Registration Information

Location: Atkinson Hall (Calit2 building)
Monday, August 13, 2007
• Tutorials
• Opening Ceremony - Wine and Cheese Party
Tuesday, August 14, 2007
• Podium and poster presentations
• Regional Computational Systems Bioinformatics
Wednesday, August 15, 2007
• Podium and poster presentations
• LSS/CSB Banquet
Thursday, August 16, 2007
• Podium presentations
Friday, August 17, 2007
• Workshops


TUESDAY, August 14, 2007
7:00 AM Breakfast
8:15 AM Opening Remarks
8:30 AM Session I: Pathways, Networks & Systems Biology I
8:30 AM Dirk Husmeier, Adriano Werhli
Bayesian Integration of Biological Prior Knowledge into the Reconstruction of Gene Networks with Bayesian Network
8:55 AM Hon Nian Chua, Kang Ning, Wing-Kin Sung, Hon Wai Leong, Limsoon Wong
Using Indirect Protein-Protein Interactions for Protein Complex Prediction
9:20 AM Henry C.M. Leung, M.H. Siu, S.M. Yiu, Francis Y.L. Chin, Ken W.K. Sung
Finding Linear Motif Pair from Protein Interaction Networks: A Probabilistic Approach
Additional paper presented as poster
Preetam Ghosh, Samik Ghosh, Kalyan Basu, Sajal K Das
A Markov Model-based Analysis of Stochastic Biochemical Systems
9:45 AM Break
10:15 AM Session II: Genomics I
10:15 AM INVITED TALK: AJ Marian Walhout
Gene-centered Protein-DNA Interactome Mapping
10:45 AM Zheng Fu, Tao Jiang
Clustering of Main Orthologs for Multiple Genomes
11:10 AM Yonghui Wu, Stefano Lonardi, Lan Liu, Timothy J. Close
Deconvoluting the Bac-gene Relationships Using a Physical Map
11:35 AM Erliang Zeng, Kalai Mathee, Giri Narasimhan
IEM: An Algorithm for Iterative Enhancement of Motifs Using Comparative Genomics Data
Additional papers presented as posters
Xi Wang, Sanghamitra Bandyopadhyay, Zhenyu Xuan, Xiaoyue Zhao, Michael Q. Zhang, Xuegong Zhang
Prediction of Transcription Start Sites Based on Feature Selection Using AMOSA
Daniel Quest, William Tapprich, Hesham Ali
A Grammar-based Methodology for Structured Motif Finding in ncRNA Database Search
12:00 PM Lunch
1:30 PM Poster Session A
2:15 PM Session III
Quantitative Aspects of Gene Regulation in Bacteria: Amplification, Threshold, and Combinatorial Control
3:15 PM Break
3:45 PM Session IV: Genomics II
3:45 PM INVITED TALK: Christina Leslie
Learning Predictive Models of Gene Regulation
4:15 PM Zefeng Zhang, Hao Lin, Ming Li
MANGO: A New Approach to Multiple Sequence Alignment
4:40 PM Xin Chen, Lingqiong Guo, Zhaocheng Fan, Tao Jiang
Learning Position Weight Matrices from Sequence and Expression Data
5:05 PM Session V: Biocomputing
5:05 PM Sven Rahmann, Tobias Wittkop, Jan Baumbach, Marcel Martin, Anke Truss, Sebastian Boecker
Exact and Heuristic Algorithms for Weighted Cluster Editing
5:30 PM Nikil Wale, George Karypis, Ian A. Watson
Methods for Effective Virtual Screening and Scaffold-hopping in Chemical Compounds
Additional paper presented as poster
Justin Wilson, Manhong Dai, Elvis Jakupovic, Stanley Watson, Fan Meng
Supercomputing with Toys: Harnessing the Power of NVIDIA 8800GTX and Play Station 3 for Bioinformatics Problems
6:00 PM Dinner
7:00 PM Regional Computational Systems Bioinformatics Opportunities
• Sourav Chatterji, University of California, Davis

Binning and Other Computer Science Challenges in Metagenomics, an Emerging Biology Research Field
• Yuhui Cheng, University of California, San Diego
Computational Biochemistry: Continuum Diffusion Modeling using SMOL
• John Wooley, University of California, San Diego
A Perspective on CSB and an Overview of a Related Grant Program: UCDISCOVERY

