John Wooley Best Paper Award and Best Poster Award WINNERS!

View and download Papers here (abstracts and full-text PDFs).

Poster abstracts (PDFs) may be viewed and downloaded from the Posters page.

Poster Presenters: Posters must be set up Tuesday morning between 7 to 11:30 AM. THe cork boards are 8 feet wide by 4 feet high. You will be sharing poster space with neighbors. CSB2010 supplies push pins, but you may prefer to bring your own.

Tuesday – August 17, 2010
8:00 AM Opening Remarks – Sean Mooney
8:05 AM Session I – Genomics and Genetics I
8:05 AM Novel Gene Discovery in the Human Malaria Parasite using Nucleosome Positioning Data
N. Pokhriyal, N. Ponts, E. Y. Harris, K. G. Le Roch and S. Lonardi
8:30 AM Inferring Haplotypes from Genotypes on a Pedigree with Mutations, Genotyping Errors and Missing Alleles
Wei-Bung Wang and Tao Jiang
8:55 AM A Genome Compression Algorithm Supporting Manipulation
Lenwood S. Heath, Ao-ping Hou, Huadong Xia and Liqing Zhang
9:20 AM Coffee Break
9:40 AM
Session II – Invited Speaker - Sandrine Dudoit UC Berkeley
Statistical Approaches for Meeting Challenges in the Analysis and Interpretation of mRNA-Seq
10:25 AM
Session III – Structural Bioinformatics I - RNA
10:25 AM
Grammar String: A Novel ncRNA Secondary Structure Representation
Rujira Achawanantakun, Seyedeh Shohreh Takyar and Yanni Sun
10:50 AM
Analyzing Modular RNA Structure Reveals Low Global Structural Entropy in microRNA Sequence
Timothy I. Shaw, Amir Manzour, Yingfeng Wang, Russell L. Malmberg and Liming Cai
11:15 AM
RNAv: Non-coding RNA Secondary Structure Variation Search via Graph Homomorphism
Zhibin Huang, Russell L. Malmberg, Mohammad Mohebbi and Liming Cai
11:40 AM LUNCH at Dohrmann Grove and Poster Session
1:10 PM Session IV – Poster Talks I
1:10 PM Simulation of "Single Molecule Real Time" (SMRT) Sequencing and Data Transformations for Use with Existing Workflow Tools
Robert Horton
1:20 PM Reanalyze Unassigned Reads In Metagenomic Data using Conserved Gene Adjacency
Daryi Wang and Francis Cheng-Hsuan Weng
1:30 PM Network Models of Clinical Trial Data
Marco D. Sorani and Geoffrey T. Manley
1:40 PM High-Throughput Detection of Epistasis in Studies of the Genetics of Complex Traits
Asta Laiho, Attila Gyenesei, András Király, János Abonyi, Colin Semple, Chris Haley and Wenhua Wei
1:50 PM Predicting Disease-Related Single Amino Acid Polymorphisms using Protein Structure
E. Capriotti and R.B. Altman
2:00 PM Genome-scale Methyltyping by Statistical Inference for Determining Methylation States in Populations
Meromit Singer, Dario Boffelli, Joseph Dhahbi, Alexander Schoenhuth, Gary P. Schroth, David I.K. Martin and Lior Pachter
2:10 PM MIDREG: A Method of Mining Developmentally Regulated Genes using Boolean Implications
D. Sahoo, J. Seita, D. Bhattacharya, M.A. Inlay, I.L. Weissman, S.K. Plevritis and D.L. Dill
2:20 PM Session V – Genomics and Genetics II
2:20 PM Comparing Multiple Protein Binding Profiles in ChIP-seq Experiments
Hatice Gulcin Ozer, Jiejun Wu, Yi-Wen Huang, Jeffrey Parvin, Tim Huang and Kun Huang
2:45 PM Coffee Break
3:10 PM Lex-SVM: Exploring the Potential of Exon Expression Profiling for Disease Classification
Xiongying Yuan, Yi Zhao, Changning Liu and Dongbo Bu
3:35 PM Kernel-based Gene Regulatory Network Inference
Yi Shi, Yuhong Guo, Guohui Lin and Dale Schuurmans
4:00 PM Session VI – Bioinformatics at the Clinical and Translational Sciences Institutes
Kent Anderson UC Davis, William K. Barnett Indiana University, Michael Kamerick UC San Francisco, Todd Ferris Stanford University and Hien Nguyen UC Davis



