Administrative requests concerning the mailing list itself, such as add/delete/address change requests, should be addressed to cse590bi-request@cs.
To: cse590bi@cs Subject: CSE 590 BI distrib. list, and variable credits Date: Fri, 05 Jan 1996 13:54:07 PST From: Martin Tompa <tompa@geoduck.cs.washington.edu> 1. We have created a mail distribution list cse590bi@cs.washington.edu from the electronic addresses you supplied in the first week. This can be used for announcements, discussion outside of class, etc. 2. As Dick mentioned, we very much want to encourage you to sign up for credit if at all possible. To accomodate this, we have changed to variable credit (anywhere between 1 and 3), with the following scheme: a. 1 credit for attending faithfully and serving as notetaker when it is your turn, b. 1 credit for homework plus the take-home final, if there is one, c. 1-2 credits for the project, depending on its magnitude, up to a maximum of 3 credits. Please choose your level of involvement and sign up for the appropriate number of credits. Monday is the last day to make such changes without penalty, I believe. Signing up for credits is good for the department and, if you're anything like me when it comes to good intentions, good for the student as well. If you have questions about the credits or would like to discuss your plan for the course, feel free to talk with any of us. If (or when) you are signed up for credit, please also send mail to Tompa saying how you intend to satisfy the number of credits you chose, so that we know who are the notetakers, who is doing a project, etc.
Date: Wed, 10 Jan 1996 14:23:44 -0800 (PST) From: Jared Roach <roach@u.washington.edu> To: cse590bi@cs.washington.edu Subject: textbooks From: Martin Tompa <tompa@cs.washington.edu> To: Jared Roach <roach@u.washington.edu> Thanks for the great pointers. Would it be o.k. for either you or me to send this to the class list, cse590bi@cs? I think they'd appreciate it. Let me know if you'd like me to do it. OK, I'll forward it. From: Jared Roach <roach@u.washington.edu> To: tompa@cs.washington.edu Subject: Algorithms notes Martin, I just wanted to alert the class to a couple of topical books. 1) Calculating the Secrets of Life Lander and Waterman, eds. 1995 National academy Press This has several good chapters, including one on yesterday and tomorrow's lectures by Gene Myers. At the end of this chapter, Gene states that the lowest bound on comparing two sequences yet found is O(NlogN), which addresses a question raised at the end of class yesterday. He claims that the fastest algorithm to date is O(N^2/log^2N) (Masek and Paterson, 1980), leaving a gap between the fastest algorithm and the highest lowest theoretical bound for algorithms, and thus an open problem. Other good chapters include one on statistical significance of comparisons by Waterman, probabilistic gene mapping by Lander, and molecular clock rates by Tavare. The book also includes four chapters on conformational computation. The UW library's copy is checked out by me and currently has a hold on it by someone else. The bookstore should have one or more copies. 2) Introduction to Computational Biology Waterman 1995 Chapman and Hall This book just came out. I ordered my copy through the bookstore and it took many weeks for it to arrive. I haven't had a chance to read it yet, but it covers many of the above areas. It is about 50% on mapping, 30% on sequence alignment and assembly, and has a chapter on RNA secondary structure and one on tree assembly. It has a 50 page chapter on the dynamic programming of yesterday and tomorrow's lectures. - -Jared - --------------------------------------------------- Jared Roach Department of Molecular Biotechnology University of Washington, Room K354 Box 357730 Seattle, WA 98195 phone 616-4536 FAX 685-7301 roach@u.washington.edu btw, dangling modifiers are not intentional, they just came out of my head that way. ------- End of Forwarded Message
Date: 11 Jan 1996 19:23 PST From: Larry Ruzzo <ruzzo@quinault.cs.washington.edu> To: cse590bi@cs Subject: extra handouts In general, Martin Tompa (Sieg 426E) will keep extras of all the handouts, in case you missed some. Handouts can also be printed from the course web pages: http://www.cs.washington.edu/education/courses/590bi
To: cse590bi@geoduck Subject: Do we have your 590bi plans? Date: Fri, 12 Jan 1996 12:14:48 PST From: Martin Tompa <tompa@geoduck.cs.washington.edu> If you have signed up for credit and haven't yet sent me the following information, please do so now: 1. How many credits? 2. Which of the options from my earlier message are you planning in order to satisfy those credits?
To: cse590bi@geoduck Subject: notetakers needed Date: Tue, 16 Jan 1996 11:07:48 PST From: Martin Tompa <tompa@geoduck.cs.washington.edu> We have a notetaker for today (1/16) but need volunteers starting Thursday (1/18). If you are signed up for credit with notetaking as part of the plan, and haven't yet taken notes, please send me mail saying which of the next several dates you can take notes. I'll then come up with a schedule.
