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PROGRAM
SPECIAL EVENTS...
All the events below are open to the public free of charge.
Monday, Aug 16, 5:30 PM Memorial Auditorium --- Francis Crick Tribute
Professor Gunther Stent, distinguished scientist from UC Berkeley, will talk about his work with Francis Crick. We will then
show a video from Sydney Brenner, Nobel Laureate (2002), which he made for this event in Singapore. He will talk about his
very close friend, Francis Crick when they were in Cambridge, UK during the Double Helix discovery.
Tuesday, Aug 17, 8:00 PM Memorial Auditorium --- High Performance Computing needed for Bioinformatics Panel
Panelists are from the Life Science divisions of HP, SUN and SIG plus many other Computer Scientists and Engineers working in this area.
more info
Tuesday, Aug 17, 8:00 PM Lower Memorial Auditorium --- Bioinformatics Education
Professor of Bioinformatics from New York City College will talk about their experiences with various workshops in the North East.
more info
Wednesday, Aug 18, 8:00 PM Memorial Auditorium --- Bioinformatics Standards Panel
Lead By John Wooley and Michael Georges together with distinguished scientists from academia and government and computer industry.
They will discuss guidelines for the most needed standards for Biological data and Bioinformatics software.
more info, including Program Outline
Thursday, Aug. 19, Noon - Dohrmann Grove --- First Bionformatics Standards Committee (BSC) meeting
BSC will be chaired by Phil Bourne, Professor and Research Director, University of California, San Diego, Department of Pharmacology,
San Diego Supercomputer Center. more info
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Tuesday, August 17, 2004 |
| 7:00–8:15 AM |
BREAKFAST and Onsite Registration |
| 8:15–8:30 AM |
OPENING REMARKS
Program Co-Chairs: Peter Markstein, Hewlett-Packard
Company and Ying Xu, University of Georgia |
| 8:30–9:45 AM |
SESSION I - Structural Bioinformatics |
| 8:30 AM |
Multiple RNA Structure Alignment - Zhuozhi Wang, Kaizhong Zhang -
Abstract, Full Paper (PDF) |
| 8:55 AM |
Weighting Features to Recognize 3D Patterns of Electron Density in X-ray Protein Crystallography -
Kreshna Gopal, Tod D. Romo, James C. Sacchettini, Thomas R. Ioerger -
Abstract, Full Paper (PDF) |
| 9:20 AM |
Reasoning About Molecular Similarity and Properties - Rahul Singh -
Abstract, Full Paper (PDF) |
Additional papers
presented as posters |
High-throughput 3D Structural Homology Detection via NMR Resonance Assignment
- Christopher Langmead, Bruce Donald - Abstract, Full Paper (PDF) |
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Pair Stochastic Tree Adjoining Grammars for Aligning and Predicting Pseudoknot
RNA Structures - Hiroshi Matsui, Kengo Sato, Yasubumi Sakakibara -
Abstract, Full Paper (PDF) |
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An Algorithm for Detecting Homologues of Known Structured RNAs in Genomes -
Shu-Yun Le, Jacob V. Maizel, Jr., Kaizhong Zhang -
Abstract, Full Paper (PDF) |
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Inverse Protein Folding in 2D HP Model -
Arvind Gupta, Ján Mañuch, Ladislav Stacho -
Abstract, Full Paper (PDF) |
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Analysis of a Systematic Search-based Algorithm for Determining
