From usenet.ucs.indiana.edu!sol.ctr.columbia.edu!spool.mu.edu!uwm.edu!rutgers!mbcl!sofer Sat Apr 3 08:23:55 EST 1993 Article: 1417 of bionet.general Path: usenet.ucs.indiana.edu!sol.ctr.columbia.edu!spool.mu.edu!uwm.edu!rutgers!mbcl!sofer From: sofer@mbcl.rutgers.edu Newsgroups: bionet.general Subject: Grad Programs in Computers/MolBiol Message-ID: <2348.2bbafefd@mbcl.rutgers.edu> Date: 1 Apr 93 18:41:01 GMT Lines: 298 Last week I asked: >Does anyone know of Universities >that have graduate programs that have >an emphasis (or program of study) in >computational molecular biology? >Bill Sofer These are the responses that I received. I tried to be careful in the attributions, but I offer no guarantees of my accuracy. In addition, I can't be responsible for any errors from the corespondents - I only collected their replies. However, if anyone has any corrections or additions, please let me know and I will post them. *** Boston University Department of Biomedical Engineering. Contact Temple Smith. (1) *** Carnegie Mellon University There are several, but I'm only going to tell you about the new program at CMU in computational biology recently funded by the Keck Foundation. Contact Prof. Robert Murphy for more information (MURPHY@A.CFR.CMU.EDU). (2) YES! Here in Pittsburgh, we have the Keck Center for Advanced Training in Computational Biology, a collaborative program between Carnegie Mellon University and the University of Pittsburgh's departments of Computer Science and Biology. For more information, you can contact Dr. Bruce Buchanan at Pitt/CS (buchanan@cs.pitt.edu) or Dr. Susan Henry at CMU/Biology (sh4b+@andrew.cmu.edu). More specifically, I'm doing research precisely on computational molecular biology. And, I'm looking for graduate students. I've appended further details to this message. Feel free to share this message. I look forward to your reply. (3) ***George Mason University A new program in Computational Science and Informatics. [I am currently teaching the bioinformatics course there.] For more information, contact Harold Morowitz (hmorowitz@gmuvax.gmu.edu) or John Evans (jevans@gmuvax2.gmu.edu). (4) *** Massachusetts Institute of Technology Eric Lander - esp. genetic mapping (5) ***Stanford University D. Brutlag (Biochem), Sam Karlin (Math - actually statistics),, D. Botstein (genetic mapping) (5) Stanford Medical School. One of the nation's best medical informatics programs, recently hired Russ Altman to teach computational biology. For information, contact Ted Shortliffe (shortliffe@sumex- aim.stanford.edu) (4) We have a program at Stanford called Medical Information Sciences which deals with molecular biological tools as well as medical diagnostics. Doug Brutlag, Ron Davis, David Botstein, Michael Walker are some key names who have demonstrated interest in furthering computational genetics. Botstein and Walker can be reached at: botstein@camis.stanford.edu, walker@camis.stanford.edu (6) Stanford Cell Biology (Michael Levitt); Stanford Medical Information Sciences (7) We have a degree granting program in Medical Information Sciences (in which all of my students participate) and we are in the midst of building a bioinformatics track (Biological Information Sciences). We have several active faculty in this area, myself, Russ Altman, Michael Levitt, Sam Karlin among others. (8) ***University of Arizona Eugene Myers, et al. (CS) - combinatorial algorithms (5) ***University of California, Berkeley Eugene Lawler (CS), R. Karp (CS) -both combinatorial algorithms, Terry Speed (Stat), others in math (e.g. DNA topology) (5) ***University of California, Davis Dan Gusfield (CS) - combinatorial algorithms (5) ***University of California, San Diego UCSD is strong in this area. Contact Doug Smith at dsmith@ucsd for info. (9) ***UC San Diego - try the CS dept - it is interdiscplinary program (5) There is a recently advertised program at UC San Diego in Genome Analysis and Informatics that seems relevant. Information is available from UC San Diego Biology Student Affairs, 0125 3300 Miramar Road La Jolla, CA 92037-9746 (10) ***University of California, San Francisco UCSF has a department of pharmaceutical chemistry which has a very strong program in computational chemistry, maybe the best in the country. (11) ***University of Colorado, Boulder Gary Stormo? (Mol. Biology) (5) ***University of Georgia The graduate program in Genetics at the University of Georgia has a program in computational molecular biology. For Further information contact: Graduate Coordinator Genetics Department University of Georgia Athens, GA 30602 (706) 542-8000 This program is folded into several training grants. (12) ***University of Illinois Then there is the Beckman Center effort at University of Illinois which is primarily an interdisciplinary program between biology and computer science. (8) ***University of Missouri We have a computer science department masters program that emphasizes molecular biology computer applications. That department is planning to offer a Ph.D. in the future. We have a