The Community for Technology Leaders
Computational Systems Bioinformatics Conference, International IEEE Computer Society (2003)
Stanford, California
Aug. 11, 2003 to Aug. 14, 2003
ISBN: 0-7695-2000-6
TABLE OF CONTENTS

Preface (PDF)

pp. xv

Program Committee (PDF)

pp. xvii

Referees (PDF)

pp. xviii
Keynote Addresses

Stepping Up the Pace of Discovery: the Genomes to Life Program (Abstract)

Gary Johnson , U.S. Department of Energy Office of Science
Edward Uberbacher , UT-Battelle, LLC
David Thomassen , U.S. Department of Energy Office of Science
Carl E. Oliver , U.S. Department of Energy Office of Science
Aristides Patrinos , U.S. Department of Energy Office of Science
Marvin Frazier , U.S. Department of Energy Office of Science
pp. 2

The Role of Algorithmic Research in Computational Genomics (PDF)

Richard M. Karp , University of California at Berkeley
pp. 10
Invited Speakers

Bridging Paradigm Gaps Between Biology and Engineering (PDF)

Johoshua Bruck , California Institute of Technology
pp. 14

Epitope Prediction Algorithms for Peptide based Vaccine Design (Abstract)

Russell Schwartz , Celera/Applied Biosystems
Stephen Hoffman , Celera/Applied Biosystems
Bjarni Halld?rsson , Celera/Applied Biosystems
Oliver Kohlbacher , Celera/Applied Biosystems
Sorin Istrail , Celera/Applied Biosystems
Liliana Florea , Celera/Applied Biosystems
pp. 17

Pathway Bioinformatics (PDF)

Peter Karp , SRI International
pp. 27

Eulerian Path Methods for Multiple Sequence Alignment (PDF)

Yu Zhang , University of Southern California
Michael S. Waterman , University of Southern California
pp. 29
Genomes to Life

Computing for the DOE Genomes to Life Program (PDF)

David Thomassen , Office of Biological and Environmental Research
Ari Patrinos , Office of Biological and Environmental Research
Marvin Frazier , Office of Biological and Environmental Research
Gary Johnson , Office of Advanced Scientific Computing Research
Ed Uberbacher , Oak Ridge National Laboratory
Carl E. Oliver , Office of Advanced Scientific Computing Research
pp. 32
Microarray Data Analysis

Clustering Binary Fingerprint Vectors with Missing Values for DNA Array Data Analysis (Abstract)

Tao Jiang , Univ. of Calif., Riverside
Andres Figueroa , Univ. of Calif., Riverside
James Borneman , Univ. of Calif., Riverside
pp. 38

Fast and Accurate Probe Selection Algorithm for Large Genomes (Abstract)

Wing-Kin Sung , National University of Singapore
Wah-Heng Lee , Genome Institute of Singapore
pp. 65

Degenerate Primer Design via Clustering (Abstract)

David N. Kuhn , Florida International University
Xintao Wei , Florida International University
Giri Narasimhan , Florida International University
pp. 75

Group Testing With DNA Chips: Generating Designs and Decoding Experiments (Abstract)

Alexander Schliep , Max-Planck-Institute for Molecular Genetics
David C. Torney , Los Alamos National Laboratory
Sven Rahmann , Max-Planck-Institute for Molecular Genetics; Freie Universit?t Berlin
pp. 84
Pathways, Networks, and Systems Biology

Can We Identify Cellular Pathways Implicated in Cancer Using Gene Expression Data? (Abstract)

Jorge Lepre , T.J. Watson Research Center
Yuhai Tu , T.J. Watson Research Center
Nigam Shah , Pennsylvania State University
Gustavo Stolovitzky , T.J. Watson Research Center
pp. 94

Combining Microarrays and Biological Knowledge for Estimating Gene Networks via Bayesian Networks (Abstract)

Takao Goto , University of Tokyo
Kousuke Tashiro , Kyushu University
Satoru Miyano , University of Tokyo
Tomoyuki Higuchi , The Institute of Statistical Mathematics
Satoru Kuhara , Kyushu University
Seiya Imoto , University of Tokyo
pp. 104
Biomedical Research and Visualization

Stochastic Stage-structured Modeling of the Adaptive Immune System (Abstract)

Dennis L. Chao , University of New Mexico
Alan S. Perelson , Los Alamos National Laboratory
Stephanie Forrest , University of New Mexico
Miles P. Davenport , University of New South Wales
pp. 124

A Personalized and Automated dbSNP Surveillance System (Abstract)

Mark Woon , Stanford Medical Informatics
Steve Lin , Stanford Medical Informatics
Russ B. Altman , Stanford Medical Informatics
Teri E. Klein , Stanford Medical Informatics
Shuo Liu , Stanford Medical Informatics
pp. 132

