IEEE Computer Society
Bioinformatics Conference

Stanford University, Palo Alto, CA
August 14 - 16, 2002

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Last update - July 19, 2002


The tutorials program is one of the highlights of the CSB Bioinformatics Conferences, offering attendees short courses in the interdisciplinary fields related to bioinformatics and the efficient implementation of large scale applications to high throughput computing. Attendees have the opportunity to interact with recognized leaders in the field and learn about the latest technology trends, theory and practical implementation of current challenging problems.

WEDNESDAY, August 14
7:30-8:30 AM
10:15-10:30 AM
BREAKFAST and Onsite Registration
Tutorial 1A

8:30-12:00 PM
Perl and Bioperl:Tools for Automated Analysis of Biological Sequence Data
Peter Schattner, Ph.D., University of Callifornia Santa Cruz
Tutorial 1B

  8:30 - 12:00 PM
Cell Signaling and Neural Networks
Raxit Jariwalla, Ph.D., California Institute for Medical Research
12:00 - 1:30 PM
3:15 - 3:30 PM
Tutorial 2A

1:30 - 5:00 PM
Comparative Genomics for Biological Discovery
Inna Dubchak, Ph.D., Lawrence Berkeley National Laboratory
Tutorial 2B

1:30 - 5:00 PM
Biology for Computer Scientists
David Keys, Ph.D., Miller Fellow, Joint Genome Institute and
Michèle Markstein, University of Chicago
Tutorial 2C

1:30 - 5:00 PM
Logical Analysis of Data and Applications to Bioinformatics
Peter L. Hammer, Ph.D.,Director of Operations Research, Rutgers University
5:30 - 7:30 PM OPENING RECEPTION- Open to all attendees


The IEEE Computer Society Bioinformatics (CSB2002) conference objective is to present cutting edge computational biology research to the largest group of computer scientists in the world. While such research has an interdisciplinary character, CSB2002 emphasizes the computational aspects of bioinformatics research.

The program committee selected computer science papers with biological relevance and biology papers stressing computational contributions.

We thank the authors for the excellent submissions, the invited and keynote speakers and the poster presenters.

