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we will meet in 
    
===>  MEB 134, 12:00-1:20 Thursday 5/9 and 5/16 <=== 

This week Tao Jiang will talk about a multiple tree alignment
problem.
<hr size=4><a name="831576080001">Date: Wed, 8 May 1996 10:21:04 -0700
From: <b>jiang (Tao Jiang)</b>
To: cse590bi
Subject: <b>CSE590bi May 9 lecture</b>
</a>

In this lecture I will give a brief survey of recent approximation
algorithms for multiple sequence alignment with guaranteed error bound.
Two popular scoring schemes are considered: tree score and sum-of-pairs
score. The latter model was also discussed in the last quarter.
The emphasis will be given to various algorithm design techniques and
some simple analyses will be sketched.

Tao Jiang
<hr size=4><a name="831681083001">Date: 9 May 1996 15:29 PDT
From: <b>Larry Ruzzo &lt;[e-mail]&gt;</b>
To: cse590bi@cs
Subject: <b>Haussler Talk.</b>
</a>

apologies if you've seen this announcement already
  &gt;  _________________________________
  &gt; From [e-mail] Wed May  8 17:00:38 1996
  &gt; 	(1.40.112.4/16.2) id AA062360060; Wed, 8 May 1996 17:01:00 -0700
  &gt; Date: Wed, 8 May 1996 17:01:00 -0700
  &gt; From: Tim Hunkapiller &lt;[e-mail]&gt;
  &gt; To: [e-mail]
  &gt; Subject: biocomp_seminars
  &gt; 
  &gt; Biocomp announcement
  &gt; for once - an early announcement!
  &gt; tim hunkapiller
  &gt; ---------------------------------------------------------------------
  &gt; 
  &gt; 
  &gt; David Haussler, from the Computer Science Department at University of
  &gt; California Santa Cruz, will be visiting the Center for Molecular
  &gt; Biotechnology Tuesday June 4 and will be presenting a lecture:
  &gt; 
  &gt; Using Hidden Markov Models for Biosequence Analysis
  &gt; (abstract at end of email)
  &gt; 
  &gt; Dr. Haussler received Ph.D. in computer science in 1982 from
  &gt; U. Colorado at Boulder.  He is a Fellow of the American Association for
  &gt; Artificial Intelligence, Associate Editor of Machine Learning,
  &gt; first chairman of the steering committee for the annual ACM Conference
  &gt; on Computational Learning Theory. His current research interests include
  &gt; computational biosequence analysis, machine learning, statistics and
  &gt; information theory.
  &gt; 
  &gt; If you would be interested in meeting with Dr. Haussler, please let me know.
  &gt; 
  &gt; Abstract:
  &gt; 
  &gt; With the databases of DNA, RNA and protein sequences growing
  &gt; at an explosive rate, the need for effective computational methods for
  &gt; biosequence analysis has become acute. In particular, we need
  &gt; good methods for locating genes in DNA sequences,
  &gt; along with their splice sites and regulatory binding sites,
  &gt; and good methods for making an initial classification of new proteins
  &gt; that detect weak homologies to other previously known proteins
  &gt; and predict possible functions for new proteins.
  &gt; Tools available for this analysis range from simple and general search
  &gt; methods such as BLAST to detailed protein folding models of
  &gt; the type used in protein threading and {\em ab initio} protein structure
  &gt; prediction. Hidden Markov Models (HMMs) lie somewhere in the middle
  &gt; of this spectrum. They are computationally efficient enough
  &gt; for use with large databases, yet flexible enough to be used in
  &gt; constructing specific, detailed statistical models of the sequence variation
  &gt; within a particular protein family, our within a family of related
  &gt; DNA binding sites. We will describe what HMMs are and how
  &gt; they are used in biosequence analysis. Then we will briefly
  &gt; discuss some new work in our lab to make these models more biologically
  &gt; accurate.
  &gt; 
<hr size=4><a name="832228312001">Date: 15 May 1996 23:27 PDT
From: <b>Larry Ruzzo &lt;[e-mail]&gt;</b>
To: cse590bi@cs
Subject: <b>NO CSE590BI THIS WEEK</b>
</a>

No class this week.  