Fourier Harmonic Approach for Visualizing Temporal Patterns of Gene Expression Data (Abstract)

Murali Ramanathan , State University of New York at Buffalo
Li Zhang , State University of New York at Buffalo
Aidong Zhang , State University of New York at Buffalo
pp. 137

Towards Index-based Similarity Search for Protein Structure Databases (Abstract)

Tamer Kahveci , University of California, Santa Barbara
Ambuj K. Singh , University of California, Santa Barbara
Orhan ?amoglu , University of California, Santa Barbara
pp. 148

Local Similarity in RNA Secondary Structures (Abstract)

Matthias H?chsmann , University of Bielefeld
Robert Giegerich , University of Bielefeld
Stefan Kurtz , University of Bielefeld
Thomas T?ller , University of Bielefeld
pp. 159

CTSS: A Robust and Efficient Method for Protein Structure Alignment Based on Local Geometrical and Biological Features (Abstract)

Yuan-Fang Wang , University of California at Santa Barbara
Tolga Can , University of California at Santa Barbara
pp. 169

Statistical Inference for Well-ordered Structures in Nucleotide Sequences (Abstract)

Jacob V. Maizel, Jr. , National Cancer Institute, NIH
Jih-H. Chen , SAIC-NCI/FCRDC
Shu-Yun Le , National Cancer Institute, NIH
pp. 190

Automated Protein NMR Resonance Assignments (Abstract)

Dong Xu , Oak Ridge National Laboratory
Carolyn M. Slupsky , University of Alberta
Guohui Lin , University of Alberta
Xiang Wan , University of Alberta
pp. 197

3D Structural Homology Detection via Unassigned Residual Dipolar Couplings (Abstract)

Bruce Randall Donald , Dartmouth Computer Science Department
Christopher James Langmead , Dartmouth Computer Science Department
pp. 209
Data Mining

Discovering Compact and Highly Discriminative Features or Feature Combinations of Drug Activities Using Support Vector Machines (Abstract)

Wei Wang , University of North Carolina
Jiong Yang , University of Illinois, Urbana-Champaign
Hwanjo Yu , University of Illinois, Urbana-Champaign
Jiawei Han , University of Illinois, Urbana-Champaign
pp. 220

Initial Large-scale Exploration of Protein-protein Interactions in Human Brain (Abstract)

Irene Ota , Myriad Proteomics, Inc.
Sudhir Sahasrabudhe , Myriad Proteomics, Inc.
Jake Y. Chen , Myriad Proteomics, Inc.
Andrey Y. Sivachenko , Myriad Proteomics, Inc.
Cornelia Kurschner , Myriad Proteomics, Inc.
Russell Bell , Myriad Proteomics, Inc.
pp. 229

An SVM-based Algorithm for Identification of Photosynthesis-specific Genome Features (Abstract)

Al Geist , Oak Ridge National Laboratory
Gong-Xin Yu , Oak Ridge National Laboratory
George Ostrouchov , Oak Ridge National Laboratory
Nagiza F. Samatova , Oak Ridge National Laboratory
pp. 235

Experimental Studies of the Universal Chemical Key (UCK)Algorithm on the NCI Database of Chemical Compounds (Abstract)

Bing Liu , University of Illinois at Chicago
Robert Grossman , University of Illinois at Chicago
Pavan Kasturi , University of Illinois at Chicago
Donald Hamelberg , University of Illinois at Chicago
pp. 244
Pattern Recognition

cWINNOWER Algorithm for Finding Fuzzy DNA Motifs (Abstract)

Shoudan Liang , NASA Ames Research Center
pp. 260

LOGOS: a modular Bayesian model for de novo motif detection (Abstract)

Eric P. Xing , University of California
Richard M. Karp , University of California, Berkeley
Michael I. Jordan , University of California, Berkeley
Wei Wu , Lawrence Berkeley National Lab
pp. 266

SMASHing regulatory sites in DNA by human-mouse sequence comparisons (Abstract)

Nikolaus Rajewsky , New York University
Terry Gaasterlamd , The Rockefeller University
Mihaela Zavolan , The Rockefeller University
Nicholas D. Socci , Albert Einstein College of Medicine
pp. 277

A Pattern Matching Algorithm for Codon Optimization and CpG Motif-Engineering in DNA Expression Vectors (Abstract)

Ravi Vijaya Satya , University of Central Florida
Udaykumar Ranga , Jawaharlal Nehru Center for Advanced Scientific Research
Amar Mukherjee , University of Central Florida
pp. 294
Sequence Alignment

ANTICLUSTAL: Multiple Sequence Alignment by Antipole Clustering and Linear Approximate 1-Median Computation (Abstract)

