The Community for Technology Leaders
Computational Systems Bioinformatics Conference, International IEEE Computer Society (2004)
Stanford, California
Aug. 16, 2004 to Aug. 19, 2004
ISBN: 0-7695-2194-0
TABLE OF CONTENTS
Microarray Analysis
Other

Preface (PDF)

pp. xvii
Introduction

Preface (PDF)

pp. xvii

Committees (PDF)

pp. xviii-xix

Referees (PDF)

pp. xx
Keynote Addresses
Invited Talks

Are We There Yet? Genomic Profiling and Mechanism in Cancer Research (PDF)

Paul Meltzer , National Human Genome Research Institute
Yidong Chen , National Human Genome Research Institute
Kristin Baird , National Human Genome Research Institute
Sean Davis , National Human Genome Research Institute
pp. 6

Spaghetti Code, Soupy Logic, and the Expression of Genes (PDF)

Jim Kent , University of California at Santa Cruz
pp. 7

High Content Cellular Analysis and Their Applications (PDF)

Stephen T.C. Wong , Harvard Medical School and Brigham & Womenés Hospital
pp. 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
Genomics

Shannon Information in Complete Genomes (Abstract)

Ta-Yuan Chen , National Central University
Li-Ching Hsieh , National Central University
Hong-Da Chen , National Central University
Liaofu Luo , Inner Mongolia University
Chang-Heng Chang , National Central 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.
Asher Zilberstein , Aventis Pharmaceuticals Inc.
Li Li , Aventis Pharmaceuticals Inc.
Chang S. Hahn , Aventis Pharmaceuticals Inc.
pp. 31-39

Recurrence Time Statistics: Versatile Tools for Genomic DNA Sequence Analysis (Abstract)

Wen-wen Tung , National Center for Atmospheric Research
Yinhe Cao , University of Florida
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)

Jude Shavlik , University of Wisconsin-Madison
Steven Smith , NimbleGen Systems, Inc.
Thomas Albert , NimbleGen Systems, Inc.
Michael Molla , University of Wisconsin-Madison and NimbleGen Systems, Inc.
Todd Richmond , NimbleGen Systems, Inc.
pp. 69-79

Space-Conserving Optimal DNA-Protein Alignment (Abstract)

Pang Ko , Iowa State University
Mahesh Narayanan , Iowa State University
Srinivas Aluru , Iowa State University
Anantharaman Kalyanaraman , Iowa State University
pp. 80-88
Evolution and Phylogeny

Rec-I-DCM3: A Fast Algorithmic Technique for Reconstructing Large Phylogenetic Trees (Abstract)

Tiffani L. Williams , University of New Mexico
Tandy Warnow , University of Texas at Austin
Bernard M. E. Moret , University of New Mexico
Usman W. Roshan , University of Texas at Austin
pp. 98-109
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)

Stephen J. Roberts , University of Oxford
Sach Mukherjee , University of Oxford
pp. 131-141

Minimum Entropy Clustering and Applications to Gene Expression Analysis (Abstract)

Keshu Zhang , Rensselaer Polytechnic Institute
Haifeng Li , University of California at Riverside
Tao Jiang , University of California at Riverside
pp. 142-151

Profile-Based String Kernels for Remote Homology Detection and Motif Extraction (Abstract)

Christina Leslie , Columbia University
Yoav Freund , Columbia University
Eugene Ie , Columbia University
Mahira Siddiqi , Columbia University
Kai Wang , Columbia University
Ke Wang , Columbia University
Rui Kuang , 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)

Jingyi Yang , University of Nebraska at Lincoln
Jitender S. Deogun , University of Nebraska at Lincoln
Zhaohui Sun , University of Nebraska at Lincoln
pp. 173-181

Biclustering in Gene Expression Data by Tendency (Abstract)

Jinze Liu , University of North Carolina
Wei Wang , University of North Carolina
Jiong Yang , University of Illinois, Urbana-Champaign
pp. 182-193