Next week Phil will do a bit more on sequence assembly, then I will
describe some approaches to &quot;biomolecular computation&quot;, e.g. the
work of Adleman, using DNA technology to solve an NP-complete
problem.
<hr size=4><a name="833424288001">Date: Wed, 29 May 1996 19:44:34 -0700
From: <b>brendan@willow (Brendan Mumey)</b>
To: cse590bi@willow
Subject: <b>tomorrow's seminar</b>
</a>


Tomorrow (30 May), Omid and I will talk about our recent work with
Dick to analyse large scale hybridization filters.  The data comes
from a new robotic system developed at MBT to determine hybridization
levels of a tissue sample against a large array of cDNA probes.  We will
present an overview of the process and discuss our efforts to
solve some new data-analysis problems which arise.  One such problem
is determining important cDNAs whose expression levels are effective
in predicting whether an unkown tissue sample is cancerous or not.

12:00, MEB 238



<hr size=4><a name="839111871001">Date: Sat, 3 Aug 1996 15:37:33 -0700 (PDT)
From: <b>Phil Green &lt;[e-mail]&gt;</b>
To: seqcourse -- Arian Smit &lt;[e-mail]&gt;,
        Beatrix Jones &lt;[e-mail]&gt;,
        Brendan Mumey &lt;[e-mail]&gt;,
        Brent Ewing &lt;[e-mail]&gt;,
        Chi-hong Tseng &lt;[e-mail]&gt;,
        Chris Abajian &lt;[e-mail]&gt;,
        Colin Wilson &lt;[e-mail]&gt;,
        David Adams &lt;[e-mail]&gt;,
        David Baker &lt;[e-mail]&gt;,
        David Gordon &lt;[e-mail]&gt;,
        Deborah Nickerson &lt;[e-mail]&gt;,
        Dick Karp &lt;[e-mail]&gt;,
        Ed Thayer &lt;[e-mail]&gt;,
        Elizabeth Thompson &lt;[e-mail]&gt;,
        Eugene Kolker &lt;[e-mail]&gt;,
        Gane Ka-Shu Wong &lt;[e-mail]&gt;,
        Jeremy Buhler &lt;[e-mail]&gt;,
        Jinko Graham &lt;[e-mail]&gt;,
        Joe Don Heath &lt;[e-mail]&gt;,
        Joe Felsenstein &lt;[e-mail]&gt;,
        Jorja Henikoff &lt;[e-mail]&gt;,
        Katrina Goddard &lt;[e-mail]&gt;,
        Larry Ruzzo &lt;[e-mail]&gt;,
        Martin Tompa &lt;[e-mail]&gt;,
        Max Robinson &lt;[e-mail]&gt;,
        Maynard Olson &lt;[e-mail]&gt;,
        Michael Parker &lt;[e-mail]&gt;,
        Scott Taylor &lt;[e-mail]&gt;,
        Sharon Guy &lt;[e-mail]&gt;,
        Simon Heath &lt;[e-mail]&gt;,
        Steve Henikoff &lt;[e-mail]&gt;, [e-mail]
Cc: &quot;A. Heidbrink-Lomer&quot; &lt;[e-mail]&gt;
Subject: <b>course on Genome Sequence Analysis</b>
</a>


As most of you already know from the message I sent out earlier, I will be
offering a course on Genome Sequence Analysis this Fall (rough outline
below). Based on the initial response, it looks as though the best meeting
times would be Tu-Th 12:00 - 1:20. Please let me know if you are
interested in the course but would be unable to attend at that time
(unfortunately though there aren't many alternative times that wouldn't
cause problems for somebody).
 I'll be sending out an announcement later with the official course number
and additional details.

Phil




Genome Sequence Analysis: Outline

(The course is intended to be reasonably self-contained in the
sense that relatively little biological or computational background will
be assumed. There will be some overlap with the course CSE 590BI offered
last winter, but I will be covering a more limited number of topics, in
substantially greater depth. In particular there will be much heavier
emphasis on the relevant biology, on statistical issues, and on pragmatic
issues (e.g. use of current computer programs).)

I. Biological background: basic concepts of molecular biology;
genes and genomes; sequence evolution.

II. Sequence interpretation.
 a. Finding protein and DNA sequence similarities.  Pairwise sequence
comparison algorithms:  Smith-Waterman, BLAST, FASTA.  Statistics of
sequence comparison and database searches: likelihood ratios,
Karlin-Altschul theory, empirical methods. Low-complexity sequences.
Optimal score matrices &amp; gap penalties.  Profiles, &quot;motifs&quot;. Multiple
comparison methods: Gibbs sampler, Hidden Markov Models.
 b. Finding genes. Detection of coding regions, codon biases.
Detection of splice sites, weight matrices.
 c. Finding repeats.
 d. Finding regulatory sites and other subtle sequence features.