V. Di Pietro , Universit? di Catania
A. Pulvirenti , Universit? di Catania
M. Scalia , Universit? di Catania
G. Pigola , Universit? di Catania
T. Maugeri , Universit? di Catania
G. Emmanuele , Universit? di Catania
D. Shasha , New York University
S. Travali , Universit? di Catania
C. Di Pietro , Universit? di Catania
M. Ragusa , Universit? di Catania
M. Purrello , Universit? di Catania
E. Modica , Universit? di Catania
A. Ferro , Universit? di Catania
V. Zimmitti , Universit? di Catania
pp. 326

Efficient Constrained Multiple Sequence Alignment with Performance Guarantee (Abstract)

N. L. Ho , The University of Hong Kong, Hong Kong
T. W. Lam , The University of Hong Kong, Hong Kong
M. Y. Chan , The University of Hong Kong, Hong Kong
Francis Y. L. Chin , The University of Hong Kong, Hong Kong
Prudence W. H. Wong , The University of Hong Kong, Hong Kong
pp. 337

A New Similarity Measure among Protein Sequences (Abstract)

Ting-Yi Sung , Academia Sinica
Wen-Lian Hsu , Academia Sinica
Kuen-Pin Wu , Academia Sinica
Hsin-Nan Lin , Academia Sinica
pp. 347

A New Approach for Gene Annotation Using Unambiguous Sequence Joining (Abstract)

Robert Norgren , University of Nebraska
Alexandre Tchourbanov , University of Nebraska
Mark Pauley , University of Nebraska
Daniel Quest , University of Nebraska
Hesham Ali , University of Nebraska
pp. 353

Efficient Reconstruction of Phylogenetic Networks with Constrained Recombination (Abstract)

Satish Eddhu , University of California, Davis
Charles Langley , University of California, Davis
Dan Gusfield , University of California, Davis
pp. 363
Data Integration

A Semantic Mediation Approach for Problems in Computational Molecular Biology (PDF)

S. Santini , U.C. San Diego
M. Chagoyen , Centro Nacional de Biotecnologia, Madrid, Spain
B. Lud?scher , U.C. San Diego
P. A. De-Alarcon , Parque Cientifico de Madrid, Madrid, Spain
J. M. Carazo , Centro Nacional de Biotecnologia, Madrid, Spain
M. E. Kurul , U.C. San Diego
A. Gupta , U.C. San Diego
pp. 386

A Query Language to Support Scientific Discovery (PDF)

Kerry Deutsch , Institute for Systems Biology
Marta Janer , Institute for Systems Biology
Barbara Eckman , IBM Life Sciences
Louiqa Raschid , University of Maryland
Zo? Lacroix , Arizona State University
pp. 388
Data Mining

Application of Singular Value Decomposition and Functional Clustering to Analyzing Gene Expression Profiles of Renal Cell Carcinoma (PDF)

Louis S. Liou , Cleveland Clinic Foundation
Ting Shi , Cleveland Clinic Foundation
Joseph A. DiDonato , Cleveland Clinic Foundation
Zhong-Hui Duan , University of Akron
pp. 392

Statistical Resynchronization and Detection of Periodic Transcripts (PDF)

Zhaohui S. Qin , Harvard University
Xin Lu , Harvard University
Jun S. Liu , Harvard University
Wen Zhang , Harvard University; Kunming Medical College
pp. 394

A Method for Tight Clustering: with Application to Microarray (PDF)

Wing H. Wong , Harvard University
George C. Tseng , University of Pittsburgh
pp. 396

Accelerating the Drug Design Process through Parallel Inductive Logic Programming Data Mining (Abstract)

Ahmed Kamal , Western Kentucky University
C. David Page , University of Wisconsin
James Graham , University of Louisville
pp. 400

Estimating Recombination Rate Distribution by Optimal Quantization (Abstract)

Stephane Boissinot , Queens College
Ihsin T. Phillips , Queens College
Robert M. Haralick , City University of New York
Mingzhou Song , Queens College
pp. 403

Statistical issues in the analysis of the array CGH data (PDF)

Donna Albertson , UCSF Comprehensive Cancer Center
Jane Fridlyand , UCSF Comprehensive Cancer Center
Antoine Snijders , UCSF Comprehensive Cancer Center
Ajay Jain , UCSF Comprehensive Cancer Center
Dan Pinkel , UCSF Comprehensive Cancer Center
pp. 407

Identification of Contaminants in Proteomics Mass Spectrometry Data (PDF)

C. Yen , University of Colorado at Denver
K. Fung , University of Colorado Health Sciences Center
K. Cios , University of Colorado at Denver
H. Wang , University of Colorado at Denver
M. Duncan , University of Colorado Health Sciences Center
pp. 409

A Computational Approach to Reconstructing Gene Regulatory Networks (PDF)