To: cse590bi@geoduck Subject: lineup of notetakers Date: Tue, 16 Jan 1996 18:37:32 PST From: Martin Tompa <tompa@geoduck.cs.washington.edu> Thanks for the many volunteers. We've got enough for the time being again. Here's the lineup. Let me know if there are any conflicts. 1/18: Mock 1/23: Fulgham 1/25: Fasulo 1/30: Mumey 2/1 : Madani 2/6 : VanVleet 2/8 : Jackson
To: cse590bi@geoduck Subject: Lecture 6 available on the web Date: Mon, 22 Jan 1996 11:50:58 PST From: Martin Tompa <tompa@geoduck.cs.washington.edu> For those of you anxious to work on the multiple string alignment homework problems, Lecture 6 is now available on the course web. We will hand out paper versions of it in Tuesday's lecture.
To: cse590bi@geoduck Subject: lineup of notetakers completed Date: Wed, 24 Jan 1996 13:46:52 PST From: Martin Tompa <tompa@geoduck.cs.washington.edu> Here's the final lineup for the remaining notetakers. If you are on this list, please check below to make sure we've agreed on the date. 1/25: Fasulo 1/30: Mumey 2/1 : Madani 2/6 : Graham 2/8 : Jackson 2/13: VanVleet 2/15: Thathachar 2/20: Adams 2/22: Chan 2/27: Fix 2/29: Lee 3/5 : Hong 3/7 : Adams
To: cse590bi@geoduck Subject: Assignment 1, problem 3 Date: Fri, 26 Jan 1996 14:01:00 PST From: Martin Tompa <tompa@geoduck.cs.washington.edu> My instructions led you down a slightly wrong path on problem 3. You should assume that n is a power of 2, rather than one more than a power of 2, for simplicity. A small bonus is that it means you can ignore all the ceiling notation in the problem. A big bonus is that it means you won't have the same misconception about how the algorithm works that I had until a few minutes ago. Sorry for misleading you.
Date: 27 Jan 1996 13:46 PST From: Larry Ruzzo <ruzzo@quinault.cs.washington.edu> To: cse590bi@cs Subject: Pevzner talks here are abstracts of the two Pevzner talks mentioned in class recently: > Date: Thu, 25 Jan 1996 14:51:02 -0800 (PST) > Subject: UW-CSE Colloq / 2-5-96 / Pevzner / USC / Genome Rearrangements, or, What Dobzhansky and Sturtevant Did Not Tell Us > > > UNIVERSITY OF WASHINGTON > Seattle, Washington 98195 > > Department of Computer Science and Engineering > Box 352350 > (206) 543-1695 > > COLLOQUIUM > > DATE: Monday, February 5, 1996 > > TIME: 3:30 pm > > PLACE: 134 Sieg Hall > > HOST: Dick Karp > > SPEAKER: Pavel Pevzner > University of Southern California > > TITLE: Genome Rearrangements, or, What Dobzhansky and Sturtevant > Did Not Tell Us > > ABSTRACT: > > Sequence comparison in computational molecular biology is a powerful tool > for deriving evolutionary or functional relationships between genes. > However, classical alignment algorithms handle only local mutations (i.e. > insertions, deletions and substitutions of one nucleotide) and ignore > global rearrangements (i.e. inversions and transpositions of long > fragments). As a result, the applications of sequence alignment to > analyze highly rearranged genomes (i.e. herpes viruses or plant > mitochondrial DNA) are very limited. I address the problem of GENOME > comparison versus classical GENE comparison and present algorithms to > analyse rearrangements in genomes evolving by inversions, transpositions > and translocations. In the simplest form the problem corresponds to > sorting by reversals, i.e. sorting of an array using reversals of > arbitrary fragments. I present polynomial algorithms and duality theorems > for sorting by reversals and genomic distance problem. I also discuss > applications of the proposed techniques to analyze evolution of herpes > viruses, plant mitochondrial DNA and mammalian chromosomes. > > This is a joint work with Vineet Bafna (DIMACS), Colombe Chappey (NIH), > Sridhar Hannenhalli (USC), and Eugene Koonin (NIH). > > > Refreshments to follow. > > Email: talk-info@cs.washington.edu > > Info: http://www.cs.washington.edu > > _________________________________ > X-Sender: egan@homer23.u.washington.edu > Date: Fri, 19 Jan 1996 14:50:35 -0800 (PST) > From: Elizabeth Egan <egan@u.washington.edu> > Subject: STC LECTURE - FEB 6 96 K069 4:00 PM > > PLEASE NOTE THAT DR. PEVZNER'S LECTURE IS AT 4:00PM Feb 6 > > > Our February 6th speaker will be Pavel Pevzner from the Department of > Mathematics University of Southern California. With this email I include > the title and abstract of his presentation as well as an invitation for > you and your group to meet Dr. Pevzner. Please let me know if you or your > laboratory would like to be included on his itinerary or if you could > suggest people/groups who may be interested. > > Spliced Alignment: a New (and Naive) Approach to Gene Recognition > > Previous attempts to solve gene recognition problem were based on > statistics and artificial intelligence and, surprisingly enough, > applications of theoretical computer science methods for gene recognition > were almost unexplored. Recent advances in large-scale cDNA sequencing > open a way towards a new combinatorial approach to gene recognition. I > describe a spliced alignment algorithm and a software tool which > explores all possible exon assemblies in polynomial time and finds the > multi-exon structure with the best fit to a related protein. Unlike other > existing methods, the algorithm successfully performs exons assemblies > even in the case of short exons or exons with unusual codon usage; we > also report correct assemblies for genes with more than 10 