III. Sequence assembly. Shotgun sequencing strategies; assembly
algorithms;  assessment of data quality; statistics of sequence accuracy.



<hr size=4><a name="839386376001">Date: Tue, 6 Aug 1996 19:52:39 -0700 (PDT)
From: <b>Phil Green &lt;[e-mail]&gt;</b>
Reply-To: Phil Green &lt;[e-mail]&gt;
To: seqcourse -- Arian Smit &lt;[e-mail]&gt;,
        Beatrix Jones &lt;[e-mail]&gt;,
        Brendan Mumey &lt;[e-mail]&gt;,
        Brent Ewing &lt;[e-mail]&gt;,
        Chi-hong Tseng &lt;[e-mail]&gt;,
        Chris Abajian &lt;[e-mail]&gt;,
        Colin Wilson &lt;[e-mail]&gt;,
        David Adams &lt;[e-mail]&gt;,
        David Baker &lt;[e-mail]&gt;,
        David Gordon &lt;[e-mail]&gt;,
        Deborah Nickerson &lt;[e-mail]&gt;,
        Dick Karp &lt;[e-mail]&gt;,
        Ed Thayer &lt;[e-mail]&gt;,
        Elizabeth Thompson &lt;[e-mail]&gt;,
        Eugene Kolker &lt;[e-mail]&gt;,
        Gane Ka-Shu Wong &lt;[e-mail]&gt;,
        Jeremy Buhler &lt;[e-mail]&gt;,
        Jinko Graham &lt;[e-mail]&gt;,
        Joe Don Heath &lt;[e-mail]&gt;,
        Joe Felsenstein &lt;[e-mail]&gt;,
        Jorja Henikoff &lt;[e-mail]&gt;,
        Katrina Goddard &lt;[e-mail]&gt;,
        Larry Ruzzo &lt;[e-mail]&gt;,
        Mark Rieder &lt;[e-mail]&gt;,
        Martin Tompa &lt;[e-mail]&gt;,
        Max Robinson &lt;[e-mail]&gt;,
        Maynard Olson &lt;[e-mail]&gt;,
        Michael Parker &lt;[e-mail]&gt;,
        Scott Taylor &lt;[e-mail]&gt;,
        Sharon Guy &lt;[e-mail]&gt;,
        Simon Heath &lt;[e-mail]&gt;,
        Steve Henikoff &lt;[e-mail]&gt;,
        Trey Ideker &lt;[e-mail]&gt;
Cc: [e-mail]
Subject: <b>599C, AU 1996 (fwd)</b>
</a>

The message below gives the room, time and course number for the
Genome Sequence Analysis course.

If you received this message because you are on the cse590bi@cs mailing
list, and want to receive further announcements about the course, but your
name does not appear on the &quot;seqcourse&quot; mailing list above, please send me
your name and email address. This is the last message that will be Cc'd to
cse590bi@cs. If you are on the above seqcourse mailing list but do not
want to be, please let me know.
Thanks,

Phil

---------- Forwarded message ----------
Date: Tue, 6 Aug 1996 09:49:24 -0700 (PDT)
From: &quot;A. Heidbrink-Lomer&quot; &lt;[e-mail]&gt;
To: [e-mail]
Subject: 599C, AU 1996


Phil,

I have set up your Special Topics Class (Sequence Analysis) for AU 1996.
Tuesdays and Thursdays from 12:00-1:20 in HSB T-473. The capacity for the
room is 50 people.

599 is MBT's general special topics course. Since 599A is Research Methods
and 599B is Research Discussions your course will fall under the 599C
section.I have also requested entry codes and a schedule line number as we
do with the other 599 sections.

Let me know if there is anything else!

Anne


==============================================================================
		*	Anne Lomer, Academic Counselor	*
                *       University of Washington        *
		*	Dept. Molecular Biotechnology	*
		*	PO Box 357730                   *
                *       Seattle, WA 98195		*
		*	Phone: [phone]		*
		*	Fax: [phone]		*
*******************************************************************************
....Life's what happens to you when your making other plans...John Lennon
===============================================================================





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