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DIMACS COMP.MOL.BIOL. YEAR

Pavel Pevzner pevzner at cse.psu.edu
Fri Jul 15 14:56:49 EST 1994


		     DIMACS SPECIAL YEAR 1994-95
				   
	    "MATHEMATICAL SUPPORT FOR MOLECULAR BIOLOGY"

	DIMACS, the Center for Discrete Mathematics and Theoretical
Computer Science, a Consortium of Rutgers and Princeton Universities
and AT&T Bell Laboratories and Bellcore, is planning a 1994-95
"special year" on the topic Mathematical Support for Molecular
Biology.  The program will start in August 1994 and run through August
1995, with some supplementary activities scheduled for the 1995-96
year.

	The Special Year will focus on those topics in molecular
biology that seem especially amenable to treatment using the methods
of discrete mathematics and the related algorithmic approaches of
theoretical computer science.  It is intended to expose a large
portion of the community of discrete mathematicians and theoretical
computer scientists to the problems of molecular biology that seem to
be fundamentally problems of their field; to provide an opportunity
for intensive collaboration to those discrete mathematicians and
theoretical computer scientists who have already discovered these
problems; to introduce some outstanding young people in the
mathematical sciences community to the field of
mathematical/computational biology in a very concentrated way; to
forge lasting partnerships between mathematical scientists and
biological scientists; to involve biologists in a primary role in
defining the agenda of computational biology; to introduce molecular
biologists to a community of mathematical scientists who are
interested in helping them solve their problems; and to develop a
long-term base and model for interdisciplinary research in this field.
	
	The DIMACS Special Year will be chaired by Joachim Messing and
Fred Roberts of Rutgers University.  It will be co-chaired by Lawrence
Shepp of AT&T Bell Laboratories and Michael Waterman of the University
of Southern California.

	The program will be supported by a distinguished steering
committee, whose members in addition to the chairs and co-chairs are
David Axelrod (Rutgers), Michael Bulmer (Rutgers), Charles Cantor
(Boston University), Martin Farach (Rutgers), Daniel Gusfield (UC
Davis), Leroy Hood (U. of Washington), Richard Karp (UC Berkeley),
Eric Lander (MIT), Eugene Lawler (UC Berkeley), Joshua Lederberg
(Rockefeller), Joseph Naus (Rutgers), Michiel Noordewier (Rutgers),
Wilma Olson (Rutgers), David B. Searls (U. Penn), William Sofer
(Rutgers), Tandy Warnow (U. Penn), Peter Winkler (Bellcore), and
Andrew Yao (Princeton).
	
	The program will include extensive collaboration with
biologists through the participation of the Waksman Institute for
Molecular Genetics at Rutgers, the Center for Molecular Biotechnology
at the University of Washington, the Genome Center at the
University of Pennsylvania, the Center for Theoretical and Applied
Genetics at Rutgers, and the Departments of Molecular Biology and of
Ecology and Evolutionary Biology at Princeton, as well as the
involvement of prominent biologists in the planning and organization
of all major activities.

	Industrial participation in the special year is welcomed.
Some companies have already agreed to sponsor a postdoctoral fellow,
plan programs of interest to the biotechnology industry, or help in
organizing workshops.  An industrial problems seminar is planned.

	The Special Year will feature a series of workshops and
mini-workshops, one or more seminar series and a distinguished lecture
series, a visitor program, an algorithm implementation challenge, and
a postdoc program.

	 DIMACS will sponsor a visitor program in which researchers
can spend some time at the Center, perhaps coordinating with a trip to
one of the special year workshops or visiting during a sabbatical
leave.  Among the prominent researchers in Biocomputing and
Biomathematics who have already agreed to visits during the special
year, some as long as a year, are Charles Cantor, Michael Gribskov,
Dan Gusfield, Timothy Havel, Herbert Hauptman, Leroy Hood, Samuel
Karlin, Richard Karp, Eric Lander, Gene Lawler, Gene Myers, Maynard
Olson, Pavel Pevzner, Steve Skiena, Temple Smith, Gary Stormo, and
Michael Waterman.  Inquiries about visiting should be sent to
special at dimacs.rutgers.edu.

