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2004 IEEE Computational Systems Bioinformatics Conference (CSB'04)
Stanford, California
August 16-August 19
ISBN: 0-7695-2194-0
Table of Contents
Microarray Analysis
Pattern Recognition
Other
Introduction
Preface (PDF)
pp. xvii
Committees (PDF)
pp. xviii-xix
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
Genomics
Chang-Heng Chang, National Central University
Li-Ching Hsieh, National Central University
Ta-Yuan Chen, National Central University
Hong-Da Chen, National Central University
Liaofu Luo, Inner Mongolia 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
Wen-wen Tung, National Center for Atmospheric Research
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
Michael Molla, University of Wisconsin-Madison and NimbleGen Systems, Inc.
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
Usman W. Roshan, University of Texas at Austin
Bernard M. E. Moret, University of New Mexico
Tandy Warnow, University of Texas at Austin
Tiffani L. Williams, University of New Mexico
pp. 98-109
Transcriptomes
Stefano Lonardi, University of California at Riverside
Yu Luo, University of California at Riverside
pp. 122-130
Haifeng Li, University of California at Riverside
Keshu Zhang, Rensselaer Polytechnic Institute
Tao Jiang, University of California at Riverside
pp. 142-151
Rui Kuang, Columbia University
Eugene Ie, Columbia University
Ke Wang, Columbia University
Kai Wang, Columbia University
Mahira Siddiqi, Columbia University
Yoav Freund, Columbia University
Christina Leslie, Columbia University
pp. 152-160
Zhaohui Sun, University of Nebraska at Lincoln
Jingyi Yang, University of Nebraska at Lincoln
Jitender S. Deogun, 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
Yonghua Han, University of Western Ontario
Bin Ma, University of Western Ontario
Kaizhong Zhang, University of Western Ontario
pp. 206-215
Tolga Can, University of California at Santa Barbara
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
Bo Yan, University of Georgia and Computational Biology Institute
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
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
Rahul Singh, San Francisco State University
pp. 266-277
Shu-Yun Le, National Cancer Institute
Jacob V. Maizel, Jr., National Cancer Institute
Kaizhong Zhang, University of Western Ontario and Simon Fraser University
pp. 300-310
Arvind Gupta, Simon Fraser University
Ján Maňuch, Simon Fraser University
Ladislav Stacho, Simon Fraser University
pp. 311-318
Pathways & Networks
Victor Olman, University of Georgia
Hanchuan Peng, University of Georgia and Oak Ridge National Laboratory
Zhengchang Su, University of Georgia and Oak Ridge National Laboratory
Ying Xu, University of Georgia and Oak Ridge National Laboratory
pp. 363-370
Applied Bioinformatics
Sarah E. Boyd, Monash University
Maria Garcia de la Banda, Monash University
Robert N. Pike, 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
Ying Liu, Georgia Institute of Technology
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
Raf M. Podowski, AstraZeneca R&D Boston and Karolinska Institutet
John G. Cleary, Reel Two, Ltd. and University of Waikato
Nicholas T. Goncharoff, Reel Two, Inc.
Gregory Amoutzias, AstraZeneca
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
Jinze Liu, University of North Carolina
Wei Wang, University of North Carolina
Jiong Yang, University of Illinois at Urbana-Champaign
pp. 436-447
Biomedical Research
Anguraj Sadanandam, University of Nebraska Medical Center
Michelle L. Varney, University of Nebraska Medical Center
Rakesh K. Singh, University of Nebraska Medical Center
pp. 450-451
Cellular Multicellular Systems
Fang-Xiang Wu, University of Saskatchewan
Wen-Jun Zhang, University of Saskatchewan
Anthony J. Kusalik, University of Saskatchewan
pp. 454-455
Comparative Genomics
Heidi J. Sofia, Pacific Northwest National Laboratory
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
Data Mining
Ian Shadforth, Cranfield University
Daniel Crowther, GlaxoSmithKline
Conrad Bessant, Cranfield University
pp. 470-471
John H. Phan, Georgia Institute of Technology and Emory University
Chang F. Quo, Georgia Institute of Technology and Emory University
Kejiao Guo, Georgia Institute of Technology and Emory University
Weimin Feng, 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
Xuanfu Wu, University of Nebraska at Omaha
Zhengxin Chen, University of Nebraska at Omaha
pp. 485-486
Zo? Lacroix, Arizona State University
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
Jeffrey Stone, University of Vermont
Xindong Wu, University of Vermont
Marc Greenblatt, University of Vermont
pp. 491-492
Huimin Geng, University of Nebraska at Omaha
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
Andrey Gorin, Oak Ridge National Laboratory
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
Hirotoshi Taira, 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
Weihong Qi, Michigan State University
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
Cheryl L. Tarr, Michigan State University
Thomas S. Whittam, Michigan State University
pp. 520-521
Functional Genomics
Allison Griggs, Rochester Institute of Technology
Shuba Gopal, Rochester Institute of Technology
pp. 528
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
Richard F. Meraz, Lawrence Berkeley National Laboratory
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
Peter M. Kasson, Stanford University
Johannes B. Huppa, Stanford University and Howard Hughes Medical Institute
Mark M. Davis, Stanford University and Howard Hughes Medical Institute
Axel T. Brunger, Stanford University and Howard Hughes Medical Institute
pp. 540-541
High Performance Computing
Zemin Ning, The Wellcome Trust Sanger Institute
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
Jung-Yup Kang, University of Southern California
Sandeep Gupta, University of Southern California
Jean-Luc Gaudiot, University of California at Irvine
pp. 552-553
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
Gaurav Tuteja, Georgia Institute of Technology
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
Shawn Martin, Sandia National Laboratories
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
Gene H. Golub, Stanford University
Haesun Park, University of Minnesota
pp. 572-573
Qian Diao, Intel China Research Center
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
Yizhou Xie, Medical College of Wisconsin
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
John A. Berger, University of California at Santa Barbara
Sampsa Hautaniemi, Tampere University of Technology
Sanjit K. Mitra, University of California at Santa Barbara
pp. 584-585
Geoffrey Yang, Affymetrix, Inc.
