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Proceedings. 2004 IEEE Computational Systems Bioinformatics Conference (2004)
Stanford, CA, USA
Aug. 19, 2004 to Aug. 19, 2004
ISBN: 0-7695-2194-0
TABLE OF CONTENTS
Pattern Recognition
Other
Preface (PDF)
pp. xvii
Introduction
Preface (PDF)
pp. xvii
Committees (PDF)
pp. xviii-xix
Referees (PDF)
pp. xx
Keynote Addresses
Invited Talks
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
pp. 6
Jim Kent , University of California at Santa Cruz
pp. 7
Stephen T.C. Wong , Harvard Medical School and Brigham & Womenés Hospital
pp. 8
Sandy Shaw , Health Discovery Corporation, Inc.
Paul Shapshak , University of Miami School of Medicine
pp. 9-17
Genomics
Li-Ching Hsieh , National Central University
Ta-Yuan Chen , National Central University
Hong-Da Chen , National Central University
Chang-Heng Chang , National Central University
Hoong-Chien Lee , National Central University and National Center for Theoretical Sciences
pp. 20-30
Hong Liu , Aventis Pharmaceuticals Inc.
Li Li , Aventis Pharmaceuticals Inc.
Asher Zilberstein , Aventis Pharmaceuticals Inc.
Chang S. Hahn , Aventis Pharmaceuticals Inc.
pp. 31-39
Yinhe Cao , University of Florida
J. B. Gao , University of Florida
pp. 40-51
Vineet Bafna , University of California at San Diego
Shaojie Zhang , University of California at San Diego
pp. 52-61
Lei Chen , Wayne State University
Shiyong Lu , Wayne State University
Jeffrey Ram , Wayne State University
pp. 62-68
Jude Shavlik , University of Wisconsin-Madison
Thomas Albert , NimbleGen Systems, Inc.
Todd Richmond , NimbleGen Systems, Inc.
Steven Smith , NimbleGen Systems, Inc.
pp. 69-79
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
Bernard M. E. Moret , University of New Mexico
Tandy Warnow , University of Texas at Austin
Usman W. Roshan , University of Texas at Austin
pp. 98-109
Transcriptomes
Stefano Lonardi , University of California at Riverside
Yu Luo , University of California at Riverside
pp. 122-130
Sach Mukherjee , University of Oxford
pp. 131-141
Haifeng Li , University of California at Riverside
Tao Jiang , University of California at Riverside
pp. 142-151
Eugene Ie , Columbia University
Ke Wang , Columbia University
Kai Wang , Columbia University
Mahira Siddiqi , Columbia University
Yoav Freund , Columbia University
Rui Kuang , Columbia University
pp. 152-160
Ryo Yoshida , Graduate University for Advanced Studies
Tomoyuki Higuchi , Institute of Statistical Mathematics
Seiya Imoto , University of Tokyo
pp. 161-172
Jingyi Yang , University of Nebraska at Lincoln
Zhaohui Sun , University of Nebraska at Lincoln
pp. 173-181
Jinze Liu , University of North Carolina
Jiong Yang , University of Illinois, Urbana-Champaign
Wei Wang , University of North Carolina
pp. 182-193
Proteomics
Bin Ma , University of Western Ontario
Yonghua Han , University of Western Ontario
pp. 206-215
Patrik D'haeseleer , Harvard Medical School
George M. Church , Harvard Medical School
pp. 216-223
Orhan Çamoğlu , 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
Chongle Pan , Computational Biology Institute and University of Tennessee
Victor N. Olman , University of Georgia and Computational Biology Institute
Bo Yan , University of Georgia and Computational Biology Institute
Ying Xu , University of Georgia and Computational Biology Institute
pp. 236-244
Structural Bioinformatics
Zhuozhi Wang , University Heath Network
Kaizhong Zhang , University of Western Ontario
pp. 246-254
Tod D. Romo , Texas A&M University
James C. Sacchettini , Texas A&M University
Thomas R. Ioerger , Texas A&M University
pp. 255-265
Rahul Singh , San Francisco State University
pp. 266-277
Jacob V. Maizel, Jr. , National Cancer Institute
Kaizhong Zhang , University of Western Ontario and Simon Fraser University
pp. 300-310
Ján Maňuch , Simon Fraser University
Arvind Gupta , Simon Fraser University
pp. 311-318
Pathways & Networks
Martin Kupiec , Tel Aviv University
Eytan Ruppin , Tel Aviv University
pp. 332-340
Zheng Yun , Nanyang Technological University
Kwoh Chee Keong , Nanyang Technological University
pp. 353-362
Hanchuan Peng , University of Georgia and Oak Ridge National Laboratory
Victor Olman , University of Georgia
Ying Xu , University of Georgia and Oak Ridge National Laboratory
pp. 363-370
Applied Bioinformatics
Maria Garcia de la Banda , Monash University
Sarah E. Boyd , Monash University
James C. Whisstock , Monash University
George B. Rudy , Walter & Eliza Hall Institute of Medical Research
pp. 372-381
Huiqing Liu , Institute for Infocomm Research
Jinyan Li , Institute for Infocomm Research
Limsoon Wong , Institute for Infocomm Research
pp. 382-392
Data Mining & Ontology
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
John G. Cleary , Reel Two, Ltd. and University of Waikato
Nicholas T. Goncharoff , Reel Two, Inc.
