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
5:30 - 6:30 PM	POSTER SESSION II
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
9:45 - 10:15 AM	POSTER SESSION III
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