edu, University of California, San Diego; 2leary@sdsc.edu, San Diego Supercomputer Center Abstract |
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J24 Catalytic and Structural Properties of Carp D-Amino Acid Oxidase Md. Golam Sarower1, Shigeru Okada2, Hiroki Abe 1aa17074@mail.ecc.u-tokyo.ac.jp, Department of Aquatic Bioscience, Graduate School of Agricultural and Life Sciences, The University of Tokyo; 2aokada@mail.ecc.u-tokyo.ac.jp, Department of Aquatic Bioscience, Graduate School of Agricultural and Life Sciences, The University of Tokyo Abstract |
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J26 Introducing a new protein structure comparison website that reports alternative alignments including structure permutations Edward S.C. Shih1, Richie Gan2, Ming-Jing Hwang 1shihds@gate.sinica.edu.tw, Institute of Biomedical Sciences, Academia Sinica; 2g39203001@ym.edu.tw, Institute of bioinformatics, National Yang-Ming University Abstract |
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J27 Comprehensive Protein Database Representation Amandeep S. Sidhu1, Tharam S. Dillon2, Baldev S. Sidhu, Henry Setiawan 1asidhu@it.uts.edu.au, Faculty of IT, UTS, Australia; 2tharam@it.uts.edu.au, Faculty of IT, UTS, Australia Abstract |
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J28 Protei-protein recognition: relationship between domain and interface cores in immunoglobulins Vladimir Potapov1, Vladimir Sobolev2, Marvin Edelman, Alexander Kister, Israel Gelfand 1vladimir.potapov@weizmann.ac.il, Weizmann Institute of Science; 2vladimir.sobolev@weizmann.ac.il, Weizmann Institute of Science Abstract |
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J29 Protein Structural Repeats Revealed in alternative Alignments of Self Structural Comparison Ching-Shu Suen1, Edward S.C. Shih2, Ming-Jing Hwang 1csuen@gate.sinica.edu.tw, Institute of Biomedical Sciences, Academia Sinica; 2shihds@gate.sinica.edu.tw, Institute of Biomedical Sciences, Academia Sinica Abstract |
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J3 Avoiding Local Optima in Single Particle Reconstruction Marshall Bern1, Jindong (JD) Chen2, H. Chi Wong 1bern@parc.com, PARC; 2jchen@parc.com, PARC Abstract |
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J30 Assignment of structural domains in proteins: why is it so difficult? Stella Veretnik1, Ilya N. Shindyalov2, Phillip E. Bourne 1veretnik@sdsc.edu, San Diego Supercomputer Center; 2shindyal@sdsc.edu, San Diego Supercomputer Center Abstract |
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J31 Training Hidden-Markov Models on Sequences of Local Structural Alphabets for Protein Fold Assignment Shiou-Ling Wang1, Chung-Ming Chen2, Ming-Jing Hwang 1r90548019@ntu.edu.tw, Institute of Biomedical Sciences, Academia Sinica; 2ming@lotus.mc.ntu.edu.tw, Institute of Biomedical Engineering, Taiwan University Abstract |
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J32 A Probability-Based Similarity Measure for Saupe Alignment Tensors with Applications to Residual Dipolar Couplings in NMR Structural Biology Anthony Yan1, Chris Langmead2, Bruce Randall Donald 1yan@cs.dartmouth.edu, Dartmouth College; 2cjl@cs.cmu.edu, Carnegie Mellon University Abstract |
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J33 When and where do protein folds come from? an evolutionary view Song Yang1, Phil Bourne2 1soyang@sdsc.edu, UCSD; 2bourne@sdsc.edu, UCSD Abstract |
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J35 Hydrophobic Moment of Multi-Domain Proteins: Magnitude and Spatial Orientational Bias Ruhong Zhou1, Ajay Royyuru2, Prasanna Athma, David Silverman 1ruhongz@us.ibm.com, IBM Research; 2ajayr@us.ibm.com, IBM Research Abstract |
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J36 Analytical Model for the Prediction of NMR Methyl-Side Chain Order Parameters in Proteins Dengming Ming1, Rafael Bruschweiler2 1dming@lanl.gov, Los Alamos Ntional Lab; 2brushweiler@nmr.clarku.edu, Clarku University Abstract |
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J37 Significance of conformational biases in Monte Carlo simulations of protein folding Teresa Przytycka1 1przytyck@ncbi.nlm.nih.gov, NIH Abstract |