	The Special Year program will be centered around a series of
workshops, open to the entire community.  Each will have two main
organizers, one from the mathematical sciences community and one from
the biological sciences community, in order to enhance collaboration
and interaction between members of the two communities.  The scheduled
workshops, with organizers and dates, are: Combinatorial Methods for
Mapping and Sequencing DNA (Charles Cantor and Pavel Pevzner, October
6-9); Sequence Alignment (Alberto Apostolico and Russel Doolittle,
November 10-12); Phylogeny (Michael Bulmer and Simon Tavare, February
6-8); and HIV Sequence Analysis (Dennis Pearl and Tom White, May 3-5).
We will also be running the fourth in a series of "DIMACS Algorithm
Implementation Challenges," to culminate in a workshop in September
1995.  Researchers will be challenged to develop algorithmic methods
for a series of benchmark problems dealing with DNA sequence
determination from shotgun sequence data.  The challenge will be
organized by Martin Vingron and Ellson Chen.

	There will be a series of one day mini-workshops, organized
around a topic of current interest, and frequently scheduled at the
last minute.  Among the topics already scheduled are programs on
Combinatorial Structures in Molecular Biology (Jerrold Griggs and Tim
Havel, November 4), DNA Topology and Regulation (Bill Bauer and Craig
Benham, December 9) and Gross and Fine Structure of DNA (Jim Fickett
and David Searls, March 6, at the Genome Center at Penn).  There will
be a series of three mini-workshops on protein structure in the period
March 20-27.  These will deal with Global Minimization of Nonconvex
Energy Functions (Panos Pardalos and David Shalloway), Sequence-Based
Methods for Protein Folding (Bonnie Berger), and Antibody Sequence and
Structure (Israel Gelfand).  A fourth miniworkshop on a related topic
will be held July 17 and 18 on the topic Geometrical Methods for
Conformational Modeling (Leo Guibas).

	In addition to the many technical reports, journal articles,
and conference volumes that usually result from a DIMACS special year,
we hope to produce a volume of papers (many of them expository) by
leaders of the field.

	The activities will commence with a tutorial program in
molecular and computational molecular biology for our postdocs, and
open to interested members of the community, in August 1994, and the
beginning of our Distinguished Lecture Series in September with
lectures by Michael Waterman (September 16) and Leroy Hood (September
22 and 23).

	We hope that, like past DIMACS special years, the year on
mathematical support for molecular biology will influence the
directions of the field for many years to come.

	Further information about the special year can be obtained
from any of the chairs or co-chairs or by sending a message to
special at dimacs.rutgers.edu.

========================================================================
========================================================================
DIMACS - Center for Discrete Mathematics and Theoretical Computer Science
  (A Consortium of Rutgers and Princeton Universities and
              AT&T Bell Labs and Bellcore)
Special Year in Mathematical Support for Molecular Biology
                     Calendar

Locations of Events:

	Events are to be held at CoRE Building, Busch Campus, Rutgers
	University, except as noted.

Special Year Seminar Series:

	Starting in September, 1994, there will be a special year
	seminar every Monday at 10 A.M., except when there is a
	workshop, miniworkshop, or Distinguished Lecture Series
	Lecture scheduled.  Most seminars will be at Rutgers, but
	some will be at the Princeton University Computer Science
	Building and others will be at the Genome Center at University
	of Pennsylvania.

August 1994: Tutorials in Molecular Biology and Computational Molecular Biology
	Week of Aug. 15: Introduction to Molelcular Biology for
	  Non-Experts (lectures by William Sofer)
	Weeks of Aug. 22 and 29: Current Computational and
	  Mathematical Approaches to Biological Problems and Current Topics in
	  Biocomputing (Lectures by Martin Farach and Michiel
	  Noordewier)
	Week of Sept. 5: Biological Maps: A Guided Tour (Lectures by
	  David Axelrod)

Sept. 1994:
	16:  Kickoff of Distinguished Lecture Series:  Michael Waterman
		
	22, 23:  Distinguished Lecture Series:  Leroy Hood

	28:      Distinguished Lecture Series:  Daniel Gusfield

Oct. 1994:
	6-9:     Workshop on Mapping and Sequencing

	20, 21:   Distinguished Lecture Series:  Samuel Karlin

	
November 1994:
	3:      Distinguished Lecture Series:  Temple Smith	

	4:       MiniWorkshop on Combinatorial Structures in Molecular Biology
	
	10-12:   Workshop on Sequence Alignment
			(To be held at Computer Science Building, Princeton U.)

