Computational Molecular Biology Journal Club
Computational Genetics Discussion Group

Effective Fall 2001, the Discussion Group has merged with the Computational Molecular Biology Journal Club.

Course Listings

The Journal Club is a cross-listed 1 hour seminar for credit:

Biol 5496 Seminar in Computational Molecular Biology
CS 6802 Research Seminar in Computational Molecular Biology

Course Masters:
Gary Stormo stormo@genetics.wustl.edu
Jeremy Buhler jbuhler@cs.wustl.edu

Website Contact:
Gary Stormo stormo@genetics.wustl.edu

Regular meetings:

4:45-5:45pm, Monday

Location: Genetics Library (Rm 823) McDonnell Sciences, Medical Campus.

Format of Group

The format will be one or two 20-30 minute presentations followed by open discussion.

Students taking it for a grade will be required to present one paper during the semester, attend the other sessions and participate in the discussions.
Other students, post-docs, faculty and others are welcome to attend and participate.
The emphasis will be on recent papers in Comp Bio, but other relevant topics can be included.
Participants can pick the papers to present or get suggestions from the Course Masters.

Spring 2004 Schedule

To sign up for an open date, email me (stormo@genetics.wustl.edu) with a date and (if possible) a topic title. If you wish to include a reference for a current paper or background review, you can send it later.

Topics:

Alternative Splicing, detection from ESTs and other sources (01/26-02/16)
Flux Balance Analysis, metabolic network modeling (02/23-03/22)
Protein Structure Prediction (CASP results) (04/05-04/29)


Date	Presenter	Topic/Paper
		TOPIC: Altenative Splicing
01/19		Organizational Meeting
01/26	Eric Nawrocki	A summary and comparison of four papers related to genomic DNA/EST alignments: EST_GENOME: CABIOS 13(4):477-8, 1997 Spidey: Genome Research 11:1952-7, 2001. Sim4: Genome Research 8:967-74, 1998. BLAT: Genome Research 12:656-64, 2002.
02/02	Jay Gertz/ KT Varley	Johnson et al, Science 302:2141-4, 2003. Wang et al, Bioinformatics 19S1:i315-322, 2003.
02/09	JW Feng	Heber et al, Bioinformatics. 2002 18 Suppl 1:S181-8.
02/16	Diana Kolbe/ Chaochun Wei	Grasso et al, PSB 2004, 29ff Sugnet et al, PSB 2004, 66ff
		TOPIC: Metabolic Flux Balance Analysis
02/23	David Granas	Kauffman et al. Current Opinion in Biotechnology 134:491-6, 2003
03/01	Hyun Seok Kim/ TaoTao Yu	Covert and Palsson, Journal of Theoretical Biology 221:309-25, 2003 Edwards and Palsson BMC Bioinformatics Vol 1 No 1 2000
03/08	No meeting	Spring Break
03/15	Jianhua Ruan/ Scott Doniger	Mahadevan R, Edwards JS, Doyle FJ 3rd. Dynamic flux balance analysis of diauxic growth in Escherichia coli. Biophys J. 2002 83:1331-40. Forster, Famili, Fu, Palsson, and Neilsen, Genome Research 13:244-53, 2003. Famili, Forster, Nielsen, and Palsson, PNAS 100:13134-9, 2003.
03/22	Yue Yun	Beard et al, Biophys J, July 2002, 83:79-86
03/29	No Meeting	RECOMB meeting in San Diego
		TOPIC: Protein Structure Prediction
04/05	Miao Zhang	Two papers as Introduction to CASP5: Proteins 53: 334-339, 340-351
04/12	Daniel Chen	Assessment of homology-based predictions in CASP5 Comparative modeling in CASP5: Progress is evident, but alignment errors remain a significant hindrance
04/19	Seolkyoung Jung/ Billy Li	CASP5 assessment of fold recognition target predictions Using multiple structure alignments, fast model building, and energetic analysis in fold recognition and homology modeling Novel use of a genetic algorithm for protein structure prediction: Searching template and sequence alignment space
04/26	Sam Gross/ Yanni Sun	Predictions without templates: New folds, secondary structure, and contacts in CASP5 Rosetta predictions in CASP5: Successes, failures, and prospects for complete automation Combining local-structure, fold-recognition, and new fold methods for protein structure prediction
		TOPIC: Wild Card
05/03	no meeting	end of semester

Looking for a topic or paper?

Computational Biology related journals

PubMed literature search at NCBI

Related Seminars:

Genetics Department Seminars (Thursdays @noon, Genetics Dept. Libarary)
Biophysical Evenings (Monthly, Tues @5:30pm, Erlander Auditorium)
Biochemistry and Biophysics Seminar Series (Wednesday @4pm, Cori Auditorium)
Computer Science Colloquia (Cupples II Room 217, Hilltop Campus)
Center for Computational Biology Seminar Series (Fridays 12:30, 2918 South Bldg)

Previous Semesters

Fall 2003 schedule
Spring 2003 schedule
Fall 2002 schedule
Spring 2002 schedule
Fall 2001 schedule
Spring 2001 schedule
Fall 2000 schedule
Spring 2000 Schedule
Fall 1999 schedule
Spring 1999 schedule
Fall 1998 schedule

If you are in the Washington University community and would like to be added to the computational genetics discussion group email list, or have further questions, please send a message to Gary Stormo stormo@genetics.wustl.edu

Last updated : Sat Jan 31 12:09:00 CDT 2004

Computational Molecular Biology Journal Club Computational Genetics Discussion Group