csb,2004 IEEE Computational Systems Bioinformatics Conference (CSB'04)

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2004 IEEE Computational Systems Bioinformatics Conference (CSB'04)

Introduction
Preface (PDF) p. xvii
Committees (PDF) pp. xviii-xix
Referees (PDF) p. xx
Keynote Addresses
Computational Dissection of Regulatory Networks Using Diverse High-Throughput Data (PDF) Ron Shamir, Tel Aviv University pp. 2-3
Whole Genome Sequencing, Comparative Genomics, and Systems Biology (PDF) Eugene Myers, University of California at Berkeley p. 4
Invited Talks
Are We There Yet? Genomic Profiling and Mechanism in Cancer Research (PDF) Paul Meltzer, National Human Genome Research Institute Sean Davis, National Human Genome Research Institute Kristin Baird, National Human Genome Research Institute Yidong Chen, National Human Genome Research Institute p. 6
Spaghetti Code, Soupy Logic, and the Expression of Genes (PDF) Jim Kent, University of California at Santa Cruz p. 7
High Content Cellular Analysis and Their Applications (PDF) Stephen T.C. Wong, Harvard Medical School and Brigham & Women’s Hospital p. 8
Fractal Genomics Modeling: A New Approach to Genomic Analysis and Biomarker Discovery (Abstract) Sandy Shaw, Health Discovery Corporation, Inc. Paul Shapshak, University of Miami School of Medicine pp. 9-17
From DNA Sequence to Network Behavior: Functional Properties of Genetic Regulatory Networks (PDF) Hamid Bolouri, Institute for Systems Biology p. 18
Genomics
Shannon Information in Complete Genomes (Abstract) Chang-Heng Chang, National Central University Li-Ching Hsieh, National Central University Ta-Yuan Chen, National Central University Hong-Da Chen, National Central University Liaofu Luo, Inner Mongolia University Hoong-Chien Lee, National Central University and National Center for Theoretical Sciences pp. 20-30
Segmental Duplications Containing Tandem Repeated Genes Encoding Putative Deubiquitinating Enzymes (Abstract) Hong Liu, Aventis Pharmaceuticals Inc. Li Li, Aventis Pharmaceuticals Inc. Asher Zilberstein, Aventis Pharmaceuticals Inc. Chang S. Hahn, Aventis Pharmaceuticals Inc. pp. 31-39
Recurrence Time Statistics: Versatile Tools for Genomic DNA Sequence Analysis (Abstract) Yinhe Cao, University of Florida Wen-wen Tung, National Center for Atmospheric Research J. B. Gao, University of Florida pp. 40-51
FastR: Fast Database Search Tool for Non-Coding RNA (Abstract) Vineet Bafna, University of California at San Diego Shaojie Zhang, University of California at San Diego pp. 52-61
Compressed Pattern Matching in DNA Sequences (Abstract) Lei Chen, Wayne State University Shiyong Lu, Wayne State University Jeffrey Ram, Wayne State University pp. 62-68
A Self-Tuning Method for One-Chip SNP Identification (Abstract) Michael Molla, University of Wisconsin-Madison and NimbleGen Systems, Inc. Jude Shavlik, University of Wisconsin-Madison Thomas Albert, NimbleGen Systems, Inc. Todd Richmond, NimbleGen Systems, Inc. Steven Smith, NimbleGen Systems, Inc. pp. 69-79
Space-Conserving Optimal DNA-Protein Alignment (Abstract) Pang Ko, Iowa State University Mahesh Narayanan, Iowa State University Anantharaman Kalyanaraman, Iowa State University Srinivas Aluru, Iowa State University pp. 80-88
Evolution and Phylogeny
Algorithms for Association Study Design Using a Generalized Model of Haplotype Conservation (Abstract) Russell Schwartz, Carnegie Mellon University pp. 90-97
Rec-I-DCM3: A Fast Algorithmic Technique for Reconstructing Large Phylogenetic Trees (Abstract) Usman W. Roshan, University of Texas at Austin Bernard M. E. Moret, University of New Mexico Tandy Warnow, University of Texas at Austin Tiffani L. Williams, University of New Mexico pp. 98-109
