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IEEE Computer Society Bioinformatics Conference (CSB'03)
Stanford, California
August 11-August 14
ISBN: 0-7695-2000-6
Table of Contents
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Referees (PDF)
pp. xviii
Keynote Addresses
Marvin Frazier, U.S. Department of Energy Office of Science
David Thomassen, U.S. Department of Energy Office of Science
Aristides Patrinos, U.S. Department of Energy Office of Science
Gary Johnson, U.S. Department of Energy Office of Science
Carl E. Oliver, U.S. Department of Energy Office of Science
Edward Uberbacher, UT-Battelle, LLC
pp. 2
Invited Speakers
Liliana Florea, Celera/Applied Biosystems
Bjarni Halld?rsson, Celera/Applied Biosystems
Oliver Kohlbacher, Celera/Applied Biosystems
Russell Schwartz, Celera/Applied Biosystems
Stephen Hoffman, Celera/Applied Biosystems
Sorin Istrail, Celera/Applied Biosystems
pp. 17
Peter Karp, SRI International
pp. 27
Michael S. Waterman, University of Southern California
Yu Zhang, University of Southern California
pp. 29
Genomes to Life
Ed Uberbacher, Oak Ridge National Laboratory
David Thomassen, Office of Biological and Environmental Research
Ari Patrinos, Office of Biological and Environmental Research
Gary Johnson, Office of Advanced Scientific Computing Research
Carl E. Oliver, Office of Advanced Scientific Computing Research
Marvin Frazier, Office of Biological and Environmental Research
pp. 32
Microarray Data Analysis
Xintao Wei, Florida International University
David N. Kuhn, Florida International University
Giri Narasimhan, Florida International University
pp. 75
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
Nigam Shah, Pennsylvania State University
Jorge Lepre, T.J. Watson Research Center
Yuhai Tu, T.J. Watson Research Center
Gustavo Stolovitzky, T.J. Watson Research Center
pp. 94
Seiya Imoto, University of Tokyo
Tomoyuki Higuchi, The Institute of Statistical Mathematics
Takao Goto, University of Tokyo
Kousuke Tashiro, Kyushu University
Satoru Kuhara, Kyushu University
Satoru Miyano, University of Tokyo
pp. 104
Biomedical Research and Visualization
Dennis L. Chao, University of New Mexico
Miles P. Davenport, University of New South Wales
Stephanie Forrest, University of New Mexico
Alan S. Perelson, Los Alamos National Laboratory
pp. 124
Shuo Liu, Stanford Medical Informatics
Steve Lin, Stanford Medical Informatics
Mark Woon, Stanford Medical Informatics
Teri E. Klein, Stanford Medical Informatics
Russ B. Altman, Stanford Medical Informatics
pp. 132
Li Zhang, State University of New York at Buffalo
Aidong Zhang, State University of New York at Buffalo
Murali Ramanathan, State University of New York at Buffalo
pp. 137
Orhan ?amoglu, University of California, Santa Barbara
Tamer Kahveci, University of California, Santa Barbara
Ambuj K. Singh, University of California, Santa Barbara
pp. 148
Matthias H?chsmann, University of Bielefeld
Thomas T?ller, University of Bielefeld
Robert Giegerich, University of Bielefeld
Stefan Kurtz, University of Bielefeld
pp. 159
Xiang Wan, University of Alberta
Dong Xu, Oak Ridge National Laboratory
Carolyn M. Slupsky, University of Alberta
Guohui Lin, University of Alberta
pp. 197
Christopher James Langmead, Dartmouth Computer Science Department
Bruce Randall Donald, Dartmouth Computer Science Department
pp. 209
Data Mining
Hwanjo Yu, University of Illinois, Urbana-Champaign
Jiong Yang, University of Illinois, Urbana-Champaign
Wei Wang, University of North Carolina
Jiawei Han, University of Illinois, Urbana-Champaign
pp. 220
Jake Y. Chen, Myriad Proteomics, Inc.