Improved Fourier Transform Method for Unsupervised Cell-Cycle Regulated Gene Prediction (Abstract)

Liu Jian Hua , Genome Institute of Singapore
Karuturi R. Krishna Murthy , Genome Institute of Singapore
pp. 194-203
Proteomics

SPIDER: Software for Protein Identification from Sequence Tags with De Novo Sequencing Error (Abstract)

Kaizhong Zhang , University of Western Ontario
Bin Ma , University of Western Ontario
Yonghua Han , 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)

Ambuj K. Singh , University of California at Santa Barbara
Tolga Can , University of California at Santa Barbara
Orhan Çamoğlu , 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)

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
Bo Yan , University of Georgia and Computational Biology Institute
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)

James C. Sacchettini , Texas A&M University
Kreshna Gopal , Texas A&M University
Thomas R. Ioerger , Texas A&M University
Tod D. Romo , Texas A&M University
pp. 255-265

Reasoning about Molecular Similarity and Properties (Abstract)

Rahul Singh , San Francisco State University
pp. 266-277

An Algorithm for Detecting Homologues of Known Structured RNAs in Genomes (Abstract)

Kaizhong Zhang , University of Western Ontario and Simon Fraser University
Shu-Yun Le , National Cancer Institute
Jacob V. Maizel, Jr. , National Cancer Institute
pp. 300-310

Inverse Protein Folding in 2D HP Mode (Extended Abstract) (Abstract)

Ladislav Stacho , Simon Fraser University
Ján Maňuch , Simon Fraser University
Arvind Gupta , Simon Fraser University
pp. 311-318
Pathways & Networks

Multi-Knockout Genetic Network Analysis: The Rad6 Example (Abstract)

Eytan Ruppin , Tel Aviv University
Alon Kaufman , Hebrew University
Martin Kupiec , Tel Aviv University
pp. 332-340

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)

Zhengchang Su , University of Georgia and Oak Ridge National Laboratory
Ying Xu , University of Georgia and Oak Ridge National Laboratory
Victor Olman , University of Georgia
Hanchuan Peng , University of Georgia and Oak Ridge National Laboratory
pp. 363-370
Applied Bioinformatics

PoPS: A Computational Tool for Modeling and Predicting Protease Specificity (Abstract)

George B. Rudy , Walter & Eliza Hall Institute of Medical Research
Robert N. Pike , Monash University
Sarah E. Boyd , Monash University
James C. Whisstock , Monash University
Maria Garcia de la Banda , Monash University
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)

Karin Borges , Emory University
Brian J. Ciliax , Emory University
Venu Dasigi , Southern Polytechnic State University
Shamkant B. Navathe , Georgia Institute of Technology
Ying Liu , Georgia Institute of Technology
Ashwin Ram , Georgia Institute of Technology
Ray Dingledine , Emory University
pp. 394-404

AZuRE, a Scalable System for Automated Term Disambiguation of Gene and Protein Names (Abstract)

William S. Hayes , AstraZeneca R&D Boston
Gregory Amoutzias , AstraZeneca
John G. Cleary , Reel Two, Ltd. and University of Waikato
Raf M. Podowski , AstraZeneca R&D Boston and Karolinska Institutet
Nicholas T. Goncharoff , Reel Two, Inc.
pp. 415-424

Comparative Analysis of Gene Sets in the Gene Ontology Space under the Multiple Hypothesis Testing Framework (Abstract)

Sheng Zhong , Harvard University
Kai-Florian Storch , Harvard Medical School
Wing H. Wong , Harvard University
Lu Tian , Harvard University
Cheng Li , Harvard University and Dana Farber Cancer Institute
pp. 425-435

Gene Ontology Friendly Biclustering of Expression Profiles (Abstract)

Wei Wang , University of North Carolina
Jiong Yang , University of Illinois at Urbana-Champaign
Jinze Liu , University of North Carolina
pp. 436-447
Biomedical Research