MinPD: Distance-Based Phylogenetic Analysis and Recombination Detection of Serially-Sampled HIV Quasispecies (Abstract) Patricia Buendia, Florida International University Giri Narasimhan, Florida International University pp. 110-119
Transcriptomes
Gridding and Compression of Microarray Images (Abstract) Stefano Lonardi, University of California at Riverside Yu Luo, University of California at Riverside pp. 122-130
A Theoretical Analysis of Gene Selection (Abstract) Sach Mukherjee, University of Oxford Stephen J. Roberts, University of Oxford pp. 131-141
Minimum Entropy Clustering and Applications to Gene Expression Analysis (Abstract) Haifeng Li, University of California at Riverside Keshu Zhang, Rensselaer Polytechnic Institute Tao Jiang, University of California at Riverside pp. 142-151
Profile-Based String Kernels for Remote Homology Detection and Motif Extraction (Abstract) Rui Kuang, Columbia University Eugene Ie, Columbia University Ke Wang, Columbia University Kai Wang, Columbia University Mahira Siddiqi, Columbia University Yoav Freund, Columbia University Christina Leslie, Columbia University pp. 152-160
A Mixed Factors Model for Dimension Reduction and Extraction of a Group Structure in Gene Expression Data (Abstract) Ryo Yoshida, Graduate University for Advanced Studies Tomoyuki Higuchi, Institute of Statistical Mathematics Seiya Imoto, University of Tokyo pp. 161-172
MISAE: A New Approach for Regulatory Motif Extraction (Abstract) Zhaohui Sun, University of Nebraska at Lincoln Jingyi Yang, University of Nebraska at Lincoln Jitender S. Deogun, University of Nebraska at Lincoln pp. 173-181
Biclustering in Gene Expression Data by Tendency (Abstract) Jinze Liu, University of North Carolina Jiong Yang, University of Illinois, Urbana-Champaign Wei Wang, University of North Carolina pp. 182-193
Improved Fourier Transform Method for Unsupervised Cell-Cycle Regulated Gene Prediction (Abstract) Karuturi R. Krishna Murthy, Genome Institute of Singapore Liu Jian Hua, Genome Institute of Singapore pp. 194-203
Proteomics
SPIDER: Software for Protein Identification from Sequence Tags with De Novo Sequencing Error (Abstract) Yonghua Han, University of Western Ontario Bin Ma, University of Western Ontario Kaizhong Zhang, University of Western Ontario pp. 206-215
Estimating and Improving Protein Interaction Error Rates (Abstract) Patrik D'haeseleer, Harvard Medical School George M. Church, Harvard Medical School pp. 216-223
Automated Protein Classification Using Consensus Decision (Abstract) Tolga Can, University of California at Santa Barbara Orhan Camoglu, University of California at Santa Barbara Ambuj K. Singh, University of California at Santa Barbara Yuan-Fang Wang, University of California at Santa Barbara pp. 224-235
Separation of Ion Types in Tandem Mass Spectrometry Data Interpretation — A Graph-Theoretic Approach (Abstract) Bo Yan, University of Georgia and Computational Biology Institute Chongle Pan, Computational Biology Institute and University of Tennessee Victor N. Olman, University of Georgia and Computational Biology Institute Robert L. Hettich, Oak Ridge National Laboratory Ying Xu, University of Georgia and Computational Biology Institute pp. 236-244
Structural Bioinformatics
Multiple RNA Structure Alignment (Abstract) Zhuozhi Wang, University Heath Network Kaizhong Zhang, University of Western Ontario pp. 246-254
Weighting Features to Recognize 3D Patterns of Electron Density in X-Ray Protein Crystallography (Abstract) Kreshna Gopal, Texas A&M University Tod D. Romo, Texas A&M University James C. Sacchettini, Texas A&M University Thomas R. Ioerger, Texas A&M University pp. 255-265
