Conference Program

The CSB2005 Conference reserves the right to make scheduling changes.
Tuesday, August 9, 2005
7:00–8:15 AM BREAKFAST and On-site Registration
Program Co-chairs: Peter Markstein, Hewlett-Packard Company and Ying Xu, University of Georgia
8:30–9:45 AM SESSION I - Genomics I
8:30 AM Islands of Tractability for Parsimony Haplotyping (PDF)
Roded Sharan, Bjarni V. Halldorsson, Sorin Istrail
8:55 AM Identifying Simple Discriminatory Gene Vectors with an Information Theory Approach (PDF)
Zheng Yun, Kwoh Chee Keong
9:20 AM Learning Yeast Gene Functions from Heterogeneous Sources of Data using Hybrid Weighted Bayesian Networks (PDF)
Xutao Deng, Huimin Geng, Hesham Ali
Additional papers presented as posters Discriminative Discovery of Transcription Factor Binding Sites from Location Data
Yuji Kawada, Yasubumi Sakakibara
  Accurate Prediction of Orthologous Gene Groups in Microbes
Hongwei Wu, Fenglou Mao, Victor Olman, Ying Xu
9:45–10:15 AM SNACK BREAK
10:15 AM–12:00 PM SESSION II - Data Mining and Ontology I
10:15 AM INVITED SPEAKER - Michael Ashburner
Professor, Dept. of Genetics, Univ. of Cambridge; EMBL - EBI
Ontologies for Biologists - A Community Model for the Annotation of Genomic Data
Biography and Abstract, Abstract (PDF)
10:45 AM Clustering Genes using Gene Expression and Text Literature Data (PDF)
Chengyong Yang, Erliang Zeng, Tao Li, Giri Narasimhan
11:10 AM Bioinformatic Insights from Metagenomics through Visualization (PDF)
Susan L. Havre, Bobbie-Jo Webb-Robertson, Anuj Shah, Christian Posse, Banu Gopalan, Fred J. Brockman
11:35 AM On Optimizing Distance-Based Similarity Search for Biological Databases (PDF)
Rui Mao, Weijia Xu, Smriti Ramakrishnan, Glen Nuckolls, Daniel P. Miranker
12:00–1:30 PM LUNCH - Dohrmann Grove
2:15–3:40 PM SESSION III - Mathematics and Biology
2:15 PM KEYNOTE SPEAKER - Jacob T. Schwartz
Professor, Computer Science, Genetics, NYU Courant Institute
3:15 PM Analysis of SNP-Expression Association Matrices (PDF)
Anya Tsalenko, Roded Sharan, Hege Edvardsen, Vessela Kristensen, Anne-Lise Børessen-Dale, Amir Ben-Dor, Zohar Yakhini
3:40–4:10 PM SNACK BREAK
4:10–5:45 PM SESSION IV - Structural Bioinformatics I
Program Manager, Defense Advanced Research Projects Agency (DARPA)
Senior Technical Advisor, Information Technology Lab, National Institute of Standards and Technology (NIST)
4:40 PM An Efficient and Accurate Algorithm for Assigning Nuclear Overhauser Effect Restraints using a Rotamer Library Ensemble and Residual Dipolar Couplings (PDF)
Lincong Wang, Bruce R. Donald
5:05 PM Multi-scale Hierarchical Structure Prediction of Helical Transmembrane Proteins (PDF)
Zhong Chen, Ying Xu
5:30 PM Deformable Modeling for Improved Calculation of Molecular Velocities from Single-Particle Tracking (PDF)
Peter M. Kasson, Mark M. Davis, Axel T. Brunger
Additional papers presented as posters An Algebraic Geometry Approach to Backbone Structure Determination from NMR Data
Lincong Wang, Ramgopal R. Mettu, Bruce R. Donald
A Tree-Decompostion Approach to Protein Structure Prediction
Jinbo Xu, Feng Jiao, Bonnie Berger
6:30 PM DINNER - Dohrmann Grove


Wednesday, August 10, 2005
7:00–8:30 AM BREAKFAST and On-site Registration
8:30–9:45 AM SESSION V - Pathways and Networks
8:30 AM A Pivoting Algorithm for Metabolic Networks in the Presence of Thermodynamic Constraints (PDF)
R. Nigam, S. Liang
8:55 AM A Topological Measurement using Weighted Protein Interaction Network (PDF)
Pengjun Pei, Aidong Zhang
9:20 AM The Generalized Monod, Wyman, Changeaux Model for Mathematical Modeling of Metabolic Enzymes with Allosteric Regulation (PDF)
Tarek S. Najdi, Chin-Rang Yang, Bruce E. Shapiro, G. Wesley Hatfield, Eric D. Mjolsness
Additional paper presented as poster Estimating Time-Dependent Gene Networks from Time Series Microarray Data by Dynamic Linear Models with Markov Switching
Ryo Yoshida, Seiya Imoto, Tomoyuki Higuchi
9:45–10:15 AM SNACK BREAK
10:15–11:50 AM SESSION VI - Medical Bioinformatics
10:15 AM INVITED SPEAKER - Lawrence Goldstein
Department of Cellular and Molecular Medicine, UC San Diego School of Medicine
10:45 AM Choosing SNPs using Feature Selection (PDF)
Tu Minh Phuong, Zhen Lin, Russ B. Altman
11:10 AM Robust and Accurate Cancer Classification with Gene Expression Profiling (PDF)
Haifeng Li, Keshu Zhang, Tao Jiang
11:35 AM A Robust Meta-classification Strategy for Cancer Diagnosis from Gene Expression Data (PDF)
Gabriela Alexe, Gyan Bhanot, Babu Venkataraghavan, Ramakrishna Ramaswamy, Jorge Lepre, Arnold J. Levine, Gustavo Stolovitzky
11:50 AM–1:20 PM LUNCH - Dohrmann Grove
2:05–3:55 PM SESSION VII - Genomics II
2:05 PM KEYNOTE SPEAKER - Sydney Brenner
Distinguished Professor of Biological Sciences, The Salk Institute
2002 Nobel Prize in Medicine and Physiology