Protein Backbone Structure from a Minimum Number of Residual Dipolar Couplings -
Lincong Wang, Bruce Donald -
Abstract, Full Paper (PDF) |
| 9:45–10:15 AM |
SNACK BREAK |
| 10:15 AM–12:05 PM |
SESSION II - Genomics 1 |
| 10:15 AM |
Shannon Information in Complete Genomes - Chang-Heng Chang, Ta-Yuan Chen, Li-Ching Hsieh,
Liaofu Luo, Hoong-Chien Lee - Abstract,
Full Paper (PDF) |
| 10:40 AM |
Segmental Duplications Containing Tandem Repeated Putative Deubiquitinating
Enzymes - Hong Liu, Li Li, Asher Zilberstein, Chang S. Hahn -
Abstract, Full Paper (PDF) |
Additional papers
presented as posters |
Compressed Pattern Matching in DNA Sequences - Lei Chen, Shiyong Lu, Jeffrey Ram -
Abstract, Full Paper (PDF) |
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A Self-Tuning Method for One-Chip SNP Identification - Michael Molla,
Jude Shavlik, Thomas Albert, Todd Richmond, Steven Smith -
Abstract, Full Paper (PDF) |
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Space-conserving Optimal DNA-protein Alignment - Pang Ko, Mahesh Narayanan,
Anantharaman Kalyanaraman, Srinivas Aluru -
Abstract, Full Paper (PDF) |
| 11:05 AM |
KEYNOTE SPEAKER - Phil Green
Professor, Genome Sciences and Adjunct Professor, Computer Science and Engineering, University of
Washington, Seattle |
| 12:05–1:35 PM |
LUNCH - Dohrmann Grove |
| 1:35–2:20 PM |
POSTER SESSION |
| 2:20–4:15 PM |
SESSION III - Transcriptomes 1 |
| 2:20 PM |
KEYNOTE SPEAKER - Ron Shamir
Professor, Computer Science Genetics, Raymond & Beverly Sackler Chair in Bioinformatics, Tel Aviv University
Computational Dissection of Regulatory Networks Using Diverse High-throughput Data -
Abstract |
| 3:20 PM |
INVITED SPEAKER - Paul Meltzer
Acting Chief & Senior Investigator, Genetics Branch and Head, Molecular Cytogenetics
Section, National Human Genome Research Institute
Are We There Yet? Genomic Profiling and Mechanism in Cancer Research -
Abstract |
| 3:50 PM |
A Theoretical Analysis of Gene Selection - S.N. Mukherjee,
S.J. Roberts -
Abstract, Full Paper (PDF) |
Additional paper
presented as poster |
Improved Fourier Transform Method for Unsupervised Cell-cycle Regulated
Gene Prediction - Karuturi Krishna Murthy, Liu Jian Hua -
Abstract, Full Paper (PDF) |
| 4:15–4:45 PM |
SNACK BREAK |
| 4:45–5:35 PM |
SESSION IV - Evolution and Phylogeny |
| 4:45 PM |
Algorithms for Association Study Design Using a Generalized Model of
Haplotype Conservation - Russell Schwartz -
Abstract, Full Paper (PDF) |
| 5:10 PM |
Rec-I-DCM3: A Fast Algorithmic Technique - Usman Roshan, Bernard M.E. Moret,
Tiffani L. Williams, Tandy Warnow -
Abstract, Full Paper (PDF) |
Additional paper
presented as poster |
MinPD: Distance-based Phylogenetic Analysis and Recombination Detection
of Serially-sampled HIV Quasispecies - Patricia Buendia, Giri Narasimhan -
Abstract, Full Paper (PDF) |
| 5:35–6:50 PM |
SESSION V - Proteomics |
| 5:35 PM |
SPIDER: Software for Protein Identification from Sequence Tags Containing De Novo
Sequencing Error - Yonghua Han, Bin Ma, Kaizhong Zhang -
Abstract, Full Paper (PDF) |
| 6:00 PM |
Estimating and Improving Protein Interaction Error Rates -
Patrick D'haeseleer, George Church -
Abstract, Full Paper (PDF) |
| 6:25 PM |
Automated Protein Classification Using Consensus Decision - Tolga Can, Orhan Camoglu,
Ambuj K. Singh, Yuan-Fang Wang -
