Co-sponsored by DIMACS and the Program in Mathematics and Molecular Biology (PMMB) of the Florida State University.
8:00 - 8:40 Continental Breakfast at DIMACS
8:40 - 8:50 Welcome to DIMACS, Fred Roberts, DIMACS Director
8:50 - 9:00 Welcome to the workshop, Sylvia Spengler, Manfred Zorn
Lawrence Berkeley Nat. Lab, Life Sciences Div., CA
9:05 - 9:25 Temple Smith, Biomolecular Engineering Research Center
Boston University, Boston, Mass.
"Protein multidomain dissection and function identification"
9:30 - 9:45 Slava Brover, RUTCOR, Rutgers University, NJ
"Recognition of Protein Domains by Amino-Acid Sequences"
9:50 - 10:00 Coffee
10:00 - 10:20 Israel Gelfand and Alexander Kister
Math Department, Rutgers University, NJ
"The classification of the human heavy chains defines
patterns, lengths of sequences and structures of the
antigen-binding regions (H1 and H2)"
10:25 - 10:45 Cassandra L. Smith and Niels Storm, Center for Advanced
Biotechnology and Departments of Biomedical Engineering,
Biology and Pharmacology, Boston University, Mass.
"Targeted Expression and Genomic Analysis of Gene Families"
10:50 - 11:00 Coffee
11:05 - 11:25 Martin Farach-Colton, DIMACS, Rutgers Univ., NJ
"On the approximability of numerical taxonomy"
11:30 - 11:50 Lev Goldfarb and John Abela, Faculty of Computer Science,
University of New Brunswick, Canada
"Inductive model for "multi-domain" sequences:
a deterministic combinatorial model"
11:50 - 1:15 Lunch at DIMACS
1:15 - 1:35 Poe Xing, Casimir Kulikowski and Ilya Muchnik,
DIMACS and CS Department, Rutgers Univ., NJ
"Analysis of ribosomal RNA sequences by
combinatorial clustering"
1:40 - 2:00 Philip E. Bourne, San Diego Supercomputer Center,
Dept. of Pharmacology, Univ. of CA, CA
"Clustering of Protein Structures using a Combinatorial
Extension Algorithm"
2:05 - 2:25 Leonid I. Perlovsky, Nichols Research Corp., MA
"Clustering With Model-Based Neural Network"
2:30 - 2:45 Vladimir Grishin, View Trends Int., OH
"Combinatorial visual clustering of multidimentional data"
2:50 - 3:00 Coffee
3:20 - 3:40 Nickolai Alexandrov, Amgen, Inc., CA
"The number of domain families"
3:45 - 4:05 Sandor Vajda, Department of Biomedical Engineering,
Boston University, MA
"Analysis and design of receptor-ligand interactions"
4:10 - 4:25 Simon Streltsov, Alphatech Inc., MA
"Making heuristic clustering algorithms globally optimal"
4:30 - 4:40 Coffee
4:40 - 5:00 Saveli Goldberg, MediSpectra Inc., MA
"Definition of anti-syndrome and empirical data
classification problems"
5:05 - 5:25 Peter Hammer, RUTCOR, Rutgers Univ., NJ
"Logical analysis of data in applications"
5:30 - 5:50 Iosif I. Vaisman, Alexander Tropsha, and Weifan Zheng,
Univ. of North Carolina, NC
"Compositional Preferences in Quadruplets of Nearest
Neighbor Residues in Protein Structures"
6:30 - 7:30 Reception,
8:00 - 8:20 Continental breakfast at DIMACS
8:20 - 8:40 Ying Xu, Computational Biosciences Section, Life Sciences
Div., ORNL, TN
"Protein threading by combinatorial optimization methods"
8:45 - 9:00 Leonard J. Schulman
Georgia Inst. Technology
"Quadratic Euclidean Clustering"
9:05 - 9:25 Valentina Di Francesco, Delwood Richardson, Jean Garnier,
Peter J. Munson and Anthony R. Kerlavage
The Institute for Genomic Research, Rockville, MD,
Math. and Stat. Computing Laboratory, National Institutes
of Health, MD
"FORESST: A database of hidden Markov models for FOld
REcognition from Secondar STructure sequences"
9:25 - 9:35 Coffee
9:35 - 9:55 Franco Armando Bignone, Dep. of Preclinical Oncology,
Lab. of Experimental Oncology, National Cancer Institute,
Italy
"A case study in genetic networks dynamics: gastrulation in
Caenorhabditis elegans as a model system"
10:00 - 10:20 Teresa Przytycka, Rajeev Aurora, and George D. Rose
przytyck@grserv.med.jhmi.edu
"Protein Classification and Secondary Structure Sequence"
10:25 - 10:40 Anders Wallqvist, Yoshifumi Fukunishi, Addi Fadel and Ronald M. Levy, ,
Department of Chemistry, Rutgers University
"Protein Fold Recognition based on Secondary Structure
Similarities."
10:45 - 10:55 Coffee
10:50 - 11:10 Steven E. Brenner, Stanford University, CA
"Recognizing Distant Evolutionary Relationships
from Protein Sequence and Structure"
11:15 - 11:35 Richard Fine and Boris Klebansky
Paradygm Technologies Inc., NJ
"Topographical and Biochemical Maps of Protein Surfaces:
Recognizing Similarity and Complementarity"
11:40 - 12:00 Donald Jacobs, Department of Phyics and Astronomy
Michigan State University, MI
"Real-time Protein Domain Evaluator and Design Tool"
12:05 - 12:25 Manfred Zorn,
Lawrence Berkeley National Laboratory
"Protein Domain Prediction in the context of
Genome Annotation"
12:30 - 1:50 Lunch and disscusion
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