Conference Program

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Tuesday, August 15, 2006
Wednesday, August 16, 2006
Thursday, August 17, 2006

The CSB2006 Conference reserves the right to make scheduling changes.

Tuesday, August 15, 2006
7:00–8:15 AM	Breakfast and On-site Registration
8:15–8:30 AM	OPENING REMARKS
8:30–9:45 AM	SESSION I - Structural Bioinformatics I
8:30 AM	Effective Optimization Algorithms for Fragment-Assembly Based Protein Structure Prediction Kevin W. DeRonne, George Karypis
8:55 AM	Transmembrane Helix and Topology Prediction Using Hierarchical SVM Classifiers and an Alternating Geometric Scoring Function Allan Lo, Hua-Sheng Chiu, Ting-Yi Sung, Wen-Lian Hsu
9:20 AM	Protein Fold Recognition Using Gradient Boost Algorithm Feng Jiao, Jinbo Xu, Libo Yu, Dale Schuurmans
Additional papers presented as posters	Identification of Alpha-Helices from Low Resolution Protein Density Mmaps Alessandro Dal Palu, Enrico Pontelli, Jing He, Yonggang Lu
	Efficient Annotation of Non-coding RNA Structures Including Pseudoknots via Automated Filters Chunmei Liu, Yinglei Song, Ping Hu, Russell L. Malmberg, Liming Cai
	Thermodynamic Matchers: Strengthening the Significance of RNA Folding Energies Thomas Hoechsmann, Matthias Hoechsmann, Robert Giegerich
9:45–10:15 AM	Coffee Break
10:15 AM–11:35 AM	SESSION II - Microarray Data Analysis and Applications
10:15 AM	PEM: A General Statistical Approach for Identifying Differentially Expressed Genes in Time-Course cDNA Microarray Experiment without Replicate Xu Han, Wing-Kin Sung, Lin Feng
10:40 AM	Efficient Generalized Matrix Approximations for Biomarker Discovery and Visualization in Gene Expression Data Wenyuan Li, Yanxiong Peng, Hung-Chung Huang, Ying Liu
11:05 AM	INVITED TALK - Jean-Christophe Olivo-Marin Movie Crunching in Biological Dynamic Imaging
11:35–12:35 PM	Lunch - Dohrmann Grove
12:35–1:20 PM	POSTER SESSION Group A
1:20–3:20 PM	SESSION III - National Centers for Biomedical Computing
1:20 PM	KEYNOTE ADDRESS - Mark Musen Don’t Know Much About Philosophy: The Confusion Over Bio-ontologies
2:20 PM	National Center for Integrative Biomedical Informatics Brian D. Athey
2:50 PM	National Center for the Multi-Scale Analysis of Genomic and Cellular Networks Chris Wiggins
3:20–4:20 PM	Coffee Break and Demos
4:20–5:40 PM	SESSION IV - Computational Genomics and Genetics – I
4:20 PM	INVITED TALK - Lincoln Stein Reactome: A Knowledgebase of Biological Pathways
4:50 PM	Turning Repeats to Advantage: Scaffolding Genomic Contigs Using LTR Retrotransposons Ananth Kalyanaraman, Srinivas Aluru, Patrick S. Schnable
5:15 PM	Whole Genome Composition Distance for HIV-1 Genotyping Xiaomeng Wu, Randy Goebel, Xiu-Feng Wan, Guohui Lin
Additional paper presented as posters	Global Correlation Analysis Between Redundant Probe Sets Using a Large Collection of Arabidopsis ATH1 Expression Profiling Data Xiangqin Cui, Ann Loraine
5:40–6:25 PM	POSTER SESSION Group B
6:25-7:45 PM	Dinner - Dohrmann Grove
7:45 PM	PANEL DISCUSSION: NIH National Centers for Biomedical Computing Review

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Wednesday, August 16, 2005
7:00–8:30 AM	Breakfast and On-site Registration
8:30–9:45 AM	SESSION V - Computational Genomics and Genetics – II
8:30 AM	Efficient Recursive Linking Algorithm for Computing the Likelihood of an Order of a Large Number of Genetic Markers S. Tewari, S. M. Bhandarkar, J. Arnold
8:55 AM	Optimal Imperfect Phylogeny Reconstruction and Haplotyping (IPPH) Srinath Sridhar, Guy E. Blelloch, R. Ravi, Russell Schwartz
9:20 AM	Toward an Algebraic Understanding of Haplotype Inference by Pure Parsimony Daniel G. Brown, Ian M. Harrower
9:45–10:15 AM	Coffee Break
10:15–12:00 PM	SESSION VI - Structural Bioinformatics – II
10:15 AM	A Graph-Based Automated NMR Backbone Resonance Sequential Assignment Xiang Wan, Guohui Lin
10:40 AM	A Data-Driven, Systematic Search Algorithm for Structure Determination of Denatured or Disordered Proteins Lincong Wang, Bruce Randall Donald
11:05 AM	Multiple Structure Alignment by Optimal RMSD Implies that the Average Structure is a Consensus Xueyi Wang, Jack Snoeyink
11:30 AM	INVITED TALK - Simon Mercer Bioinformatics Research at Microsoft
12:00 AM–1:00 PM	Lunch - Dohrmann Grove
1:00–1:45 PM	POSTER SESSION Group A
1:45–3:35 PM	SESSION VII - Computational Genomics and Genetics – III
1:45 PM	KEYNOTE ADDRESS - Marvin Frazier Exploring the Ocean's Microbes: Sequencing the Seven Seas
2:45 PM	Efficient Computation of Minimum Recombination with Genotypes (not Haplotypes) Yufeng Wu, Dan Gusfield
3:10 PM	Sorting Genomes by Translocations and Deletions Xingqin Qi, Shuguang Li, Guojun Li, Ying Xu
3:35–4:05 PM	Coffee Break
4:05–5:05 PM	SESSION VIII - Protein Functions and Computational Proteomics – I
4:00 PM	Cavity-Aware Motifs Reduce False Positives in Protein Function Prediction Brian Y. Chen, Drew H. Bryant, Viacheslav Y. Fofanov, David M. Kristensen, Amanda E. Cruess, Marek Kimmel, Olivier Lichtarge, Lydia E. Kavraki
4:25 PM	Protein Subcellular Localization Prediction Based on Compartment-Specific Biological Features Chia-Yu Su, Allan Lo, Hua-Sheng Chiu, Ting-Yi Sung, Wen-Lian Hsu
4:50 PM	Predicting the Binding Affinity of MHC Class II Peptides Fatih Altiparmak, Altuna Akalin, Hakan Ferhatosmanoglu
Additional paper presented as posters	Complexity and Scoring Function of MS/MS Peptide De Novo Sequencing Changjiang Xu, Bin Ma
5:05–6:30 PM	SESSION IX - Biomedical Applications - I
5:05 PM	INVITED TALK - Mark Ellisman Biomedical Informatics Research Network (BIRN): Building a National Collaboratory for BioMedical and Brain Research
5:50 PM	Expectation-Maximization Method for Reconstructing Tumor Phylogenies from Single-Cell Data Gregory Pennington, Charles A. Smith, Stanley Shackney, Russell Schwartz
6:30–8:15 PM	Dinner - Stanford Faculty Club
8:15 PM	LSS Annual Meeting – Stanford Faculty Club

