COMBINATORIAL METHODS IN DNA MAPPING AND SEQUENCING (schedule)

[Pavel Pevzner]

                    DIMACS Computational Molecular Biology Year
  
                                   WORKSHOP

               COMBINATORIAL METHODS FOR DNA MAPPING AND SEQUENCING
                              (Preliminary Program)

 DIMACS, Rutgers University, CoRE Building 431, October, 6 - October, 9, 1994

 Program Committee:     

 C.Cantor (co-chair),
 P.Gillevet,
 R.Karp, 
 G.Myers,
 M.Olson,
 P.Pevzner (co-chair), 
 M.Yannakakis 

 For questions regarding registration/accomodation/driving directions
 contact Pat Toci  toci at dimacs.rutgers.edu (phone (908) 932-5930)

********************************************************************************
*NOTE: THE DIMACS CONFERENCE CENTER AT RUTGERS CAN ACCOMODATE 150 PARTICIPANTS.*
*THE NUMBER OF REGISTERED PARTICIPANTS IS FASTLY APPROACHING THIS LIMIT.       *
*TO ENSURE PARTICIPATION IN THE CONFERENCE PLEASE REGISTER AS SOON AS POSSIBLE.*
********************************************************************************

Thursday, October, 6


8:15 a.m.  Registration and  Coffee in CoRE 401 

8:45 a.m.   Opening Session
            Fred Roberts, Department of Mathematics and DIMACS, Chair of Special Year 
            Joachim Messing, Director, Waksman Inst. for Mol.Gen.,Chair of Special Year 
            Andras Hajnal, Director, DIMACS 
            Joseph Seneca, Vice President for Academic Affairs, Rutgers University 
  

Session DNA MAPPING I (chair: P.Pevzner) 

9:00 a.m.   Richard Karp,  Dept. of Computer  Sci., University of California at Berkeley 
	    A Survey of Algorithmic Problems in Physical Mapping

10:20 a.m   Coffee Break

10:50 a.m.  Maynard Olson, Department of Molecular Biotechnology, University of Washington
	    Computing High-resolution Restriction-site Maps:  Past, Present, and Future.

11:40 a.m.  Ron Shamir,  Computer Science Department, Tel Aviv University 
	    Graph-theoretic Support for Physical Mapping of DNA

12:30 a.m   Lunch 


Session DNA MAPPING II (chair: M.Olson)  

2:00 p.m.   Michael Waterman, Department of Math. and Mol. Biol., U. of South. California 
	    Statistical Models of Physical Mapping

2:50 p.m.   Jim Orlin,    MIT  and Whitehead Institute 
	    Creating a Physical Map of the Human Genome 

3:40 p.m.   Coffee Break 

4:10 p.m.   Contributed talks
            B. Bruno,D.Balding,E,Knill,D. Torney,  Los Alamos Nat. Lab. and U. of London 
	    Combinatorial Methods for Screening Libraries of Clones

            A. Bonner, E. Harley,   Dept. of. Computer Science, University of Toronto  
	    Genome Map Assembly using Noisy Data


            W. Gillet, M.V.Olson,  Washington U., St.Louis and U. of Washington U.,Seattle
	    Assembling High-resolution Restriction Maps Using Multiple Complete Digestions

            M.W. Perlin, C.W. Richard III,  Carnegie Mellon U. and  U. of Pittsburgh 
	    Inner Product Mapping: Validation on chromosome 11 data 
         
******************************************************************************************
Friday,  October, 7

      
Session DNA SEQUENCING BY HYBRIDIZATION I  (chair: R.Karp) 

9:00 a.m.   Charles Cantor,  Center for Advanced Biotechnology, Boston University
            Parallel Processing in Genome Mapping and Sequencing 

9:50 a.m.   Coffee Break 

10:05 a.m.  Robert Lipshutz,   Affymetrix
            Oligonucleotide Arrays and Sequence Analysis by Hybridization: a Survey 
         
11:25 a.m.  Coffee Break 

11:40 a.m.  Steven Skiena,  Department of Computer Science, SUNY at Stony Brook 
            Reconstructing Strings from Substrings 
        
12:30 a.m.  Lunch 


Session DNA  SEQUENCING BY HYBRIDIZATION II  (chair: C.Cantor) 

2:00 p.m.   Radoje Drmanac,   Argonne National Laboratory 
            Informatics of DNA Screening, Mapping, and Sequencing by Hybridization
            with 30-3000 Oligomers
        