Andrey Y. Sivachenko, Myriad Proteomics, Inc.
Russell Bell, Myriad Proteomics, Inc.
Cornelia Kurschner, Myriad Proteomics, Inc.
Irene Ota, Myriad Proteomics, Inc.
Sudhir Sahasrabudhe, Myriad Proteomics, Inc.
pp. 229
Gong-Xin Yu, Oak Ridge National Laboratory
George Ostrouchov, Oak Ridge National Laboratory
Al Geist, Oak Ridge National Laboratory
Nagiza F. Samatova, Oak Ridge National Laboratory
pp. 235
Robert Grossman, University of Illinois at Chicago
Pavan Kasturi, University of Illinois at Chicago
Donald Hamelberg, University of Illinois at Chicago
Bing Liu, University of Illinois at Chicago
pp. 244
Pattern Recognition
Eric P. Xing, University of California
Wei Wu, Lawrence Berkeley National Lab
Michael I. Jordan, University of California, Berkeley
Richard M. Karp, University of California, Berkeley
pp. 266
Mihaela Zavolan, The Rockefeller University
Nicholas D. Socci, Albert Einstein College of Medicine
Nikolaus Rajewsky, New York University
Terry Gaasterlamd, The Rockefeller University
pp. 277
Ravi Vijaya Satya, University of Central Florida
Amar Mukherjee, University of Central Florida
Udaykumar Ranga, Jawaharlal Nehru Center for Advanced Scientific Research
pp. 294
Sequence Alignment
C. Di Pietro, Universit? di Catania
V. Di Pietro, Universit? di Catania
G. Emmanuele, Universit? di Catania
A. Ferro, Universit? di Catania
T. Maugeri, Universit? di Catania
E. Modica, Universit? di Catania
G. Pigola, Universit? di Catania
A. Pulvirenti, Universit? di Catania
M. Purrello, Universit? di Catania
M. Ragusa, Universit? di Catania
M. Scalia, Universit? di Catania
D. Shasha, New York University
S. Travali, Universit? di Catania
V. Zimmitti, Universit? di Catania
pp. 326
Francis Y. L. Chin, The University of Hong Kong, Hong Kong
N. L. Ho, The University of Hong Kong, Hong Kong
T. W. Lam, The University of Hong Kong, Hong Kong
Prudence W. H. Wong, The University of Hong Kong, Hong Kong
M. Y. Chan, The University of Hong Kong, Hong Kong
pp. 337
Kuen-Pin Wu, Academia Sinica
Hsin-Nan Lin, Academia Sinica
Ting-Yi Sung, Academia Sinica
Wen-Lian Hsu, Academia Sinica
pp. 347
Alexandre Tchourbanov, University of Nebraska
Daniel Quest, University of Nebraska
Hesham Ali, University of Nebraska
Mark Pauley, University of Nebraska
Robert Norgren, University of Nebraska
pp. 353
Dan Gusfield, University of California, Davis
Satish Eddhu, University of California, Davis
Charles Langley, University of California, Davis
pp. 363
Data Integration
M. Chagoyen, Centro Nacional de Biotecnologia, Madrid, Spain
M. E. Kurul, U.C. San Diego
P. A. De-Alarcon, Parque Cientifico de Madrid, Madrid, Spain
S. Santini, U.C. San Diego
B. Lud?scher, U.C. San Diego
J. M. Carazo, Centro Nacional de Biotecnologia, Madrid, Spain
A. Gupta, U.C. San Diego
pp. 386
Barbara Eckman, IBM Life Sciences
Kerry Deutsch, Institute for Systems Biology
Marta Janer, Institute for Systems Biology
Zo? Lacroix, Arizona State University
Louiqa Raschid, University of Maryland
pp. 388
Xin Lu, Harvard University
Wen Zhang, Harvard University; Kunming Medical College
Zhaohui S. Qin, Harvard University
Jun S. Liu, Harvard University
pp. 394
Jane Fridlyand, UCSF Comprehensive Cancer Center
Antoine Snijders, UCSF Comprehensive Cancer Center
Dan Pinkel, UCSF Comprehensive Cancer Center
Donna Albertson, UCSF Comprehensive Cancer Center