High-Throughput Computational and Experimental Biology Strategy in Identifying Tumor Expressing CAMs (PDF)

Michelle L. Varney , University of Nebraska Medical Center
Anguraj Sadanandam , 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)

Anthony J. Kusalik , University of Saskatchewan
Fang-Xiang Wu , University of Saskatchewan
Wen-Jun Zhang , University of Saskatchewan
pp. 454-455

Nonlinear Modeling on Protein Kinase C(PKC)-Epsilon Inverse Regulation of Stress Fibers in Oncogenically Transformed Cells (PDF)

Julie A. Barnes , Bowling Green State University
Yingxin Li , Bowling Green State University
Carol A. Heckman , Bowling Green State University
pp. 456-457
Comparative Genomics

Exploring Genomic Context Patterns for Rhodobacter Sphaeroides in the HERBE Knowledge Discovery Environment (PDF)

Eric G. Stephan , Pacific Northwest National Laboratory
Heidi J. Sofia , Pacific Northwest National Laboratory
George Chin , Pacific Northwest National Laboratory
Kyle R. Klicker , Pacific Northwest National Laboratory
Abigail L. Corrigan , Pacific Northwest National Laboratory
pp. 462-463

RepeatAssembler: A Package for Annotation of Full-Length Repetitive DNA Sequences in Fungal Genomes (Abstract)

Chuck Staben , University of Kentucky
Jerzy W. Jaromczyk , University of Kentucky
Mark L. Farman , University of Kentucky
Joshua W. Gilkerson , University of Kentucky
pp. 464-467
Data Mining

Search-Space Reduction of a Non-Redundant Peptide Database (PDF)

Ian Shadforth , Cranfield University
Conrad Bessant , Cranfield University
Daniel Crowther , GlaxoSmithKline
pp. 470-471

Development of a Knowledge-Based Multi-Scheme Cancer Microarray Data Analysis System (PDF)

Kejiao Guo , Georgia Institute of Technology and Emory University
Weimin Feng , Georgia Institute of Technology and Emory University
Geoffrey Wang , Georgia Institute of Technology
John H. Phan , Georgia Institute of Technology and Emory University
Chang F. Quo , Georgia Institute of Technology and Emory University
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
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
Marilyn Safran , Weizmann Institute of Science
Doron Lancet , Weizmann Institute of Science
Michael Shmoish , Weizmann Institute of Science
pp. 478-479

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)

Stephen J. Roberts , University of Oxford
Sach Mukherjee , University of Oxford
pp. 487-488

Automating the Biological Data Collection Process with Agents (PDF)

I. V. Ramakrishnan , State University of New York
Nikeeta Julasana , State University of New York
Zo? Lacroix , Arizona State University
Hasan Davulcu , Arizona State University
Kaushal Parekh , Arizona State University
pp. 489-490

An Intelligent Digital Library System for Biologists (PDF)

Marc Greenblatt , University of Vermont
Xindong Wu , University of Vermont
Jeffrey Stone , University of Vermont
pp. 491-492

A New Approach to Clustering Biological Data Using Message Passing (PDF)

Hesham Ali , University of Nebraska at Omaha
Huimin Geng , University of Nebraska at Omaha
Dhundy Bastola , University of Nebraska Medical Center
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

Probability Profile Method — New Approach to Data Analysis in Tandem Mass Spectrometry (Abstract)

Tema Fridman , Oak Ridge National Laboratory
Michael B. Strader , Oak Ridge National Laboratory
Robert M. Day , Oak Ridge National Laboratory
Andrey Borziak , Oak Ridge National Laboratory
Andrey Gorin , Oak Ridge National Laboratory
Gregory B. Hurst , Oak Ridge National Laboratory
pp. 499-502

Assigning Gene Ontology Categories (GO) to Yeast Genes Using Text-Based Supervised Learning Methods (PDF)

Hirotoshi Taira , NTT Communication Science Laboratories
Tomonori Izumitani , NTT Communication Science Laboratories
Eisaku Maeda , NTT Communication Science Laboratories
Hideto Kazawa , 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

