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Computational Systems Bioinformatics Conference, International IEEE Computer Society (2002)
Stanford, California
Aug. 14, 2002 to Aug. 16, 2002
ISBN: 0-7695-1653-X
TABLE OF CONTENTS
Introduction

Preface (PDF)

pp. ix

Referees (PDF)

pp. xii

Keynote Speakers (PDF)

pp. xiii
Invited Talk Abstracts

Genome Annotation and Protein Structure (PDF)

Steven E. Brenner , University of California at Berkeley
pp. 4

Decoding Noncoding Regulatory DNAs in Metazoan Genomes (PDF)

Peter Markstein , University of California at Berkeley and Joint Genome Institute
Dave Keys , University of California at Berkeley and Joint Genome Institute
Michele Markstein , University of California at Berkeley and Joint Genome Institute
Vicky Markstein , University of California at Berkeley and Joint Genome Institute
Dan Rokshar , University of California at Berkeley and Joint Genome Institute
Byung-in Lee , University of California at Berkeley and Joint Genome Institute
Angela Stathopoulos , University of California at Berkeley and Joint Genome Institute
Mike Levine , University of California at Berkeley and Joint Genome Institute
Paul Richardson , University of California at Berkeley and Joint Genome Institute
Naoe Harafuji , University of California at Berkeley and Joint Genome Institute
pp. 5
Phylogenetics

Φ-LOG: A Domain Specific Language for Solving Phylogenetic Inference Problems (Abstract)

G. Gupta , University of Texas at Dallas
B. Milligan , New Mexico State University
D. Ranjan , New Mexico State University
E. Pontelli , New Mexico State University
pp. 9

AxML: A Fast Program for Sequential and Parallel Phylogenetic Tree Calculations Based on the Maximum Likelihood Method (Abstract)

Marty J. Wolf , Bemidji State University
Harald Meier , Technical University of Munich
Alexandros P. Stamatakis , Technical University of Munich
Thomas Ludwig , Ruprecht-Karls-University
pp. 21
Motif Finding

Rapid Large-Scale Oligonucleotide Selection for Microarrays (Abstract)

Sven Rahmann , MPI for Molecular Genetics and Free University of Berlin
pp. 54
Genotype-Phenotype

Automated Identification of Single Nucleotide Polymorphisms from Sequencing Data (Abstract)

Mark Lathrop , Centre National de Genotypage
Nino Margetic , Centre National de Genotypage
Masazumi Takahashi , Centre National de Genotypage
Fumihiko Matsuda , Centre National de Genotypage
pp. 87
Database Mining

A Multi-Level Text Mining Method to Extract Biological Relationships (Abstract)

Mathew Palakal , Indiana University Purdue University Indianapolis
Snehasis Mukhopadhyay , Indiana University Purdue University Indianapolis
Simon Rhodes , Indiana University Purdue University Indianapolis
Rajeev Raje , Indiana University Purdue University Indianapolis
Matthew Stephens , Indiana University Purdue University Indianapolis
pp. 97

A Literature Based Method for Identifying Gene-Disease Connections (Abstract)

Dennis Wilkinson , HP Laboratories
Lada A. Adamic , HP Laboratories
Eytan Adar , HP Laboratories
Bernardo A. Huberman , HP Laboratories
pp. 109

Protein-Based Analysis of Alternative Splicing in the Human Genome (Abstract)

Ann E. Loraine , Affymetrix, Inc.
Michael A. Siani-Rose , Affymetrix, Inc.
Gregg A. Helt , Affymetrix, Inc.
Melissa S. Cline , Affymetrix, Inc.
pp. 118
Comparative Genomics

Constrained Multiple Sequence Alignment Tool Development and Its Application to RNase Family Alignment (Abstract)

Hao-Teng Chang , National Tsing Hua University
Yuh-Ju Sun , National Tsing Hua University
Chin Lung Lu , National Center for High-Performance Computing
Yu-Han Chiou , National Tsing Hua University
Yin-Te Tsai , Providence University
Kun-Mao Chao , National Yang-Ming University
Jia-Ming Chang , National Tsing Hua University
Wei-I Chou , National Tsing Hua University
Margaret Dah-Tsyr Chang , National Tsing Hua University
Chia-Mao Wu , National Tsing Hua University
Chuan Yi Tang , National Tsing Hua University
pp. 127