exons provided > a homologous protein is already known. On a test sample of human genes > with known mammalian relatives the average overlap between the predicted > and the actual genes was 99\%, which is remarkably well as compared to > other existing methods. At that, the algorithm absolutely correctly > reconstructed 87\% of genes. The rare discrepancies between the predicted > and real exon-intron structues were restricted either to extremely short > initial or terminal exons (less than 5 amino acids) or proved to be > results of alternative splicing. Moreover, the algorithm performs > reasonably well with non-vertebrate and even prokaryote targets. The main > result of the paper is that a relatively simple algorithm based on > combinatorial common sense and some biological intuition can outperform > many approaches developed for gene recognition in the last fifteen years. > > This is a joint work with M.Gelfand and A.Mironov. > > For more information: > elizabeth a egan > center for molecular biotechnology > (an NSF Science & Technology Center) > university of washington, box 35-7730 > seattle, washington 98195-7730 > TEL: (206) 685-1894 > FAX: (206) 685-7301 > email: egan@u.washington.edu > >
To: cse590bi@geoduck Subject: CSE 590 BI projects Date: Thu, 08 Feb 1996 16:28:36 PST From: Martin Tompa <tompa@geoduck.cs.washington.edu> If you are going to do a project in CSE 590BI, please send me mail with your schedule for next week (Feb 12-16). We're going to try to arrange a meeting to discuss projects.
To: cse590bi@geoduck Subject: some course project suggestions Date: Fri, 09 Feb 1996 10:44:24 PST From: Martin Tompa <tompa@geoduck.cs.washington.edu> Here are a few project ideas for CSE 590BI, to get you thinking about them. If you are doing a project and have your own ideas about what you would like to do, please come talk with us about them. If anyone else on this mailing list has interesting suggestions for course projects, please send them to us. CLASSIFICATION OF PROSTATE CANCER TUMORS This project is related to research in Lee Hood's laboratory on the classification of prostate cancer tumors. It is believed that a disease category such as prostate cancer or ovarian cancer includes a number of distinct disease types that may require very different kinds of medical treatment. Some prostate cancers develop so slowly that they present no threat to mortality, while others require immediate medical intervention. The existing diagnostic tests do not distinguish the different variants of the disease. Molecular biology may provide new experimental techniques that will distinguish the different types of prostate cancer or ovarian cancer. It is now possible to extract the mRNA from a tumor and transcribe it back to cDNA. By hybridizing the mix of cDNAs from a tumor against a large number of genes from normal tissue and measuring the amounts of hybridization product produced, one obtains a profile of the gene expression taking place in the tumor. Experiments are now getting under way which will use this hybridization technique to obtain 25,000 measurements of gene expression in each of 600 prostate cancer tumors, and data will be available by late March. These experiments will provide much more detailed "fingerprints" of tumors than has been available up to now. The computational challenge is to use this large body of data to classify the tumors into clusters and, based on this classification, to determine rules that can be used to classify tumors in the future. One special feature of the problem is the high dimensionality of the data; i.e., the large number of measurements for each tumor. It is likely that only a small subset of these measurements will be important for the clasification, but we cannot know in advance which ones these will be. The project will consist of looking into the literature of clustering and classification to discover appropriate computational methods and software packages, as well as devising special methods suited to this particular problem. Since real data will not be available by the end of the quarter, it may be desirable to test out different methods on simulated data. MULTIPLE SEQUENCE ALIGNMENT There are a few different ideas for projects concerned with multiple sequence alignment, as introduced in Lecture 6 and Homework 1. The general issues to explore are the various methods of valuation of alignments (sum-of-pairs, consensus, Steiner, phylogenetic tree), and efficient algorithms for achieving good alignments under any of these valuation schemes. Because no one knows efficient algorithms for optimal alignments under any of these valuation schemes, the project could explore ideas for heuristics or approximation algorithms. Dick Karp has a divide and conquer heuristic that he would be interested in sharing. There is a minimum spanning tree heuristic hinted at in problem 10 of Homework 1, and more details of what is done in practice are available in Gusfield's manuscript and other sources. Exploring such heuristics could be done experimentally, or analytically. Data for experimentation might come from exisiting databases containing multiple aligned sequences, or could be generated synthetically. cDNA MATCHING Another project to explore is introduced in problem 4 of Homework 1: For the cDNA matching problem, experiment with realistic gap penalties reflecting what is known about intron lengths.
