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Computational Systems Bioinformatics Conference, International IEEE Computer Society (2005)
Stanford, California
Aug. 8, 2005 to Aug. 11, 2005
ISBN: 0-7695-2344-7
TABLE OF CONTENTS
Workshop Abstracts
Introduction

Referees (PDF)

pp. xii,xiii

Preface (PDF)

pp. ix
Introduction

Committees (PDF)

pp. x-xi
Keynote Addresses
Invited Talks

The Center for Computational Biology (PDF)

Arthur W. Toga , University of California at Los Angeles School of Medicine
pp. 9
Genomics

Identifying Simple Discriminatory Gene Vectors with an Information Theory Approach (Abstract)

Kwoh Chee Keong , Nanyang Technological University
Zheng Yun , Nanyang Technological University
pp. 13-24

Learning Yeast Gene Functions from Heterogeneous Sources of Data Using Hybrid Weighted Bayesian Networks (Abstract)

Xutao Deng , University of Nebraska at Omaha
Hesham Ali , University of Nebraska at Omaha
Huimin Geng , University of Nebraska - Medical Center
pp. 25-34

Consensus Genetic Maps: A Graph Theoretic Approach (Abstract)

Patrick S. Schnable , Iowa State University
Benjamin N. Jackson , Iowa State University
Srinivas Aluru , Iowa State University
pp. 35-43

Gene Teams with Relaxed Proximity Constraint (Abstract)

Jeong-Hyeon Choi , Indiana University
Sun Kim , Indiana University
Jiong Yang , Case Western Reserve University
pp. 44-55

Islands of Tractability for Parsimony Haplotyping (Abstract)

Roded Sharan , Tel-Aviv University
Bjarni V. Halldórsson , deCode Genetics
Sorin Istrail , California Institute of Technology
pp. 65-72

Accurate Prediction of Orthologous Gene Groups in Microbes (Abstract)

Hongwei Wu , University of Georgia and Oak Ridge National Laboratory
Fenglou Mao , Oak Ridge National Laboratory
Ying Xu , University of Georgia and Oak Ridge National Laboratory
Victor Olman , Oak Ridge National Laboratory
pp. 73-79

Motif Extraction and Protein Classification (Abstract)

Eytan Ruppin , Tel Aviv University
David Horn , Tel Aviv University
Shimon Edelman , Cornell University
Vered Kunik , Tel Aviv University
Zach Solan , Tel Aviv University
pp. 80-85
Phylogeny and Evolution

Reconstructing Phylogenetic Networks Using Maximum Parsimony (Abstract)

John Mellor-Crummey , Rice University
Luay Nakhleh , Rice University
Fengmei Zhao , Rice University
Guohua Jin , Rice University
pp. 93-102

An Efficient Algorithm for Perfect Phylogeny Haplotyping (Abstract)

Ravi VijayaSatya , University of Central Florida
Amar Mukherjee , University of Central Florida
pp. 103-110
Transcriptomes

Multi-Metric and Multi-Substructure Biclustering Analysis for Gene Expression Data (Abstract)

Man-Wai Mak , Hong Kong Polytechnic University
S. Y. Kung , Princeton University
Ilias Tagkopoulos , Princeton University
pp. 123-134

Analysis of SNP-Expression Association Matrices (Abstract)

Amir Ben-Dor , Agilent Technologies
Anne-Lise B?rresen-Dale , University of Oslo
Roded Sharan , Tel-Aviv University
Vessela Kristensen , University of Oslo
Zohar Yakhini , Agilent Technologies
Anya Tsalenko , Agilent Technologies
Hege Edvardsen , University of Oslo
pp. 135-143

A Learned Comparative Expression Measure for Affymetrix GeneChip DNA Microarrays (Abstract)

Eli Upfal , Brown University
John Sedivy , Brown University
Will Sheffler , University of Washington
William Stafford Noble , University of Washington
pp. 144-154
Proteomics

Identification of Post-Translational Modifications via Blind Search of Mass-Spectra (Abstract)

Vineet Bafna , University of California at San Diego
Dekel Tsur , University of California at San Diego
Ebrahim Zandi , University of Southern California
Stephen Tanner , University of California at San Diego
Pavel A. Pevzner , University of California at San Diego
pp. 157-166

Discover True Association Rates in Multi-protein Complex Proteomics Data Sets (Abstract)

Lang Li , Indiana University
Changyu Shen , Indiana University
Jake Yue Chen , Indiana University and Purdue University
pp. 167-174

Peptide Charge State Determination for Low-Resolution Tandem Mass Spectra (Abstract)

Aaron A. Klammer , University of Washington
William Stafford Noble , University of Washington
Christine C. Wu , University of Colorado
Michael J. MacCoss , University of Washington
pp. 175-185
Structural Bioinformatics

Multi-Scale Hierarchical Structure Prediction of Helical Transmembrane Proteins (Abstract)

Zhong Chen , University of Georgia
Ying Xu , University of Georgia
pp. 203-207

PSIST: Indexing Protein Structures Using Suffix Trees (Abstract)