Reasoning about Molecular Similarity and Properties (Abstract) Rahul Singh, San Francisco State University pp. 266-277
High-Throughput 3D Structural Homology Detection via NMR Resonance Assignment (Abstract) Christopher James Langmead, Carnegie Mellon University Bruce Randall Donald, Dartmouth University pp. 278-289
Pair Stochastic Tree Adjoining Grammars for Aligning and Predicting Pseudoknot RNA Structures (Abstract) Hiroshi Matsui, Keio University Kengo Sato, Keio University Yasubumi Sakakibara, Keio University pp. 290-299
An Algorithm for Detecting Homologues of Known Structured RNAs in Genomes (Abstract) Shu-Yun Le, National Cancer Institute Jacob V. Maizel, Jr., National Cancer Institute Kaizhong Zhang, University of Western Ontario and Simon Fraser University pp. 300-310
Inverse Protein Folding in 2D HP Mode (Extended Abstract) (Abstract) Arvind Gupta, Simon Fraser University Jan Manuch, Simon Fraser University Ladislav Stacho, Simon Fraser University pp. 311-318
Analysis of a Systematic Search-Based Algorithm for Determining Protein Backbone Structure from a Minimum Number of Residual Dipolar Couplings (Abstract) Lincong Wang, Dartmouth University Bruce Randall Donald, Dartmouth University pp. 319-330
Pathways & Networks
Multi-Knockout Genetic Network Analysis: The Rad6 Example (Abstract) Alon Kaufman, Hebrew University Martin Kupiec, Tel Aviv University Eytan Ruppin, Tel Aviv University pp. 332-340
A Hierarchical Mixture of Markov Models for Finding Biologically Active Metabolic Paths Using Gene Expression and Protein Classes (Abstract) Hiroshi Mamitsuka, Kyoto University Yasushi Okuno, Kyoto University pp. 341-352
Dynamic Algorithm for Inferring Qualitative Models of Gene Regulatory Networks (Abstract) Zheng Yun, Nanyang Technological University Kwoh Chee Keong, Nanyang Technological University pp. 353-362
Mapping of Microbial Pathways through Constrained Mapping of Orthologous Genes (Abstract) Victor Olman, University of Georgia Hanchuan Peng, University of Georgia and Oak Ridge National Laboratory Zhengchang Su, University of Georgia and Oak Ridge National Laboratory Ying Xu, University of Georgia and Oak Ridge National Laboratory pp. 363-370
Applied Bioinformatics
PoPS: A Computational Tool for Modeling and Predicting Protease Specificity (Abstract) Sarah E. Boyd, Monash University Maria Garcia de la Banda, Monash University Robert N. Pike, Monash University James C. Whisstock, Monash University George B. Rudy, Walter & Eliza Hall Institute of Medical Research pp. 372-381
Selection of Patient Samples and Genes for Outcome Prediction (Abstract) Huiqing Liu, Institute for Infocomm Research Jinyan Li, Institute for Infocomm Research Limsoon Wong, Institute for Infocomm Research pp. 382-392
Data Mining & Ontology
Comparison of Two Schemes for Automatic Keyword Extraction from MEDLINE for Functional Gene Clustering (Abstract) Ying Liu, Georgia Institute of Technology Brian J. Ciliax, Emory University Karin Borges, Emory University Venu Dasigi, Southern Polytechnic State University Ashwin Ram, Georgia Institute of Technology Shamkant B. Navathe, Georgia Institute of Technology Ray Dingledine, Emory University pp. 394-404
Calculation, Visualization, and Manipulation of MASTs (Maximum Agreement Subtrees) (Abstract) Shiming Dong, University of Georgia Eileen Kraemer, University of Georgia pp. 405-414
AZuRE, a Scalable System for Automated Term Disambiguation of Gene and Protein Names (Abstract) Raf M. Podowski, AstraZeneca R&D Boston and Karolinska Institutet John G. Cleary, Reel Two, Ltd. and University of Waikato Nicholas T. Goncharoff, Reel Two, Inc. Gregory Amoutzias, AstraZeneca William S. Hayes, AstraZeneca R&D Boston pp. 415-424
