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                             Joe Felsenstein

                     of the Department of Genetics
                    will teach a 3-credit course in

                         Phylogenetic Inference

            at 11:30-12:20 MWF in room J280 Health Sciences Building

This course will cover, at the graduate level, the biology, statistics, and
computation of estimating phylogenies (evolutionary trees), inferring how much
uncertainty we have about the estimates, and making use of phylogenies in other
kinds of inferences.

Prerequisite is enough background in biology to know what DNA is, enough
statistics to know what likelihood is, and enough mathematics to be able to
understand what a matrix is.

Topics covered will include:

         What is a phylogeny?        restriction sites and RAPDs
         Parsimony methods           gene frequencies
         Compatibility methods       morphology and quantitative characters
         Distance matrix methods     comparative methods
         Likelihood methods          coalescent trees of genes
         Searching tree space        consensus trees and tree distances
         nucleotide sequences        tests based on tree shape
         proteins

There will also be computer exercises.

---- 
Joe Felsenstein         [e-mail]     (IP No. 128.95.12.41)
 Dept. of Genetics, Univ. of Washington, Box 357360, Seattle, WA 98195-7360 USA
 phone: [phone]
<hr size=4><a name="827367172001">Date: 20 Mar 1996 14:39 PST
From: <b>Larry Ruzzo &lt;[e-mail]&gt;</b>
To: cse590bi@cs
Subject: <b>CSE 590BI continues...</b>
</a>

We are planning to run a somewhat more informal continuation of CSE
590BI (Computation, Molecular Biology, etc.)  during Spring quarter.
We hope to revisit in more depth some topics introduced last quarter
(e.g. perhaps sequence assembly, MCD mapping), as well as explore
some new ones (perhaps protein folding, biomolecular computing,
genome rearrangement).  The topic list is not finalized; feel free
to send suggestions if you have particular interests.

Time:    Thursdays, 12:00-1:30 (starting next week, 3/28) 
         Note it's just one day per week.  
Place:   MEB 238
Grading: Credit/No Credit
Units:   Variable (1-3).  1 unit will again entail light housework,
         at worst.  2 or 3 units for more substantive involvement,
	 e.g., reading and presenting paper(s); negotiable.  
         (I don't have the SLN yet; it should appear in the official
	 time schedule tomorrow.)
<hr size=4><a name="827539407001">To: cse590bi@geoduck
cc: [e-mail]
Subject: <b>course on Protein Stucture Prediction</b>
Date: Fri, 22 Mar 1996 14:18:07 PST
From: <b>Martin Tompa &lt;[e-mail]&gt;</b>
</a>


------- Forwarded Message

Date:    Fri, 22 Mar 1996 14:04:02 -0800
From:    David Baker &lt;[e-mail]&gt;
To:      Martin Tompa &lt;[e-mail]&gt;
Subject: Re: computational biology course


Martin,
	Here is an announcement for a course next quarter that may interest
you or people attending your class last quarter.  Could you send it to
people on your class mailing list?
thanks,
David

Protein Stucture Prediction			David Baker

	This seminar course will focus on recent developments in methods 
for protein structure prediction and amino acid sequence comparison.  The 
course will meet Tuesdays and Thursdays 12:30- 2:00 from March 26 to 
April 30 in HSB J-412.  Students taking the course for (one) credit will 
propose new developments/ improvements to current approaches to structure 
prediction in a short paper.

March 26 	David Baker (Biochemistry)	
Introduction

March 28	Phil Green	(Molecular Biotechnology) 
Conserved sequence families

April 2 Kam Zhang (FHCRC) 
The 3D profile and threading methods for structure prediction

April 4 Scott Presnell (Zymogenetics)
From EST to Structure

April 9 John Moult (Center for Advanced Research in Biotechnology)
The current state of protein structure prediction

April 11	Terry Lybrand	(Bioengineering)
Protein 3D Model Building: Homology and Constraint-based de novo Modeling 
Methods.

April 16	Steve Henikoff  (FHCRC)
Scores for sequence searches and alignments

April 18	Valerie Daggett	(Medicinal Chemistry)
Lessons from molecular dynamics

April 30	David Baker  Conclusion



------- End of Forwarded Message

<hr size=4><a name="827948936001">Date: 27 Mar 1996 09:32 PST
From: <b>Larry Ruzzo &lt;[e-mail]&gt;</b>
To: cse590bi@cs, cs-grads@cs
Cc: [e-mail]
Subject: <b>CSE590BI schedule change</b>
</a>

We suspect that many people who would be interested in the
continuation of our computational bio seminar will also be
interested in David Baker's seminar on protein structure prediction.
Unfortunately there's a time conflict, and rescheduling our class is
difficult at this late date.  However, Baker's course only runs 4.5
weeks, so what we've decided to do is delay starting ours until 
*** Thursday, April 25 ***, continuing on the 5 subsequent
Thursday's.  This should avoid the conflicts.  So, until 4/25,
you're encouraged to go to Baker's seminar if interested, and to
join us for CSE590bi in MEB 238, 12:00-1:20 Thursdays, starting
4/25.  We'll work  out and distribute a schedule of topics in
advance of that.