Ajay Jain, UCSF Comprehensive Cancer Center
pp. 407
M. Duncan, University of Colorado Health Sciences Center
K. Fung, University of Colorado Health Sciences Center
H. Wang, University of Colorado at Denver
C. Yen, University of Colorado at Denver
K. Cios, University of Colorado at Denver
pp. 409
Xutao Deng, University of Nebraska at Omaha
Hesham Ali, University of Nebraska at Omaha
pp. 413
Tema Fridman, Computer Science and Mathematics Division
Robert Day, Computer Science and Mathematics Division
Jane Razumovsbya, Life Sciences Division
Dong Xu, Life Sciences Division
Andrey Gorin, Computer Science and Mathematics Division
pp. 415
Eric G. Stephan, Pacific Northwest National Laboratories
George Chin Jr., Pacific Northwest National Laboratories
Kyle R. Klicker, Pacific Northwest National Laboratories
Abigail L. Corrigan, Pacific Northwest National Laboratories
Heidi J. Sofia, Pacific Northwest National Laboratories
pp. 419
Jane Razumovskaya, Oak Ridge National Laboratory; University of Tennessee, Knoxville
Victor Olman, Oak Ridge National Laboratory
Dong Xu, Oak Ridge National Laboratory; University of Tennessee, Knoxville
Ed Uberbacher, Oak Ridge National Laboratory; University of Tennessee, Knoxville
Nathan Verbermoes, University of Tennessee, Knoxville
Ying Xu, Oak Ridge National Laboratory; University of Tennessee, Knoxville
pp. 421
Functional Genomics
Zhangjun Fei, Texas A&M University; Cornell University
Xuemei Tang, Cornell University
Rob Alba, Cornell University
Paxton Payton, Cornell University
Jim Giovannoni, Cornell University; USDA Plant, Soil, and Nutrition Laboratory
pp. 424
Harpreet Kaur Gill, Christian Medical College and Hospital
pp. 426
Marilyn Safran, the Weizmann Institute of Science
Vered Chalifa-Caspi, the Weizmann Institute of Science
Orit Shmueli, the Weizmann Institute of Science
Naomi Rosen, the Weizmann Institute of Science
Hila Benjamin-Rodrig, the Weizmann Institute of Science
Ron Ophir, the Weizmann Institute of Science
Itai Yanai, the Weizmann Institute of Science
Michael Shmoish, the Weizmann Institute of Science
Doron Lancet, the Weizmann Institute of Science
pp. 427
Taku A. Tokuyasu, UCSF Cancer Center
Donna Albertson, UCSF Cancer Center
Dan Pinkel, UCSF Cancer Center
Ajay Jain, UCSF Cancer Center
pp. 429
Wenwu Cui, University of Delaware
Jianchang Ning, University of Delaware
Ulhas P. Naik, University of Delaware
Melinda K. Duncan, University of Delaware
pp. 433
Bartosz Wilczynski, Warsaw University
Torgeir Hvidsten, Linnaeus Centre for Bioinformatics
Andriy Kryshtafovych, Lawrence Livermore National Laboratory
Lisa Stubbs, Lawrence Livermore National Laboratory
Jan Komorowski, Linnaeus Centre for Bioinformatics
Krzysztof Fidelis, Lawrence Livermore National Laboratory
pp. 435
Qing Dong, Stanford University School of Medicine
Rama Balakrishnan, Stanford University School of Medicine
Gail Binkley, Stanford University School of Medicine
Karen R. Christie, Stanford University School of Medicine
Maria Costanzo, Stanford University School of Medicine
Kara Dolinski, Stanford University School of Medicine
Selina S. Dwight, Stanford University School of Medicine
Stacia Engel, Stanford University School of Medicine
Dianna G. Fisk, Stanford University School of Medicine
Jodi Hirschman, Stanford University School of Medicine