Xutao Deng , University of Nebraska at Omaha
Hesham Ali , University of Nebraska at Omaha
pp. 413

Probability Profiles - Novel Approach in Tandem Mass Spectrometry De Novo Sequencing (Abstract)

Robert Day , Computer Science and Mathematics Division
Tema Fridman , Computer Science and Mathematics Division
Jane Razumovsbya , Life Sciences Division
Andrey Gorin , Computer Science and Mathematics Division
Dong Xu , Life Sciences Division
pp. 415

A Symbolic Logic Strategy For Mapping Biological Concepts in the HERBE Prototype (PDF)

Eric G. Stephan , Pacific Northwest National Laboratories
Abigail L. Corrigan , Pacific Northwest National Laboratories
Heidi J. Sofia , Pacific Northwest National Laboratories
Kyle R. Klicker , Pacific Northwest National Laboratories
George Chin Jr. , Pacific Northwest National Laboratories
pp. 419

A Computational Method for Assessing Peptide-Identification Reliability in Tandem Mass Spectrometry Analysis with SEQUEST (PDF)

Dong Xu , Oak Ridge National Laboratory; University of Tennessee, Knoxville
Ying Xu , Oak Ridge National Laboratory; University of Tennessee, Knoxville
Victor Olman , Oak Ridge National Laboratory
Jane Razumovskaya , Oak Ridge National Laboratory; University of Tennessee, Knoxville
Nathan Verbermoes , University of Tennessee, Knoxville
Ed Uberbacher , Oak Ridge National Laboratory; University of Tennessee, Knoxville
pp. 421
Functional Genomics

Tomato Expression Database (TED) - An Interactive Management Tool for Tomato Expression Profiling Data (PDF)

Rob Alba , Cornell University
Zhangjun Fei , Texas A&M University; Cornell University
Xuemei Tang , Cornell University
Jim Giovannoni , Cornell University; USDA Plant, Soil, and Nutrition Laboratory
Paxton Payton , Cornell University
pp. 424

Oncogenetics Tree Models - An Estimation (PDF)

Harpreet Kaur Gill , Christian Medical College and Hospital
pp. 426

The GeneCards<sup>TM</sup> Family of Databases: GeneCards, GeneLoc, GeneNote and GeneAnnot (PDF)

Doron Lancet , the Weizmann Institute of Science
Naomi Rosen , the Weizmann Institute of Science
Marilyn Safran , the Weizmann Institute of Science
Michael Shmoish , the Weizmann Institute of Science
Vered Chalifa-Caspi , the Weizmann Institute of Science
Ron Ophir , the Weizmann Institute of Science
Hila Benjamin-Rodrig , the Weizmann Institute of Science
Itai Yanai , the Weizmann Institute of Science
Orit Shmueli , the Weizmann Institute of Science
pp. 427

Wavelet Transforms for the Analysis of Microarray Experiments (PDF)

Donna Albertson , UCSF Cancer Center
Ajay Jain , UCSF Cancer Center
Taku A. Tokuyasu , UCSF Cancer Center
Dan Pinkel , UCSF Cancer Center
pp. 429

OptiRNai, a Web-based Program to Select siRNA Sequences (PDF)

Wenwu Cui , University of Delaware
Ulhas P. Naik , University of Delaware
Jianchang Ning , University of Delaware
Melinda K. Duncan , University of Delaware
pp. 433

A rule-based framework for gene regulation pathways discovery (PDF)

Jan Komorowski , Linnaeus Centre for Bioinformatics
Torgeir Hvidsten , Linnaeus Centre for Bioinformatics
Andriy Kryshtafovych , Lawrence Livermore National Laboratory
Krzysztof Fidelis , Lawrence Livermore National Laboratory
Bartosz Wilczynski , Warsaw University
Lisa Stubbs , Lawrence Livermore National Laboratory
pp. 435

Gene Function, Metabolic Pathways and Comparative Genomics in Yeast (PDF)

Laurie Issel-Tarver , Stanford University School of Medicine
Rama Balakrishnan , Stanford University School of Medicine
Shuai Weng , Stanford University School of Medicine
David Botstein , Stanford University School of Medicine
Rob Nash , Stanford University School of Medicine
Qing Dong , Stanford University School of Medicine
Gail Binkley , Stanford University School of Medicine
Dianna G. Fisk , Stanford University School of Medicine
Stacia Engel , Stanford University School of Medicine
Karen R. Christie , Stanford University School of Medicine
Eurie L. Hong , Stanford University School of Medicine
J. Michael Cherry , Stanford University School of Medicine
Selina S. Dwight , Stanford University School of Medicine
Kara Dolinski , Stanford University School of Medicine
Jodi Hirschman , Stanford University School of Medicine
Chandra L. Theesfeld , Stanford University School of Medicine
Maria Costanzo , Stanford University School of Medicine
Anand Sethuraman , Stanford University School of Medicine
pp. 437

