This special focus is jointly sponsored by the Center for Discrete Mathematics and Theoretical Computer Science (DIMACS), the Biological, Mathematical, and Physical Sciences Interfaces Institute for Quantitative Biology (BioMaPS), and the Rutgers Center for Molecular Biophysics and Biophysical Chemistry (MB Center).
Wednesday, May 11, 2005 8:15 - 9:00 Breakfast and Registration 9:00 - 9:15 Welcoming Remarks Brenda Latka, DIMACS Associate Director; Cenk Sahinalp for Conference Organizers 9:20 - 10:05 Modeling Cells with Protein Networks Trey Ideker, University of California, San Diego 10:10 - 10:55 Duplication and the Evolution of the Vertebrate Insulin Signaling Pathway Dannie Durand, Carnegie Mellon University 10:55 - 11:15 Break 11:15 - 12:00 Conserved Patterns of Protein-Protein Interaction in Yeast, Worm and Fly Richard Karp, University of California, Berkeley 12:00 - 1:30 Lunch 1:30 - 2:15 Reconstructing Temporal Ordering of Proteins in Biological Pathways Using Protein-protein Interactions Martin Farach-Colton, Rutgers University 2:20 - 3:05 Network Topology and Evolution of Hard to Gain and Hard to Loose Attributes Teresa Przytycka, NCBI/NIH 3:05 - 4:35 Break 4:35 - 4:20 Duplication Based Models for Proteome Network Evolution Cenk Sahinalp, Simon Fraser University and Gurkan Bebek, Case Western Reserve 4:25 - 5:10 Multi-Molecular Assemblies by Multiple Combinatorial Docking and Biomolecular Networks Ruth Nussinov, Tel Aviv and NCI/NIH 5:30 Poster Session and Banquet An evolution-based clustering method to separate orthologous genes from out-paralogs Raja Jothi, Elena Zotenko, Asba Tasneem, Teresa Przytycka NIH/NLM/NCBI Studying Disease Dynamics Using a Network Model Jacqueline Dresch and Amy Zielinski, SUNY Geneseo, Geneseo NY Modelling plant-herbivore evolutionary rates using a graph theoretical approach Presenter: Shuya Kyu, SUNY Geneseo, Geneseo, NY Group testing to annihilate added hyperedges in a hypergraph Niels Hanson, SUNY Geneseo A Faster Algorithm For Network Motif Detection Sebastian Wernicke, Institut für Informatik Friedrich-Schiller-Universität Jena A Comprehensive Phylogeny of ART-LGIC Superfamily Asba Tasneem +, Lakshminarayan M. Iyer #, Eric Jakobsson + and L. Aravind #* +National Center for Biotechnology Information #National Center for Supercomputing Applications, Beckman Institute for Advance Science and Technology, University of Illinois at Urbana-Champaign *Corresponding Author Two applications of Delaunay contact graphs in the analysis of protein structures Todd Taylor and Iosif Vaisman, School of Computational Sciences, George Mason University Graph theoretic properties of contact networks formed by the Delaunay tessellation of protein structures Todd Taylor and Iosif Vaisman, School of Computational Sciences George Mason University A new method for protein secondary structure assignment based on a simple topological descriptor Todd Taylor and Iosif Vaisman, School of Computational Sciences George Mason University Direct identification of network modules from gene-expression measurement Michael Hornquist, Department of Science and Technology, Linköping University, Campus Norrköping, Sweden Thursday, May 12, 2005 8:15 - 9:00 Breakfast and Registration 9:00 - 9:45 Evolution of Mammalian Gene Sequence and Gene Expression Networks I. King Jordan, NCBI/NIH 9:50 - 10:35 Functional Organization of Cellular Networks Zoltan Oltvai, University of Pittsburgh 10:40 - 11:10 Break 11:15 - 12:00 Alfonso Valencia, National Center of Biotechnology, Spain 12:00 - 1:30 Lunch 1:30 - 2:15 Mapping Biological Networks Joel Bader, Johns Hopkins University 2:20 - 3:05 Predicting and Analyzing Protein Interaction Networks Mona Singh, Princeton University 3:05 - 3:35 Break 3:35 - 4:20 A Random Graph Approach to Protein Structure Determination Gopal Pandurangan, Purdue University 4:25 - 5:10 Dynamical Properties of the Yeast Cell Cycle Network Chao Tang, University of California San Francisco Speaker's dinner Friday, May 13, 2005 8:15 - 9:00 Breakfast and Registration 9:00 - 9:45 An Informatics Analysis of Protein Factors and Binding Sites on Yeast DNA Yi-Kuo Yu, NCBI/NIH 9:50 - 10:35 Integrative Analyses of Interaction Networks Underlying the Cellular Circuitry in Yeast Ron Pinter, Technion 10:40 - 11:15 Break 11:15 - 12:00 Computational Proteins: Understanding Protein Function on a Genome-scale using Networks Mark Gerstein, Yale University 12:00 - 1:30 Lunch 1:30 - 2:15 Glimpses on the Evolution of Transcription Regulation Networks Ron Shamir, Tel Aviv 2:20 - 3:05 Degree Distributions of BFS Trees in Random Graphs David Kempe, USC