Abstract, Full Paper (PDF) |
Additional paper
presented as poster |
Separation of Ion Types in Tandem Mass Spectrometry Data Interpretation—
A Graph-theoretic Approach - Bo Yan, Chongle Pan, Victor Olman, Robert Hettich, Ying Xu
- Abstract, Full Paper (PDF) |
| 6:50 PM |
DINNER - Dohrmann Grove |
| 8:00 PM |
High Performance and Grid Computing SIG -
chaired by Bob Lashley |
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Bioinformatics Education SIG -
chaired by Yuying Gosser |
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Wednesday, August 18, 2004 |
| 7:00–8:30 AM |
BREAKFAST and Onsite Registration |
| 8:30–10:15 AM |
SESSION VI - Transcriptomes 2 |
| 8:30 AM |
Minimum Entropy Clustering and Applications
to Gene Expression Analysis - Haifeng Li, Tao Jiang -
Abstract, Full Paper (PDF) |
| 8:55 AM |
A Mixed Factors Model for Dimension Reduction and Extraction of a Group Structure in Gene Expression Data
- Ryo Yoshida, Tomoyuki Higuchi, Seiya Imoto -
Abstract, Full Paper (PDF) |
| 9:20 AM |
Gridding and Compression of Microarray Images - Stefano Lonardi, Yu Luo -
Abstract, Full Paper (PDF) |
| 9:45 AM |
INVITED SPEAKER - Jim Kent
Research Scientist, Baskin School of Engineering, University of California Santa Cruz
Spaghetti Code, Soupy Logic, and the Expression of Genes - Abstract |
| 10:15–10:45 AM |
SNACK BREAK |
| 10:45 AM–12:05 PM |
SESSION VII - Applied Bioinformatics |
| 10:45 AM |
INVITED SPEAKER - Stephen Wong
Director, HCNR Center for Bioinformatics and Associate Professor, Department of Radiology, Harvard
Medical School and Brigham & Women's Hospital
High Content Cellular Analysis and Their Applications - Abstract |
| 11:15 AM |
PoPS: A Computational Tool for Modeling and Predicting Protease Specificity -
S.E. Boyd, M. Garcia de la Banda, R.N. Pike, G.B. Rudy, J.C. Whisstock -
Abstract, Full Paper (PDF) |
| 11:40 AM |
Selection of Patient Samples and Genes for Outcome Prediction -
Huiqing Liu, Jinyan Li, Limsoon Wong -
Abstract, Full Paper (PDF) |
| 12:05 - 12:15 PM |
PLoS |
| 12:15–1:45 PM |
LUNCH - Dohrmann Grove |
| 1:45–2:30 PM |
POSTER SESSION |
| 2:30–4:15 PM |
SESSION VIII - Data Mining and Ontology 1 |
| 2:30 PM |
INVITED SPEAKER - Michael Eisen
Assistant Adjunct Professor of Genetics & Development, University of California Berkeley and Scientist,
Life Sciences Division, Lawrence Berkeley Lab |
| 3:00 PM |
Comparison of Two Schemes for Automatic Keyword Extraction from MEDLINE for Functional Gene Clustering -
Ying Liu, Brian J. Ciliax, Karin Borges, Venu Dasigi, Ashwin Ram, Shamkant B. Navathe, Ray Dingledine -
Abstract, Full Paper (PDF) |
| 3:25 PM |
Calculation, Visualization, and Manipulation of MASTs (Maximum Agreement Subtrees) -
Shiming Dong, Eileen Kraemer -
Abstract, Full Paper (PDF) |
| 3:50 PM |
AzuRE, A Scalable System for Automated Term Disambiguation of Gene and Protein Names -
Raf M. Podowski, John G. Cleary, Nicholas Goncharoff, William S. Hayes -
Abstract, Full Paper (PDF) |
| 4:15–4:45 PM |
SNACK BREAK |
| 4:45–6:15 PM |
SESSION IX - Fractals and Bioinformatics |
| 4:45 PM |
KEYNOTE SPEAKER - Benoit Mandelbrot
Sterling Professor of Mathematical Sciences, Yale University and IBM Fellow Emeritus, IBM TJ Watson
Research Center |
| 5:45 PM |
INVITED SPEAKER - Sandy Shaw
Vice President, Fractal Technology, Health Discovery Corporation