Raf M. Podowski , AstraZeneca R&D Boston and Karolinska Institutet
William S. Hayes , AstraZeneca R&D Boston
pp. 415-424
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
Wei Wang , University of North Carolina
Jinze Liu , University of North Carolina
pp. 436-447
Biomedical Research
Anguraj Sadanandam , University of Nebraska Medical Center
Rakesh K. Singh , University of Nebraska Medical Center
pp. 450-451
Cellular Multicellular Systems
Wen-Jun Zhang , University of Saskatchewan
Anthony J. Kusalik , University of Saskatchewan
pp. 454-455
Comparative Genomics
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
Joshua W. Gilkerson , University of Kentucky
Mark L. Farman , University of Kentucky
Chuck Staben , University of Kentucky
pp. 464-467
Data Mining
Ian Shadforth , Cranfield University
Daniel Crowther , GlaxoSmithKline
Conrad Bessant , Cranfield University
pp. 470-471
Chang F. Quo , Georgia Institute of Technology and Emory University
Kejiao Guo , Georgia Institute of Technology and Emory University
John H. Phan , 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
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
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
Mehmet Koyutürk , Purdue University
Wojciech Szpankowski , Purdue University
Ananth Grama , Purdue University
pp. 480-484
Xuanfu Wu , University of Nebraska at Omaha
Zhengxin Chen , University of Nebraska at Omaha
pp. 485-486
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
Xindong Wu , University of Vermont
Jeffrey Stone , University of Vermont
pp. 491-492
Dhundy Bastola , University of Nebraska Medical Center
Hesham Ali , University of Nebraska at Omaha
pp. 493-494
Daniel Quest , University of Nebraska at Omaha
Hesham Ali , University of Nebraska at Omaha
pp. 495-496
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
Tomonori Izumitani , NTT Communication Science Laboratories
Hideto Kazawa , NTT Communication Science Laboratories
Eisaku Maeda , NTT Communication Science Laboratories
pp. 503-504
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
Boris Budagyan , California State University at Hayward
Ann Loraine , University of Alabama at Birmingham
pp. 515-516
Francisca Zanoguera , Serono Pharmaceutical Research Institute
Massimo de Francesco , Serono Pharmaceutical Research Institute
pp. 517-519
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
Weihong Qi , Michigan State University
Thomas S. Whittam , Michigan State University
pp. 520-521
Fei Nan , West Virginia University
Donald Adjeroh , West Virginia University
pp. 522-526
Functional Genomics
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
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
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
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
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
Grace Steele , Morgan State University
Vojislav Stojkovic , Morgan State University
pp. 546-551
Jung-Yup Kang , University of Southern California
Jean-Luc Gaudiot , University of California at Irvine
pp. 552-553
Microarray Analysis
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
Weimin Feng , Georgia Institute of Technology and Emory University
May D. Wang , Georgia Institute of Technology and Emory University
pp. 562-563
Bill Martin , Attotron Biosensor Corporation
Robert M. Horton , Attotron Biosensor Corporation
pp. 564-565
George Davidson , Sandia National Laboratories
Elebeoba May , Sandia National Laboratories
Jean-Loup Faulon , Sandia National Laboratories
Margaret Werner-Washburne , University of New Mexico
pp. 566-569
Hyunsoo Kim , University of Minnesota
Haesun Park , University of Minnesota
pp. 572-573
We Hu , Intel China Research Center
Hao Zhong , Intel China Research Center
Juntao Li , Intel China Research Center
Feng Xue , Intel China Research Center
Tao Wang , Intel China Research Center
Yimin Zhang , Intel China Research Center
pp. 574-575
Danny Barash , Ben-Gurion University
Dorin Comaniciu , Siemens Corporate Research
pp. 578-579
Soumitra Ghosh , Medical College of Wisconsin
Parthav Jailwalia , Medical College of Wisconsin
Xujing Wang , Medical College of Wisconsin
pp. 580-581
Hui Fang , University of Illinois at Urbana-Champaign
Chengxiang Zhai , University of Illinois at Urbana-Champaign
Lei Liu , University of Illinois at Urbana-Champaign
Jiong Yang , University of Illinois at Urbana-Champaign
pp. 582-583
Ming-Hsiu Ho , Affymetrix, Inc.