Embedded Computation of Maximum-Likelihood Phylogeny Inference Using Platform FPGA (Abstract)

K. P. Lam , Chinese University of Hong Kong
Terrence S. T. Mak , 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)

Lindsey M. Ouellette , Michigan State University
Cheryl L. Tarr , Michigan State University
Alyssa C. Bumbaugh , Michigan State University
Thomas S. Whittam , Michigan State University
David W. Lacher , Michigan State University
Teresa M. Large , Michigan State University
Weihong Qi , Michigan State University
Katie E. Hyma , 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)

Shuba Gopal , Rochester Institute of Technology
Allison Griggs , Rochester Institute of Technology
pp. 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
Wen-wen Tung , National Center for Atmospheric Research
Jianbo Gao , University of Florida
Yinhe Cao , University of Florida and BioSieve
pp. 531-532

Positive Sample Only Learning (PSOL) for Predicting RNA Genes in E. coli (Abstract)

Xiaofeng He , Lawrence Berkeley National Laboratory
Stephen R. Holbrook , Lawrence Berkeley National Laboratory
Richard F. Meraz , Lawrence Berkeley National Laboratory
Chris H.Q. Ding , Lawrence Berkeley National Laboratory
pp. 535-538
High Content Analysis

Quantitative Analysis of Membrane Protein Localization and Signaling (PDF)

Mark M. Davis , Stanford University and Howard Hughes Medical Institute
Johannes B. Huppa , Stanford University and Howard Hughes Medical Institute
Peter M. Kasson , Stanford University
Axel T. Brunger , Stanford University and Howard Hughes Medical Institute
pp. 540-541
High Performance Computing

The SSAHA Trace Server (PDF)

Antony Cox , The Wellcome Trust Sanger Institute
Steven Leonard , The Wellcome Trust Sanger Institute
William Spooner , The Wellcome Trust Sanger Institute
Adam Spargo , The Wellcome Trust Sanger Institute
Zemin Ning , The Wellcome Trust Sanger Institute
Mark Rae , 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)

Sandeep Gupta , University of Southern California
Jung-Yup Kang , University of Southern California
Jean-Luc Gaudiot , University of California at Irvine
pp. 552-553
Microarray Analysis

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
Zhong-Hui Duan , University of Akron
Joseph A. DiDonato , Cleveland Clinic Foundation
John D. Carpten , Translational Genomics Research Institute
Jianping Zhu , University of Akron
pp. 558-559

EGOMinor: A Genomics and Proteomics Data Computation and Interpretation System for Biomedical Applications (PDF)

Gaurav Tuteja , Georgia Institute of Technology
Weimin Feng , Georgia Institute of Technology and Emory University
May D. Wang , Georgia Institute of Technology and Emory University
pp. 562-563

A Java Program to Create Simulated Microarray Images (PDF)

Bill Martin , Attotron Biosensor Corporation
Robert M. Horton , Attotron Biosensor Corporation
pp. 564-565

Inferring Genetic Networks from Microarray Data (Abstract)

Elebeoba May , Sandia National Laboratories
Shawn Martin , Sandia National Laboratories
George Davidson , Sandia National Laboratories
Jean-Loup Faulon , Sandia National Laboratories
Margaret Werner-Washburne , University of New Mexico
pp. 566-569

Extracting Characteristic Patterns from Genome - Wide Expression Data by Non-Negative Matrix Factorization (PDF)

Simon J. Shepherd , University of Bradford
Nini Rao , University of Electronic Science and Technology
pp. 570-571

Imputation of Missing Values in DNA Microarray Gene Expression Data (PDF)

Gene H. Golub , Stanford University
Hyunsoo Kim , University of Minnesota
Haesun Park , University of Minnesota
pp. 572-573

Disease Gene Explorer: Display Disease Gene Dependency by Combining Bayesian Networks with Clustering (PDF)