To: cse590bi@geoduck Subject: student and postdoc financial support to workshop Date: Wed, 21 Feb 1996 08:52:29 PST From: Martin Tompa <tompa@geoduck.cs.washington.edu> ------- Forwarded Message Date: Tue, 20 Feb 1996 20:04:15 -0800 From: "William E. Hart" <wehart@cs.sandia.gov> To: Local Distribution <theory-net@JUNE.CS.WASHINGTON.EDU> Subject: Financial Support for Second SNL Workshop on Computational Molecular B iology UPDATE*UPDATE**UPDATE*UPDATE*UPDATE**UPDATE*UPDATE*UPDATE $$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$ The Second Sandia National Laboratories Workshop on Computational Molecular Biology March 4-6, 1996 Albuquerque, New Mexico Organized in collaboration with DIMACS Special Year on Mathematical Support for Molecular Biology Funded by DOE MICS Office of Scientific Computing Applied Mathematics Program Dr. Fred Howes, Director and DOE Office of Health and Environmental Research Human Genome Program Dr. A. Patrinos, Director We are pleased to announce that the DOE Office of Health and Environmental Research, Human Genome Program has generously provided some financial support for graduate students and postdocs to attend the 2nd SNL Workshop on Computational Molecular Biology. Accordingly, we will be granting partial financial support for ten graduate students and/or postdocs. Please send email or contact Sorin Istrail. Include a vita and a description of current research. A decision will be made by February 21, 1996. We apologize for the late date of this announcement, but our efforts to obtain this funding have just recently succeeded. Interested parties should also finalize their travel arrangements immediately, as space is limited. For further information on the workshop can be obtained at http://www.cs.sandia.gov/cmb_workshop96.html Sorin Istrail, Workshop Chair Sandia National Laboratories Massively Parallel Computing Research Laboratory Algorithms and Discrete Mathematics Albuquerque, NM 87185-1110 Phone: (505) 845-7612 Secretary: (505) 845-7432 Fax : (505) 845-7442 Email: scistra@cs.sandia.gov ------- End of Forwarded Message
To: cse590bi@geoduck Subject: lecture notes drafts Date: Wed, 21 Feb 1996 09:00:52 PST From: Martin Tompa <tompa@geoduck.cs.washington.edu> If you are working on HW2 but don't have the polished lecture notes you need, you can find unedited drafts of most of them on the course web: http://www.cs.washington.edu/education/courses/590bi/
To: cse590bi@geoduck Subject: sequel to CSE 590BI Date: Tue, 27 Feb 1996 15:50:47 PST From: Martin Tompa <tompa@geoduck.cs.washington.edu> We are considering holding a less formal sequel to CSE 590BI next quarter, to explore some of the many topics that we couldn't get into deeply enough this quarter. The format is very much up in the air: it might meet only once a week, might consist largely of student presentations, etc. This message is to see how much interest there is in the audience (both student and faculty) for such a sequel. If you are interested in continuing next quarter, please send me information such as 1. interested in 1 day per week or 2? 2. any topics you would be particularly interested in exploring? 3. ideas on format?
From: Joe Felsenstein <joe@genetics.washington.edu> Subject: Phylogeny course Sprinq Quarter To: cse590bi@cs.washington.edu Date: Mon, 18 Mar 1996 15:06:32 -0800 (PST) (apologies to those for whom this is "junk mail" or who get it multiple times) NEW COURSE Spring Quarter, 1996 under the Topics in Genetics number (GENET 554) 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 joe@genetics.washington.edu (IP No. 128.95.12.41) Dept. of Genetics, Univ. of Washington, Box 357360, Seattle, WA 98195-7360 USA phone: 543-0150
Date: 20 Mar 1996 14:39 PST From: Larry Ruzzo <ruzzo@quinault.cs.washington.edu> To: cse590bi@cs Subject: CSE 590BI continues... 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.)