Using Rule Induction Methods to Analyze Gene Expression Data (PDF)

Liwu Hao , Univ. of Massachusetts, Lowell
Gary Livingston , Univ. of Massachusetts, Lowell
Xiao Li , Univ. of Massachusetts, Lowell
Guangyi Li , Univ. of Massachusetts, Lowell
Jiangping Zhou , Univ. of Massachusetts, Lowell
pp. 439
Genomic Annotation

A New Approach to Gene Prediction Using the Self-Organizing Map (PDF)

Terry J. Smith , National Centre for Biomedical Engineering Science, NUI, Galway
Aaron Golden , Department of Information Technology, NUI, Galway
Shaun Mahony , National Centre for Biomedical Engineering Science, NUI, Galway
James O. McInerney , Bioinformatics and Pharmacogenomics Laboratory, NUI, Maynooth, Co.
pp. 444

On Gene Prediction by Cross-Species Comparative Sequence Analysis (PDF)

Hesham Ali , University of Nebraska at Omaha
Rong Chen , University of Nebraska at Omaha
pp. 446

CUBIC: Identification of Regulatory Binding Sites Through Data Clustering (PDF)

Victor Olman , Oak Ridge National Laboratory
Dong Xu , Oak Ridge National Laboratory
Ying Xu , Oak Ridge National Laboratory
pp. 448
Genotyping and SNPs

SNP Analysis System for Detecting Complex Disease Associated Sites (PDF)

Masanori Baba , HuBit Genomix, Inc.
Hirohito Matsumine , HuBit Genomix, Inc.
Masaaki Muramatsu , HuBit Genomix, Inc.; Tokyo Medical Dental University
Takashi Kido , HuBit Genomix, Inc.
Yoko Higashi , NTT Data Co. Ltd.
Hirotaka Higuchi , NTT Data Co. Ltd.
Toshihiko Morimoto , NTT Data Co. Ltd.
pp. 450

Haplotype Pattern Mining & Classification for detecting disease associated Site (PDF)

Masanori Baba , HuBit Genomix, Inc.
Yoko Higashi , NTT Data Co. Ltd.
Hirohito Matsumine , HuBit Genomix, Inc.
Hirotaka Higuchi , NTT Data Co. Ltd.
Masaaki Muramatsu , HuBit Genomix, Inc.; Tokyo Medical Dental University
Takashi Kido , HuBit Genomix, Inc.
pp. 452
Molecular Simulation

What makes IgG binding domain of protein L fold up to native state: a simulation study with physical oriented energy functions coupled to topology induced terms (PDF)

Yoshimi Fujitsuka , Kobe University
Seung Yup Lee , Korea Advanced Institute of Science and Technology
Shoji Takada , Kobe University; Japan Science and Technology Corporation
Do Hyun Kim , Korea Advanced Institute of Science and Technology
pp. 456

Substrate Recognition by Enzymes: a Theoretical Study (PDF)

Kaori Ueno-Noto , Ochanomizu University
Keiko Takano , Ochanomizu University
Miki Hara-Yokoyama , Ochanomizu University
pp. 462

Computational Simulation of Lipid Bilayer Reorientation at Gaps (Abstract)

Vijay S. Pande , Stanford University
Peter M. Kasson , Stanford University
pp. 464
Phylogeny and Evolution

Search for Evolution-Related-Oligonucleotides and Conservative Words in rRNA Sequences (PDF)

Fengmin Ji , Northern Jiaotong University
Mengwen Jia , Inner Mongolia University
H.C. Lee , National Central University
Liaofu Luo , Inner Mongolia University
Li-Ching Hsieh , National Central University
pp. 468

High Speed GAML-based Phylogenetic Tree Reconstruction Using HW/SW Codesign (Abstract)

K. P. Lam , The Chinese University of Hong Kong
Terrence S. T. Mak , The Chinese University of Hong Kong
pp. 470

Evidence for Growth of Microbial Genomes by Short Segmental Duplications (PDF)

Liaofu Luo , Inner Mongolia University
Li-Ching Hsieh , National Central University, Taiwan
H.C. Lee , National Central University, Taiwan; Inner Mongolia University
pp. 474

PTC: An Interactive Tool for Phylogenetic Tree Construction (PDF)

Chen Yang , San Jose State University
Sami Khuri , San Jose State University
pp. 476

Iterative Rank based Methods for Clustering (PDF)

S?ren W. Perrey , University of Applied Sciences of Gelsenkirchen, Germany
Achim Zielesny , University of Applied Sciences of Gelsenkirchen, Germany
Heinrich Brinck , University of Applied Sciences of Gelsenkirchen, Germany
pp. 478

