 Program |
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Opening Ceremony & Networking Reception* Monday, August 11, 2003 at 5:00 pm–7:00 pm Dohrmann Grove, Stanford University, CA (across from Memorial Auditorium) *The Opening Ceremony and Networking Reception is open to all attendees. To celebrate the second annual Computational Systems Bioinformatics (CSB) Conference at Stanford University, CSB cordially invites you to attend the Opening Ceremony and Networking Reception. The reception will attract attendees, speakers and special guests and will take place in the pastoral setting of Dorhmann Grove. It's an ideal setting for attendees to meet their colleagues, visit the poster displays to preview the latest technologies while enjoying wine and cheese. Special Events are planned for Tuesday and Wednesday evenings. Tuesday is a Bioethics Panel on Dangerous Knowledge. Wednesday is the DOE/GTL Dinner Workshop. Everyone is invited, but space is limited. So sign up for this event when you register for the conference. Sponsorship opportunities available. See details at http://conferences.computer.org/bioinformatics/CSB2003/Sponsor.html |
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Special Interest Groups—CSBB (Biomedical science) and CSBHPC (High
Performance Computing) Monday, August 11, 2003 at 7:00 pm–9:30 pm Stanford University(meeting room to be announced) Details |
| PODIUM
AND POSTER PRESENTATIONS The IEEE Computer Society Bioinformatics 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, CSB2003 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, the invited and keynote speakers, and the poster exhibitors for their excellent presentations. |
| TUESDAY, August 12, 2003 | |
| 7:00 - 8:00 AM | BREAKFAST and Onsite Registration |
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SESSION I Microarray Data Analysis Chair - Jake Chen |
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| 8:00 - 8:15 AM | OPENING
REMARKS - Program Co-Chairs Peter Markstein, Principal Scientist, Hewlett-Packard Co. Ying Xu,Senior Staff Scientist/Group Leader, Oak Ridge National Laboratory |
| 8:15 - 8:45 AM |
Clustering Binary Fingerprint Vectors with Missing Values for DNA Array Data Analysis
Abstract, Full Paper Andres Figueroa, James Borneman, Tao Jiang |
| 8:45 - 9:15 AM |
Clustering Time-varying Gene Expresssion Profiles Using Scale-space Signals
Abstract, Full Paper Tanveer Syeda-Mahmood |
| 9:15 - 9:45 AM | INVITED
SPEAKER - Jehoshua Bruck Gordon and Betty Moore Professor of Computation and Neural Systems & Electrical Engineering, California Institute of Technology Bridging Paradigm Gaps Between Biology and Engineering |
| 9:45 - 10:00 AM | SNACK BREAK |
| SESSION II Microarray Data Analysis (Continued) Chair - Suchendra Bhandarkar |
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| 10:00 - 10:30 AM | INVITED
SPEAKER - John Wooley Assoc. Vice Chancellor for Research/Depts. of Pharmacology, Chemistry, and Biochemistry/ San Diego Supercomputer Center, UC San Diego Cyberinfrastructure and The Frontier between Computing and Biology |
| 10:30 - 11:00 AM |
Fast and Sensitive Probe Selection for DNA Chips Using Jumps in Matching Statistics
Abstract, Full Paper Sven Rahmann |
| 11:00 - 11:30 AM |
Fast and Accurate Probe Selection Algorithm for Large Genomes
Abstract, Full Paper Wing-Kin Sung, Wah-Heng Lee |
| 11:30 AM - 12:00 PM |
Degenerate Primer Design via Clustering
Abstract, Full Paper Xintao Wei, Giri Narasimhan, David N. Kuhn |
| * | FULL
PAPER PRESENTED AS POSTER Group Testing with DNA Chips: Generating Designs and Decoding Experiments Abstract, Full Paper Alexander Schliep, David C. Torney, Sven Rahmann |
| 12:00 - 1:15 PM | LUNCH |
| 1:15 - 2:00 PM | POSTER
SESSION I - Presentation by Section A authors All posters will be up for all sessions. |
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SESSION III
Molecular Structure Chair - Antonio Piccolboni |
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| 2:00 - 2:30 PM |
Experimental Studies of the Universal Chemical Key (UCK) Algorithm on the NCI Database of Chemical Compounds
Abstract, Full Paper Robert Grossman, Donald Hamelberg, Pavan Kasturi, Bing Liu |
| 2:30 - 3:30 PM | KEYNOTE
SPEAKER- Christian Burks Chief Scientific Officer, Affinium Pharmaceuticals |
| 3:30 - 3:45 PM | SNACK BREAK |
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SESSION IV Pathways, Networks and System Biology Chair - Gustavo Stolovitzky |
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| 3:45 - 4:15 PM |
Can We Identify Cellular Pathways Implicated in Cancer Using Gene Expression Data?