Mohammed J. Zaki , Rensselaer Polytechnic Institute
Feng Gao , Rensselaer Polytechnic Institute
pp. 212-222

Tree Decomposition Based Fast Search of RNA Structures Including Pseudoknots in Genomes (Abstract)

Russell Malmberg , University of Georgia
Chunmei Liu , University of Georgia
Yinglei Song , University of Georgia
Liming Cai , University of Georgia
Fangfang Pan , University of Georgia
pp. 223-234

An Algebraic Geometry Approach to Protein Structure Determination from NMR Data (Abstract)

Lincong Wang , Dartmouth University
Bruce Randall Donald , Dartmouth University
Ramgopal R. Mettu , Dartmouth University
pp. 235-246

A Tree-Decomposition Approach to Protein Structure Prediction (Abstract)

Jinbo Xu , Massassachusetts Institute of Technology
Bonnie Berger , Massassachusetts Institute of Technology
Feng Jiao , University of Waterloo
pp. 247-256
Pathways and Networks

A Topological Measurement for Weighted Protein Interaction Network (Abstract)

Pengjun Pei , State University of New York at Buffalo
Aidong Zhang , State University of New York at Buffalo
pp. 268-278

Application of a Generalized MWC Model for the Mathematical Simulation of Metabolic Pathways Regulated by Allosteric Enzymes (Abstract)

Bruce E. Shapiro , California Institute of Technology
Chin-Rang Yang , University of California at Irvine
Tarek S. Najdi , University of California at Irvine
G. Wesley Hatfield , University of California at Irvine
Eric D. Mjolsness , University of California at Irvine
pp. 279-288

Estimating Time-Dependent Gene Networks from Time Series Microarray Data by Dynamic Linear Models with Markov Switching (Abstract)

Ryo Yoshida , Institute of Statistical Mathematics
Tomoyuki Higuchi , Institute of Statistical Mathematics
Seiya Imoto , University of Tokyo
pp. 289-298
Applied Bioinformatic

Choosing SNPs Using Feature Selection (Abstract)

Zhen Lin , Stanford University
Tu Minh Phuong , Institute of Technology - Hanoi
Russ B. Altman , Stanford University
pp. 301-309

Robust and Accurate Cancer Classification with Gene Expression Profiling (Abstract)

Tao Jiang , University of California at Riverside
Haifeng Li , University of California at Riverside
Keshu Zhang , Motorola, Inc.
pp. 310-321

A Robust Meta-classification Strategy for Cancer Diagnosis from Gene Expression Data (Abstract)

Ramakrishna Ramaswamy , Institute for Advanced Study
Gustavo Stolovitzky , IBM T.J. Watson Research Center
Arnold J. Levine , Institute for Advanced Study and Robert Wood Johnson School of Medicine and Dentistry
Babu Venkataraghavan , Institute for Advanced Study
Gyan Bhanot , IBM T.J. Watson Research Center
Jorge Lepre , IBM T.J. Watson Research Center
Gabriela Alexe , IBM T.J. Watson Research Center
pp. 322-325
Data Mining and Ontology

Clustering Genes Using Gene Expression and Text Literature Data (Abstract)

Giri Narasimhan , Florida International University
Tao Li , Florida International University
Chengyong Yang , Florida International University
Erliang Zeng , Florida International University
pp. 329-340

Bioinformatic Insights from Metagenomics through Visualization (Abstract)

Banu Gopalan , Pacific Northwest National Laboratory
Christian Posse , Pacific Northwest National Laboratory
Anuj Shah , Pacific Northwest National Laboratory
Susan L. Havre , Pacific Northwest National Laboratory
Bobbie-Jo Webb-Robertson , Pacific Northwest National Laboratory
Fred J. Brockman , Pacific Northwest National Laboratory
pp. 341-350

On Optimizing Distance-Based Similarity Search for Biological Databases (Abstract)

Weijia Xu , University of Texas at Austin
Glen Nuckolls , University of Texas at Austin
Smriti Ramakrishnan , University of Texas at Austin
Daniel P. Miranker , University of Texas at Austin
Rui Mao , University of Texas at Austin
pp. 351-361

Computational Method for Temporal Pattern Discovery in Biomedical Genomic Databases (Abstract)

Amar K. Das , Stanford Medical Informatics
Mohammed I. Rafiq , Stanford Medical Informatics
Martin J. O?Connor , Stanford Medical Informatics
pp. 362-365

Investigation into Biomedical Literature Classification Using Support Vector Machines (Abstract)

Ramprasad Ramnarayanan , Georgia Institute of Technology
Ying Liu , Georgia Institute of Technology
Nalini Polavarapu , Georgia Institute of Technology
Abrar ul Haque , Georgia Institute of Technology
Saurav Sahay , Georgia Institute of Technology
Shamkant B. Navathe , Georgia Institute of Technology
pp. 366-374
Miscellaneous
Author Index

Author Index (PDF)

pp. 403-404
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