Fractal Genomics Modeling: A New Approach to Genomic Analysis and Biomarker Discovery -
Abstract |
| 6:15–7:00 PM |
POSTER SESSION |
| 7:00 PM |
DINNER - Dohrmann Grove |
| 8:00 PM |
Bioinformatics Standards Committee (BSC) Panel discussion - led by John
Wooley and George Michaels - Memorial Auditorium |
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Thursday, August 19, 2004 |
| 7:00–8:30 AM |
BREAKFAST and Onsite Registration |
| 8:30–9:20 AM |
SESSION X - Data Base and Ontology 2 |
| 8:30 AM |
Comparative Analysis of Gene Sets in the Gene Ontology Space under the Multiple Hypothesis Testing
Framework - Sheng Zhong, Lu Tian, Cheng Li, Wing H. Wong -
Abstract, Full Paper (PDF) |
| 8:55 AM |
Gene Ontology Friendly Biclustering of Expression Profiles - Jinze Liu, Wei Wang,
Jiong Yang - Abstract, Full Paper (PDF) |
| 9:20–10:10 AM |
SESSION XI - Pathways and Networks 1 |
| 9:20 AM |
Dynamic Algorithm for Inferring Qualitative Models of Gene Regulatory Networks -
Zheng Yun, Kwoh Chee Keong -
Abstract, Full Paper (PDF) |
| 9:45 AM |
Mapping of Microbial Pathways through Constrained Mapping of Orthologous Genes -
Victor Olman, Hanchuan Peng, Zhengchang Su -
Abstract, Full Paper (PDF) |
| 10:10–10:40 AM |
SNACK BREAK |
| 10:40 AM–12:00 PM |
SESSION XII - Pathways and Networks 2 |
| 10:40 AM |
INVITED SPEAKER - Hamid Bolouri
Professor, Institute for Systems Biology
From DNA Sequence to Network Behavior: Functional Properties of Genetic Regulatory Networks -
Abstract |
| 11:10 AM |
Multi-Knockout Genetic Network Analysis: The Rad6 Example -
Alon Kaufman, Martin Kupiec, Eytan Ruppin -
Abstract, Full Paper (PDF) |
| 11:35 AM |
A Hierarchical Mixture of Markov Models for Finding Biologically Active Metabolic Paths using Gene
Expression and Protein Classes - Hiroshi Mamitsuka, Yasuchi Okuno -
Abstract, Full Paper (PDF) |
| 12:00–2:00 PM |
Kickoff Bioinformatics Standards Committee (BSC) -
chaired by Phil Bourne - Dohrmann Grove |
| 12:00–1:30 PM |
LUNCH - Dohrmann Grove |
| 1:30–2:15 PM |
POSTER SESSION |
| 2:15–4:05 PM |
SESSION XIII - Genomics 2 |
| 2:15 PM |
KEYNOTE SPEAKER - Gene Myers
Professor, Computer Science, University of California Berkeley
Whole Genome Sequencing, Comparative Genomics, and Systems Biology - Abstract |
| 3:15 PM |
FastR: Fast Database Search Tool for Non-coding RNA -
Vineet Bafna, Shaojie Zhang -
Abstract, Full Paper (PDF) |
| 3:40 PM |
Recurrence Time Statistics: Versatile Tools for Genomic DNA Sequence Analysis -
Yinhe Cao, Wen-wen Tung, Jianbo Gao -
Abstract, Full Paper (PDF) |
| 4:05–4:35 PM |
SNACK BREAK |
| 4:35–5:50 PM |
SESSION XIV - Transcriptomes 3 |
| 4:35 PM |
Profile-based String Kernels for Remote Homology Detection and Motif Extraction -
Rui Kuang, Engene Ie, Ke Wang, Kai Wang, Mahira Siddiqi, Yoav Freund, Christina Leslie -
Abstract, Full Paper (PDF) |
| 5:00 PM |
MISAE: A New Approach for Regulatory Motif Extraction -
Zhaohui Sun, Jingyi Yang, Jitender S. Deogun -
Abstract, Full Paper (PDF) |
| 5:25 PM |
Biclustering in Gene Expression Data by Tendency -
Jinze Liu, Jiong Yang, Wei Wang -
Abstract, Full Paper (PDF) |
| 5:50 PM |
CONCLUDING REMARKS; BEST PAPER AND BEST POSTER AWARDS |
The CSB2004 Conference reserves the right to make scheduling changes.
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