Abstract, Full Paper Nigam Shah, Jorge Lepre, Yuhai Tu, Gustavo Stolovitzky |
| 4:15 - 4:45 PM |
Statistical Inference for Well-ordered Structures in Nucleotide Sequences
Abstract, Full Paper Shu-Yun Le, Jih-H. Chen, Jacob V. Maizel, Jr. |
| 4:45 - 5:15 PM | INVITED
SPEAKER - Eric Davidson Norman Chandler Professor of Biology, California Institute of Technology The Sea Urchin Endomesoderm Gene Regulatory Network, an Encoded Logic Map for Early Development |
| 5:15 - 5:45 PM |
Combining Microarrays and Biological Knowledge for Estimating Gene Networks via Bayesian Networks
Abstract, Full Paper Seiya Imoto, Tomoyuki Higuchi, Takao Goto, Kousuke Tashiro, Satoru Kuhara, Satoru Miyano |
| * | FULL
PAPER PRESENTED AS POSTER Two Operative Concepts for the Post-genomic Era: The "mémoire vive" of the Cell and a Molecular Algebra Abstract, Full Paper Simone Bentolila |
| 5:45 - 6:15 PM | POSTER
SESSION II - Presentation by Section B authors All posters will be up for all sessions. |
| 6:15 - 7:30 PM | DINNER - Dohrmann Grove |
| 7:30 PM |
PANEL DISCUSSION - Bioethics |
| WEDNESDAY, August 13, 2003 | |
| 7:00 - 8:00 AM | BREAKFAST and Onsite Registration |
| SESSION V Biomedical Research Chair - Ann Loraine | |
| 8:00 - 8:30 AM | Stochastic Stage-structured
Modeling of the Adaptive Immune System
Abstract, Full Paper Dennis L. Chao, Stephanie Forrest, Miles P. Davenport, Alan S. Perelson |
| 8:30 - 9:00 AM |
A Personalized and Automated dbSNP Surveillance System
Abstract, Full Paper Shuo Liu, Steve Lin, Mark Woon, Teri E. Klein, Russ B. Altman |
| 9:00 - 9:30 AM | INVITED
SPEAKER - Stephen Wong Director and Associate Professor, HCNR Center of Bioinformatics, Harvard Medical School Integrating Bioinformatics Advances into Disease Management Systems to Improve Quality of Care |
| * | FULL
PAPER PRESENTED AS POSTER Fourier Harmonic Approach for Visualizing Temporal Patterns of Gene Expression Data Abstract, Full Paper Li Zhang, Aidong Zhang, Murali Ramanathan |
| 9:30 - 9:45 AM | SNACK BREAK |
| SESSION VI Protein/RNA Structure Prediction and Modeling Chair - Sridhar Govindarajan | |
| 9:45 - 10:15 AM | INVITED
SPEAKER - Sorin Istrail Senior Director of Informatics Research, Celera Genomics Epitope prediction algorithms for peptide-based vaccine design |
| 10:15 - 10:45 AM |
Towards Index-based Similarity Search for Protein Structure Databases
Abstract, Full Paper Orhan Camoglu, Tamer Kahveci, Ambuj K. Singh |
| 10:45 - 11:15 AM |
Local Similarity in RNA Secondary Structures
Abstract, Full Paper Matthias Höchsmann, Thomas Töller, Robert Giegerich, Stefan Kurtz |
| 11:15 - 11:45 PM |
CTSS: A Robust and Efficient Method for Protein Structure Alignment
Based on Local Geometrical and Biological Features
Abstract, Full Paper Tolga Can, Yuan-Fang Wang |
| 11:45 AM - 1:00 PM | LUNCH |
| 1:00 - 2:00 PM | POSTER
SESSION III - Presentation by Section B authors All posters will be up for all sessions. |
| SESSION VII Data Mining and GTL Project Chair - Satoru Miyano | |
| 2:00 - 2:30 PM |
Discovering Compact and Highly Discriminative Features or Feature
Combinations of Drug Activities Using Support Vector Machine
Abstract, Full Paper Hwanjo Yu, Jiong Yang, Wei Wang, Jiawei Han |
| 2:30 - 3:30 PM | KEYNOTE