December 1994:
	9:	 MiniWorkshop on DNA Topology and Structure

January 1995:
	24:  Distinguished Lecture Series:  Joachim Messing

February 1995:
	3:       Distinguished Lecture Series:  Richard Karp
	 
	6-8:      Workshop on Phylogeny
			(To be held at Computer Science Building, Princeton U.)

	10 or 13?: Distinguished Lecture Series:  Eugene Lawler

March 1995:

	6:  Miniworkshop on Gene Finding and Gene Prediction
		 (To be held at the Genome Center at Univ. of Pennsylvania)
	
	10:  Distinguished Lecture series: Eric Lander

	20-27:   Three MiniWorkshops on protein structure.

		 20-21: Global Minimization of Nonconvex Energy Functions
			 including a Distinguished Lecture Series Lecture by 
			 Herbert Hauptman
		 22:    Antibody Structure and Sequence
                 24:    Sequence-Based Methods for Protein Folding
		 

April 1995:
	17, 18:  Distinguished Lecture series (two lectures) by Charles Cantor

May 1995:
	3-5:  Workshop on HIV Sequence Data 
	12?:  MiniWorkshop on Database Aspects of Biological Data
		(probable topic)
			
July 1995:
	17, 18: MiniWorkshop on Geometrical Methods for Conformational
		Modeling

September 1995:
	Dates to be Decided:  Algorithm Implementation Challenge Workshop
		(DNA Sequence Determination from Shotgun Sequence Data)


Organizers: Joachim Messing and Fred Roberts (chairs), Lawrence Shepp
	and Michael Waterman (co-chairs)

Further information:  special at dimacs.rutgers.edu, (908)455-5928
==========================================================================
==========================================================================
		Dimacs Summer 1994 Tutorial on Molecular Biology

	Preliminary to the opening of the DIMACS 1994-95 Special Year
on Mathematical Support for Molecular Biology, the Center is holding a
tutorial on molecular biology.  Emphasis will be on presenting topics
in molecular biology for non-experts and introducing approaches from
the mathematics and computer science sides to problems of molecular
biology.  The tutorial program is scheduled to start August 15 and
continue until the beginning of the week of September 12, and it is
open without charge to members of the research community (faculty,
industrial and government researchers, postdocs, graduate students,
etc.).  Participation is on a preregistered basis only and will be
limited.  The Special Year is under the direction of Fred Roberts and
Joachim Messing of Rutgers University, with co-chairs Michael Waterman
of University of Southern California and Lawrence Shepp of AT&T Bell
Laboratories.  Further information about other special year activities
can be obtained by sending a message to special at dimacs.rutgers.edu.

	It is expected that each day of the tutorial program will have
two group sessions featuring presentations by an expert in molecular
biology and/or biomath/biocomputing.  Although each day might be
different, a typical day might have a one hour lecture in the morning,
followed by discussion of lecture topics and suggested readings, a
similar format in the afternoon, plus time for presentations (formal
or informal) by participants.  During the week of August 15, Professor
William Sofer of the Waksman Institute for Molecular Genetics at
Rutgers University will present "An Introduction to Molecular Biology
for Non-Experts."  During the weeks of August 22 and 29, Professors
Martin Farach of the Rutgers Computer Science Department and Michiel
Noordewier of the Rutgers Computer Science Department and the Waksman
Institute will make presentations on "Current Topics in Biocomputing"
and "Current Computational and Mathematical Approaches to Biological
Problems," respectively.  After a break for the Labor Day weekend,
Professor David Axelrod of the Waksman Institute will present
"Biological Maps: A Guided Tour," beginning on September 7.

	In addition to the tutorial lectures, there will be informal
seminar sessions devoted to current literature and presentations by
some of the participants.  Background reading will be suggested by the
principal lecturers.

	Further information about the tutorial program can be obtained
by sending an email message to Martin Farach at farach at dimacs.rutgers.edu
or by calling him at 908-932-4580.  Space is limited and those who wish to
participate need to preregister.  Places will be filled on a
first-come first-served basis.  However, those who cannot make a
commitment to stay for at least the first two weeks of the program
might have confirmation of their participation deferred until we
understand how many people are interested in attending.  To
preregister, send a message stating your interest and whether or not
you are able to stay for the first two weeks to Martin Farach.

	There will be no charge for participation.   DIMACS will
provide office space for participants and make available its computer
facilities.  However, transportation and local expenses are the
responsibility of the participants.



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