2:50 p.m.   Pavel Pevzner,  Dept.  of Comp. Sci. and Eng., Penn State University 
            Rearrangements of Maps, Sequences and Genomes 
        
3:40 p.m.   Coffee Break

4:10 p.m.   Ming Li,   Department of Computer Science, University of Waterloo 
            DNA Sequencing and Learning 

5:00 p.m.   Open Problems Session and Software Demonstration  

******************************************************************************************
Saturday, October, 8 

  
Session  DNA  SEQUENCING I  (chair: M.Yannakakis)

9:00 a.m.   Leroy  Hood,   Department of Molecular Biotechnology, University of Washington
            Computational Challenges in the Human Genome Project

9:50 a.m.   Gene Myers,   Department of Computer Science, University of Arizona
            An Alternative Formulation of Sequence Assembly 

10:40       Coffee Break 

11:10 a.m.  S. Rao Kosaraju,  Department of Computer Science, The Johns Hopkins University
            Experiments on Large Scale DNA Sequence Assembly
                 

12:00 a.m.  Contributed talks 
            R. Idury, M.S. Waterman, Dept. of Math. and Mol.Biol., U. of South. California
            A new method for shotgun sequence assembly         

            C.Armen, C.Stein,   Dept. of Computer Science, Dartmouth College 
            Short Superstrings and the Structure of Overlapping Strings 

12:30 a.m.  Lunch 


Session: DNA SEQUENCING II  (chair: E.Myers)  

2:00 p.m.   Richard  Wilson,  Dept. of Genetics, Washington University School of Medicine 
            The C. elegans Genome Sequencing Project 
       

2:50 p.m.   John Kececioglu, Department of Computer Science,  U. of California at Davis 
            DNA sequencing in the Presence of Errors
         
3:40 p.m.   Coffee Break 


4:10 p.m.   Pat Gillevet,  National Center for Human Genome Research 
            Automatic Analysis and Annotation of Data from Mycoplasma capricolum Project
        
5:00 p.m.   Contributed talks  
            R.Parsons,   University  of Central Florida 
            Stochastic Methods for Genome Sequence Assembly

            C.Burks,  Los Alamos National   Laboratory
            Optimization Tools for Genome Sequence Assembly 
         
*****************************************************************************************
Sunday, October, 9 


Session  DNA MAPPING III  (chair: P.Gillevet)

9:00 a.m.   Hans  Lehrach,   Genome Analysis Laboratory, Imperial Cancer Research Fund 
            TBA

9:50 a.m.   Alan Frieze,   Dept. of Mathematics, Carnegie Mellon University
            Ordering Clone Libraries in Computational Biology 
         

10:40 a.m.  Coffee Break 

11:10 a.m.  Phil Green,  Department of Molecular Biotechnology, University of Washington
            Methods for Assembly and Error Identification in Mapping and Sequencing 
        


12:00 a.m.  Contributed talks 
            A.Chetverin,  M. S. Gelfand, O.I. Razgulyaev,   A.R.Rubinov 
            Protein Research Institute,  Russian Acad. of Sci., Puschino, Russia 
            DNA Sequencing by Nested Strand Hybridization 
        
12:30 a.m.  Lunch  






Session  DNA MAPPING IV  (chair: P.Pevzner) 

2:00 p.m.   Tom Marr,  Cold Spring Harbor Laboratory 
            Genome Topographer: Computer Science, Systems and Software Engineering, 
            and the Study of Complex Genetic Diseases 

2:50 p.m.   Sorin Istrail,  Sandia National Laboratories 
            Algorithmic strategies for handling errors in physical mapping:
            Chimerism and Deletions 

3:40 p.m.   Coffee Break  

4:00 p.m.   Contributed talks 

            S. McDougall, R. Lindstrom, J. Orlin,  H. Safer, 
            Collaborative Research, Inc. and MIT. 
            Using Double-Ended Sequencing to Assemble  through Repeats 

            A.Milosavljevic,  Argonne National Laboratory 
            DNA Sequence Recognition by Hybridization to Short Oligomers 
    
            J.C. Roach,   Dept. of Molecular Biotechnology University of Washington
            Distribution Models for Random Subcloning: 
            Applications to Mapping and Sequencing 

            P.Zhang,  Department of Genetics, Columbia University
            Probe Interval Mapping and its Applications in Physical Mapping
            of Human Chromosomes