DIMACS Workshop on Combinatorial Clustering and Multi-Domain Protein Structure Analysis

June 26-27, 1998
DIMACS Center, CoRE Building (Room 431), Rutgers University, Busch Campus, Piscataway, NJ

Principal Organizers:

Presented under the auspices of the Special Year on Massive Data Sets and the Special Year in Mathematical Support for Molecular Biology.

Co-sponsored by DIMACS and the Program in Mathematics and Molecular Biology (PMMB) of the Florida State University.

Workshop Program:

Friday, June 26, 1998

Morning Session I, Chair - Casimir Kulikowski

 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 

Afternoon Session I, Chair - Manfred Zorn

  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, 

Saturday, June 27, 1998

Morning Session II,Chair - Nickolai Alexandrov

 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, 

                   "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

                    "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 

 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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Document last modified on April 13, 1998.