Computational Molecular Biology Journal Club
Computational Genetics Discussion Group

Course Listings

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

Biol 5496 Seminar in Computational Molecular Biology
CS 7804 Research Seminar in Computational Molecular Biology

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

Fall 2008 Schedule

To sign up for an open date, email me (stormo@genetics.wustl.edu) with a date and (if possible) a paper you wish to present.


Date	Presenter	Topic/Paper
Sept 8		Organization Meeting: We will decide the topics to be discussed this semester
		TOPIC 1: Flux Balance Analysis
Sept 15	Gary Stormo	An introduction to flux balance analysis: Advances in flux balance analysis, KJ Kauffman, P Prakash and JS Edwards Current Opinion in Biotechnology, Volume 14, Issue 5, October 2003, Pages 491-496
Sept 22	No meeting
Sept 29	Yue Yun	Integrating metabolic, transcriptional regulatory and signal transduction models in Escherichia coli by Covert et al. Bioinformatics (2008) 24:2044-2050
Oct 6	Yue Zhao	Wild Card: Human-Specific Gain of Function in a Developmental Enhancer, Prabhakar et al. Science 321:1346 - 1350
Oct 13	No meeting
		TOPIC 2: Metagenomics
Oct 20	Jeremy Buhler	Bioinformatics for Whole-Genome Shotgun Sequencing of Microbial Communities K. Chen and L. Pachter, PLOS Comp. Bio. 1(2):e24, 2005.
Oct 27	Alejandro Reyes	The Marine Viromes of Four Oceanic Regions, by Angly, F.E et al. PLoS Biol. 4:e368.	Topic 2: mapping short reads to genomic sequence
Nov 3
		TOPIC 3: Evolution of networks
Nov 10	Gurmukh Sahota	Evolution of Evolvability in Gene Regulatory Networks, by Crombach and Hogeweg PLoS Comput Biol. 4:e1000112
Nov 17	No meeting
Nov 24	Steven Zhang	Design of genetic networks with specified functions by evolution in silico. François P, Hakim V (2004) Proc Natl Acad Sci U S A 101: 580–585
Dec 1	Francesco Vallania	Predictive Behavior Within Microbial Genetic Networks, by Ilias, Liu and Tavazoie Science. 320:1313-7.