THURSDAY, August 15
7:00 - 8:00 AM BREAKFAST and Onsite Registration
8:00 - 8:15 AM Opening Remarks
Program Chair - Peter Markstein
8:15 - 8:45 AM Fast and Sensitive Alignment of Large Genomic Sequences
Michael Brudno, Department of Computer Science, Stanford University, Stanford, CA, USA
8:45 - 9:15 AM An Efficient Branch-and-Bound Algorithm for the Assignment of Protein Backbone NMR Peaks
Dong Xu, Protein Informatics Group, Oak Ridge National Laboratory,TN, USA
9:15 - 10:15 AM Keynote Speaker -
Professor Bernhard Palsson, Ph.D., UC San Diego, USA
10:15 - 10:30 AM COFFEE BREAK
10:30 - 11:00 AM Bayesian Network and Nonparametric Heteroscedastic Regression for Nonlinear Modeling of Genetic Network
Seiya Imoto, Human Genome Center, Institute of Medical Science, University of Tokyo, Tokyo, Japan
11:00 - 11:30 AM A Literature Based Method for Identifying Gene-Disease Connections
Dr. Lada A. Adamic, HP Laboratories, 1501 Page Mill Road, Palo Alto, CA, USA
11:00 - 12:00 PM Invited Speaker -
Suffix Trees Come of Age: Applications in Genomic-Scale Bioinformatics
Dan Gusfield, Professor Computer Science, UC Davis
12:00 - 12:30 PM POSTER SESSION I
12:30 - 1:45 PM LUNCH
1:45 - 2:45 PM Keynote Speaker -
Leroy Hood, M.D.,Ph.D., President and Director Institute for Systems Biology
2:45 - 3:15 PM Some Histograms Generated from the Counting of K-tuples in Genomes
Huimin Xie, Suzhou Univeristy, Peoples Republic of China
3:15 - 3:30 PM COFFEE BREAK
3:30 - 4:00 PM Invited Speaker -
Professor Steven Brenner, UC Berkeley
4:00 - 4:30 PM Automated Identification of Single Nucleotide Polymorphisms from Sequence Data
Masazumi Takahashi, Centre National de Genotypage, France
4:30 - 5:00 PM PheGe, the Platform for Exploring Genotype/Phenotype Relations on Cellular and Organism Level
Klaus Seidl, German Research Centre for Biotechnology, Germany
5:00 - 5:30 PM Parallelizing a DNA Simulation Code for the Cray MTA-2
Shahid H. Bokhari, EE, University of Engineering & Technology, Lahore, Pakistan
6:15 - 7:30 PM DINNER
7:30 - 9:00 PM Panel Discussion
"How Open Should Bioinformatics Be?"
9:00 - 9:30 PM DESSERTS
FRIDAY, August 16
7:00 - 8:00 AM BREAKFAST and Onsite Registration
8:00 - 8:30 AM A Multi-level Text Mining Method to Extract Biological Relationships
Mathew Palakal, CS and Biology, Indiana University Purdue University, Indianapolis, IN
8:30 - 9:00 AM DNA Sequence Compression Using the Burrows-Wheeler Transform
Adjeroh D.A, CS and EE West Virginia University
9:00 - 9:30 AM Constrained Multiple Sequence Alignment Tool Development and Its Application to RNase Family Alignment
ChuanYi Tang, National Tsing Hua University, Hsinchu 300, Taiwan
9:30 - 9:45 AM COFFEE BREAK
10:15 - 10:45 AM Fast and Sensitive Algorithm for Aligning ESTs to Human Genome
Jun Ogasawara, Computer Science, University of Tokyo, Japan
10:45 - 11:15 AM Protein-based Analysis of Alternative Splicing in the Human Genome
Ann E. Loraine, Affymetrix, Inc., Emeryville, CA, USA
11:15 - 12:15 PM Keynote Speaker -
Challenges for Knowledge Management in Biomedical Informatics
Russ Altman, M.D.,Ph.D., Associate Professor of Genetics and Medicine (and Computer Science by courtesy), Stanford University, CA
12:15 - 1:30 PM LUNCH
1:30 - 2:00 PM Invited Speaker -
Decoding Regulatory DNAs in Complex Genomes
Michael Levine, Professor of Genetics and Development, UC Berkeley, CA, USA
2:00 - 2:30 PM Rapid Large-Scale Oligonucleotide Selection for Microarrays
Sven Rahmann, MPI for Molecular Genetics, Berlin, Germany
2:30 - 3:00 PM ΦLOG: a Domain Specific Language for Solving Phylogenetic Inference Problems
E. Pontelli, CS and Biology, New Mexico State University, USA
3:00 - 3:30 PM Prediction of Protein Function Using Protein-Protein Interaction Data
Fengzhu Sun, Molecular and Computational Biology, University of Southern California, Los Angeles, CA, USA
3:30 -3:45 PM COFFEE BREAK
3:45 - 4:15 PM A Maximum Entropy Algorithm for Rhythmic Analysis of Genome-Wide Expression Patterns
Christopher James Langmead, Dartmouth Computer Science, Hanover, NH, USA
4:15 - 4:45 PM A Bi-Recursive Neural Network Architecture for the Prediction of Protein Coarse Contact Maps
Paolo Frasconi, Systems and Computer Science, University of Florence, Firenze, Italy
4:45 - 5:15 PM Towards Automatic Clustering of Protein Sequences
Jiong Yang, IBM T. J. Watson Research Center, Hawthorne, NY, USA
5:15 - 5:45 PM Best Paper and Best Poster
Closing Remarks
Conference Chair - Vicky Markstein

© 2002 IEEE Computer Society Bioinformatics