To: cse590bi@geoduck cc: baker@ben.bchem.washington.edu Subject: course on Protein Stucture Prediction Date: Fri, 22 Mar 1996 14:18:07 PST From: Martin Tompa <tompa@geoduck.cs.washington.edu> ------- Forwarded Message Date: Fri, 22 Mar 1996 14:04:02 -0800 From: David Baker <baker@BEN.bchem.washington.edu> To: Martin Tompa <tompa@cs.washington.edu> 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
Date: 27 Mar 1996 09:32 PST From: Larry Ruzzo <ruzzo@quinault.cs.washington.edu> To: cse590bi@cs, cs-grads@cs Cc: baker@ben.bchem.washington.edu Subject: CSE590BI schedule change 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 <baker@BEN.bchem.washington.edu> 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
To: cse590bi@geoduck, baker@ben.bchem.washington.edu Subject: University of Pennsylvania Conference on Computational Biology Date: Tue, 09 Apr 1996 12:23:58 PDT From: Martin Tompa <tompa@geoduck.cs.washington.edu> ------- Forwarded Message Date: Tue, 09 Apr 1996 12:50:07 -0400 From: Tandy Warnow <tandy@central.cis.upenn.edu> To: tompa@cs.washington.edu 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&T) Eero Simoncelli (CIS, Penn) Michael Waterman (Math and Molecular Biology, USC). REGISTRATION: A registration form is appended at the end of this announcement. Participants should submit their registration applications by e-mail, using this form, to Sandy Barbu at barbu@cs.princeton.edu. There is no charge for registering, but registration will be limited to 150 applicants. GRADUATE STUDENTS AND POSTDOCS: Funds are available to partly defray the costs of attending this conference for graduate students and postdocs. Please arrange for a letter of recommendation to be sent by your advisor or other appropriate senior scientist. Students and postdocs will also be expected to participate either by giving a contributed talk or presenting a poster. DISCUSSANT AWARDS: Awards to help cover travel to the conference are available, primarily for biologists. All recipients of these awards are expected to participate either through a poster or through a contributed talk. To apply for a discussant award, please send a CV and a letter describing your intended contribution to the Conference Organizer. (See information below.) Awards will be announced by mid-April. APPLICATION PROCEDURE: To apply for a discussant or travel award, please send a vita, a one page abstract of a poster of contributed talk, and a letter of recommendation to the Conference Organizer (see below). BANQUET: A banquet will be held Firday evening at the University of Pennsylvania as part of the ENIAC celebration. This will include a distinguished lecture on the History of Science. There will be a moderate charge for the banquet, reduced for students. Transportation to Penn and back will be provided. PROCEEDINGS: A proceedings will be published. SUBMISSIONS: We are limiting the contributed talks so as to leave sufficient time for general and technical discussion. However, we will have a poster session as part of the wine and cheese reception Saturday evening. If you are interested in providing a contributed talk, please send a short abstract *as soon as possible* to Tandy Warnow (address below). Posters may be submitted until May 1, 1996, and - if space permits - after that date. Selection of contributed talks will be made and announced by April 20, 1996. Selection of posters will be announced by May 10, 1996. Simultaneous submission to conferences or journals is acceptable. CONFERENCE ORGANIZERS: Craig Benham and Tandy Warnow send correspondence to: Tandy Warnow Department of Computer and Information Science University of Pennsylvania Philadelphia, PA 19105-6389 tandy@central.cis.upenn.edu PROGRAM COMMITTEE: Craig Benham (Mount Sinai) Martin Farach (Rutgers) Sampath Kannan (Penn) Tandy Warnow (Penn) LOCATION: Nassau Inn, Princeton NJ, and the Computer Science Building of Princeton University, located at 35 Olden Street. LODGING: A block of 50 rooms has been set aside for conference participants at the Nassau Inn, and another 25 rooms have been set aside at the Palmer Inn. These rooms are available at reduced rates for participants registering before *April 21st.* Be sure to inform the registration desk that you are registering for the Penn/DIMACS Computational Biology Conference held at Princeton University in order to receive the reduced rate. Nassau Inn Dbl/Single $105 1 Palmer Square Princeton, NJ Phone: (609) 921-7500 FAX: (608) 921-6530 1-800-862-7728 The Nassau Inn is located in the center of downtown Princeton within walking distance of the Computer Science Building. Palmer Inn Single $ 64 3499 Rt. 1 South Double $ 66 Princeton, NJ Phone: (609) 452-2500 FAX: (609) 452-1371 (800) 688-0500 The Palmer Inn is not within walking distance, but they do provide van service. The above rate includes a continental breakfast. Bed and Breadfast of Princeton P. O. Box 571 Princeton, NJ 08542 Phone: (609) 924-3189 FAX: (609) 921-6271 Email: CompuServe 71035.757@compuserve.com (John Hurley) Single:$40-$50, Dbl. $50-$60 Please make reservations directly with hotels or bed & breakfast. When making reservations at either hotel, specify it is a DIMACS reservation. (This isn't necessary at the B & B.) ___________________________________________________________________ *Watch the DIMACS WWW page for updates in the schedule ------- End of Forwarded Message