Comparative Analysis of Gene Sets in the Gene Ontology Space under the Multiple Hypothesis Testing Framework (Abstract) Sheng Zhong, Harvard University Lu Tian, Harvard University Cheng Li, Harvard University and Dana Farber Cancer Institute Kai-Florian Storch, Harvard Medical School Wing H. Wong, Harvard University pp. 425-435
Gene Ontology Friendly Biclustering of Expression Profiles (Abstract) Jinze Liu, University of North Carolina Wei Wang, University of North Carolina Jiong Yang, University of Illinois at Urbana-Champaign pp. 436-447
Biomedical Research
High-Throughput Computational and Experimental Biology Strategy in Identifying Tumor Expressing CAMs (PDF) Anguraj Sadanandam, University of Nebraska Medical Center Michelle L. Varney, University of Nebraska Medical Center Rakesh K. Singh, University of Nebraska Medical Center pp. 450-451
Cellular Multicellular Systems
State-Space Model for Gene Regulatory Networks with Time Delays (PDF) Fang-Xiang Wu, University of Saskatchewan Wen-Jun Zhang, University of Saskatchewan Anthony J. Kusalik, University of Saskatchewan pp. 454-455
Nonlinear Modeling on Protein Kinase C(PKC)-Epsilon Inverse Regulation of Stress Fibers in Oncogenically Transformed Cells (PDF) Yingxin Li, Bowling Green State University Carol A. Heckman, Bowling Green State University Julie A. Barnes, Bowling Green State University pp. 456-457
Analysis of Population Dynamics in Beta-Cell Destruction Lead to Identification of Novel Candidate Genes for Type 1 Diabetes (PDF) Yizhou Xie, Medical College of Wisconsin Xujing Wang, Medical College of Wisconsin pp. 458-459
Comparative Genomics
Exploring Genomic Context Patterns for Rhodobacter Sphaeroides in the HERBE Knowledge Discovery Environment (PDF) Heidi J. Sofia, Pacific Northwest National Laboratory Abigail L. Corrigan, Pacific Northwest National Laboratory Kyle R. Klicker, Pacific Northwest National Laboratory George Chin, Pacific Northwest National Laboratory Eric G. Stephan, Pacific Northwest National Laboratory pp. 462-463
RepeatAssembler: A Package for Annotation of Full-Length Repetitive DNA Sequences in Fungal Genomes (Abstract) Mark L. Farman, University of Kentucky Joshua W. Gilkerson, University of Kentucky Jerzy W. Jaromczyk, University of Kentucky Chuck Staben, University of Kentucky pp. 464-467
Data Mining
Search-Space Reduction of a Non-Redundant Peptide Database (PDF) Ian Shadforth, Cranfield University Daniel Crowther, GlaxoSmithKline Conrad Bessant, Cranfield University pp. 470-471
Automated and Rapid Bacterial Identification Using LC-Mass Spectrometry with a Relational Database Management System (PDF) Samir V. Deshpande, Science & Technology Corporation Rabih E. Jabbour, Geo-Centers, Inc. Charles Wick, US Army RDECOM A. Peter Snyder, US Army RDECOM pp. 472-473
Development of a Knowledge-Based Multi-Scheme Cancer Microarray Data Analysis System (PDF) John H. Phan, Georgia Institute of Technology and Emory University Chang F. Quo, Georgia Institute of Technology and Emory University Kejiao Guo, Georgia Institute of Technology and Emory University Weimin Feng, Georgia Institute of Technology and Emory University Geoffrey Wang, Georgia Institute of Technology May D. Wang, Georgia Institute of Technology and Emory University pp. 474-475
FigSearch: Using Maximum Entropy Classifier to Categorize Biological Figures (PDF) Fang Liu, Norwegian Radium Hospital and PubGene AS Tor-Kristian Jenssen, PubGene AS Vegard Nygaard, Norwegian Radium Hospital John Sack, Stanford University Eivind Hovig, Norwegian Radium Hospital pp. 476-477
