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: Center for Genome Sciences Classroom;

4444 Forest Park Blvd, Room 5206, Med School 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 2009 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
Aug 31		Organization Meeting: We will decide the topics to be discussed this semester
Sep 7	No meeting	Labor Day
		Topic 1: Aligning Networks
Sep 14	No meeting
Sep 21	No meeting
Sep 28	No meeting
Oct 5	Yue Zhao	Alignment and prediction of cis-regulatory modules based on a probabilistic model of evolution. He X, Ling X, Sinha S. PLos Comput Biol. 2009 5:e1000299. (Saurabh Sinha will be the Genetics seminar speaker on Oct 8)
Oct 12	Roman Sloutsky	Modeling cellular machinery through biological network comparison Roded Sharan& Trey Ideker Nature Biotechnology 24, 427 - 433 (2006)
Oct 19	No meeting
Oct 26	Ryan Christensen	A systematic characterization of factors that regulate Drosophila segmentation via a bacterial one-hybrid system. Noyes MB, Meng X, Wakabayashi A, Sinha S, Brodsky MH, Wolfe SA. Nucleic Acids Res. 36:2547-60. (2008) [Scot Wolfe will be Genetics seminar speaker on Oct 29]	Topic 2: mapping short reads to genomic sequence
		Topic 2: Short read alignment to reference genomes
Nov 2	No meeting
Nov 9	Jeremy Buhler	How to map billions of short reads onto genomes Cole Trapnell & Steven L Salzberg, Nature Biotechnology 27, 455 - 457 (2009) Mapping short DNA sequencing reads and calling variants using mapping quality scores Heng Li, Jue Ruan, and Richard Durbin, Genome Res. 2008 18: 1851-1858. Fast and accurate short read alignment with Burrows-Wheeler transform Heng Li and Richard DurbinBioinformatics. 2009 25: 1754-1760.
Nov 16	GiNell Elliott	Fast Mapping of Short Sequences with Mismatches, Insertions and Deletions Using Index Structures Hoffman et al., PLoS Comput Biol. 2009 September; 5(9): e1000502.
Nov 23	Claire Schulkey	SNP detection for massively parallel whole-genome resequencing. Li, et al. Genome Res. June 2009 19: 1124-1132
Nov 30	No meeting

Journals with many Comp Bio articles:

PLoS Comp Bio

Bioinformatics

J. Comp Bio

BMC Bioinformatics

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Related Seminars:

• Genetics Department Seminars  (Thursdays @noon, Genetics Dept. Library)
• Biophysical Evenings (Monthly, Tues @5:30pm, Erlanger Auditorium)
• Biochemistry and Biophysics Seminar Series
• Computer Science Colloquia
• Center for Computational Biology Seminar Series

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Previous Semesters

Spring 2009 schedule

Fall 2008 schedule

Spring 2008 schedule

Fall 2007 schedule

Spring 2007 schedule

Fall 2006 schedule
Spring 2006 schedule
Fall 2005 schedule
Spring 2005 schedule
Fall 2004 schedule
Spring 2004 schedule
Fall 2003 schedule
Spring 2003 schedule
Fall 2002 schedule

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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 : Thursday Feb. 7, 2008