To: cse590bi@geoduck Subject: Graduate Research Position in Theoretical Biology @ LANL Date: Sat, 13 Apr 1996 17:30:17 PDT From: Martin Tompa <tompa@geoduck.cs.washington.edu> ------- Forwarded Message Date: Fri, 12 Apr 1996 20:19:26 -0700 From: Emanuel Knill <knill@c3serve.c3.lanl.gov> To: Local Distribution <theory-net@JUNE.CS.WASHINGTON.EDU> Subject: Graduate Research Position in Theoretical Biology @ LANL The Theoretical Biology Group (T10) at Los Alamos National Laboratory invites applications for a Graduate Research Assistantship. This opening is for someone who will contribute to our ongoing theoretical research in support of the human genome project. The specific project involves developing methods for analyzing long sequences of DNA. One aspect of this includes algorithm development for inducing a Hidden Markov Model of DNA. The project can be expected to include research into new algorithms as well as software implementation of algorithms we have developed. It is hoped that this work will be suitable for a thesis or scientific publication. The most qualified students will have the following skills: competence in C++ programming (non-negotiable) interest in "real" applications of theory, in particular, to DNA sequences some knowledge of probability and/or statistics interest in AI /machine learning willingness to read the current relevant literature - ---------------------------------------------------------------------------- The Theoretical Biology Group (T10) T10 has a long history of research excellence in theoretical biophysics and mathematical biology. T10 collaborates closely with the Center for Human Genome Studies at Los Alamos National Laboratory. To contribute to the mapping of the human genome we have developed novel techniques for constructing maps of clones. T10 houses several nationally recognized sequence databases databases including HIV. Ongoing theoretical research also includes HIV pathogenesis; protein and DNA dynamics; signaling kinetics; immune response and cellular dynamics. - ---------------------------------------------------------------------------- Los Alamos National Laboratory The Los Alamos National Laboratory, operated by the University of California for the U.S. Department of Energy, is a multiprogram national laboratory, operated by the University of California. In accordance with the Laboratory mission, "Science Serving Society", the scope of research has expanded from the original charge of designing nuclear weapons to include a wide spectrum of programs including biomedicine, computational science, science education, environmental protection and materials science. In staff and technical capability, Los Alamos is one of the largest multidisciplinary laboratories in the world with world-class theoretical and applied researchers. The Laboratory offers a research atmosphere designed to foster innovative interdisciplinary collaborations. The Laboratory has consistently led the world in the area of high performance computing. Los Alamos provides an excellent computing environment including leading technologies from Thinking Machines Corporation; Cray Research, Inc.; IBM;, Motorola; Silicon Graphics, Inc.; and Sun Microsystems to name a few. Los Alamos is one of 2 DOE High Performance Computing Research Centers. The Laboratory's Integrated Computing Network, used by approximately 9,000 people distributed throughout the nation, constitutes one of the most powerful scientific computing facilities in the world. - ---------------------------------------------------------------------------- Graduate Research Assistantships Applications for Graduate Research Assistantships are accepted on a year-round basis. Eligibility requires that you * are currently enrolled or anticipating acceptance in an accredited graduate program within the next 12 months. * OR have received your degree (BS, BA, MS, MA, PhD) within the last 12 months. In this case, a Graduate Research Assistantship at Los Alamos is an excellent opportunity for recent graduates to gain applied research experience before moving on to further graduate work or industry. Traditional positions are full-time, 90-day summer appointments, but longer-term appointments, starting at any time and extending throughout the year, are also available. Part-time status is an option for those with appointments of at least one year in length. Salaries are based on education and relevant experience. They currently range from approx. $11 to approx. $17 /hr. Benefits depend on appointment length. Participants residing outside a fifty-mile radius of Los Alamos are reimbursed for one round-trip from point-of-hire each calendar year. They are also reimbursed for the shipment of up to 100 pounds of personal belongings. Eligibility is limited to applicants with a cumulative GPA of at least 2.5 who have completed a bachelor's degree by date-of-hire and who intend to continue with graduate studies. To remain in the program longer than one year, students must furnish proof of progress toward a graduate degree. Non-U.S. citizens are eligible to apply. - ---------------------------------------------------------------------------- The Community Los Alamos is a small alpine community in the mountains of Northern New Mexico, an area of diverse cultures and great scenic beauty. Year-round outdoor activities include skiing, hiking, mountain biking, and white water rafting. Los Alamos is approximately 40 minutes from Santa Fe and 90 minutes from Taos. Santa Fe and the surrounding area comprise the 2nd largest art market in the United States. Santa Fe is home to a number of cultural events such as the internationally acclaimed