From msong@cs.qc.edu Wed Mar 3 19:03:22 2004 From: msong@cs.qc.edu (Mingzhou Song) Date: Wed, 3 Mar 2004 14:03:22 -0500 Subject: [ CS-Bioinf ] slides Message-ID: <000201c40152$3323d970$6cd30495@cs.qc.edu> This is a multi-part message in MIME format. ------=_NextPart_000_0003_01C40128.4A504270 Content-Type: text/plain; charset="US-ASCII" Content-Transfer-Encoding: 7bit Dear students: New slides are put online. Please download. Mingzhou ------=_NextPart_000_0003_01C40128.4A504270 Content-Type: text/html; charset="US-ASCII" Content-Transfer-Encoding: quoted-printable

Dear students:

 

New slides are put online.  Please download.

 

Mingzhou

 

------=_NextPart_000_0003_01C40128.4A504270-- From msong@cs.qc.edu Fri Mar 5 00:03:10 2004 From: msong@cs.qc.edu (M. Song) Date: Thu, 4 Mar 2004 19:03:10 -0500 Subject: [ CS-Bioinf ] Hw#1 Prob 4 Message-ID: This is a multi-part message in MIME format. ------=_NextPart_000_001B_01C4021B.56A6EFD0 Content-Type: text/plain; charset="US-ASCII" Content-Transfer-Encoding: 7bit The T in the RNA should be U. Please make the correction. ------=_NextPart_000_001B_01C4021B.56A6EFD0 Content-Type: text/html; charset="US-ASCII" Content-Transfer-Encoding: quoted-printable

The T in the RNA should be U.  Please make the correction.

------=_NextPart_000_001B_01C4021B.56A6EFD0-- From msong@cs.qc.edu Fri Mar 5 00:20:40 2004 From: msong@cs.qc.edu (M. Song) Date: Thu, 4 Mar 2004 19:20:40 -0500 Subject: [ CS-Bioinf ] HW#1 Prob 5 Message-ID: This is a multi-part message in MIME format. ------=_NextPart_000_002F_01C4021D.C88F7B10 Content-Type: text/plain; charset="US-ASCII" Content-Transfer-Encoding: 7bit In prob 5, assume the frequencies or probabilities of A,T,G,C in DNA are all 0.25. ------=_NextPart_000_002F_01C4021D.C88F7B10 Content-Type: text/html; charset="US-ASCII" Content-Transfer-Encoding: quoted-printable

In prob 5, assume the frequencies or probabilities of A,T,G,C in DNA are all 0.25.

------=_NextPart_000_002F_01C4021D.C88F7B10-- From msong@cs.qc.edu Fri Mar 12 18:28:05 2004 From: msong@cs.qc.edu (Mingzhou Song) Date: Fri, 12 Mar 2004 13:28:05 -0500 Subject: [ CS-Bioinf ] phylogenetic tree slides Message-ID: <000201c4085f$c30bc3e0$6cd30495@cs.qc.edu> This is a multi-part message in MIME format. ------=_NextPart_000_0003_01C40835.DA35BBE0 Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: 7bit Are now available online. Have a good weekend! ------=_NextPart_000_0003_01C40835.DA35BBE0 Content-Type: text/html; charset="us-ascii" Content-Transfer-Encoding: quoted-printable

Are now available = online.

 

Have a good weekend!

 

------=_NextPart_000_0003_01C40835.DA35BBE0-- From msong@cs.qc.edu Sun Mar 21 23:48:58 2004 From: msong@cs.qc.edu (Mingzhou Song) Date: Sun, 21 Mar 2004 18:48:58 -0500 Subject: [ CS-Bioinf ] Previous Project Reports Message-ID: <000a01c40f9f$144e77c0$6cd30495@cs.qc.edu> This is a multi-part message in MIME format. ------=_NextPart_000_000B_01C40F75.2B786FC0 Content-Type: text/plain; charset="US-ASCII" Content-Transfer-Encoding: 7bit You can go to the course website: www.cs.qc.edu/~msong/780 and the project section to find project reports done by other students when I offered Bioinformatics course. Mingzhou Song Assistant Professor Department of Computer Science Queens College City University of New York Homepage: http://www.cs.qc.edu/~msong Email: msong@cs.qc.edu Phone: 718-997-3584 Fax: 718-997-3513 ------=_NextPart_000_000B_01C40F75.2B786FC0 Content-Type: text/html; charset="US-ASCII" Content-Transfer-Encoding: quoted-printable

You can go to the course website: www.cs.qc.edu/~msong/780 = and the project section to find project reports done by other students when I = offered Bioinformatics course.

