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Proceedings of the 2003 IEEE Bioinformatics Conference. CSB2003 (2003)
Stanford, CA, USA
Aug. 11, 2003 to Aug. 14, 2003
ISBN: 0-7695-2000-6
TABLE OF CONTENTS
Preface (PDF)
pp. xv
pp. xvii
Referees (PDF)
pp. xviii
Keynote Addresses
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
Marvin Frazier , U.S. Department of Energy Office of Science
pp. 2
Richard M. Karp , University of California at Berkeley
pp. 10
Invited Speakers
Johoshua Bruck , California Institute of Technology
pp. 14
Bjarni Halld?rsson , Celera/Applied Biosystems
Oliver Kohlbacher , Celera/Applied Biosystems
Russell Schwartz , Celera/Applied Biosystems
Stephen Hoffman , Celera/Applied Biosystems
Liliana Florea , Celera/Applied Biosystems
pp. 17
Peter Karp , SRI International
pp. 27
Genomes to Life
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
James Borneman , Univ. of Calif., Riverside
Tao Jiang , Univ. of Calif., Riverside
pp. 38
Wing-Kin Sung , National University of Singapore
Wah-Heng Lee , Genome Institute of Singapore
pp. 65
Xintao Wei , 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
Jorge Lepre , T.J. Watson Research Center
Nigam Shah , Pennsylvania State University
Gustavo Stolovitzky , T.J. Watson Research Center
pp. 94
Tomoyuki Higuchi , The Institute of Statistical Mathematics
Takao Goto , University of Tokyo
Kousuke Tashiro , Kyushu University
Satoru Kuhara , Kyushu University
Seiya Imoto , 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
Steve Lin , Stanford Medical Informatics
Mark Woon , Stanford Medical Informatics
Teri E. Klein , Stanford Medical Informatics
Shuo Liu , Stanford Medical Informatics
pp. 132
Aidong Zhang , State University of New York at Buffalo
Murali Ramanathan , State University of New York at Buffalo
pp. 137
Tamer Kahveci , University of California, Santa Barbara
Orhan ?amoglu , 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
Jih-H. Chen , SAIC-NCI/FCRDC
Shu-Yun Le , National Cancer Institute, NIH
pp. 190
Dong Xu , Oak Ridge National Laboratory
Carolyn M. Slupsky , University of Alberta
Xiang Wan , University of Alberta
pp. 197
Data Mining
Jiong Yang , University of Illinois, Urbana-Champaign
Hwanjo Yu , University of Illinois, Urbana-Champaign
Jiawei Han , University of Illinois, Urbana-Champaign
pp. 220
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
George Ostrouchov , Oak Ridge National Laboratory
Al Geist , Oak Ridge National Laboratory
Nagiza F. Samatova , Oak Ridge National Laboratory
pp. 235
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
Shoudan Liang , NASA Ames Research Center
pp. 260
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
Nicholas D. Socci , Albert Einstein College of Medicine
Mihaela Zavolan , The Rockefeller 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
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
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
Hsin-Nan Lin , Academia Sinica
Kuen-Pin Wu , Academia Sinica
Wen-Lian Hsu , Academia Sinica
pp. 347
Daniel Quest , University of Nebraska
Hesham Ali , University of Nebraska
Mark Pauley , University of Nebraska
Robert Norgren , University of Nebraska
pp. 353
Satish Eddhu , University of California, Davis
Dan Gusfield , University of California, Davis
pp. 363
Data Integration
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
Kerry Deutsch , Institute for Systems Biology
Barbara Eckman , IBM Life Sciences
Zo? Lacroix , Arizona State University
Louiqa Raschid , University of Maryland
pp. 388
Data Mining
Wen Zhang , Harvard University; Kunming Medical College
Zhaohui S. Qin , Harvard University
Jun S. Liu , Harvard University
pp. 394
Stephane Boissinot , Queens College
Robert M. Haralick , City University of New York
Mingzhou Song , Queens College
pp. 403
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
K. Fung , University of Colorado Health Sciences Center
H. Wang , University of Colorado at Denver
C. Yen , University of Colorado at Denver
M. Duncan , University of Colorado Health Sciences Center
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
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
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
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
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
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
Torgeir Hvidsten , Linnaeus Centre for Bioinformatics
Andriy Kryshtafovych , Lawrence Livermore National Laboratory
Lisa Stubbs , Lawrence Livermore National Laboratory
Bartosz Wilczynski , Warsaw University
Krzysztof Fidelis , Lawrence Livermore National Laboratory
pp. 435
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
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
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
Victor Olman , Oak Ridge National Laboratory
Dong Xu , Oak Ridge National Laboratory
Ying Xu , Oak Ridge National Laboratory
pp. 448
Genotyping and SNPs
Hirotaka Higuchi , NTT Data Co. Ltd.
Takashi Kido , HuBit Genomix, Inc.
Hirohito Matsumine , HuBit Genomix, Inc.
Yoko Higashi , NTT Data Co. Ltd.
Toshihiko Morimoto , NTT Data Co. Ltd.