Please contact Karp, Tompa, or me if you have questions about
registration, credits, or other administrative or substantive
issues.

Here's a repeat of Baker's announcement.  Note the room has been
changed to K-450, not J-something as reported below.


Date:    Fri, 22 Mar 1996 14:04:02 -0800
From:    David Baker &lt;[e-mail]&gt;


Protein Stucture Prediction			David Baker

	This seminar course will focus on recent developments in methods 
for protein structure prediction and amino acid sequence comparison.  The 
course will meet Tuesdays and Thursdays 12:30- 2:00 from March 26 to 
April 30 in HSB J-412.  Students taking the course for (one) credit will 
propose new developments/ improvements to current approaches to structure 
prediction in a short paper.

March 26 	David Baker (Biochemistry)	
Introduction

March 28	Phil Green	(Molecular Biotechnology) 
Conserved sequence families

April 2 Kam Zhang (FHCRC) 
The 3D profile and threading methods for structure prediction

April 4 Scott Presnell (Zymogenetics)
From EST to Structure

April 9 John Moult (Center for Advanced Research in Biotechnology)
The current state of protein structure prediction

April 11	Terry Lybrand	(Bioengineering)
Protein 3D Model Building: Homology and Constraint-based de novo Modeling 
Methods.

April 16	Steve Henikoff  (FHCRC)
Scores for sequence searches and alignments

April 18	Valerie Daggett	(Medicinal Chemistry)
Lessons from molecular dynamics

April 30	David Baker  Conclusion



------- End of Forwarded Message

<hr size=4><a name="829077850001">To: cse590bi@geoduck, [e-mail]
Subject: <b>University of Pennsylvania Conference on Computational Biology</b>
Date: Tue, 09 Apr 1996 12:23:58 PDT
From: <b>Martin Tompa &lt;[e-mail]&gt;</b>
</a>


------- Forwarded Message

Date:    Tue, 09 Apr 1996 12:50:07 -0400
From:    Tandy Warnow &lt;[e-mail]&gt;
To:      [e-mail]
Subject: conference in Computational Biology


Martin,

    I wanted to let you know about a conference I'm organizing
which will take place the week before FCRC. We'd very much like
to have people involved in training in computational biology
at the conference, so especially would like to have people from
Washington (your department and Biotechnology as well).  Would
you please distribute this to anyone who might be interested?

     Thanks very much,

           Tandy


NOTE: The Nassau Inn is holding rooms only until April 21. Please
reserve rooms now to be sure of space.



                   ANNOUNCEMENT AND CALL FOR PAPERS

    The University of Pennsylvania Conference on Computational Biology
             to honor the 50th anniversary of the ENIAC,

                            sponsored by: 

  The University of Pennsylvania Training Program in Computational Biology, 

   DIMACS - The NSF Center for Discrete Mathematics and Computer Science, 

       IRCS - The Institute for Research in Cognitive Science, an
             NSF Center for Science and Technology at 
                 the University of Pennsylvania,

                SmithKline Beecham Pharmaceuticals,

                               Merck,

                and the National Science Foundation. 



The conference will be held at DIMACS and Princeton University, May 17-19, 
1996.  (The timing of the conference enables attendees to attend this 
and the FCRC, which will take place in Philadelphia, one hour away,
the following week.)


Historical Note:

    The University of Pennsylvania Training Program in Computational 
Biology, DIMACS, and IRCS are pleased to jointly host this conference on 
computational biology as part of the ENIAC Symposium.  This conference 
will be one of the activities in the Commemorative, Technical and 
Historical Symposium on the occasion of 50th anniversary of the Moore 
School Lectures.  These Lectures were held during the summer of 1946 
to bring together the leading specialists in high-speed digital 
computation in order to lay the foundations of the yet-to-be-defined 
fields of computer engineering and computer science.  With this 
symposium, we again hope to assemble researchers in current computer
science disciplines to advance the state of the field.  On this 
occasion we also invite historians of technology and computing, in 
order to understand the past so that we may proceed more knowingly 
into the future.


About the Conference:

The conference will have invited and contributed talks, and will be 
based around sessions focusing on important research areas within 
the field.  There will be ample time allocated for discussions 
and interactions among biologists, computer scientists and mathematicians.  

This year's special research topics will include: Structure Prediction, 
Tandem Repeats, Databases, Sequencing and Mapping, and Genome 
Rearrangements.  There also will be a special session on 
interdisciplinary education in computational biology, in which directors 
and students in various training programs throughout the country will 
participate.  

Invited speakers include: 

    Craig Benham (Biomathematics, Mt. Sinai School of Medicine),
    Gary Benson (Biomathematics, Mt. Sinai School of Medicine),
    Bonnie Berger (Math, MIT), 
    Bill Bialek (NEC)
    Susan Davidson (CIS, Penn),
    Sampath Kannan (CIS, Penn),
    Rob Lipschutz (Affymetrix),
    Joshua Lederberg (Rockefeller),
    Pavel Pevzner (Math, USC), and
    David Sankoff (Math, Montreal)
    Jeanette Schmidt (Brooklyn Polytechnic)
    Peter Shor (AT&amp;T)
    Eero Simoncelli (CIS, Penn)