GeneTide: Terra Incognita Discovery Endeavor Mining ESTs and Expression Data to Elucidate Known and De-Novo GeneCards Genes (PDF) Maxim Shklar, Weizmann Institute of Science Orit Shmueli, Weizmann Institute of Science Liora Strichman-Almashanu, Weizmann Institute of Science Michael Shmoish, Weizmann Institute of Science Doron Lancet, Weizmann Institute of Science Marilyn Safran, Weizmann Institute of Science pp. 478-479
Biclustering Gene-Feature Matrices for Statistically Significant Dense Patterns (Abstract) Mehmet Koyuturk, Purdue University Wojciech Szpankowski, Purdue University Ananth Grama, Purdue University pp. 480-484
Recognition of Exon/Intron Boundaries Using Dynamic Ensembles (PDF) Xuanfu Wu, University of Nebraska at Omaha Zhengxin Chen, University of Nebraska at Omaha pp. 485-486
Probabilistic Consistency Analysis for Gene Selection (PDF) Sach Mukherjee, University of Oxford Stephen J. Roberts, University of Oxford pp. 487-488
Automating the Biological Data Collection Process with Agents (PDF) Lacroix Lacroix, Arizona State University Kaushal Parekh, Arizona State University Hasan Davulcu, Arizona State University I. V. Ramakrishnan, State University of New York Nikeeta Julasana, State University of New York pp. 489-490
An Intelligent Digital Library System for Biologists (PDF) Jeffrey Stone, University of Vermont Xindong Wu, University of Vermont Marc Greenblatt, University of Vermont pp. 491-492
A New Approach to Clustering Biological Data Using Message Passing (PDF) Huimin Geng, University of Nebraska at Omaha Dhundy Bastola, University of Nebraska Medical Center Hesham Ali, University of Nebraska at Omaha pp. 493-494
Ontology Specific Data Mining Based on Dynamic Grammars (PDF) Daniel Quest, University of Nebraska at Omaha Hesham Ali, University of Nebraska at Omaha pp. 495-496
Application of Relief-F Feature Filtering Algorithm to Selecting Informative Genes for Cancer Classification Using Microarray Data (PDF) Yuhang Wang, Dartmouth College Fillia Makedon, Dartmouth College pp. 497-498
Probability Profile Method — New Approach to Data Analysis in Tandem Mass Spectrometry (Abstract) Andrey Gorin, Oak Ridge National Laboratory Robert M. Day, Oak Ridge National Laboratory Andrey Borziak, Oak Ridge National Laboratory Michael B. Strader, Oak Ridge National Laboratory Gregory B. Hurst, Oak Ridge National Laboratory Tema Fridman, Oak Ridge National Laboratory pp. 499-502
Assigning Gene Ontology Categories (GO) to Yeast Genes Using Text-Based Supervised Learning Methods (PDF) Tomonori Izumitani, NTT Communication Science Laboratories Hirotoshi Taira, NTT Communication Science Laboratories Hideto Kazawa, NTT Communication Science Laboratories Eisaku Maeda, NTT Communication Science Laboratories pp. 503-504
PPM-Chain De novo Peptide Identification Program Comparable in Performance to Sequest (Abstract) Robert M. Day, Oak Ridge National Laboratory Andrey Borziak, Oak Ridge National Laboratory Andrey Gorin, Oak Ridge National Laboratory pp. 505-508
Evolution and Phylogenetics
Comparative Genomics of Cyclin-Dependent Kinases Suggest Co-Evolution of the RNAP II C-Terminal Domain and CTD-Directed CDKs (PDF) Zhenhua Guo, East Carolina University John W. Stiller, East Carolina University pp. 510-511
Embedded Computation of Maximum-Likelihood Phylogeny Inference Using Platform FPGA (Abstract) Terrence S. T. Mak, Chinese University of Hong Kong K. P. Lam, Chinese University of Hong Kong pp. 512-514
Gene Length and Alternative Transcription in Fruit Fly (PDF) Boris Budagyan, California State University at Hayward Ann Loraine, University of Alabama at Birmingham pp. 515-516