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Thursday, August 17, 2005
7:00–8:30 AM	Breakfast and Onsite Registration
8:30–9:55 AM	SESSION X - Biomedical Applications – II
8:30 AM	A Combined Data Mining Approach for Infrequent Events: Analyzing HIV Mutation Changes Based on Treatment History Ray S. Lin, Soo-Yon Rhee, Robert W. Shafer, Amar K. Das
8:45 AM	A Systems Biology Case Study of Ovarian Cancer Drug Resistance Jake Y. Chen, Changyu Shen, Zhong Yan, Dawn P. G. Brown, Andrey Sivachenko, Mu Wang
9:10 AM	Simulating In Vitro Epithelial Morphogenesis in Multiple Environments Mark R. Grant, Sean H. J. Kim, C. Anthony Hunt
9:25 AM	INVITED TALK - Eric Jakobsson Systems Biology in Two Dimensions: Understanding and Engineering Membranes as Dynamical Systems
9:55–10:25 AM	Coffee Break
10:25–12:10 AM	SESSION XI - Protein Functions and Computational Proteomics – II
10:25 AM	Codon-Based Detection of Positive Selection Can Be Biased by Heterogeneous Distribution of Polar Amino Acids along Protein Sequences Xuhua Xia, Sudhir Kumar
10:50 AM	Bayesian Data Integration: A Functional Perspective Curtis Huttenhower, Olga Troyanskaya
11:15 AM	An Iterative Algorithm to Quantify the Factors Influencing Peptide Fragmentation for MS/MS Spectrum Chungong Yu, Yu Lin, Shiwei Sun, Zhuo Zhang, Jinjin Cai, Jingfen Zhang, Runsheng Chen, Dongbo Bu
11:40 AM	INVITED TALK - Trey Ideker Protein Network Comparative Genomics
12:10–1:10 PM	Lunch - Dohrmann Grove
1:10–1:55 PM	POSTER SESSION Group B
1:55 PM	KEYNOTE ADDRESS - Drew Endy On a System for Engineering Genetic Machines
2:55 PM	INVITED TALK - Christina Smolke Engineering Nucleic Acid-Based Molecular Sensors for Probing and Programming Cellular Systems
3:25–3:55 PM	Coffee Break
3:55–5:10 PM	SESSION XII - Motif Sequence Identification
3:55 PM	Distance-based Identification of Spatial Motifs in Proteins Using Constrained Frequent Subgraph Mining Jun Huan, Deepak Bandyopadhyay, Jan Prins, Jack Snoeyink, Alexander Tropsha, Wei Wang
4:20 PM	An Improved Gibbs Sampling Method for Motif Discovery via Sequence Weighting Xin Chen, Tao Jiang
4:45 PM	Detection of Cleavage Sites for HIV-1 Protease in Native Proteins Liwen You
Additional paper presented as posters	A Methodology for Motif Discovery Employing Iterated Cluster Re-assignment Osman Abul, Geir Kjetil Sandve, Finn Drabløs
5:10–6:00 PM	SESSION XIII - Biological Pathways
5:10 PM	Identifying Biological Pathways via Phase Decomposition and Profile Extraction Yi Zhang, Zhidong Deng
5:35 PM	Expectation-Maximization Algorithms for Fuzzy Assignment of Genes to Cellular Pathways Liviu Popescu, Golan Yona
Additional papers presented as posters	Classification of Drosophila Embryonic Developmental Stage Range Based on Gene Expression Pattern Images Jieping Ye, Jianhui Chen, Qi Li, Sudhir Kumar
	Evolution versus Intelligent Design: Comparing the Topology of Protein-Protein Interaction Networks to the Internet Qiaofeng Yang, Georgos Siganos, Michalis Faloutsos, Stefano Lonardi
6:00 PM	Closing Remarks and Awards for Best Paper and Best Poster

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