Santa Fe Opera. - ---------------------------------------------------------------------------- How to Apply Send e-mail indicating your interest to: cam@t10.lanl.gov Please include: * A paragraph about your current research interests (250 words maximum). * Your curriculum vitae * Names, addresses, and phone numbers for at least three references Please submit ASCII versions of the above, we will not be able to process any other formats at this time. We will screen all applications before we ask for official laboratory applications or letters of reference. We are ready to hire now and will do so as we find suitable candidates. Therefore, to receive full consideration, let us know of your interest as soon as possible. However, we consider applications on an on-going basis. Los Alamos National Laboratory is an Affirmative Action/Equal Opportunity Employer. ------- End of Forwarded Message
Date: 22 Apr 1996 16:23 PDT From: Larry Ruzzo <ruzzo@quinault.cs.washington.edu> To: cse590bi@cs Subject: CSE 590BI Comp. Bio. Seminar Restarts We will be restarting our computational biology seminar THIS THURSDAY 4/25 12:00-1:20 in MEB 238. The first 3 meetings will be: 4/25: 4 short talks on physical mapping: (OK, I confess. We're double-dipping a bit, and practicing some talks that will also be given to another audience, but they'll still be great...) Richard Karp - Physical Mapping: Computational Tools for Exploring the Human Genome Tao Jiang - The Complexity of Restriction Mapping Dan Fasulo - A Computer Program for Restriction Mapping Brendan Mumey-A Powerful Clone Overlap Test 5/2 Phil Green: More on his sequence assembly algorithm, which he barely got started explaining to us last quarter. 5/9 Tao Jiang: approximation algorithms for tree alignment (a variant of multiple alignment) 5/16 \ 5/23 }-- TBA. Probable topics include "Biomolecular Computation", 5/30 / and cluster analysis of data from the prostate study. More details later. Hope to see you Thursday.
Date: 7 May 1996 20:17 PDT From: Larry Ruzzo <ruzzo@quinault.cs.washington.edu> To: cse590bi@cs Subject: cse590bi ROOM CHANGE ME department has asked us to switch rooms, to avoid the room conflict we had last week. So, for this week and next (at least), 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.
Date: Wed, 8 May 1996 10:21:04 -0700 From: jiang (Tao Jiang) To: cse590bi Subject: CSE590bi May 9 lecture 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
Date: 9 May 1996 15:29 PDT From: Larry Ruzzo <ruzzo@quinault.cs.washington.edu> To: cse590bi@cs Subject: Haussler Talk. apologies if you've seen this announcement already > _________________________________ > From tim@mudhoney.mbt.washington.edu Wed May 8 17:00:38 1996 > (1.40.112.4/16.2) id AA062360060; Wed, 8 May 1996 17:01:00 -0700 > Date: Wed, 8 May 1996 17:01:00 -0700 > From: Tim Hunkapiller <tim@mudhoney.mbt.washington.edu> > To: ruzzo@cs.washington.edu > Subject: biocomp_seminars > > Biocomp announcement > for once - an early announcement! > tim hunkapiller > --------------------------------------------------------------------- > > > David Haussler, from the Computer Science Department at University of > California Santa Cruz, will be visiting the Center for Molecular > Biotechnology Tuesday June 4 and will be presenting a lecture: > > Using Hidden Markov Models for Biosequence Analysis > (abstract at end of email) > > Dr. Haussler received Ph.D. in computer science in 1982 from > U. Colorado at Boulder. He is a Fellow of the American Association for > Artificial Intelligence, Associate Editor of Machine Learning, > first chairman of the steering committee for the annual ACM Conference > on Computational Learning Theory. His current research interests include > computational biosequence analysis, machine learning, statistics and > information theory. > > If you would be interested in meeting with Dr. Haussler, please let me know. > > Abstract: > > With the databases of DNA, RNA and protein sequences growing > at an explosive rate, the need for effective computational methods for > biosequence analysis has become acute. In particular, we need > good methods for locating genes in DNA sequences, > along with their splice sites and regulatory binding sites, > and good methods for making an initial classification of new proteins > that detect weak homologies to other previously known proteins > and predict possible functions for new proteins. > Tools available for this analysis range from simple and general search > methods such as BLAST to detailed protein folding models of > the type used in protein threading and {\em ab initio} protein structure > prediction. Hidden Markov Models (HMMs) lie somewhere in the middle > of this spectrum. They are computationally efficient enough > for use with large databases, yet flexible enough to be used in > constructing specific, detailed statistical models of the sequence variation > within a particular protein family, our within a family of related > DNA binding sites. We will describe what HMMs are and how > they are used in biosequence analysis. Then we will briefly > discuss some new work in our lab to make these models more biologically > accurate. >
Date: 15 May 1996 23:27 PDT From: Larry Ruzzo <ruzzo@quinault.cs.washington.edu> To: cse590bi@cs Subject: NO CSE590BI THIS WEEK No class this week. Next week Phil will do a bit more on sequence assembly, then I will describe some approaches to "biomolecular computation", e.g. the work of Adleman, using DNA technology to solve an NP-complete problem.