Yimin Zhang , Intel China Research Center
We Hu , Intel China Research Center
Feng Xue , Intel China Research Center
Qian Diao , Intel China Research Center
Juntao Li , Intel China Research Center
Tao Wang , Intel China Research Center
Hao Zhong , Intel China Research Center
pp. 574-575

DNA Microarray Image Analysis Using Active Contour Model (PDF)

Cheng-Wei Huang , Fu Jen University
Yuan-Kai Wang , Fu Jen University
pp. 576-577

Meanshift Clustering for DNA Microarray Analysis (PDF)

Danny Barash , Ben-Gurion University
Dorin Comaniciu , Siemens Corporate Research
pp. 578-579

The Dynamic Range of Gene Expressions Depend on Their Ontology (PDF)

Xujing Wang , Medical College of Wisconsin
Soumitra Ghosh , Medical College of Wisconsin
Yizhou Xie , Medical College of Wisconsin
Parthav Jailwalia , Medical College of Wisconsin
pp. 580-581

Subspace Clustering for Microarray Data Analysis: Multiple Criteria and Significance Assessment (PDF)

Hui Fang , University of Illinois at Urbana-Champaign
Chengxiang Zhai , University of Illinois at Urbana-Champaign
Jiong Yang , University of Illinois at Urbana-Champaign
Lei Liu , University of Illinois at Urbana-Champaign
pp. 582-583

Comparative Analysis of Gene Expression and DNA Copy Number Data for Pancreatic and Breast Cancers Using an Orthogonal Decomposition (PDF)

Sampsa Hautaniemi , Tampere University of Technology
Sanjit K. Mitra , University of California at Santa Barbara
John A. Berger , University of California at Santa Barbara
pp. 584-585

High-Throughput Microarray-Based Genotyping (PDF)

Earl Hubbell , Affymetrix, Inc.
Ming-Hsiu Ho , Affymetrix, Inc.
Geoffrey Yang , Affymetrix, Inc.
pp. 586-587
Other

Navigating through the Biological Maze (PDF)

Kaushal Parekh , Arizona State University
Maria Esther Vidal , Universidad Sim?n Bol?var
Louiqa Raschid , University of Maryland
Zo? Lacroix , Arizona State University
pp. 594-595

How Biological Source Capabilities May Affect the Data Collection Process (PDF)

Zo? Lacroix , Arizona State University
Vidyadhari Edupuganti , Arizona State University
pp. 596-597
Pathways Networks Systems Biology

A New Hierarchical Method for Identification of Dynamic Regulatory Pathways from Time-Series DNA Microarray Data (PDF)

K. Gopalakrishnan , University of North Carolina at Charlotte
R. H. Zadeh , University of North Carolina at Charlotte
Kayvan Najarian , University of North Carolina at Charlotte
Alireza Darvish , University of North Carolina at Charlotte
E. Bak , University of North Carolina at Charlotte
pp. 602-603

Boosted PRIM with Application to Searching for Oncogenic Pathway of Lung Cancer (Abstract)

Jonathan Pollack , Stanford University
Robert Tibshirani , Stanford University
Pei Wang , Stanford University
Young Kim , Stanford University
pp. 604-609

A. Genetic Algorithm for Inferring Time Delays in Gene Regulatory Networks (PDF)

Wen-Jun Zhang , University of Saskatchewan
Anthony J. Kusalik , University of Saskatchewan
Fang-Xiang Wu , University of Saskatchewan
pp. 610-611

A Knowledge Base for Computational Pathway Reconstruction (PDF)

Peng Wang , University of Georgia
Phuongan Dam , University of Georgia
Zhengchang Su , University of Georgia
Ying Xu , University of Georgia
pp. 612-613

In Silico Construction of the Carbon Fixation Pathway in Synechococcus sp. WH8102 (PDF)