Eurie L. Hong, Stanford University School of Medicine
Rob Nash, Stanford University School of Medicine
Laurie Issel-Tarver, Stanford University School of Medicine
Anand Sethuraman, Stanford University School of Medicine
Chandra L. Theesfeld, Stanford University School of Medicine
Shuai Weng, Stanford University School of Medicine
David Botstein, Stanford University School of Medicine
J. Michael Cherry, Stanford University School of Medicine
pp. 437
Gary Livingston, Univ. of Massachusetts, Lowell
Xiao Li, Univ. of Massachusetts, Lowell
Guangyi Li, Univ. of Massachusetts, Lowell
Liwu Hao, Univ. of Massachusetts, Lowell
Jiangping Zhou, Univ. of Massachusetts, Lowell
pp. 439
Genomic Annotation
Shaun Mahony, National Centre for Biomedical Engineering Science, NUI, Galway
Terry J. Smith, National Centre for Biomedical Engineering Science, NUI, Galway
James O. McInerney, Bioinformatics and Pharmacogenomics Laboratory, NUI, Maynooth, Co.
Aaron Golden, Department of Information Technology, NUI, Galway
pp. 444
Rong Chen, University of Nebraska at Omaha
Hesham Ali, University of Nebraska at Omaha
pp. 446
Victor Olman, Oak Ridge National Laboratory
Dong Xu, Oak Ridge National Laboratory
Ying Xu, Oak Ridge National Laboratory
pp. 448
Genotyping and SNPs
Yoko Higashi, NTT Data Co. Ltd.
Hirotaka Higuchi, NTT Data Co. Ltd.
Takashi Kido, HuBit Genomix, Inc.
Hirohito Matsumine, HuBit Genomix, Inc.
Masanori Baba, HuBit Genomix, Inc.
Toshihiko Morimoto, NTT Data Co. Ltd.
Masaaki Muramatsu, HuBit Genomix, Inc.; Tokyo Medical Dental University
pp. 450
Takashi Kido, HuBit Genomix, Inc.
Masanori Baba, HuBit Genomix, Inc.
Hirohito Matsumine, HuBit Genomix, Inc.
Yoko Higashi, NTT Data Co. Ltd.
Hirotaka Higuchi, NTT Data Co. Ltd.
Masaaki Muramatsu, HuBit Genomix, Inc.; Tokyo Medical Dental University
pp. 452
Molecular Simulation
Seung Yup Lee, Korea Advanced Institute of Science and Technology
Yoshimi Fujitsuka, Kobe University
Shoji Takada, Kobe University; Japan Science and Technology Corporation
Do Hyun Kim, Korea Advanced Institute of Science and Technology
pp. 456
Kaori Ueno-Noto, Ochanomizu University
Keiko Takano, Ochanomizu University
Miki Hara-Yokoyama, Ochanomizu University
pp. 462
Phylogeny and Evolution
Liaofu Luo, Inner Mongolia University
Li-Ching Hsieh, National Central University
Fengmin Ji, Northern Jiaotong University
Mengwen Jia, Inner Mongolia University
H.C. Lee, National Central University
pp. 468
Li-Ching Hsieh, National Central University, Taiwan
Liaofu Luo, Inner Mongolia University
H.C. Lee, National Central University, Taiwan; Inner Mongolia University
pp. 474
Chen Yang, San Jose State University
Sami Khuri, San Jose State University
pp. 476
S?ren W. Perrey, University of Applied Sciences of Gelsenkirchen, Germany
Heinrich Brinck, University of Applied Sciences of Gelsenkirchen, Germany
Achim Zielesny, University of Applied Sciences of Gelsenkirchen, Germany
pp. 478
Ghislain Bidaut, Fox Chase Cancer Center; Structural and Genetic Information Laboratory
Karsten Suhre, Structural and Genetic Information Laboratory
Jean-Michel Claverie, Structural and Genetic Information Laboratory
Michael F. Ochs, Fox Chase Cancer Center
pp. 480
Yunfeng Shan, Dalhousie University
Evangelos E. Milios, Dalhousie University