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J38 Structure-based assessment of missense mutations in the HMGB domain of SRY identified in 46,XY females with sex reversal Sharmila Banerjee-Basu1, Andread D. Baxevanis2 1sharmib@mail.nih.gov, NHGRI; 2, Abstract |
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J39 Sequence and Structural Templates For Protein Protein Recognition Motifs Owen Lancaster1, Simon Hubbard2, Jo Avis 1O.Lancaster@postgrad.umist.ac.uk, UMIST; 2, UMIST Abstract |
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J4 Discrete-event Simulation of Self-Assembly Systems Sue Yi Chew1, Rorianne Rohlfs2, Russell Schwartz 1syc@andrew.cmu.edu, Carnegie Mellon University; 2rrohlfs@andrew.cmu.edu, Carnegie Mellon University Abstract |
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J40 Partition Function and Base-Pairing Probability Algorithms for
Nucleic Acid Secondary Structure Including Pseudoknots Robert M. Dirks1, Niles A. Pierce2 1dirks@caltech.edu, Caltech; 2niles@caltech.edu, Caltech Abstract |
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J41 Profile--profile methods provide improved fold--recognition. A study of different profile-profile alignment methods. Tomas 1, Arne2, Björn Wallner 1tomasoh@sbc.su.se, Ohlson; 2arne@sbc.su.se, Elofsson Abstract |
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J5 A Dynamical Monte Carlo Algorithm to Study Protein Folding Pathways Andres Colubri1 1acolubri@uchicago.edu, University of Chicago Abstract |
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J6 Assessment of Replica Exchange Method for Protein Structure Prediciton Gelonia Dent1, Ruhong Zhou2, Ajay Royyuru, Prasanna Athma 1gdent@us.ibm.com, IBM TJ Watson Research Center; 2ruhongz@us.ibm.com, IBM TJ Watson Research Center Abstract |
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J7 Predicting disulfide bond partners Fabrizio Ferre1, Peter Clote2 1ferref@bc.edu, Boston College; 2clote@bc.edu, Boston College Abstract |
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J8 Visualization and Analysis of Eukaryotic Gene Vivek Gopalan1, Shang Liang2, Dr. Tin wee Tan, Dr. Shoba Ranganathan 1vivek@bic.nus.edu.sg, National University of Singapore; 2sci11162@nus.edu.sg, National University of Singapore Abstract |
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Recognition of genes and regulatory elements |
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K1 The Probability of Occurence in a Single Sequence Ezekiel F. Adebiyi1 1adebiyi@informatik.uni-tuebingen.de, Department of Computer & Information Technology, College of Science & Technology, Covenant University Abstract |
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K10 Identification of Regulatory Controls for Sets of Co-expressed Genes Shannan J. Ho Sui1, James Mortimer2, Brian P. Kennedy, Chris J. Walsh, Wyeth W. Wasserman 1shosui@cmmt.ubc.ca, Centre for Molecular Medicine and Therapeutics; 2james_mortimer@merck.com, Merck Frosst Centre for Therapeutic Research Abstract |
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K11 Splign: a Hybrid Approach to Spliced Sequence Alignments Yuri Kapustin1, Alexender Souvorov2, Tatiana Tatusova 1kapustin@ncbi.nlm.nih.gov, NCBI; 2souvorov@ncbi.nlm.nih.gov, NCBI Abstract |
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K12 In silico studies of the transcriptional regulation of the genes coding for the novel IL28A, IL28B, and IL29 protein family: A computational screening approach applicable on a genomic scale. William Krivan1, Brian Fox2, Emily Cooper, Teresa Gilbert, Frank Grant, Betty Haldeman, Katherine Henderson, Wayne Kindsvogel, Kevin Klucher, Gary McKnight, Patrick O'Hara, Scott Presnell, Monica Tackett, David Taft, Paul Sheppard 1krivan@zgi.com, ZymoGenetics, Inc.; 2bfox@zgi.com, ZymoGenetics, Inc. Abstract |
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K13 Gene modeling using cDNA or amino acid to genomic sequence alignments Roland Luethy1 1rolandl@timelogi.com, TimeLogic Corp. Abstract |