Protein Classification into Domains of Life Using Markov Chain Models (Abstract) Francisca Zanoguera, Serono Pharmaceutical Research Institute Massimo de Francesco, Serono Pharmaceutical Research Institute pp. 517-519
EcMLST: An Online Database for Multi Locus Sequence Typing of Pathogenic Escherichia coli (PDF) Weihong Qi, Michigan State University David W. Lacher, Michigan State University Alyssa C. Bumbaugh, Michigan State University Katie E. Hyma, Michigan State University Lindsey M. Ouellette, Michigan State University Teresa M. Large, Michigan State University Cheryl L. Tarr, Michigan State University Thomas S. Whittam, Michigan State University pp. 520-521
On Complexity Measures for Biological Sequences (Abstract) Fei Nan, West Virginia University Donald Adjeroh, West Virginia University pp. 522-526
Functional Genomics
A Markov Model Based Gene Discrimination Approach in Trypanosomes (PDF) Allison Griggs, Rochester Institute of Technology Shuba Gopal, Rochester Institute of Technology p. 528
Predicting Gene Ontology Annotations from Sequence Data Using Kernel-Based Machine Learning Algorithms (PDF) J. J. Ward, University College London J. S. Sodhi, University College London B. F. Buxton, University College London D. T. Jones, University College London pp. 529-530
Deriving a Novel Codon Index by Combining Period-3 and Fractal Features of DNA Sequences (PDF) Yan Qi, Johns Hopkins University Jianbo Gao, University of Florida Yinhe Cao, University of Florida and BioSieve Wen-wen Tung, National Center for Atmospheric Research pp. 531-532
Exploring the Use of Stem-Loop Characteristics for Pinpointing Structural RNA Genes (PDF) Kirt Noel, Simon Fraser University Kay C. Wiese, Simon Fraser University pp. 533-534
Positive Sample Only Learning (PSOL) for Predicting RNA Genes in E. coli (Abstract) Richard F. Meraz, Lawrence Berkeley National Laboratory Xiaofeng He, Lawrence Berkeley National Laboratory Chris H.Q. Ding, Lawrence Berkeley National Laboratory Stephen R. Holbrook, Lawrence Berkeley National Laboratory pp. 535-538
High Content Analysis
Quantitative Analysis of Membrane Protein Localization and Signaling (PDF) Peter M. Kasson, Stanford University Johannes B. Huppa, Stanford University and Howard Hughes Medical Institute Mark M. Davis, Stanford University and Howard Hughes Medical Institute Axel T. Brunger, Stanford University and Howard Hughes Medical Institute pp. 540-541
High Performance Computing
The SSAHA Trace Server (PDF) Zemin Ning, The Wellcome Trust Sanger Institute William Spooner, The Wellcome Trust Sanger Institute Adam Spargo, The Wellcome Trust Sanger Institute Steven Leonard, The Wellcome Trust Sanger Institute Mark Rae, The Wellcome Trust Sanger Institute Antony Cox, The Wellcome Trust Sanger Institute pp. 544-545
Agent-Oriented Approach to DNA Computing (Abstract) Grace Steele, Morgan State University Vojislav Stojkovic, Morgan State University pp. 546-551
Accelerating the Kernels of BLAST with an Efficient PIM (Processor-In-Memory) Architecture (PDF) Jung-Yup Kang, University of Southern California Sandeep Gupta, University of Southern California Jean-Luc Gaudiot, University of California at Irvine pp. 552-553
Microarray Analysis
Qvalue Method May Not Always Control False Discovery Rate in Genomics Applications (PDF) Xiao Yang, Monsanto Company pp. 556-557
Application of a Genetic Algorithm/K-Nearest Neighbor Method to the Classification of Renal Cell Carcinoma (PDF) Dongqing Liu, University of Akron Ting Shi, Cleveland Clinic Foundation Joseph A. DiDonato, Cleveland Clinic Foundation John D. Carpten, Translational Genomics Research Institute Jianping Zhu, University of Akron Zhong-Hui Duan, University of Akron pp. 558-559

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