DIMACS Workshop on Detecting and Processing Regularities in High Throughput Biological Data

June 20 - 22, 2005
DIMACS Center, CoRE Building, Rutgers University

Laxmi Parida, IBM T J Watson Research, parida@us.ibm.com
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:

Monday, June 20, 2005

 8:00 -   8:45 Breakfast and Registration

 8:45 -   9:00 Welcoming Remarks
               Fred Roberts, DIMACS Director
               Laxmi Parida, Workshop Organizer

Morning chair: Gyan Bhanot

 9:00 -  10:00 Chains of collective reasoning in biological publications (RELEVANT PAPERS)
               Andrey Rzhetsky, Columbia University
10:00 - 10:30  False Negatives and False Positives in HTS (SLIDES)
               Vlado Dancik, Millennium Pharmaceuticals
10:30 - 11:00  Tea/Coffee Break

11:00 - 11:30  The structures of about eight thousand sandwich proteins
               can be described by few supermotifs
               A.E. Kister, Univ of Medicine and Dentistry of New Jersey & Rutgers University
11:30 - 12:00  Detecting synchronization between the signals from multivariate
               and univariate biological data (SLIDES)
               Mikhail Prokhorov, Saratov Inst of RadioEngineering & Electronics
12:00 -  1:30  Lunch

Afternoon chair: Steffen Heber

 1:30 -  2:30  Statistical and algorithmic approaches to genome rearrangements
               based on sequence data
               David Sankoff, University of Ottawa
 2:30 -  3:00  Common Intervals of Graphs (SLIDES)
               Steffen Heber, N C State University
 3:00 -  3:30  Tea/Coffee Break

 3:30 -  4:00  Multiple alignment using hydrophobic clusters:
               a tool to identify and align distantly related proteins (SLIDES)
               J. Baussand, Université Pierre et Marie Curie
 4:00 -  4:30  Locating conserved genes in whole genome scale (SLIDES)
               Prudence Wong, University of Liverpool
 4:30 -  5:00  Gene expression patterns of breast cancer phenotype revealed (SLIDES)
               by molecular profiling
               Gyan Bhanot, IBM T J Watson Research

 5:00 -  5:30  Inferring Phylogeny using Permutation Patterns in Genomic Data (SLIDES)
               Md Enamul Karim, University of Louisiana
Tuesday, June 21, 2005

 8:15 -   9:00 Breakfast and Registration

Morning Chair: Alberto Apostolico

 9:00 -  10:00 Mining and Pattern Analysis in Large Data Sets for
               Biological Information (SLIDES)
               David Mount, University of Arizona
10:00 - 10:30  Logical Analysis of Diffuse Large B-Cell Lymphomas   (SLIDES)
               D. Weissmann, Robert Wood Johnson University Hospital
10:30 - 11:00  Tea/Coffee Break

11:00 - 11:30  Deciphering the Information Encoded in RNA Viral Genomes (SLIDES)
               Christine Heitsch, University of Wisconsin
11:30 - 12:00  Robust diagnosis of non-Hodgkin lymphoma phenotypes validated on gene
               expression data from different laboratories  (SLIDES)
               Gabriela Alexe, Institute for Advanced Study, Princeton
12:00 -  1:30  Lunch

Afternoon chair: Vlado Dancik

 1:30 -  2:30  Discovering key modulators of genetic activity by network reverse engineering
               Andrea Califano, Columbia University
 2:30 -  3:00  ActiveNetworks: A Framework for Cross-Condition Analysis of Functional 
               Genomic Data (SLIDES)
               T M Murali, Virginia Polytechnic Institute
 3:00 -  3:30  Tea/Coffee Break

 3:30 -  4:00  Efficient probe selection in microarray design (SLIDES)
               Cindy Li, University of Liverpool
 4:00 -  4:30  TriCluster: Mining Coherent Clusters in 3D Microarray Data (SLIDES)
               Mohammed Zaki, Rensselaer Polytechnic Institute

 4:30 -  5:00  A method for aligning RNA secondary structures
               and its application to RNA motif detection (SLIDES)
               Jason Wang, NJIT
 5:00 - 5:30   Animated Terrain Evolution for Visual Analysis
               of Protein Folding Trajectory (SLIDES)
               Kush Kapila, Matrox Imaging
 7:00          Workshop Banquet at the Holiday Inn
               Banquet speaker: Ajay Royyuru, IBM T J Watson Research
               The Genographic Project

Wednesday, June 22, 2005

 8:15 -   9:00 Breakfast and Registration

Morning chair: Mohammed Zaki
 9:00 -  10:00 Comparative genomics: The lion, the leopard, 
		the wolf or the boar, Why not more? (SLIDES)
               Bud Mishra, New York University
10:00 - 10:30  Analysis of High Bandwidth Molecular Dynamics Results
               from the Blue Gene Project (SLIDES)
               Frank Suits, IBM T J Watson Research
10:30 - 11:00  Tea/Coffee Break

11:00 - 11:30  Novel Computational and Integrative Tools for the Analysis
               of Gene Co-Expression Data (SLIDES)
               Michael A. Langston, Univ of Tennessee & Oak Ridge National Lab
11:30 - 12:00  An Algorithm for Exploring Patterns in Clinical Genomic Data (SLIDES)
               Richard Mushlin, IBM T J Watson Research
12:00 -  1:30  Lunch

Afternoon chair: Leszek Gasieniec

 1:30 -  2:30  The Unbearable Monotony of Surprises
               Alberto Apostolico, Purdue University & University of Padova
 2:30 -  3:00  Linear Manifold Embeddings of Pattern Clusters (SLIDES)
               Rave Harpaz, City University of New York
 3:00 -  3:30  Tea/Coffee Break

 3:30 -  4:00  Efficient Algorithms for Motif Search (SLIDES)
               Sudha Balla, University of Connecticut
 4:00 -  4:30  Varun: Extraction of Over-Represented Extensible Patterns (SLIDES)
               Matteo Comin, University of Padova

 4:30 -  5:00  Predicting Novel Genes and Interactions using the Scale Free
               Behavior of Genetic Networks (SLIDES)
               Ugur Sezerman, Sabanci University

DIMACS Homepage, Workshop Pictures

Document last modified on June 22, 2005.