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K14 Detecting Functional Modules of Transcription Factor Binding Sites in the Human Genome T. Manke1, Ch. Dieterich2, M. Vingron 1manke@molgen.mpg.de, MPI; 2dieteric@molgen.mpg.de, MPI Abstract |
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K15 SHADOWER: A generalized hidden Markov phylogeny for
multiple-sequence functional annotation Jon D. McAuliffe1, Lior Pachter2, Michael I. Jordan 1jon@stat.berkeley.edu, UC Berkeley Statistics; 2lpachter@math.berkeley.edu, UC Berkeley Mathematics Abstract |
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K16 Longer sequence surrounding motif distinguishes regulatory elements from false positives Emily Rocke1, James Thomas2 1ecrocke@gs.washington.edu, University of Washington; 2jht@u.washington.edu, University of Washington Abstract |
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K17 Gnomon – a multi-step combined gene prediction program Alexandre Souvorov1, Tatiana Tatusova2, David Lipman 1souvorov@ncbi.nlm.nih.gov, National Center for Biotechnology Information; 2tatiana@ncbi.nlm.nih.gov, National Center for Biotechnology Information Abstract |
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K18 Experimental tools to determine DNA binding sites of KRAB zinc finger proteins in their candidate target genes – a challenge in computational biology of transcriptional regulatory networks Lorenz, P.1, Dietmann, S.2, Sina, C, Koczan, D., Moeller, S., Thiesen, H.-J. 1peter.lorenz@med.uni-rostock.de, Institute of Immunology; 2sabine.dietmann@med.uni-rostock.de, Institute of Immunology Abstract |
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K19 A Systematic Analysis of Stress Induced DNA Duplex Destabilization (SIDD) Sites in the E. coli Genome: Implications of SIDD Analysis for Promoter and Operon prediction in Prokaryotes Huiquan Wang1, Craig J. Benham2 1hqwang@ucdavis.edu, Genome Center, UC Davis; 2cjbenham@ucdavis.edu, Genome Center, UC Davis Abstract |
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K2 A Minimization Entropy-Based Bipartite Algorithm with Application to PXR/RXRα Binding Sites Chengpeng Bi1, Carrie A. Vyhlidal2, J. Steve Leeder, Peter K. Rogan 1cbi@cmh.edu, Children's Mercy Hospital; 2cvyhlidal@cmh.edu, Children's Mercy Hospital Abstract |
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K20 Blind Operon Finding in Genomes with Insufficient Training Data Benjamin Westover1, Jeremy Buhler2, Jeff Gordon, Justin Sonnenburg 1ben@cse.wustl.edu, Washington University; 2jbuhler@cse.wustl.edu, Washington University Abstract |
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K21 Bayesian Variable Selection to Identify Quantiative Trait Loci Dabao Zhang1, Min Zhang2, Kristi L. Montooth, Martin Wells, Carlos Bustamante, Andrew G. Clark 1dzhang@bst.rochester.edu, University of Rochester Medical Center; 2mz35@cornell.edu, Cornell University Abstract |
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K22 The Estimations of Motif Effects with Longitudinal Mixed Model in Temporal Gene Expression Analysis Jiuzhou Song1, Jaime Bjarnason 2, Mike Surette 1songj@ucalgary.ca, University of Calgary; 2jbjarnso@ucalgary.ca, University of Calgary Abstract |
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K23 Excess Information at T7-like Promoters and Classification of T7-like Phages Zehua Chen1, Thomas D. Schneider2 1chenze@ncifcrf.gov, LECB, NCI-Frederick; 2toms@ncifcrf.gov, LECB, NCI-Frederick Abstract |
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K3 Identification of Regulatory Elements in Archaea using Self-Organizing Maps Alan P. Boyle1, John A. Boyle2, Susan M. Bridges 1apb22@cse.msstate.edu, Mississippi State University; 2jab@ra.msstate.edu, Mississippi State University Abstract |
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K4 Gene finding in the presence of RNA editing Ralf Bundschuh1, Jonatha Gott2 1bundschuh@mps.ohio-state.edu, The Ohio State University; 2jmg13@po.cwru.edu, Case Western Reserve University Abstract |