grant from the National Library of Medicine "Integrating the Tools for Molecular Biology" that is to develop integrated tools for computer applications across heterogeneous platforms. This is a cooperative arrangement between Computer Science, Biochemistry, and Microbiology faculty on this campus with personnel at the Pittsburgh Supercomputing Center. For additional information either write to me or to Dr. Gordon Springer Computer Science Department University of Missouri Columbia, Missouri 65212 (13) ***University of North Carolina I know that at the Univ. of North Carolina in Chapel Hill, we have a curriculum called Program in Molecular Biology and Biotechnology (PMBB). Faculties from Dept. of Microbiology and PMBB offer a few courses in computational molecular biology. I have also heard some rumors that they may start such a program explicitly. I myself have an interest in this field and have been collaborating with researchers from departments above and the biochemistry in developing computational tools and techniques for various purposes such as biological sequence analysis, protein folding etc. Hope this helps. (14) *** University of Pennsylvania Pavel Pevzner (Math) at University Park (?) [Is this perhaps Penn State? - Bill S.] (5) *** University of Pennsylvania Medical School(?) Chris Overton and David Searles = logic programming / syntactic approaches to genomic sequence analysis (5) ***University of Pittsburgh *University of Pittsburgh (in conjunction with Carnegie Mellon). A new program in computational biology, funded by the Keck Foundation. For information on that program, contact Bruce Buchanan (buchanan@cs.pitt.edu). (4) (See also Carnegie-Mellon University) *** University of Southern California Mike Waterman (Math, Statistics),genomic sequence statistics, algorithms, statistics of mapping (5) ***University of Utah Math Dept. (5) *** University of Washington, Seattle Genetics Dept., Biotech Dept. - computational genetics, ?? (5) The new biotechnology department at the Univ. of Washington has as part of its area of interest computational molecular biology. Since Lee Hood has only just this year arrived, there is no track record yet in terms of what kind of students will actually be part of the department. (15) Depending on what you want to compute, the molecular biotechnology department at the university of washington definitely has a strong computational bent. We are not degree granting yet, but probably will be within 12 months. Current grads are in the immunology (me), bioengineering, or genetics departments. Currently, Lee's vision of a graduate program has a graduate student work both on a cutting edge problem in molecular biology as well as a tool to solve it. Such a tool could obviously be computational. Of course, visions do not always become reality... (16) ***University of Wisconsin I think that the computer science department at U of Wisconsin has such a program. You might send email to shavlik@cs.wisc.edu (Jude Shavlik) to inquire. He is on the faculty there. (17) Deborah Joseph (CS) - algorithms, Jude Shavlik (CS) machine learning (5) ***Washington State University, Pullman A program in computational science including biology that has been going for at least three years. For more information, contact Keith Dunker (dunker@bobcat.csc.wsu.edu). (4) Washington State University has a program that may be applicable -I'd suggest you contact Robert Miller (rmiller@eeecs.wsu.edu) as he is working in the program. (18) ***Washington University CS. Dept - Medical Informatics Program (5) Washington University, St. Louis. They have just instituted a new Institute for Biological Computing, which will begin admitting students next fall. For more information contact David States (states@wucs1.wustl.edu). (4) *** W.M. Keck Center for Computational Biology, Houston, TX A collaborative effort between Rice University, Baylor College of Medicine, and the University of Houston, has been offering graduate studies in computational biology since 1990. For more information, contact George Phillip, Jr. (georgep@rice.edu) (4) *** Yale University My department has a Center for Computational Ecology. (19) *** Others In addition, David Olafson (20) mentioned Virginia Commonwealth University (Biomedical Engineering Program) and the University of Virginia (Dept. Biomedical Engineering) as possibilities. ***Respondents (1) Charles R. Cantor (2) Peter B. Berget (3) Mark.Perlin@J.GP.CS.CMU.EDU (4) hunter@ncbi.nlm.nih.gov (Larry Hunter) (5) Frank Olken olken@ux5.lbl.gov (6) mahtani@CAMIS.Stanford.EDU (Melanie Mahtani) (7) epr@leland.stanford.edu (edwin rock) (8) Doug Brutlag (9) elkan@cs.ucsd.edu (Charles Elkan) (10) Robert Robbins (11) Xiaowu Chen XO3@PSUVM.psu.edu (12) Jonathan Arnoldarnold@bscf.uga.edu (13) Cannon@medsci.mbp.missouri.edu (John Cannon) (14) Raj Kumar Singh (15) wijsman@u.washington.edu (Ellen Wijsman) (16) Jared Roach (17) Kathleen McKusick (18) jfletche@eecs.wsu.edu (Justin Fletcher) (19) Una Smith smith-una@yale.edu (20) rurik@brc.uconn.edu (David M. Olafson)