 

Mingzhou Song

Assistant = Professor

Department of = Computer Science

Queens College

City University of New = York

Homepage: http://www.cs.qc.edu/~msong

Email: = msong@cs.qc.edu<= font face=3D"Arial Narrow">

Phone: = 718-997-3584

Fax: = 718-997-3513

 

------=_NextPart_000_000B_01C40F75.2B786FC0-- From msong@cs.qc.edu Sun Mar 21 23:49:29 2004 From: msong@cs.qc.edu (Mingzhou Song) Date: Sun, 21 Mar 2004 18:49:29 -0500 Subject: [ CS-Bioinf ] mutliple sequence alignment Message-ID: <000f01c40f9f$268120f0$6cd30495@cs.qc.edu> This is a multi-part message in MIME format. ------=_NextPart_000_0010_01C40F75.3DAB18F0 Content-Type: text/plain; charset="US-ASCII" Content-Transfer-Encoding: 7bit Slides are now on the web site, please download. Mingzhou ------=_NextPart_000_0010_01C40F75.3DAB18F0 Content-Type: text/html; charset="US-ASCII" Content-Transfer-Encoding: quoted-printable

Slides are now on the web site, please = download.

 

Mingzhou

 

------=_NextPart_000_0010_01C40F75.3DAB18F0-- From msong@u.washington.edu Fri Mar 26 14:04:20 2004 From: msong@u.washington.edu (M. Song) Date: Fri, 26 Mar 2004 09:04:20 -0500 Subject: [ CS-Bioinf ] Computational Biology Summer Intern at Institute for Systems Biology at Seattle Message-ID: FYI > Computational Biology Summer Intern - 04-005 > > The Institute for Systems Biology is seeking a summer intern in the > area of > computational biology. > > Responsibilities: > > Contribute to an effort to understanding one or more of the following: > > . The transcriptome of macrophages, and the signaling > networks in > stimulated macrophages. > > . Markers involved in the development of prostate cancer. > > . Juvenile diabetes. > > Annotate genes and gene networks with information from multiple > databases. > Some of this annotation will be manual, and some will be automated. > Particularly well-qualified candidates will contribute to the > automation of > this effort. > > A highly-motivated candidate will draw inferences from datasets, and > will > have the opportunity to write or contribute to a peer-reviewed > publication. > This analysis will require the use of current computational biology > tools > and programming skills. > > Requirements: > > . Some undergraduate study with coursework in genetics or > equivalent. > > . Experience in computer programming. Candidates without > experience > in PERL are urged to learn PERL basics prior to starting. > > . Good written and oral communications skills. > > . Considering a career in biomedical research. > > Compensation: > > $10/hr; hours and dates of employment flexible but are anticipated to > span > summer 2004. > > > > Downloadable application forms are available at http://www.systemsbiology.org/Default.aspx?pagename=careeropportunities _______________________________________________ Compbio-group mailing list Compbio-group@cs.washington.edu http://mailman.cs.washington.edu/mailman/listinfo/compbio-group From msong@cs.qc.edu Fri Mar 26 15:48:43 2004 From: msong@cs.qc.edu (M. Song) Date: Fri, 26 Mar 2004 10:48:43 -0500 Subject: [ CS-Bioinf ] FW: [Publicity-list] DIMACS Workshop on the Interface between Biology and Game Theory Message-ID: -----Original Message----- From: publicity-list-admin@dimax.rutgers.edu [mailto:publicity-list-admin@dimax.rutgers.edu] On Behalf Of Linda Casals Sent: Thursday, March 25, 2004 9:01 To: publicity-list@dimacs.rutgers.edu; dmanet@zpr.uni-koeln.de; theory-a@listserv.nodak.edu; sy-compmolecbio-global@dimacs.rutgers.edu; sy-compmolecbio-local@dimacs.rutgers.edu; sy-compmolecbio-rutgers@dimacs.rutgers.edu Subject: [Publicity-list] DIMACS Workshop on the Interface between Biology and Game Theory ********REGISTRATION DEADLINE March 29, 2004****************** ************************************************************** DIMACS Workshop on the Interface between Biology and Game Theory April 5, 2004 DIMACS Center, CoRE Building, Rutgers University Organizers: Adam Arkin, Lawrence Berkeley Labs and UC Berkeley Vijay Vazirani, Georgia Tech, vazirani@cc.gatech.edu Denise Wolf, Lawrence Berkeley Labs, dmwolf@lbl.gov Presented under the auspices of the Special Focus on Computational Molecular Biology. ********************************************************************* Starting with the pioneering work of John Maynard Smith, game theory has been increasingly used to explain, understand, and predict biological phenomena. In a sense, game theory is even more readily applicable to biology than to economics, for which it was initially intended, because the concept of human rationality, a rather uncomfortable assumption, can be replaced by more robust notions such as evolutionary stability. In recent years, game theory has been used to explain RNA phage dynamics, viral latency, chromosome segragation subversion in sexual species, E. coli mutant proliferation under environmental stress, and aspects of competitive bacterial ecology. At this workshop, the first of its kind, we hope to not only see some of the best work being done on