Masaaki Muramatsu , HuBit Genomix, Inc.; Tokyo Medical Dental University
pp. 450
Masanori Baba , HuBit Genomix, Inc.
Hirohito Matsumine , HuBit Genomix, Inc.
Yoko Higashi , NTT Data Co. Ltd.
Hirotaka Higuchi , NTT Data Co. Ltd.
Takashi Kido , HuBit Genomix, Inc.
pp. 452
Molecular Simulation
Seung Yup Lee , Korea Advanced Institute of Science and Technology
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
Li-Ching Hsieh , National Central University
Fengmin Ji , Northern Jiaotong University
Liaofu Luo , Inner Mongolia University
H.C. Lee , National Central University
pp. 468
Li-Ching Hsieh , National Central University, Taiwan
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
Evangelos E. Milios , Dalhousie University
Andrew J. Roger , Dalhousie University
Christian Blouin , Dalhousie University
Edward Susko , Dalhousie University
pp. 482
Jan Prins , University of North Carolina at Chapel Hill
Jun Huan , University of North Carolina at Chapel Hill
Todd Vision , University of North Carolina at Chapel Hill
pp. 484
John P. Rose , University of Georgia
Bi-Cheng Wang , University of Georgia
Yuhong Wang , Jilin University
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
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
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
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
Torgeir R. Hvidsten , Uppsala University, Uppsala, Sweden
Jan Komorowski , Uppsala University, Uppsala, Sweden
Andriy Kryshtafovych , Lawrence Livermore National Laboratory, Livermore, CA
pp. 517
Gary D. Stormo , Washington University in St. Louis
Jianhua Ruan , Washington University in St. Louis
pp. 519
Tomonori Izumitani , NTT Communication Science Laboratories
Eisaku Maeda , NTT Communication Science Laboratories
Takeshi Suzuki , Nagaoka University of Technology
pp. 521
Chris Ding , University of California, Berkeley
pp. 523
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
Chia H. Yeh , University of Southern California
Shih-Chieh Su , University of Southern California
pp. 539
Wenhui Ren , Purdue University
Wojciech Szpankowski , Purdue University
pp. 541
Carl E. McMillin , Attotron Biosensor Corporation
Robert M. Horton , Attotron Biosensor Corporation
pp. 547
Yanwei Niu , University of Delaware
Jizhu Lu , University of Delaware
Weirong Zhu , University of Delaware
pp. 549
Tamer Kahveci , University of California, Santa Barbara
Ambuj K. Singh , University of California, Santa Barbara
pp. 551
Ozgur Ozturk , Ohio State University
Hong Sun , Ohio State University
pp. 553
Strings, Graphs, and Algorithms
Michael J. Melzer , University of Hawaii at Manoa
John S. Hu , University of Hawaii at Manoa
pp. 560
F. R. Hsu , Taichung Healthcare and Management University, Taiwan
J. F. Chen , Taichung Healthcare and Management University, Taiwan
pp. 564
Suchendra M. Bhandarkar , The University of Georgia
Jinling Huang , The University of Georgia
Jonathan Arnold , The University of Georgia
pp. 567
Xiaolu Huang , University of Nebraska at Omaha
Hesham Ali , University of Nebraska at Omaha
pp. 573
T. Angel , Chemistry & Biochemistry
B. Kirkpatrick , Departments of Computer Sciences
B. Mumey , Departments of Computer Sciences
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
pp. 587
Yunkai Liu , West Virginia University
Elaine M. Eschen , West Virginia University
Keqiang Wu , West Virginia University
pp. 593
Matthew Palensky , University of Nebraska at Omaha
Hesham Ali , University of Nebraska at Omaha
pp. 598
Structural Biology
Igor B. Kuznetsov , Mount Sinai School of Medicine
S. Rackovsky , Mount Sinai School of Medicine
pp. 604
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
Doug L. Brutlag , Stanford Medical Informatics
Mike P. Liang , Stanford Medical Informatics
pp. 613
Keum Joo Kim , University of Connecticut, Storrs
Eugene Santos Jr. , University of Connecticut, Storrs
pp. 615
Systems Biology
Steven Eker , SRI International
Carolyn Talcott , SRI International
Patrick Lincoln , SRI International
Keith Laderoute , SRI International
pp. 618
Karen Chancellor , Arizona State University
Nam Tran , Arizona State University
Nhan Tran , Translational Genomics Research Institute
pp. 623
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
Z. Su , Oak Ridge National Laboratory
pp. 631
Text Mining and Ontologies
Steve Racunas , The Pennsylvania State University
Nina V. Fedoroff , The Pennsylvania State University
pp. 634
Stanley J. Watson , University of Michigan, Ann Arbor
Huda Akil , University of Michigan, Ann Arbor
Weijian Xuan , University of Michigan, Ann Arbor
pp. 639
Miscellaneous
Lori Deneke , University of West Florida
John Eme , University of West Florida
Wayne Bennett , University of West Florida
Melanie A. Sutton , University of West Florida
pp. 654
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
Joseph Gerrein , Columbia University School of Engineering and Applied Sciences
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
Author Index (PDF)
pp. 661
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