Analysis of Phylogenetic Profiles Using Bayesian Decomposition (PDF)

Ghislain Bidaut , Fox Chase Cancer Center; Structural and Genetic Information Laboratory
Karsten Suhre , Structural and Genetic Information Laboratory
Michael F. Ochs , Fox Chase Cancer Center
Jean-Michel Claverie , Structural and Genetic Information Laboratory
pp. 480

Automatic Recognition of Regions of Intrinsically Poor Multiple Alignment Using Machine Learning (PDF)

Christian Blouin , Dalhousie University
Yunfeng Shan , Dalhousie University
Edward Susko , Dalhousie University
Evangelos E. Milios , Dalhousie University
Andrew J. Roger , Dalhousie University
pp. 482

Reconstruction of Ancestral Gene Order after Segmental Duplication and Gene Loss (PDF)

Todd Vision , University of North Carolina at Chapel Hill
Wei Wang , University of North Carolina at Chapel Hill
Jun Huan , University of North Carolina at Chapel Hill
Jan Prins , University of North Carolina at Chapel Hill
pp. 484

Reconstruction of Ancient Operons From Complete Microbial Genome Sequences (PDF)

John P. Rose , University of Georgia
Dawei Lin , University of Georgia
Bi-Cheng Wang , University of Georgia
Yuhong Wang , Jilin University
pp. 486
Predictive Methods

Gene Selection for Multi-Class Prediction of Microarray Data (Abstract)

Dechang Chen , Unifonned Services University of the Health Sciences
Dong Hua , The George Washington University
Xiuzhen Cheng , The George Washington University
Jaques Reifman , US Army Medical Research and Materiel Command
pp. 492

Latent Structure Models for the Analysis of Gene Expression Data (Abstract)

Abdou Youssef , The George Washington University
Dong Hua , The George Washington University
Xiuzhen Cheng , The George Washington University
Dechang Chen , Uniformed Services University of the Health Sciences
pp. 496

Molecular Evaluation using Comparative Molecular Interaction Profile Analysis system (PDF)

Yoshiharu Hayashi , KLIMERS Co., LTD; Toyohashi University of Technology
Nao Iwata , KLIMERS Co., LTD
Katsuyoshi Sakaguchi , KLIMERS Co., LTD
Masaki Kobayashi , KLIMERS Co., LTD
pp. 500

Probe Design for Large-Scale Molecular Biology Applications (PDF)

Minoru S.H. Ko , National Institutes of Health, National Institute on Aging
Vincent VanBuren , National Institutes of Health, National Institute on Aging
Toshiyuki Yoshikawa , National Institutes of Health, National Institute on Aging
Toshio Hamatani , National Institutes of Health, National Institute on Aging
pp. 502

A Statistical Model of Proteolytic Digestion (Abstract)

Christopher P. Diehl , Johns Hopkins University Applied Physics Lab
I-Jeng Wang , Johns Hopkins University Applied Physics Lab
Fernando J. Pineda , Johns Hopkins Bloomberg School of Public Health
pp. 506

Preliminary Wavelet Analysis of Genomic Sequences (PDF)

Jianchang Ning , University of Delaware, Newark
J. Clare Nelson , Kansas State University, Manhattan
Charles N. Moore , Kansas State University, Manhattan
pp. 509

Fold Recognition Using Sequence Fingerprints of Protein Local Substructures (PDF)

Torgeir R. Hvidsten , Uppsala University, Uppsala, Sweden
Krzysztof Fidelis , Lawrence Livermore National Laboratory, Livermore, CA
Jan Komorowski , Uppsala University, Uppsala, Sweden
Andriy Kryshtafovych , Lawrence Livermore National Laboratory, Livermore, CA
pp. 517

An Iterative Loop Matching Approach to the Prediction of RNA Secondary Structures with Pseudoknots (PDF)

Weixiong Zhang , Washington University in St. Louis
Gary D. Stormo , Washington University in St. Louis
Jianhua Ruan , Washington University in St. Louis
pp. 519

A New Method for Predicting RNA Secondary Structure (PDF)

Eisaku Maeda , NTT Communication Science Laboratories
Hirotoshi Taira , NTT Communication Science Laboratories
Takeshi Suzuki , Nagaoka University of Technology
Tomonori Izumitani , NTT Communication Science Laboratories
pp. 521

Minimum Redundancy Feature Selection from Microarray Gene Expression Data (Abstract)

Hanchuan Peng , University of California, Berkeley
Chris Ding , University of California, Berkeley
pp. 523
Sequence Comparison

Automatic Parameter Selection for Sequence Similarity Search (PDF)

Jianping Zhou , Univ. of Mass., Lowell
Georges Grinstein , Univ. of Mass, Lowell
Gary Livingston , Univ. of Mass., Lowell
pp. 530