Date: Wed, 29 May 1996 19:44:34 -0700 From: brendan@willow (Brendan Mumey) To: cse590bi@willow Subject: tomorrow's seminar 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
Date: Sat, 3 Aug 1996 15:37:33 -0700 (PDT) From: Phil Green <phg@u.washington.edu> To: seqcourse -- Arian Smit <asmit@u.washington.edu>, Beatrix Jones <trix@stat.washington.edu>, Brendan Mumey <brendan@cs.washington.edu>, Brent Ewing <bge@u.washington.edu>, Chi-hong Tseng <tseng@stat.washington.edu>, Chris Abajian <chrisa@cirque.mbt.washington.edu>, Colin Wilson <colin@u.washington.edu>, David Adams <blue145@u.washington.edu>, David Baker <baker@BEN.bchem.washington.edu>, David Gordon <gordon@tahoma.mbt.washington.edu>, Deborah Nickerson <debnick@u.washington.edu>, Dick Karp <karp@cs.washington.edu>, Ed Thayer <ed@bozeman.mbt.washington.edu>, Elizabeth Thompson <thompson@stat.washington.edu>, Eugene Kolker <eugene@genome.biotech.washington.edu>, Gane Ka-Shu Wong <gksw@u.washington.edu>, Jeremy Buhler <jbuhler@cs.washington.edu>, Jinko Graham <graham@biostat.washington.edu>, Joe Don Heath <jdheath@u.washington.edu>, Joe Felsenstein <joe@genetics.washington.edu>, Jorja Henikoff <jorja@howard.fhcrc.org>, Katrina Goddard <katrina@biostat.washington.edu>, Larry Ruzzo <ruzzo@cs.washington.edu>, Martin Tompa <tompa@cs.washington.edu>, Max Robinson <max@u.washington.edu>, Maynard Olson <mvo@u.washington.edu>, Michael Parker <mparker@fhcrc.org>, Scott Taylor <stay@droog.mbt.washington.edu>, Sharon Guy <sharon@stat.washington.edu>, Simon Heath <heath@stat.washington.edu>, Steve Henikoff <steveh@howard.fhcrc.org>, cse590bi@cs.washington.edu Cc: "A. Heidbrink-Lomer" <alomer@u.washington.edu> Subject: course on Genome Sequence Analysis 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 & gap penalties. Profiles, "motifs". 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.
Date: Tue, 6 Aug 1996 19:52:39 -0700 (PDT) From: Phil Green <phg@u.washington.edu> Reply-To: Phil Green <phg@u.washington.edu> To: seqcourse -- Arian Smit <asmit@u.washington.edu>, Beatrix Jones <trix@stat.washington.edu>, Brendan Mumey <brendan@cs.washington.edu>, Brent Ewing <bge@u.washington.edu>, Chi-hong Tseng <tseng@stat.washington.edu>, Chris Abajian <chrisa@cirque.mbt.washington.edu>, Colin Wilson <colin@u.washington.edu>, David Adams <blue145@u.washington.edu>, David Baker <baker@BEN.bchem.washington.edu>, David Gordon <gordon@tahoma.mbt.washington.edu>, Deborah Nickerson <debnick@u.washington.edu>, Dick Karp <karp@cs.washington.edu>, Ed Thayer <ed@bozeman.mbt.washington.edu>, Elizabeth Thompson <thompson@stat.washington.edu>, Eugene Kolker <eugene@genome.biotech.washington.edu>, Gane Ka-Shu Wong <gksw@u.washington.edu>, Jeremy Buhler <jbuhler@cs.washington.edu>, Jinko Graham <graham@biostat.washington.edu>, Joe Don Heath <jdheath@u.washington.edu>, Joe Felsenstein <joe@genetics.washington.edu>, Jorja Henikoff <jorja@howard.fhcrc.org>, Katrina Goddard <katrina@biostat.washington.edu>, Larry Ruzzo <ruzzo@cs.washington.edu>, Mark Rieder <mjr@droog.mbt.washington.edu>, Martin Tompa <tompa@cs.washington.edu>, Max Robinson <max@u.washington.edu>, Maynard Olson <mvo@u.washington.edu>, Michael Parker <mparker@fhcrc.org>, Scott Taylor <stay@droog.mbt.washington.edu>, Sharon Guy <sharon@stat.washington.edu>, Simon Heath <heath@stat.washington.edu>, Steve Henikoff <steveh@howard.fhcrc.org>, Trey Ideker <trey@droog.mbt.washington.edu> Cc: cse590bi@cs.washington.edu Subject: 599C, AU 1996 (fwd) 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 "seqcourse" 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: "A. Heidbrink-Lomer" <alomer@u.washington.edu> To: phg@u.washington.edu 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: (206) 616-7297 * * Fax: (206) 685-7301 * ******************************************************************************* ....Life's what happens to you when your making other plans...John Lennon ===============================================================================