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).
Monday, June 20, 2005 8:00 - 8:45 Breakfast and Registration 8:45 - 9:00 Welcoming Remarks Brenda Latka, DIMACS Associate Director Laxmi Parida, Workshop Organizer Morning chair: Gyan Bhanot 9:00 - 10:00 Chains of collective reasoning in biological publications Andrey Rzhetsky, Columbia University 10:00 - 10:30 False Negatives and False Positives in HTS 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 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 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 J. Baussand, Université Pierre et Marie Curie 4:00 - 4:30 Locating conserved genes in whole genome scale Prudence Wong, University of Liverpool 4:30 - 5:00 Gene expression patterns of breast cancer phenotype revealed by molecular profiling Gyan Bhanot, IBM T J Watson Research 5:00 - 5:30 Inferring Phylogeny using Permutation Patterns in Genomic Data 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 David Mount, University of Arizona 10:00 - 10:30 Logical Analysis of Diffuse Large B-Cell Lymphomas 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 Christine Heitsch, University of Wisconsin 11:30 - 12:00 Robust diagnosis of non-Hodgkin lymphoma phenotypes validated on gene expression data from different laboratories 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 T M Murali, Virginia Polytechnic Institute 3:00 - 3:30 Tea/Coffee Break 3:30 - 4:00 Efficient probe selection in microarray design Cindy Li, University of Liverpool 4:00 - 4:30 TriCluster: Mining Coherent Clusters in 3D Microarray Data Mohammed Zaki, Rensselaer Polytechnic Institute 4:30 - 5:00 A method for aligning RNA secondary structures and its application to RNA motif detection Jason Wang, NJIT 5:00 - 5:30 Animated Terrain Evolution for Visual Analysis of Protein Folding Trajectory 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? Bud Mishra, New York University 10:00 - 10:30 Analysis of High Bandwidth Molecular Dynamics Results from the Blue Gene Project 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 Michael A. Langston, Univ of Tennessee & Oak Ridge National Lab 11:30 - 12:00 An Algorithm for Exploring Patterns in Clinical Genomic Data 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 Rave Harpaz, City University of New York 3:00 - 3:30 Tea/Coffee Break 3:30 - 4:00 Efficient Algorithms for Motif Search Sudha Balla, University of Connecticut 4:00 - 4:30 Varun: Extraction of Over-Represented Extensible Patterns Matteo Comin, University of Padova 4:30 - 5:00 Predicting Novel Genes and Interactions using the Scale Free Behavior of Genetic Networks Ugur Sezerman, Sabanci University