Fast and Sensitive Alignment of Large Genomic Sequences (Abstract)

Burkhard Morgenstern , Universität Bielefeld
Michael Brudnd , Stanford University
pp. 138
Biological Networks

Design of Genetic Switches with Only Positive Feedback Loops (Abstract)

Luonan Chen , Osaka Sangyo University
Kazuyuki Aihara , University of Tokyo
Tetsuya Kobayashi , University of Tokyo
pp. 151
Proteomics

An Efficient Branch-and-Bound Algorithm for the Assignment of Protein Backbone NMR Peaks (Abstract)

Ying Xu , Oak Ridge National Laboratory
Tao Jiang , University of California at Riverside
Jianjun Wen , University of California at Riverside
Zhi-Zhong Chen , Tokyo Denki University
Dong Xu , Oak Ridge National Laboratory
Guohui Lin , University of Alberta
pp. 165

Towards Automatic Clustering of Protein Sequences (Abstract)

Jiong Yang , IBM T.J. Watson Research Center
Wei Wang , University of North Carolina at Chapel Hill
pp. 175

Prediction of Protein Function Using Protein-Protein Interaction Data (Abstract)

Ting Chen , University of Southern California
Minghua Deng , University of Southern California
Fengzhu Sun , University of Southern California
Kui Zhang , University of Southern California
Shipra Mehta , University of Southern California
pp. 197

Accelerating Approximate Subsequence Search on Large Protein Sequence Databases (Abstract)

Jiong Yang , IBM T.J. Watson Research
Wei Wang , University of North Carolina at Chapel Hill
Yi Xia , University of California at Los Angeles
Philip S. Yu , IBM T. J. Watson Research
pp. 207
Gene Expression

Bayesian Network and Nonparametric Heteroscedastic Regression for Nonlinear Modeling of Genetic Network (Abstract)

Sachiyo Aburatani , Kyushu University
Kim Sunyong , University of Tokyo
Kousuke Tashiro , Kyushu University
Takao Goto , University of Tokyo
Satoru Miyano , University of Tokyo
Satoru Kuhara , Kyushu University
Seiya Imoto , University of Tokyo
pp. 219

An Index Structure for Pattern Similarity Searching in DNA Microarray Data (Abstract)

Philip S. Yu , IBM T. J. Watson Research Center
Chang-Shing Perng , IBM T. J. Watson Research Center
Haixun Wang , IBM T. J. Watson Research Center
Wei Fan , IBM T. J. Watson Research Center
pp. 256

A New Clustering Method for Microarray Data Analysis (Abstract)

Louxin Zhang , National University of Singapore
Song Zhu , Labs for Information Technology
pp. 268

An Adaptive Meta-Clustering Approach: Combining the Information from Different Clustering Results (Abstract)

Yujing Zeng , University of Delaware
Guang R. Gao , University of Delaware
Jianshan Tang , University of Delaware
Javier Garcia-Frias , University of Delaware
pp. 276
Computer Science and Biology

Parallelizing a DNA Simulation Code for the Cray MTA-2 (Abstract)

Jon R. Sauer , Eagle Research & Development
Matthew A. Glaser , University of Colorado
Shahid H. Bokhari , University of Engineering & Technology
Yves Lansac , University of Colorado
Bart Van Zeghbroeck , Eagle Research & Development
Harry F. Jordan , University of Colorado
pp. 291

DNA Sequence Compression Using the Burrows-Wheeler Transform (Abstract)

Don Adjeroh , West Virginia University
Amar Mukherjee , University of Central Florida
Matt Powell , University of Canterbury
Tim Bell , University of Canterbury
Yong Zhang , West Virginia University
pp. 303

A Security System for Personal Genome Information at DNA Level (Abstract)

Yumi Kawazoe , Hokkaido University
Masahito Yamamoto , Hokkaido University and Japan Science and Technology Cooperation
Toshikazu Shiba , FUJIREBIO Inc. and Japan Science and Technology Cooperation
Azuma Ohuchi , Hokkaido University and Japan Science and Technology Cooperation
pp. 314

