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
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