A Linear Programming Based Algorithm for Multiple Sequence Alignments (PDF)

Fern Y. Hunt , National Institute of Standards and Technology
Anthony J. Kearsley , National Institute of Standards and Technology
Agnes O?Gallagher , National Institute of Standards and Technology
pp. 532

Prediction of Protein Function Using Signal Processing of Biochemical Properties (Abstract)

Kayvan Najarian , University of North Carolina at Charlotte
Krishna Gopalakrishnan , University of North Carolina at Charlotte
pp. 536

Genomic Sequence Analysis Using Gap Sequences and Pattern Filtering (PDF)

Chia H. Yeh , University of Southern California
C. -C. Jay Kuo , University of Southern California
Shih-Chieh Su , University of Southern California
pp. 539

An Optimal DNA Segmentation Based on the MDL Principle (Abstract)

Lukasz Szpankowski , University of Michigan
Wenhui Ren , Purdue University
Wojciech Szpankowski , Purdue University
pp. 541

The Cybertory Sequence File System for Managing Large DNA Sequences (PDF)

Carl E. McMillin , Attotron Biosensor Corporation
Robert M. Horton , Attotron Biosensor Corporation
pp. 547

Implementing Parallel Hmm-pfam on the EARTH Multithreaded Architecture (PDF)

Yanwei Niu , University of Delaware
Guang R. Gao , University of Delaware
Jizhu Lu , University of Delaware
Weirong Zhu , University of Delaware
pp. 549

Genome on Demand: Interactive Substring Searching (PDF)

Tamer Kahveci , University of California, Santa Barbara
Ambuj K. Singh , University of California, Santa Barbara
pp. 551

CoMRI: A Compressed Multi-Resolution Index Structure for Sequence Similarity Queries (Abstract)

Hakan Ferhatosmanoglu , Ohio State University
Ozgur Ozturk , Ohio State University
Hong Sun , Ohio State University
pp. 553
Strings, Graphs, and Algorithms

Genetic Algorithm Approach for the Closest String Problem (PDF)

John S. Hu , University of Hawaii at Manoa
Holger Mauch , University of Hawaii at Manoa
Michael J. Melzer , University of Hawaii at Manoa
pp. 560

GenericBioMatch: A novel generic pattern match algorithm for biological sequences (PDF)

A. Fazel Famili , National Research Council Canada
Youlian Pan , National Research Council Canada
pp. 562

Aligning ESTs to Genome Using Multi-Layer Unique Makers (Abstract)

F. R. Hsu , Taichung Healthcare and Management University, Taiwan
J. F. Chen , Taichung Healthcare and Management University, Taiwan
pp. 564

A Parallel Genetic Algorithm for Physical Mapping of Chromosomes (Abstract)

Suchendra M. Bhandarkar , The University of Georgia
Jonathan Arnold , The University of Georgia
Jinling Huang , The University of Georgia
pp. 567

RCIS: A Common Interval Searching Algorithm for Amino Acid Sequences (PDF)

Xiaolu Huang , University of Nebraska at Omaha
Hesham Ali , University of Nebraska at Omaha
pp. 573

Exact and Heuristic Algorithms for the DNA Fragment Assembly Problem (PDF)

Sami Khuri , San Jose State University
Yimin Jing , San Jose State University
pp. 581

Finding Higher Order Motifs under the Levenshtein Measure (PDF)

Tinuke Dipe , University of Ilorin, Ilorin
Ezekiel F. Adebiyi , University of Ilorin, Ilorin
pp. 583

Mapping Discontinuous Antibody Epitopes to Reveal Protein Structure and Changes in Structure Related to Function (PDF)

T. Angel , Chemistry & Biochemistry
E. Dratz , Chemistry & Biochemistry
B. Bailey , NIH-NIAAA
B. Mumey , Departments of Computer Sciences
B. Kirkpatrick , Departments of Computer Sciences
P. Hargrave , Univ. of Florida, Gainesville, FL
A. Jesaitis , Montana State Univ., Bozeman, MT
pp. 585

The SCP and Compressed Domain Analysis of Biological Sequences (Abstract)

Jianan Feng , West Virginia University, Morgantown
Donald Adjeroh , West Virginia University, Morgantown
pp. 587

Identifying Regulatory Signals in DNA-Sequences with a Non-statistical Approximation Approach (Abstract)

Keqiang Wu , West Virginia University
Cun-Quan Zhang , West Virginia University
Yunkai Liu , West Virginia University
Elaine M. Eschen , West Virginia University
pp. 593

A Genetic Algorithm for Simplifying The Amino Acid Alphabet (PDF)

Matthew Palensky , University of Nebraska at Omaha
Hesham Ali , University of Nebraska at Omaha
pp. 598
Structural Biology

