CSB2007 Conference Program
| 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 Opportunities |
| 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 |
| 2:15 PM | KEYNOTE ADDRESS: Terry Hwa 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 |
| 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 | |
| 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 |
| 3:10 PM |
INVITED TALKS AND PANEL DISCUSSION 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.