Ying Xu , University of Georgia at Athens and Oak Ridge National Laboratory
Phuongan Dam , University of Georgia at Athens and Oak Ridge National Laboratory
Zhengchang Su , University of Georgia at Athens and Oak Ridge National Laboratory
Victor Olman , University of Georgia at Athens
pp. 614-615

A Finite Model Theory for Biological Hypotheses (Abstract)

Christopher Griffin , Penn State University
Stephen Racunas , Penn State University
Nigam Shah , Penn State University
pp. 616-620

Bacillus Subtilis Protein Interaction Network Analysis (Abstract)

Peter Andras , University of Newcastle upon Tyne
Olusola C. Idowu , University of Newcastle upon Tyne
Steven J. Lynden , University of Newcastle upon Tyne
Malcolm P. Young , University of Newcastle upon Tyne
pp. 623-625

Dynamical Robustness in Gene Regulatory Networks (PDF)

Shawn Martin , Sandia National Laboratories
Robert D. Carr , Sandia National Laboratories
Jean-Loup Faulon , Sandia National Laboratories
pp. 626-627

Synchronized Oscillations and Chaos in Coupled Genetic Repressilators (PDF)

Jesse Bridgewater , University of California at Los Angeles
Vwani P. Roychowdhury , University of California at Los Angeles
Jianbo Gao , University of Florida
pp. 630-631

Inference of Gene Regulatory Network Based on Module Network Model with Gene Functional Classifications (PDF)

Reiji Teramoto , Sumitomo Pharmaceuticals Co., Ltd.
Hideo Matsuda , Osaka University
Yoichi Takenaka , Osaka University
Kohei Taki , Osaka University
pp. 632-633

Parallel Extreme Pathway Computation for Metabolic Networks (Abstract)

Kwok Ko , Stanford Linear Accelerator Center
Lie-Quan Lee , Stanford Linear Accelerator Center
Jeff Varner , Genencor International, Inc
pp. 636-639

Computational Construction of Nitrogen Assimilation Pathway in Cyanobacteria Synechococcus sp. WH8102 (PDF)

Z. Su , University of Georgia and Oak Ridge National Laboratory
T. Jiang , University of California at Riverside
V. Olman , University of Georgia and Oak Ridge National Laboratory
X. Chen , University of California at Riverside
P. Dam , University of Georgia and Oak Ridge National Laboratory
Y. Xu , University of Georgia and Oak Ridge National Laboratory
pp. 640-641

Pathway Mapping with Operon Information: An Integer-Programming Method (PDF)

Ying Xu , University of Georgia and Oak Ridge National Laboratory
Fenglou Mao , University of Georgia and Oak Ridge National Laboratory
Victor Olman , University of Georgia and Oak Ridge National Laboratory
David Chuang , University of Georgia and Oak Ridge National Laboratory
Zhengchang Su , University of Georgia and Oak Ridge National Laboratory
pp. 642-643

Analysis of Signaling Pathways in Human T-Cells Using Bayesian Network Modeling of Single Cell Data (PDF)

Dana Pe?er , Harvard Medical School
Garry P. Nolan , Stanford University School of Medicine
Douglas A. Lauffenburger , Massachusetts Institute of Technology
David K. Gifford , Massachusetts Institute of Technology
Tommi S. Jaakkola , Massachusetts Institute of Technology
Karen Sachs , Massachusetts Institute of Technology
Omar D. Perez , Stanford University School of Medicine
pp. 644

Applying Two-Level Simulated Annealing on Bayesian Structure Learning to Infer Genetic Networks (PDF)

Guoliang Xue , Arizona State University
Jeffrey W. Touchman , Arizona State University
Tie Wang , Arizona State University
pp. 647-648
Pattern Recognition

A Efficient Algorithm for Unique Signature Discovery on Whole-Genome EST Databases (PDF)

Yin Te Tsai , Providence University - Taiwan
Chuan Yi Tang , National Tsing-Hua University
Tzu Fang Sheu , National Tsing-Hua University
Ching Hua Shih , National Tsing-Hua University
Hsiao Ping Lee , National Tsing-Hua University
pp. 650-651