An Exact Algorithm For Determining Protein Backbone Structure From NH Residual Dipolar Couplings (PDF)

Lincong Wang , Dartmouth Computer Science Department, Hanover, NH
Ramgopal R. Mettu , Dartmouth Computer Science Department, Hanover, NH
Ryan Lilien , Dartmouth Computer Science Department, Hanover, NH
Bruce Randall Donald , Dartmouth Computer Science Department, Hanover, NH
pp. 611

Automatic Construction of 3D Structural Motifs for Protein Function Prediction (PDF)

Doug L. Brutlag , Stanford Medical Informatics
Russ B. Altman , Stanford Medical Informatics
Mike P. Liang , Stanford Medical Informatics
pp. 613

Local Minima-Based Exploration for Off-Lattice Protein Folding (PDF)

Eunice E. Santos , Virginia Polytechnic Institute and State University
Keum Joo Kim , University of Connecticut, Storrs
Eugene Santos Jr. , University of Connecticut, Storrs
pp. 615
Systems Biology

Pathway Logic Modeling of Protein Functional Domains in Signal Transduction (PDF)

Merrill Knapp , SRI International
Patrick Lincoln , SRI International
Carolyn Talcott , SRI International
Keith Laderoute , SRI International
Steven Eker , SRI International
pp. 618

Development of a Massively-Parallel, Biological Circuit Simulator (Abstract)

Elebeoba E. May , Sandia National Laboratories
Richard L. Schiek , Sandia National Laboratories
pp. 620

Representing and reasoning about signal networks: an illustration using NF\kappaB dependent signaling pathways (Abstract)

Nam Tran , Arizona State University
Chitta Baral , Arizona State University
Nhan Tran , Translational Genomics Research Institute
Karen Chancellor , Arizona State University
pp. 623

Noise-Attenuation in Artificial Genetic Networks (PDF)

Kazuyuki Aihara , The University of Tokyo
Yoshihiro Morishita , The University of Tokyo
pp. 629

Computational Inference of Regulatory Pathways in Microbes (PDF)

V. Olman , Oak Ridge National Laboratory
B. Palenik , University of California at San Diego
X. Chen , Univ. of California at Riverside
Y. Xu , Oak Ridge National Laboratory
T. Jiang , Univ. of California at Riverside
P. Dam , Oak Ridge National Laboratory
Z. Su , Oak Ridge National Laboratory
pp. 631
Text Mining and Ontologies

A Contradiction-Based Framework for Testing Gene Regulation Hypotheses (Abstract)

Nigam Shah , The Pennsylvania State University
Steve Racunas , The Pennsylvania State University
Nina V. Fedoroff , The Pennsylvania State University
pp. 634

Identifying Gene and Protein Names from Biological Texts (Abstract)

Huda Akil , University of Michigan, Ann Arbor
Fan Meng , University of Michigan, Ann Arbor
Stanley J. Watson , University of Michigan, Ann Arbor
Weijian Xuan , University of Michigan, Ann Arbor
pp. 639

Refining the Extraction of Relevant Documents from Biomedical Literature to Create a Corpus for Pathway Text Mining (PDF)

Stephen Osborn , PPD Discovery, Inc.
Yan Lu , PPD Discovery, Inc.
Rachel Harte , PPD Discovery, Inc.
David Dehoney , PPD Discovery, Inc.
Daniel Chin , PPD Discovery, Inc.
pp. 644

Using Natural Language Processing and the Gene Ontology to Populate a Structured Pathway Database (PDF)

Yan Lu , PPD Discovery, Inc
David Dehoney , PPD Discovery, Inc
Rachel Harte , PPD Discovery, Inc
Daniel Chin , PPD Discovery, Inc
pp. 646
Miscellaneous

Development and Assessment of Bioinformatics Tools for Species Conservation and Habitat Management (PDF)

John Eme , University of West Florida
Wayne Bennett , University of West Florida
Frank Wray , University of West Florida
Lori Deneke , University of West Florida
Melanie A. Sutton , University of West Florida
pp. 654

MedfoLink: Bridging the Gap between IT and the Medical Community (PDF)

Alvin Wald , Columbia University Department of Biomedical Engineering
Armen Kherlopian , Columbia University School of Engineering and Applied Sciences
Mitchell Berman , Columbia University College of Physicians and Surgeons
Vezen Wu , Columbia University Information Technology Programs
Joseph Gerrein , Columbia University School of Engineering and Applied Sciences
pp. 656

TC-DB: An Architecture for Membrane Transport Protein Analysis (PDF)

Can V. Tran , University of California at San Diego, La Jolla
Nelson M. Yang , University of California at San Diego, La Jolla
Milton H. Saier, Jr. , University of California at San Diego, La Jolla
pp. 658

Author Index (PDF)

pp. 661
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