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K5 Computational Identification of Noncoding RNA Genes through Phylogenetic Shadowing Kushal Chakrabarti1, Daniel L. Ong2 1kushalc@uclink.berkeley.edu, University of California, Berkeley; 2dlong@ocf.berkeley.edu, University of California, Berkeley Abstract |
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K6 Discovering Transcription Factor Binding Sites in the Yeast Saccharomyces Cerevisiae Xue-wen Chen1, Jianwen Fang2, Xinkun Wang 1xwchen@ku.edu, The University of Kansas; 2jwfang@ku.edu, The University of Kansas Abstract |
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K7 Mammalian Promoter Database: Information resource of mammalian gene promoters Hao Sun1, Saranyan K. Palaniswamy2, Twyla T. Pohar; Ramana V. Davuluri 1sun.143@osu.edu, The Ohio State University; 2Palaniswamy-1@medctr.osu.edu, The Ohio State University Abstract |
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K8 From Motif-Finding to Promoter Structure Chun Ye1, Eleazar Eskin2 1yimmieg@ucsd.edu, Univeristy of California, San Diego; 2eeskin@cs.ucsd.edu, University of California, San Diego Abstract |
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K9 A Whole-genome Analysis of Transcription Factor Binding Sites for Human and Mouse Orthologs Caroline Finnerty1, James McInerney2 1caroline.s.finnerty@may.ie, NUI Maynooth; 2james.o.mcinerney@may.ie, NUI Maynooth Abstract |
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Structural and functional genomics |
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L1 Analysis of Ataxin-2 and other Lsm domain proteins Mario Albrecht1, Markus Ralser2, Hans Lehrach, Sylvia Krobitsch, Thomas Lengauer 1mario.albrecht@mpi-sb.mpg.de, Max-Planck-Institute for Informatics; 2ralser@molgen.mpg.de, Max-Planck-Institute for Molecular Genetics Abstract |
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L10 A target selection informatics resource for structural genomics Ana Rodrigues1, Guy G. Dodson2, Roderick E. Hubbard 1rodrigues@ysbl.york.ac.uk, University of York; 2ggd@ysbl.york.ac.uk, University of York Abstract |
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L11 Structural Kinomics - Structural Genomics of the Human Kinome Kenneth D Schwinn1, Christopher R Hansen2, Ian M Miller, Shane Atwell, Sean G Buchanan, J Michael Sauder 1ken@stromix.com, SGX; 2chansen@stromix.com, SGX Abstract |
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L12 The SWISS-MODEL Repository of annotated 3 dimensional protein structure homology models Juergen Kopp1, Torsten Schwede2 1Juergen.Kopp@unibas.ch, Biozentrum & Swiss Instititute of Bioinformatics; 2Torsten.Schwede@unibas.ch, Biozentrum & Swiss Instititute of Bioinformatics Abstract |
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L13 Quantifying Structure-Function Uncertainty: A Graph Theoretical Exploration Into the Origins and Limitations of Protein Annotation Shaknnovich1, Harvey2 1borya@acs.bu.edu, BU; 2max10@bu.edu, BU Abstract |
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L14 Use of limited suboptimal alignment in homology modeling Christopher L Tang1, Donald S Petrey2, Marc Fasnacht, Mickey Kosloff, Emil Alexov, Barry Honig 1clt47@columbia.edu, Columbia University; 2dsp18@columbia.edu, Columbia University Abstract |
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L15 Contact Map Prediciton via Maximum Entropy Degui Zhi1, Charles Elkan2 1dzhi@ucsd.edu, UCSD; 2elkan@cs.ucsd.edu, UCSD Abstract |
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L16 Application of a Two-stage Method to Identify Protein-Protein Interface Residues Changhui Yan1, Vasant Honavar2, Drena Dobbs 1chhyan@iastate.edu, Iowa State University; 2honavar@cs.iastate.edu, Iowa State University Abstract |
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L17 High-Throughput 3D Homology Detection via NMR Resonance Assignment Christopher James Langmead1, Bruce Randall Donald2 1cjl@cs.cmu.edu, Carnegie Mellon University Department of Computer Science; 2brd@cs.dartmouth.edu, Dartmouth Department of Computer Science Abstract |
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L19 Efficiently computing the landscape of
locally optimal RNA secondary structures Peter Clote1 1clote@bc.edu, Boston College Abstract |