VirusFinder: A Web-Based Virus Identification System Using Viral Nucleotide Signatures (PDF)

Yan Ding , American Type Culture Collection
Shu Wen , Dalian Medical University
Hong Cao , American Type Culture Collection
pp. 652-653

Incremental and Decremental Least Squares Support Vector Machine and Its Application to Drug Design (PDF)

Hyunsoo Kim , University of Minnesota - Twin Cities
Haesun Park , University of Minnesota - Twin Cities
pp. 656-657

A Prediction Model for the Drug Efficacy of Interferon in CHC Patients Based on SNPs (PDF)

Yuchi Hwang , Vita Genomics, Inc.
Dennis Chen , Vita Genomics, Inc.
Z. John Gu , Vita Genomics, Inc.
Eugene Lin , Vita Genomics, Inc.
Ashely Chang , Vita Genomics, Inc.
pp. 658-659

RNA Motif Search Using the Structure to String (STR²) Method (PDF)

Oriel Bergig , Ben-Gurion University
Danny Barash , Ben-Gurion University
Klara Kedem , Ben-Gurion University
pp. 660-661

PRUNER: Algorithms for Finding Monad Patterns in DNA Sequences (Abstract)

Amar Mukherjee , University of Central Florida
Ravi VijayaSatya , University of Central Florida
pp. 662-665

CUBIC: Search for Binding Sites (PDF)

Ying Xu , University of Georgia and Oak Ridge National Laboratory
Victor Olman , University of Georgia
Zhengchang Su , Oak Ridge National Laboratory
PhuongAn Dam , Oak Ridge National Laboratory
Jizhu Lu , University of Georgia
pp. 666-667

A Hidden Markov Model for Gene Function Prediction from Sequential Expression Data (PDF)

Hesham Ali , University of Nebraska at Omaha
Xutao Deng , University of Nebraska at Omaha
pp. 670-671

Using Enhancing Signals to Improve Specificity of ab initio Splice Site Sensors (PDF)

Jitender Deogun , University of Nebraska-Lincoln
Alexandre Tchourbanov , University of Nebraska at Omaha
Hesham H. Ali , University of Nebraska at Omaha
pp. 672-673

SRPVS: A New Motif Searching Algorithm for Protein Analysis (PDF)

Anguraj Sadanandam , University of Nebraska Medical Center
Hesham Ali , University of Nebraska at Omaha
Xiaolu Huang , University of Nebraska at Omaha
Rakesh Singh , University of Nebraska Medical Center
pp. 674-675

Locating All Tandem Repeat Families in a Sequence (Abstract)

Donald Adjeroh , West Virginia University
Jianan Feng , West Virginia University
pp. 676-681
Promoter Analysis

Selection of Putative Cis-Regulatory Motifs through Regional and Global Conservation (PDF)

Fazel A. Famili , National Research Council Canada
Marianna Sikorska , National Research Council Canada
Roy Walker , National Research Council Canada
Youlian Pan , National Research Council Canada
Brandon Smith , National Research Council Canada
Hung Fang , National Research Council Canada
pp. 684-685

Promoter Recognition for E. coli DNA Segments by Independent Component Analysis (Abstract)

Yasuo Matsuyama , Waseda University
Ryo Kawamura , Sony-Kihara Research Center Inc.
pp. 686-691
Protein Structure Analysis

Computational Analysis and Classification of p53 Mutants According to Primary Structure (PDF)

Kayvan Najarian , University of North Carolina at Charlotte
Alireza Darvish , University of North Carolina at Charlotte
R. H. Zadeh , University of North Carolina at Charlotte
Krishna Gopalakrishnan , University of North Carolina at Charlotte
pp. 694-695

In-Silico Prediction of Surface Residue Clusters for Enzyme-Substrate Specificity (PDF)