Wednesday – August 18, 2010
8:00 AM Session VII – Structural Bioinformatics II
8:00 AM Approximating Conserved Regions of Protein Structures
Yi Wei, Mingfu Shao, Jishuang Yang, Chao Wang, Shuai Cheng Li and Dongbo Bu
8:25 AM Optimization of Therapeutic Proteins to Delete T-cell Epitopes while Maintaining Beneficial Residue Interactions
Andrew S. Parker, Karl E. Griswold and Chris Bailey-Kellogg
8:50 AM Session VIII – Biological Pathways and Networks
8:50 AM Modeling of Hysteresis in a Mammalian Gene Regulatory Network
J. Hu, K.R. Qin, C. Xiang and T.H. Lee
9:15 AM Generating Executable Models from Signaling Network Connectivity and Semi-quantitative Proteomic Measurements
Derek Ruths and Luay Nakhleh
9:40 AM Coffee Break
10:00 AM
Modeling Perturbations using Gene Networks
Nirmalya Bandyopadhyay, Manas Somaiya, Tamer Kahveci and Sanjay Ranka
10:25 AM
Temporal Graphical Models for Cross-Species Gene Regulatory Network Discovery
Yan Liu, Alexandru Niculescu-Mizil, Aurelie Lozano and Yong Lu
10:50 AM
Session IX – Keynote Talk – Mike Snyder Stanford University
Personal and Non-Personal Genomes: Their Analysis and Variation
11:50 AM LUNCH at Dohrmann Grove and Poster Session
1:20 PM Session X – Poster Talks II
1:20 PM Greatly Improved Allele-specific Tumor Copy Numbers with DNA Microarrays when a Matched Normal is Available
Pierre Neuvial, Henrik Bengtsson and Terence P. Speed
1:30 PM Analysis of a Local Huntington Protein Interaction Network
C. Powell, C. Tourette, R. Bell, S. Mooney and R. Hughes
1:40 PM Reanalyze Unassigned Reads in Metagenomic Data using Conserved Gene Adjacency
Daryi Wang, Francis Cheng-Hsuan Weng, Huai-Kuang Tsai, Chien-Hao Su, Ming-Tsung Hsu and Tse-Yi Wang
1:50 PM Exploring the Protein University from General Principles
L. Apeltsin and T. E. Ferrin
2:00 PM Genome-wide Mouse Encode Data at UC Santa Cruz
Melissa Cline, Kate Rosenbloom, Tim Drezer, Brian Raney, Cricket Sloan, Venkat Malladi, Galt Barber, Krishna Roskin, Bernard Suh, Angie Hinrichs, Ann Zwieg, Pauline Fujita, Katrina Learned, Brooke Rhead, Vanessa Swing, Antonio Coehlo, Robert Kuhn, Donna Karolchik, David Haussler and W. James Kent
2:10 PM Large-scale Evolutionary Simulations of Complex Microbial Behaviors in Dynamic Environments
V. Mozhayskiy and I. Tagkopoulos
2:20 PM Session XI – Invited Talk – Steven Brenner UC Berkeley
Progress and Aspirations of the Genome Commons
3:05 PM Coffee Break
3:25 PM Session XII – Genetics and Genomics III
3:25 PM Algorithmic Strategies for Estimating the Amount of Reticulation from a Collection of Gene Trees
H. J. Park, G. Jin and L. Nakhleh
3:50 PM Hierarchical Boosting for Gene Function Prediction
Noor Alaydie, Chandan K. Reddy and Farshad Fotouhi
4:15 PM Accurate Identification of Ortholog Groups among Multiple Genomes
Guanqun Shi, Meng-Chih Peng and Tao Jiang
4:40 PM Classification of Large Microarray Data Sets using Fast Random Forest Construction
E. A. Manilich, Z. M. Ozsoyoglu, V. Trubachev and T. Radivoyevitch
5:05 PM Session XIII – Invited Talk – Brian Naughton 23 and Me
5:50 PM Closing Remarks
Awards - The John Wooley Award for Best Paper and the Award for Best Poster

CSB2010 reserves the right to make scheduling changes at any time if necessary.


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