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L2 Secondary structure prediction of RNA pairs Mirela Andronescu1, Anne Condon2 1andrones@cs.ubc.ca, University of British Columbia; 2condon@cs.ubc.ca, University of British Columbia Abstract |
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L20 Evidence for a subpopulation of alternative splicing events under selection pressure for protein reading frame preservation Alissa Resch1, Yi Xing2, Alexander Alekseyenko, Barmak Modrek, Christopher Lee 1aresch@mbi.ucla.edu, UCLA-DOE Center for Genomics and Proteomics; 2yxing@ucla.edu, UCLA-DOE Center for Genomics and Proteomics Abstract |
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L22 Hardness of RNA Secondary Structure Design Rosalia Aguirre-Hernandez1, Holger H Hoos2, Anne Condon 1rosalia@cs.ubc.ca, UBC; 2hoos@cs.ubc.ca, UBC Abstract |
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L23 Data Mining Atomic Motions from Computer Simulations of Nucleic Acids: A Wavelet Study of the Differential Bending of d[GA4T4C]n and d[GT4A4C]n Elijah Gregory1, Thomas E. Cheatham, III2, Julio C. Facelli 1dwee@chpc.utah.edu, CHPC, University of Utah; 2tec3@utah.edu, Departments of Medicinal Chemistry and of Pharmaceutics and Pharmaceutical Chemsitry, University of Utah Abstract |
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L24 The Alternative Splicing Gallery (ASG) – Visualizing Gene Structure and Alternative Splicing Jeremy Leipzig1, Steffen Heber2 1jnleipzi@ncsu.edu, NCSU Department of Computer Science; 2sheber@ncsu.edu, NCSU Department of Computer Science Abstract |
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L25 Computer modeling of DNA unknotting by type II topoisomerases Barath Raghavan1, Diana Nguyen2, Javier Arsuaga, Mariel Vazquez 1barath@ucsd.edu, CSE, UC San Diego; 2dnguyen@uclink.berkeley.edu, Bioengineering Department, UC Berkeley Abstract |
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L26 Analysis of Shotgun Sequence Data from Microbial Ecosystems Peter Salamon1, Mya Breitbart2, J. Mahaffy, J. Nulton, B. Felts, B. Rodriguez Brito, D. Bangor, and F. Rohwer 1salamon@sdsu.edu, San Diego State University; 2mya@sunstroke.sdsu.edu, San Diego State University Abstract |
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L3 A comparison of transmembrane topologies greatly improves the comprehensive functional classification and identification of prokaryotic transmembrane proteins Masafumi Arai1, Kosuke Okumura2, Masanobu Satake, Toshio Shimizu 1d01603@si.hirosaki-u.ac.jp, Hirosaki University; 2gs03406@si.hirosaki-u.ac.jp, Hirosaki University Abstract |
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L4 Insertions and deletions in protein alignment Charlotte Deane1, Gerton Lunter2, Jacob Pedersen 1deane@stats.ox.ac.uk, Oxford University; 2lunter@stats.ox.ac.uk, Oxford University Abstract |
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L6 Predicted Secondary Structure Slightly Enhances
Ortholog Detection Ying Lin1, John Case2, Hsing-Kuo Kenneth Pao, Joan Burnside 1ylin@cis.udel.edu, Univeristy of Delaware; 2case@cis.udel.edu, University of Delaware Abstract |
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L7 Application of Variable Order Markov Models to Identifying CpG Islands Zhenqiu Liu1, Dechang Chen2, Jaques Reifman 1liu@bioanalysis.org, TATRC; 2dchen@usuhs.mil, Uniformed Services University of the Health Sciences Abstract |
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L8 Using an RNA Secondary Structure Partition Function to Determine Confidence in Base Pairs Predicted by Free Energy Minimization David H. Mathews1 1David_Mathews@urmc.rochester.edu, University of Rochester Medical Center Abstract |
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L9 Annotation of 3D Protein Chains in PDB with GO terms via Structural Homology Julia V. Ponomarenko1, Philip E. Bourne2, Ilya N. Shindyalov 1jpon@sdsc.edu, San Diego Supercomputer Center, University of California, San Diego; 2bourne@sdsc.edu, San Diego Supercomputer Center, University of California, San Diego Abstract |
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