this exciting interface, but also think of future directions for exploring it. ********************************************************************** Program: 8:00 - 8:50 Registration - First Floor Lobby of the CoRE Building Breakfast - 4th Floor, Lounge, CoRE Building 8:50 - 9:00 Welcome and Opening Remarks Mel Janowitz, DIMACS Associate Director 9:00 - 9:40 Rock-Paper-Scissors for the Adult Player Keynote Speaker: Karl Sigmund, University of Vienna 9:45 - 10:25 Behavioral Game Theory, Evolutionary Game Theory, and the Explanation of Social Cooperation Herbert Gintis, Columbia University 10:25 - 10:40 Discussion 10:40 - 11:00 Break 11:00 - 11:30 A game theoretic analysis of random phase variation and other microbial diversificaiton strategies Denise Wolf, Lawrence Berkeley National Laboratories 11:30 - 12:00 Cooperation in social dilemmas: Effects of population structures Christoph Hauert, University of British Columbia 12:00 - 1:00 Lunch 1:00 - 1:30 Clinical Trials and Game Theory Sorin Istrail, Applied Biosystems 1:30 - 2:00 Sperm Competition Games: the "risk" model Mike Ball, University of Liverpool 2:00 - 2:30 Entering Stationary Phase: Senescence, Death and Selfish Survivors Marin Vulic, Getique Moleculaire Evolutive et Medicale 2:30 - 3:00 Bet-hedging in herpes viruses Michael Stumpf, Imperial College 3:00 - 3:30 Break 3:30 - 4:00 Evolutionary Game Dynamics in Finite Populations Christine Taylor, MIT 4:00 - 4:30 Equilibrium selection in the evolution of mutualism: The Red King effect Carl Bergstrom, Washington State University 4:30 - 5:00 Evolutionary game dynamics and the evolution of trait variation: will an ESS evolve? Steven Orzack, Fresh Pond Research Institute ********************************************************************** Registration Fees: (Pre-registration deadline: March 29, 2004) Please see website for additional registration information. ********************************************************* Information on participation, registration, accommodations, and travel can be found at: http://dimacs.rutgers.edu/Workshops/Biogame/ **PLEASE BE SURE TO PRE-REGISTER EARLY** ********************************************************* _______________________________________________ Publicity-list mailing list Publicity-list@dimax.rutgers.edu http://dimax.rutgers.edu/mailman/listinfo/publicity-list From msong@cs.qc.edu Fri Mar 26 20:26:12 2004 From: msong@cs.qc.edu (Mingzhou Song) Date: Fri, 26 Mar 2004 15:26:12 -0500 (EST) Subject: [ CS-Bioinf ] project ideas and proposal Message-ID: Please check out our course website for a list of three project ideas. You can come with your own not limited by the ideas given. You need to write a proposal and email it to me in one week by April 2. The proposal will account for a portion of the project grade. The instruction for the proposal can be found on the same page with the project ideas. Mingzhou From msong@cs.qc.edu Fri Mar 26 20:29:23 2004 From: msong@cs.qc.edu (Mingzhou Song) Date: Fri, 26 Mar 2004 15:29:23 -0500 (EST) Subject: [ CS-Bioinf ] proposal Message-ID: You are welcome to come up with your own project ideas and then formulate your proposal. In your proposal, you will: 1. state the biology motivation of your project 2. define the computational approach that you use 3. give the data source 4. explain what your solution 5. show a week by week plan for the project From msong@cs.qc.edu Sat Mar 27 00:02:23 2004 From: msong@cs.qc.edu (M. Song) Date: Fri, 26 Mar 2004 19:02:23 -0500 Subject: [ CS-Bioinf ] FW: [Colloq] 3/30/04 CS Colloquium: Ilya Nemenman - "Estimatinginformation content of biological data" Message-ID: New York University Department of Computer Science COMPUTER SCIENCE COLLOQUIUM Tuesday, March 30, 2004 11:30 a.m. Room 1302 Warren Weaver Hall 251 Mercer Street New York, NY 10012-1185 Speaker: Ilya Nemenman, UCSB Title: Estimating information content of biological data Abstract: In many biological applications, notably in computational neuroscience and bioinformatics, information theoretic methods are now routinely being used. The major hurdle in applying such methods is the reliable estimation of entropy and information from small samples. I will discuss this difficult problem, approaches that the others have taken, and then present a Bayesian estimator of entropies introduced by us recently. I will analyze properties of the estimator and explain when it is expected to work well and how to diagnose errors. Throughout the talk I will focus on applications to biological examples (mainly to a fly visual system neuroscience experiment) to illustrate the potentials of the method. Refreshments will be served at 11:15 a.m. in room 1302 Warren Weaver Hall Host: Richard Cole cole@cs.nyu.edu, (212) 998-3119 Directions: http://cs.nyu.edu/csweb/Location/directions.html Colloquium Information: http://cs.nyu.edu/csweb/Calendar/colloquium/index.html _______________________________________________ Colloq mailing list Colloq@cs.nyu.edu http://www.cs.nyu.edu/mailman/listinfo/colloq