Ming-Hsiu Ho, Affymetrix, Inc.
Earl Hubbell, Affymetrix, Inc.
pp. 586-587
Xiequn Xu, Donald Danforth Plant Science Center
W. Bradley Barbazuk, Donald Danforth Plant Science Center
Yucheng Feng, Donald Danforth Plant Science Center
Karel Schubert, 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
Zo? Lacroix, Arizona State University
Kaushal Parekh, Arizona State University
Louiqa Raschid, University of Maryland
Maria Esther Vidal, Universidad Sim?n Bol?var
pp. 594-595
Pathways Networks Systems Biology
Alireza Darvish, University of North Carolina at Charlotte
E. Bak, University of North Carolina at Charlotte
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
pp. 602-603
Fang-Xiang Wu, University of Saskatchewan
Anthony J. Kusalik, University of Saskatchewan
Wen-Jun Zhang, 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
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
Ying Xu, University of Georgia at Athens and Oak Ridge National Laboratory
pp. 614-615
Stephen Racunas, Penn State University
Christopher Griffin, Penn State University
Nigam Shah, Penn State University
pp. 616-620
Olusola C. Idowu, University of Newcastle upon Tyne
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
Jean-Loup Faulon, Sandia National Laboratories
Shawn Martin, Sandia National Laboratories
Robert D. Carr, Sandia National Laboratories
pp. 626-627
Jianbo Gao, University of Florida
Jesse Bridgewater, University of California at Los Angeles
Vwani P. Roychowdhury, University of California at Los Angeles
pp. 630-631
Lie-Quan Lee, Stanford Linear Accelerator Center
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
Fenglou Mao, University of Georgia and Oak Ridge National Laboratory
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
Karen Sachs, Massachusetts Institute of Technology
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
Tommi S. Jaakkola, Massachusetts Institute of Technology
Douglas A. Lauffenburger, Massachusetts Institute of Technology
pp. 644
Hsiao Ping Lee, National Tsing-Hua University
Tzu Fang Sheu, National Tsing-Hua University
Yin Te Tsai, Providence University - Taiwan
Ching Hua Shih, National Tsing-Hua University
Chuan Yi Tang, 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
Eugene Lin, Vita Genomics, Inc.
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
Victor Olman, University of Georgia
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
Xutao Deng, University of Nebraska at Omaha
Hesham Ali, University of Nebraska at Omaha
pp. 670-671
Alexandre Tchourbanov, University of Nebraska at Omaha
Hesham H. Ali, University of Nebraska at Omaha
Jitender Deogun, University of Nebraska-Lincoln
pp. 672-673
Xiaolu Huang, University of Nebraska at Omaha
Hesham Ali, University of Nebraska at Omaha
Anguraj Sadanandam, University of Nebraska Medical Center
Rakesh Singh, University of Nebraska Medical Center
pp. 674-675
Promoter Analysis
Youlian Pan, National Research Council Canada
Brandon Smith, National Research Council Canada
Hung Fang, National Research Council Canada
Fazel A. Famili, National Research Council Canada
Marianna Sikorska, National Research Council Canada
Roy Walker, National Research Council Canada
pp. 684-685
Protein Structure Analysis
Krishna 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
pp. 694-695
Gong-Xin Yu, Oak Ridge National Laboratory
Byung-Hoon Park, Oak Ridge National Laboratory
Praveen Chandramohan, Oak Ridge National Laboratory
Al Geist, Oak Ridge National Laboratory
Nagiza F. Samatova, Oak Ridge National Laboratory
pp. 696-697
Chenyang Cui, Zhejiang University
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
Barrett Abel, University of Nevada Reno
Martin Gollery, University of Nevada Reno
pp. 704-705
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
Christopher Maher, Cold Spring Harbor Laboratory
Marja Timmermans, Cold Spring Harbor Laboratory
Lincoln Stein, Cold Spring Harbor Laboratory
Doreen Ware, Cold Spring Harbor Laboratory
pp. 718-723
Sequence Alignment
Daniela Puiu, Virginia Commonwealth University
pp. 736-737
Aaron E. Darling, University of Wisconsin-Madison
Bob Mau, University of Wisconsin-Madison
Mark Craven, 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
Ruiqi Wang, Osaka Sangyo University
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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