Andrew J. Roger, Dalhousie University
Christian Blouin, Dalhousie University
Edward Susko, Dalhousie University
pp. 482
Jun Huan, University of North Carolina at Chapel Hill
Jan Prins, University of North Carolina at Chapel Hill
Wei Wang, University of North Carolina at Chapel Hill
Todd Vision, University of North Carolina at Chapel Hill
pp. 484
Yuhong Wang, Jilin University
John P. Rose, University of Georgia
Bi-Cheng Wang, University of Georgia
Dawei Lin, University of Georgia
pp. 486
Predictive Methods
Dechang Chen, Unifonned Services University of the Health Sciences
Dong Hua, The George Washington University
Jaques Reifman, US Army Medical Research and Materiel Command
Xiuzhen Cheng, The George Washington University
pp. 492
Dong Hua, The George Washington University
Dechang Chen, Uniformed Services University of the Health Sciences
Xiuzhen Cheng, The George Washington University
Abdou Youssef, The George Washington University
pp. 496
Yoshiharu Hayashi, KLIMERS Co., LTD; Toyohashi University of Technology
Katsuyoshi Sakaguchi, KLIMERS Co., LTD
Nao Iwata, KLIMERS Co., LTD
Masaki Kobayashi, KLIMERS Co., LTD
pp. 500
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
Minoru S.H. Ko, National Institutes of Health, National Institute on Aging
pp. 502
I-Jeng Wang, Johns Hopkins University Applied Physics Lab
Christopher P. Diehl, Johns Hopkins University Applied Physics Lab
Fernando J. Pineda, Johns Hopkins Bloomberg School of Public Health
pp. 506
Jianchang Ning, University of Delaware, Newark
Charles N. Moore, Kansas State University, Manhattan
J. Clare Nelson, Kansas State University, Manhattan
pp. 509
Andriy Kryshtafovych, Lawrence Livermore National Laboratory, Livermore, CA
Torgeir R. Hvidsten, Uppsala University, Uppsala, Sweden
Jan Komorowski, Uppsala University, Uppsala, Sweden
Krzysztof Fidelis, Lawrence Livermore National Laboratory, Livermore, CA
pp. 517
Jianhua Ruan, Washington University in St. Louis
Gary D. Stormo, Washington University in St. Louis
Weixiong Zhang, Washington University in St. Louis
pp. 519
Hirotoshi Taira, NTT Communication Science Laboratories
Tomonori Izumitani, NTT Communication Science Laboratories
Eisaku Maeda, NTT Communication Science Laboratories
Takeshi Suzuki, Nagaoka University of Technology
pp. 521
Sequence Comparison
Jianping Zhou, Univ. of Mass., Lowell
Gary Livingston, Univ. of Mass., Lowell
Georges Grinstein, Univ. of Mass, Lowell
pp. 530
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
Shih-Chieh Su, University of Southern California
Chia H. Yeh, University of Southern California
C. -C. Jay Kuo, University of Southern California
pp. 539
Carl E. McMillin, Attotron Biosensor Corporation
Robert M. Horton, Attotron Biosensor Corporation
pp. 547
Weirong Zhu, University of Delaware
Yanwei Niu, University of Delaware
Jizhu Lu, University of Delaware
Guang R. Gao, University of Delaware
pp. 549
Tamer Kahveci, University of California, Santa Barbara
Ambuj K. Singh, University of California, Santa Barbara
pp. 551
Strings, Graphs, and Algorithms
Holger Mauch, University of Hawaii at Manoa
Michael J. Melzer, University of Hawaii at Manoa
John S. Hu, University of Hawaii at Manoa
pp. 560
Youlian Pan, National Research Council Canada
A. Fazel Famili, National Research Council Canada
pp. 562