From Biological Computation to Computational Biology
3:05 PM Consensus Genetic Maps: A Graph Theoretic Approach (PDF)
Benjamin N. Jackson, Srinivas Aluru, Patrick S. Schnable
3:30 PM Gene Teams with Relaxed Proximity Constraint (PDF)
Sun Kim, Jeong-Hyeon Choi, Jiong Yang
3:55–4:25 PM SNACK BREAK
4:25–5:45 PM SESSION VIII - Transcriptomics
4:25 PM INVITED SPEAKER - Daniel Rokhsar
Program Head, Computational Genomics, JGI
Professor, Molecular Cell Biology, Physics, UC Berkeley
4:55 PM Multi-metric and Multi-substructure Biclustering Analysis for Gene Expression Data (PDF)
S.Y. Kung, M.W. Mak, I. Tagkopoulos
5:20 PM Automated Validation of Polymerase Chain Reactions using Amplicon Melting Curves (PDF)
Tobias P. Mann, Richard Humbert, John A. Stamatoyannopolous, William S. Noble
Additional paper presented as poster A Learned Comparative Expression Measure for Affymetrix GeneChip DNA Microarrays
Will Sheffler, Eli Upfal, John Sedivy, William S. Noble
6:00 PM DINNER - Stanford Faculty Club


Thursday, August 11, 2005
7:00–8:30 AM BREAKFAST and Onsite Registration
8:30–9:10 AM SESSION IX - Genomics III
8:30 AM Efficient Algorithms and Software for Detection of Full-Length LTR Retrotransposons (PDF)
Anantharaman Kalyanaraman, Srinivas Aluru
8:45 AM Motif Extraction and Protein Classification
Vered Kunik, Zach Solan, Shimon Edelman, Eytan Ruppin, David Horn
9:10–9:50 AM SESSION X - Phylogeny and Evolution
9:10 AM Reconstructing Phylogenetic Networks using Maximum Parsimony (PDF)
Luay Nakhleh, Guohua Jin, Fengmei Zhao, John Mellor-Crummey
9:35 AM An Efficient Algorithm for Perfect Phylogeny Haplotyping (PDF)
Ravi Vijaya Satya, Amar Mukherjee
Additional paper presented as poster TreeRefiner: A Tool for Refining a Multiple Alignment on a Phylogenetic Tree
Aswath Manohar, Serafim Batzoglou
9:50–10:20 AM SNACK BREAK
10:20–11:10 AM SESSION XI - Proteomics
10:20 AM Identification of Posttranslational Modifications via Blind Search of Mass-Spectra (PDF)
Dekel Tsur, Stephen Tanner, Ebrahim Zandi, Vineet Bafna, Pavel A. Pevzner
10:45 AM Peptide Charge State Determination for Low-Resolution Tandem Mass Spectra (PDF)
Aaron A. Klammer, Christine C. Wu, Michael J. MacCoss, William S. Noble
Additional paper presented as poster Discover True Association Rates in Multi-protein Complex Proteomics Data Sets
Changyu Shen, Lang Li, Jake Y. Chen
11:10 –11:50 AM SESSION XII - Data Mining and Ontology II
11:10 AM Computational Method for Temporal Pattern Discovery in Biomedical Genomic Databases (PDF)
Mohammed I. Rafiq, Martin J. O'Connor, Amar K. Das
11:25 AM Investigation into Biomedical Literature Classification using Support Vector Machines (PDF)
Nalini Polavarapu, Shamkant B. Navathe, Ramprasad Ramnarayanan, Abrar ul Haque, Saurav Sahay, Ying Liu
11:50 AM –12:20 PM INVITED SPEAKER - Sharon Settnek
Program Manager, Assistant Vice President, Deputy Division Manager, Science Applications International Corporation
Data Mining and Federated IT Systems Enabling Translational Research Across the Cancer Research Community
Biography and Abstract
12:20–1:50 PM LUNCH - Dohrmann Grove
2:35–4:35 PM SESSION XIII - National Centers for Biomedical Computing
2:35 PM KEYNOTE SPEAKER - Russ Altman
Professor, Genetics, Bioengineering, Medicine, Computer Science, Stanford University
Challenges in Creating an Infrastructure for Physics-Based Simulation of Biological Structures
Biography and Abstract, Abstract (PDF)
3:35 PM INVITED SPEAKER - Ron Kikinis
Director of the Surgical Planning Laboratory of the Department of Radiology, Brigham and Women's Hospital and Harvard Medical School; Professor of Radiology at Harvard Medical School
The National Alliance for Medical Imaging Computing (NA-MIC)
Biography and Abstract, Abstract (PDF)
4:05 PM INVITED SPEAKER - Isaac S. Kohane
Associate Professor of Pediatrics and Medicine, Harvard Medical School; Associate Henderson Professor of Health Sciences and Technology; Director, Children's Hospital Informatics Program
4:35–5:05 PM SNACK BREAK
5:05–5:55 PM SESSION XIV - Structural Bioinformatics II
5:05 PM PSIST: Indexing Protein Structure using Suffix Trees (PDF)
Feng Gao, Mohammed J. Zaki
5:30 PM Tree Decomposition Based Fast Search of RNA Structures including Pseudoknots in Genomes (PDF)
Yinglei Song, Chunmei Liu, Russell Malmberg, Fangfang Pan, Liming Cai




To download full papers or abstracts, click on links for the paper in the conference program.