SPEAKER- Marvin E. Frazier Director, Life Sciences Division, Office of Biological & Environmental Research, U.S. Dept. of Energy Stepping up the Pace of Biological Discovery: The DOE Genomes to Life Program Abstract (PDF), Presentation Slides |
| 3:30 - 3:45 PM | SNACK BREAK |
| SESSION VIII Pattern Recognition Chair - Mark Borodovsky | |
| 3:45 - 4:15 PM |
cWINNOWER Algorithm for Finding Fuzzy DNA Motifs
Abstract, Full Paper Shoudan Liang |
| 4:15 - 4:45 PM |
LOGOS: A Modular Bayesian Model for de novo Motif Detection
Abstract, Full Paper Eric P. Xing, Wei Wu, Michael I. Jordan, Richard M. Karp |
| 4:45 - 5:15 PM |
INVITED SPEAKER- Jun Liu Professor, Dept. of Statistics, Harvard Univ. BPPS: An Algorithm for Analyzing Protein Sequence Alignments |
| 5:15 - 5:45 PM |
A Block Coding Method That Leads to Significantly Lower Entropy Values
for the Proteins of Haemophilus influenza and Its Coding Sections
Abstract, Full Paper G Sampath |
| * |
FULL PAPERS PRESENTED AS POSTERS Codon Optimization for DNA Vaccines and Gene Therapy Using Pattern Matching Abstract, Full Paper Ravi Vijaya Satya, Amar Mukherjee, Udaykumar Ranga Haplotype Motifs: An Algorithmic Approach to Locating Evolutionary Conserved Patterns in Haploid Sequences Abstract, Full Paper Russell Schwartz |
| 6:00 - 9:30 PM | DINNER -
Stanford Faculty Club DOE/GTL WORKSHOP - Marvin Frazier, Adam Arkin, Grant Heffelfinger, Michael Knotek, Maddalena Coppi, Ed Uberbacher Abstract (PDF), Presentation Slides |
| THURSDAY, August 14, 2003 | |
| 7:00 - 8:00 AM | BREAKFAST and Onsite Registration |
| SESSION IX Protein/RNA Structure Prediction and Modeling (Continued) Chair - Ying Xu |
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| 8:00 - 8:30 AM |
Statistical and Visual Morph Movie Analysis of Crystallographic Mutant Selection Bias in
Protein Mutation Resource Data
Abstract, Full Paper Werner G. Krebs, Phil Bourne |
| 8:30 - 9:00 AM |
A New Similarity Measure Among Protein Sequences
Abstract, Full Paper Kuen-Pin Wu, Hsin-Nan Lin, Ting-Yi Sung, Wen-Lian Hsu |
| 9:00 - 9:30 AM | INVITED
SPEAKER - Philip Bourne Dept. of Pharmacology/San Diego Supercomputer Center, UC San Diego High Performance Computational Biology—Past Progress and Future Promise |
| * |
FULL PAPERS PRESENTED AS POSTERS Automated Protein NMR Resonance Assignments Abstract, Full Paper Xiang Wan, Dong Xu, Carolyn M. Slupsky, Guohui Lin 3D Structural Homology Detection via Unassigned Residual Dipolar Couplings Abstract, Full Paper Christopher James Langmead, Bruce Randall Donald |
| 9:30 - 9:45 AM | SNACK BREAK |
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SESSION X Sequence Alignment Chair - Peter Markstein |
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| 9:45 - 10:15 AM | INVITED
SPEAKER - Michael Waterman Professor, Dept. of Computational and Molecular Biology, USC Eulerian Path Methods for Multiple Sequence Alignment |
| 10:15 - 10:45 AM |
Computing Highly Specific and Mismatch Tolerant Oligomers Efficiently
Abstract, Full Paper Tomoyuki Yamada, Shinichi Morishita |
| 10:45 - 11:15 AM |
ANTICLUSTAL: Multiple Sequence Alignment by Antipole Clustering and Linear Approximate 1-Median Selection
Abstract, Full Paper C. Di Peitro, A. Ferro, T. Maugeri, G. Pigola, A. Pulvirenti, D. Shasha, V. Di Pietro, G. Emmanuele, E. Modica, M. Purrello, M. Ragusa, M. Scalia, S. Travali, V. Zimmitti |
| 11:15 - 11:45 AM |