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WEDNESDAY, August 15, 2007
7:00 AM Breakfast
8:30 AM Session VI: Structural Bioinformatics I
8:30 AM Xiaoyu Zhang, Chandrajit Bajaj
Extraction, Visualization and Quantification of Protein Pockets
8:55 AM Zeyar Aung, Soon-Heng Tan, See-Kiong Ng, Kian-Lee Tan
Uncovering the Structural Basis of Protein Interactions with Efficient Clustering of 3-D Interaction Interfaces
9:20 AM Xin Gao, Dongbo Bu, Shuai Cheng Li, Ming Li, Jinbo Xu
Consensus Contact Prediction by Linear Programming
Additional papers presented as posters
Hong Sun, Yusu Wang, Hakan Ferhatosmanoglu
Enhanced Partial Order Curve Comparison over Multiple Protein Folding
Huzefa Rangwala, George Karypis
fRMSDPred: Predicting Local RMSD Between Structural Fragments Using Sequence Information
Mary Ellen Bock, Claudio Garutti, Concettina Guerra
Effective Labeling of Molecular Surface Points for Cavity Detection and Location of Putative Binding Sites
Brian Y. Chen, Drew H. Bryant, Amanda E. Cruess, Joseph H. Bylund, Viacheslav Y. Fofanov, David M. Kristensen, Marek Kimmel, Olivier Lichtarge, Lydia E. Kavraki
Composite Motifs Integrating Multiple Protein Structures Increase Sensitivity for Function Prediction
9:45 AM Break
10:15 AM Session VII: Transcriptomics & Phylogeny
10:15 AM Sergio Anibal de Carvalho Junior, Sven Rahmann
Improving the Design of GeneChip Arrays by Combining Placement and Embedding
10:40 AM Wenyuan Li, Ying Liu
Modeling Species-Genes Data for Efficient Phylogenetic Inference
11:05 AM Benjamin Vernot, Maureen Stolzer, Aiton Goldman, Dannie Durand
Reconciliation with Non-Binary Species Trees
11:30 AM INVITED TALK: Kimmen Sjölander
The Phylofacts Phylogenomic Encyclopedia: Structural Phylogenomic Analysis Across the Tree of Life
12:15 PM Lunch
1:45 PM Poster Session B
2:30 PM Session VIII: Structural Bioinformatics II
2:30 PM KEYNOTE ADDRESS: Mike Levine
Whole-genome Analysis of Dorsal Gradient Thresholds in the Drosophila Embryo
3:30 PM Kyle Ellrott, Jun-tao Guo, Victor Olman, Ying Xu
Improvement in Protein Sequence-Structure Alignment Using Insertion/Deletion Frequency Arrays
3:55 PM Break
4:25 PM Session IX: Ontology, Data Bases & Text Mining
4:25 PM Weijian Xuan, Manhong Dai, Barbara Mirel, Justin Wilson, Brian Athey, Stanley J. Watson, Fan Meng
An Active Visual Search Interface for Medline
4:50 PM William Lau, Kevin Becker, Calvin Johnson
Rule-based Human Gene Normalization in Biomedical Text with Confidence Estimation
5:15 PM Chitta Baral, Graciela Gonzalez, Anthony Gitter, Craig Teegarden, Amanda Zeigler, G. Joshi-Topé
CBioC: Beyond a Prototype for Collaborative Annotation of Molecular Interactions from the Literature
5:30 PM Session X: Pathways, Networks & Systems Biology II
5:30 PM Manjunatha Jagalur, David Kulp
An Information Theoretic Method for Reconstructing Local Regulatory Network Modules from Polymorphic Samples
5:55 PM Arvind Rao, Alfred O. Hero III, David J. States, James Douglas Engel
Using Directed Information to Build Biologically Relevant Influence Networks
7:00 PM LSS/CSB Banquet - La Jolla Shores Hotel
INVITED SPEAKER: Shannon Williamson
Extreme Metagenomics: Investigations of Virus-Host Interactions in Deep-Sea Environments

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THURSDAY, August 16, 2007
7:00 AM Breakfast
8:30 AM Session XI: Proteomics
8:30 AM Kang Ning, Hon Wai Leong
Algorithm for Peptide Sequencing by Tandem Mass Spectrometry Based on Better Preprocess and Anti-symmetric Computational Model
8:55 AM Wei Zheng, Xiaoduan Ye, Alan M. Friedman, Chris Bailey-Kellogg
Algorithms for Selecting Breakpoint Locations to Optimize Diversity in Protein Engineering by Site-directed Protein Recombination
Additional paper presented as poster
Timothy Lee, Rahul Singh, Ten-Yang Yen, Bruce Macher
An Algorithmic Approach to Automated High-Throughput Identification of Disulfide Connectivity in Proteins Using Tandem Mass Spectrometry
9:20 AM INVITED TALK: Kavitha Venkatesan
Mapping and Analysis of the Human Interactome Network
9:50 AM Break
10:20 AM Session XII: Biomedical Applications
10:20 AM Xiaoxu Han
Cancer Molecular Pattern Discovery by Subspace Consensus Kernel Classification
10:45 AM Lan Liu, Yonghui Wu, Stefano Lonardi, Tao Jiang
Efficient Algorithms for Genome-wide TagSNP Selection across Populations via the Linkage Disequilibrium Criterion
Additional paper presented as poster
Huiqing Liu, Stephen Dalton, Ying Xu
Transcriptional Profiling of Definitive Endoderm Derived from Human Embryonic Stem Cells
11:10 AM INVITED TALK: Adam Godzik
Bioinformatics Challenges of High Throughput Biology
11:40 AM Lunch
1:10 PM Session XIII
1:10 PM KEYNOTE ADDRESS: Chris Somerville
Scientific Issues Associated with the Development of Biofuels
2:10 PM INVITED TALK: Pavel Pevzner
De Novo Shotgun Protein Sequencing via Spectral Networks Analysis
2:40 PM Break
3:10 PM Session XIV: Bioinformatics Education
John Dehlin
The OpenCourseWare Movement and Cross-Institutional Development of Open Course Materials
Philip Bourne, Co-Director, Protein Data Bank, UCSD
4:40 PM Session XV: Pathways, Networks & Systems Biology III
4:40 PM Xiao-Li Li, Chuan-Sheng Foo, See-Kiong Ng
Discovering Protein Complexes in Dense Reliable Neighborhoods of Protein Interaction Networks
5:05 PM Seungchan Kim, Ina Sen, Michael Bittner
Mining Molecular Contexts of Cancer via In Silico Conditioning
5:30 PM Award Ceremony and Closing Remarks

The CSB2007 Program Committee reserves the right to make scheduling changes at their discretion.

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