Visualization Techniques for Genomic Data (Abstract)

Ann E. Loraine , Affymetrix, Inc.
Gregg A. Helt , Affymetrix, Inc.
pp. 321
Poster Abstracts

A Bayesian Modeling Framework for Genetic Regulation (Abstract)

Guang Gao , University of Delaware
Javier Garcia-Frias , University of Delaware
Rishi Khan , University of Delaware
Yujing Zeng , University of Delaware
pp. 330

Complexity and Application of Pedigree Analysis Programme GTree (Abstract)

Masato Nose , Ehime University
Daisuke Ogino , Yamagata University
Hideki Sawada , Yamagata University
Shiro Mori , Tohoku University
pp. 333

Designing Oscillators in Synthetic Gene Networks Based on Multi-Scale Dynamics (PDF)

Tetsuya Kobayashi , University of Tokyo
Luonan Chen , Osaka Sangyo University
Kazuyuki Aihara , University of Tokyo
pp. 336

Electronic Polymerase Chain Reaction (EPCR) Search Algorithm (PDF)

James A. Foster , University of Idaho
Conrad Shyu , University of Idaho
Larry J. Forney , University of Idaho
pp. 338

GeneCards™ 2002: An Evolving Human Gene Compendium (PDF)

Naomi Rosen , Weizmann Institute of Science
Nir Esterman , Weizmann Institute of Science
Irina Solomon , Weizmann Institute of Science
Doron Lancet , Weizmann Institute of Science
Shai Shen-Orr , Weizmann Institute of Science
Marilyn Safran , Weizmann Institute of Science
Avital Adato , Weizmann Institute of Science
Tsviya Olender , Weizmann Institute of Science
Orit Shmueli , Weizmann Institute of Science
Uri Ben-Dor , Weizmann Institute of Science
Vered Chalifa-Caspi , Weizmann Institute of Science
Michal Lapidot , Weizmann Institute of Science
Inga Peter , Weizmann Institute of Science
pp. 339

HIV Protease Structural Database (PDF)

Alexander Wlodawer , National Cancer Institute-Frederick
Jiri Vondrasek , National Cancer Institute-Frederick
Gary Gilliland , National Institute of Standards and Technology
T. N. Bhat , National Institute of Standards and Technology
V. Ravichandran , National Institute of Standards and Technology
pp. 340

MiCA: Web-Based Computational Tools for the Analysis of Microbial Community Structure and Compisition Based on T-RFLP of 16S rRNA Genes (PDF)

L. J. Forney , University of Idaho
K. Sale , University of Idaho
K. X. Liao , University of Idaho
S. J. Bent , University of Idaho
J. A. Foster , University of Idaho
C. Shyu , University of Idaho
T. Soule , University of Idaho
pp. 341

P-quasi Complete Linkage Analysis for Gene-Expression Data (PDF)

Hideo Matsuda , Osaka University
Shigeto Seno , Osaka University
Reiji Teramoto , Osaka University
pp. 342

A Reference Database for Medicago Truncatula Genes, Protiens, and Metabolites (PDF)

Aejaaz Kamal , Virginia Tech
Dianjing Guo , Virginia Tech
Olga Brazhnik , Virginia Tech
Pedro Mendes , Virginia Tech
Xingjing Li , Virginia Tech
pp. 343

Wavelet Profiles: Their Application in Oryza sativa DNA Sequence Analysis (PDF)

Nobuyuki Kawagashira , National Institute of Agrobiological Sciences
Yoshihide Hayashizaki , RIKEN (The Institute of Physical and Chemical Research)
Jun Kawai , RIKEN (The Institute of Physical and Chemical Research)
Kenichi Matsubara , Foundation for Advancement of International Science
Kazuo Murakami , Foundation for Advancement of International Science
Yasuhiro Ohtomo , Foundation for Advancement of International Science
Piero Carninci , RIKEN (The Institute of Physical and Chemical Research)
Shoshi Kikuchi , National Institute of Agrobiological Sciences
pp. 345
Author Index

Author Index (PDF)

pp. 347
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