Geoffrey Yang , Affymetrix, Inc.
pp. 586-587
Other
W. Bradley Barbazuk , Donald Danforth Plant Science Center
Yucheng Feng , Donald Danforth Plant Science Center
Xiequn Xu , Donald Danforth Plant Science Center
Agnes P. Chan , The Institute of Genomics Research
Geo Pertea , The Institute of Genomics Research
Li Zheng , The Institute of Genomics Research
Foo Cheung , The Institute of Genomics Research
Yuandan Lee , The Institute of Genomics Research
pp. 594-595
Kaushal Parekh , Arizona State University
Louiqa Raschid , University of Maryland
Zo? Lacroix , Arizona State University
pp. 594-595
Zo? Lacroix , Arizona State University
Vidyadhari Edupuganti , Arizona State University
pp. 596-597
Pathways Networks Systems Biology
E. Bak , University of North Carolina at Charlotte
K. Gopalakrishnan , University of North Carolina at Charlotte
Alireza Darvish , University of North Carolina at Charlotte
Kayvan Najarian , University of North Carolina at Charlotte
pp. 602-603
Young Kim , Stanford University
Pei Wang , Stanford University
Robert Tibshirani , Stanford University
pp. 604-609
Anthony J. Kusalik , University of Saskatchewan
Fang-Xiang Wu , University of Saskatchewan
pp. 610-611
Peng Wang , University of Georgia
Zhengchang Su , University of Georgia
Phuongan Dam , University of Georgia
Ying Xu , University of Georgia
pp. 612-613
Zhengchang Su , University of Georgia at Athens and Oak Ridge National Laboratory
Victor Olman , University of Georgia at Athens
Ying Xu , University of Georgia at Athens and Oak Ridge National Laboratory
pp. 614-615
Stephen Racunas , Penn State University
Nigam Shah , Penn State University
pp. 616-620
Hee Young Kang , Chungbuk National University
Hak Yong Kim , Chungbuk National University
pp. 621-622
Steven J. Lynden , University of Newcastle upon Tyne
Malcolm P. Young , University of Newcastle upon Tyne
Peter Andras , University of Newcastle upon Tyne
pp. 623-625
Shawn Martin , Sandia National Laboratories
Jean-Loup Faulon , Sandia National Laboratories
pp. 626-627
Jesse Bridgewater , University of California at Los Angeles
Jianbo Gao , University of Florida
pp. 630-631
Jeff Varner , Genencor International, Inc
Kwok Ko , Stanford Linear Accelerator Center
pp. 636-639
Z. Su , University of Georgia and Oak Ridge National Laboratory
P. Dam , University of Georgia and Oak Ridge National Laboratory
X. Chen , University of California at Riverside
V. Olman , University of Georgia and Oak Ridge National Laboratory
T. Jiang , University of California at Riverside
Y. Xu , University of Georgia and Oak Ridge National Laboratory
pp. 640-641
Zhengchang Su , 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
Ying Xu , University of Georgia and Oak Ridge National Laboratory
pp. 642-643
Omar D. Perez , Stanford University School of Medicine
Dana Pe?er , Harvard Medical School
Garry P. Nolan , Stanford University School of Medicine
David K. Gifford , Massachusetts Institute of Technology
Karen Sachs , Massachusetts Institute of Technology
Douglas A. Lauffenburger , Massachusetts Institute of Technology
pp. 644
Pattern Recognition
Tzu Fang Sheu , National Tsing-Hua University
Yin Te Tsai , Providence University - Taiwan
Ching Hua Shih , National Tsing-Hua University
Hsiao Ping Lee , National Tsing-Hua University
pp. 650-651
Yan Ding , American Type Culture Collection
Hong Cao , American Type Culture Collection
Shu Wen , Dalian Medical University
pp. 652-653
Hyunsoo Kim , University of Minnesota - Twin Cities
Haesun Park , University of Minnesota - Twin Cities
pp. 656-657
Dennis Chen , Vita Genomics, Inc.