Al Geist , Oak Ridge National Laboratory
Praveen Chandramohan , Oak Ridge National Laboratory
Nagiza F. Samatova , Oak Ridge National Laboratory
Byung-Hoon Park , Oak Ridge National Laboratory
Gong-Xin Yu , Oak Ridge National Laboratory
pp. 696-697

Comparing 3D Protein Structures Similarity by Using Fractal Features (PDF)

Jiaoying Shi , Zhejiang University
Chenyang Cui , Zhejiang University
Donghui Wang , Zhejiang University
pp. 698-699

Structural Analysis of FGFR1 Kinase Activation through Molecular Dynamics Simulation (PDF)

Peng Wang , University of Georgia
Zhengchang Su , University of Georgia
Juntao Guo , University of Georgia
Ying Xu , University of Georgia
pp. 700-701

Automatic Prediction of Functional Site Regions in Low-Resolution Protein Structures (PDF)

Jaspreet Singh Sodhi , University College London
Lorenz Wernisch , University College London
David T. Jones , University College London
Jonathan J. Ward , University College London
Kevin Bryson , University College London
Liam J. McGuffin , University College London
pp. 702-703

BPAP: A Computational Tool for Whole Genome Analysis and Annotation (PDF)

Martin Gollery , University of Nevada Reno
Barrett Abel , University of Nevada Reno
pp. 704-705

Molecular Modeling of Full-Length OxyR from Shewanella oneidensis MR-1 and Molecular Dynamics Studies of the Activation Domain (PDF)

Ying Xu , University of Georgia and Oak Ridge National Laboratory
Jun-tao Guo , University of Georgia
pp. 708-709
RNAi Analysis

Contraction Graphs for Representation and Analysis of RNA Secondary Structure (PDF)

Chris H. Q. Ding , Lawrence Berkeley National Laboratory
Stephen R. Holbrook , Lawrence Berkeley National Laboratory
Richard F. Meraz , Lawrence Berkeley National Laboratory
Xiaofeng He , Lawrence Berkeley National Laboratory
pp. 716-717

Identifying MicroRNAs in Plant Genomes (Abstract)

Doreen Ware , Cold Spring Harbor Laboratory
Lincoln Stein , Cold Spring Harbor Laboratory
Christopher Maher , Cold Spring Harbor Laboratory
Marja Timmermans , Cold Spring Harbor Laboratory
pp. 718-723
Sequence Alignment

SUPERCONTIGS: A Contig Scaffolding Tool (PDF)

Daniela Puiu , Virginia Commonwealth University
pp. 736-737

Multiple Alignment of Rearranged Genomes (PDF)

Mark Craven , University of Wisconsin-Madison
Bob Mau , University of Wisconsin-Madison
Aaron E. Darling , University of Wisconsin-Madison
Nicole T. Perna , University of Wisconsin-Madison
pp. 738-739

An Exhaustive Genome Assembly Algorithm Using K-Mers to Indirectly Perform N-Squared Comparisons in O(N) (PDF)

Maulik K. Shah , Arizona State University and Translational Genomics Research Institute
Stephanie A. Rogers , Arizona State University
HoJoon Lee , Arizona State University
Jeffrey W. Touchman , Translational Genomics Research Institute and Arizona State University
pp. 740-741
SNPs and Haplotyping

Association Tests and Estimation of Haplotype Frequencies and of Penetrance-Related Parameters in a Case-Control Study (PDF)

Shiori Furihata , Japan Biological Informatics Consortium
Toshikazu Ito , Mitsubishi Research Institute, INC.
Naoyuki Kamatani , TokyoWomen?s Medical University
pp. 744-745
Synthetic Biological Systems

Designing Synthetic Biological Systems by Multiple Time Scale Networks (PDF)

Luonan Chen , Osaka Sangyo University
Ruiqi Wang , Osaka Sangyo University
Junya Nakai , Osaka Sangyo University
Mitsuyasu Seo , Osaka Sangyo University
pp. 748-749
Author Index

Author Index (PDF)

pp. 753-756
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