F. R. Hsu, Taichung Healthcare and Management University, Taiwan
J. F. Chen, Taichung Healthcare and Management University, Taiwan
pp. 564
Xiaolu Huang, University of Nebraska at Omaha
Hesham Ali, University of Nebraska at Omaha
pp. 573
Yimin Jing, San Jose State University
Sami Khuri, San Jose State University
pp. 581
Ezekiel F. Adebiyi, University of Ilorin, Ilorin
Tinuke Dipe, University of Ilorin, Ilorin
pp. 583
B. Mumey, Departments of Computer Sciences
T. Angel, Chemistry & Biochemistry
B. Kirkpatrick, Departments of Computer Sciences
B. Bailey, NIH-NIAAA
P. Hargrave, Univ. of Florida, Gainesville, FL
A. Jesaitis, Montana State Univ., Bozeman, MT
E. Dratz, Chemistry & Biochemistry
pp. 585
Donald Adjeroh, West Virginia University, Morgantown
Jianan Feng, West Virginia University, Morgantown
pp. 587
Matthew Palensky, University of Nebraska at Omaha
Hesham Ali, University of Nebraska at Omaha
pp. 598
Structural Biology
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
Mike P. Liang, Stanford Medical Informatics
Doug L. Brutlag, Stanford Medical Informatics
Russ B. Altman, Stanford Medical Informatics
pp. 613
Eugene Santos Jr., University of Connecticut, Storrs
Keum Joo Kim, University of Connecticut, Storrs
Eunice E. Santos, Virginia Polytechnic Institute and State University
pp. 615
Systems Biology
Carolyn Talcott, SRI International
Steven Eker, SRI International
Merrill Knapp, SRI International
Patrick Lincoln, SRI International
Keith Laderoute, SRI International
pp. 618
Chitta Baral, Arizona State University
Karen Chancellor, Arizona State University
Nam Tran, Arizona State University
Nhan Tran, Translational Genomics Research Institute
pp. 623
Yoshihiro Morishita, The University of Tokyo
Kazuyuki Aihara, The University of Tokyo
pp. 629
Z. Su, Oak Ridge National Laboratory
P. Dam, Oak Ridge National Laboratory
X. Chen, Univ. of California at Riverside
V. Olman, Oak Ridge National Laboratory
T. Jiang, Univ. of California at Riverside
B. Palenik, University of California at San Diego
Y. Xu, Oak Ridge National Laboratory
pp. 631
Text Mining and Ontologies
Steve Racunas, The Pennsylvania State University
Nigam Shah, The Pennsylvania State University
Nina V. Fedoroff, The Pennsylvania State University
pp. 634
Weijian Xuan, University of Michigan, Ann Arbor
Stanley J. Watson, University of Michigan, Ann Arbor
Huda Akil, University of Michigan, Ann Arbor
Fan Meng, University of Michigan, Ann Arbor
pp. 639
Rachel Harte, PPD Discovery, Inc.
Yan Lu, PPD Discovery, Inc.
Stephen Osborn, PPD Discovery, Inc.
David Dehoney, PPD Discovery, Inc.
Daniel Chin, PPD Discovery, Inc.
pp. 644
Miscellaneous
Melanie A. Sutton, University of West Florida
Lori Deneke, University of West Florida
John Eme, University of West Florida
Wayne Bennett, University of West Florida
Frank Wray, University of West Florida
pp. 654
Joseph Gerrein, Columbia University School of Engineering and Applied Sciences
Armen Kherlopian, Columbia University School of Engineering and Applied Sciences
Vezen Wu, Columbia University Information Technology Programs
Mitchell Berman, Columbia University College of Physicians and Surgeons
Alvin Wald, Columbia University Department of Biomedical Engineering
pp. 656
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
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