Efficient Constrained Multiple Sequence Alignment with Performance Guarantee
Abstract, Full Paper Francis Y.L. Chin, N.L. Ho, T.W. Lam |
| * | FULL
PAPER PRESENTED AS POSTER A New Approach for Gene Annotation Using Unambiguous Sequence Joint Abstract, Full Paper Alexandre Tchourbanov, Daniel Quest, Hesham Ali, Mark Pauley, Robert Norgren |
| 11:45 AM - 1:00 PM | LUNCH |
| 1:00 - 1:30 PM | POSTER
SESSION IV - Presentation by Section A authors All posters will be up for all sessions. |
| SESSION XI Comparative Genomics and Phylogenetic Analysis Chair - Liping Wei |
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| 1:30 - 2:00 PM |
Efficient Reconstruction of Phylogenetic Networks (of SNPs) with Constrained Recombination
Abstract, Full Paper Dan Gusfield, Satish Eddhu, Charles Langley |
| 2:00 - 2:30 PM |
Prokaryote Phylogeny without Sequence Alignment: From Avoidance Signature
to Composition Distance
Abstract, Full Paper Bailin Hao, Ji Qi, Bin Wang |
| 2:30 - 3:30 PM | KEYNOTE
SPEAKER- Richard Karp Professor, Depts. of Bioengineering, Electrical Engineering & Computer Science, and Mathematics, UC Berkeley The Role of Algorithmic Research in Computational Genomics Abstract, Presentation Slides |
| 3:30 - 3:45 PM | SNACK BREAK |
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SESSION XII Data Mining (Continued) Chair - Sean Mooney |
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| 3:45 - 4:15 PM |
SMASHing Regulatory Sites in DNA by Human-mouse Sequence Comparisons
Abstract, Full Paper Mihaela Zavolan, Terry Gaasterland, Nikolaus Rajewsky, Nicholas D. Socci |
| 4:15 - 4:45 PM | INVITED
SPEAKER - Peter Karp Director, Bioinformatics Research Group, SRI International, Palo Alto, CA Pathway Bioinformatics |
| 4:45 - 5:15 PM |
Initial Large-scale Exploration of Protein-Protein Interactions in the Human Brain
Abstract, Full Paper Jake Y. Chen, Andrey Y. Sivachenko, Russell Bell, Connie Kurschner, Irene Ota, Sudhir Sahasrabudhe |
| 5:15 - 5:45 PM |
An SVM-based Algorithm for Identification of Photosynthesis-Specific Genome Features
Abstract, Full Paper Gong-Xin Yu, Al Geist, George Ostrouchov, Nagiza F. Samatova |
| * | FULL
PAPER PRESENTED AS POSTER A Probabilistic Model for Identifying Protein Names and Their Name Boundaries Abstract, Full Paper Kazuhiro Seki, Javed Mostafa |
| 5:45 PM | BEST PAPER/POSTER -
HP Laptop Awards CLOSING REMARKS - Vicky Markstein, retired Staff Member, Watson IBM Research, IEEE CS Bioinformatics Technical Chair and CSB General Chair |
 ABSTRACTS KEYNOTE SPEAKERS INVITED SPEAKERS DOE GTL WORKSHOP Click on presentation title or speaker name for abstract/full paper PODIUM PRESENTATIONS This is a listing of Abstracts only. For Full Papers as Proceedings pdf files, click on "Full Paper" next to the presentation title on the program. FULL PAPERS PRESENTED AS POSTERS This is a listing of Abstracts only. For Full Papers as Proceedings pdf files, click on "Full Paper" next to the poster title on the program. POSTERS Section A Data Integration Data Mining Functional Genomics Genotyping and SNPs Strings, Graphs, and Algorithms Structural Biology Text Mining and Ontologies Section B Genomic Annotation Molecular Simulation Phylogeny and Evolution Predictive Methods Sequence Comparison Systems Biology Miscellaneous
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