DIMACS Workshop on Biomolecular Networks: Topological Properties and Evolution

May 11 - 13, 2005
DIMACS Center, CoRE Building, Rutgers University

Petra Berenbrink, Simon Fraser University, petra@cs.sfu.ca
Joe Nadeau, Case Western Reserve University, jhn4@po.cwru.edu
Teresa Przytycka, NCBI/NLM/NIH, przytyck@ncbi.nlm.nih.gov
Cenk Sahinalp, Simon Fraser University, cenk at cs.sfu.ca
Presented under the auspices of the DIMACS/BioMaPS/MB Center Special Focus on Information Processing in Biology.

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).

Workshop Program:

This is a preliminary program.

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

               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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Document last modified on May 3, 2005.