Yuchi Hwang , Vita Genomics, Inc.
Ashely Chang , Vita Genomics, Inc.
Z. John Gu , Vita Genomics, Inc.
pp. 658-659
Oriel Bergig , Ben-Gurion University
Danny Barash , Ben-Gurion University
Klara Kedem , Ben-Gurion University
pp. 660-661
Ravi VijayaSatya , University of Central Florida
pp. 662-665
Jizhu Lu , University of Georgia
PhuongAn Dam , Oak Ridge National Laboratory
Zhengchang Su , Oak Ridge National Laboratory
Ying Xu , University of Georgia and Oak Ridge National Laboratory
pp. 666-667
Hesham H. Ali , University of Nebraska at Omaha
Jitender Deogun , University of Nebraska-Lincoln
pp. 672-673
Hesham Ali , University of Nebraska at Omaha
Xiaolu Huang , University of Nebraska at Omaha
Rakesh Singh , University of Nebraska Medical Center
pp. 674-675
Donald Adjeroh , West Virginia University
Jianan Feng , West Virginia University
pp. 676-681
Promoter Analysis
Brandon Smith , National Research Council Canada
Hung Fang , National Research Council Canada
Youlian Pan , National Research Council Canada
Marianna Sikorska , National Research Council Canada
Roy Walker , National Research Council Canada
pp. 684-685
Yasuo Matsuyama , Waseda University
Ryo Kawamura , Sony-Kihara Research Center Inc.
pp. 686-691
Protein Structure Analysis
R. H. Zadeh , University of North Carolina at Charlotte
Kayvan Najarian , University of North Carolina at Charlotte
Krishna Gopalakrishnan , University of North Carolina at Charlotte
pp. 694-695
Byung-Hoon Park , Oak Ridge National Laboratory
Praveen Chandramohan , Oak Ridge National Laboratory
Al Geist , Oak Ridge National Laboratory
Gong-Xin Yu , Oak Ridge National Laboratory
pp. 696-697
Donghui Wang , Zhejiang University
Jiaoying Shi , Zhejiang University
pp. 698-699
Peng Wang , University of Georgia
Zhengchang Su , University of Georgia
Juntao Guo , University of Georgia
Ying Xu , University of Georgia
pp. 700-701
Jaspreet Singh Sodhi , University College London
Liam J. McGuffin , University College London
Kevin Bryson , University College London
Jonathan J. Ward , University College London
Lorenz Wernisch , University College London
David T. Jones , University College London
pp. 702-703
RNAi Analysis
Chris H. Q. Ding , Lawrence Berkeley National Laboratory
Richard F. Meraz , Lawrence Berkeley National Laboratory
Xiaofeng He , Lawrence Berkeley National Laboratory
Stephen R. Holbrook , Lawrence Berkeley National Laboratory
pp. 716-717
Marja Timmermans , Cold Spring Harbor Laboratory
Christopher Maher , Cold Spring Harbor Laboratory
Doreen Ware , Cold Spring Harbor Laboratory
pp. 718-723
Sequence Alignment
Robert C. Edgar , University of California at Berkeley
pp. 728-729
Daniela Puiu , Virginia Commonwealth University
pp. 736-737
Bob Mau , University of Wisconsin-Madison
Aaron E. Darling , University of Wisconsin-Madison
Nicole T. Perna , University of Wisconsin-Madison
pp. 738-739
Maulik K. Shah , Arizona State University and Translational Genomics Research Institute
HoJoon Lee , Arizona State University
Stephanie A. Rogers , Arizona State University
Jeffrey W. Touchman , Translational Genomics Research Institute and Arizona State University
pp. 740-741
SNPs and Haplotyping
Shiori Furihata , Japan Biological Informatics Consortium
Toshikazu Ito , Mitsubishi Research Institute, INC.
Naoyuki Kamatani , TokyoWomen?s Medical University
pp. 744-745
Synthetic Biological Systems
Junya Nakai , Osaka Sangyo University
Mitsuyasu Seo , Osaka Sangyo University
Luonan Chen , Osaka Sangyo University
pp. 748-749
Author Index
Author Index (PDF)
pp. 753-756
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