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 2007 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.
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Date
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Presenter
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Topic/Paper
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Sept. 10
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Organization Meeting: We will decide the topics to be
discussed this semester
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Sept. 17
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No meeting
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TOPIC 1:
Conditional Random Fields
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Sept 24
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Jeremy Buhler
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Conditional Random
Fields: Probabilistic Models for Segmenting and Labeling Sequence Data
Lafferty, McCallum and Pereira
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Oct 1
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Hongtao Sun
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CONTRAlign: Discriminative Training for Protein Sequence Alignment CB Do, SS Gross, S Batzoglou - RECOMB 2006, LNBI 3909, pp.160-174,2006 |
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Oct
8
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Sung
Chun
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Protein-protein interaction site prediction based on conditional random fields,
by Li et al. Bioinformatics 2007.
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Oct
15
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Zhehao
Zhang
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Gene Prediction with Conditional Random Fields
Aron Culotta, David Kulp and Andrew McCallum
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Oct
22
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Yue
Zhao
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CONTRAST: A Discriminative,
Phylogeny-free Approach to Multiple Informant De Novo Gene Prediction
A submitted paper by Samuel S. Gross,
Chuong B. Do, Marina Sirota, and Serafim Batzoglou
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Oct
29
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Gary
Stormo
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Genomic dissection of behavioral maturation in the honey bee.
Proc Natl Acad Sci U
S A. 2006 103(44):16068-75.
and
Genome scan for cis-regulatory DNA motifs associated with
social behavior in honey bees.
Proc Natl Acad Sci U
S A. 2006 103(44):16352-7.
by
Gene Robinson and colleagues (Genetics seminar speaker on Nov 1)
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Topic 2: Protein-Protein Docking
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Nov
5
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Diana
Wong
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Protein-ligand docking: current status and future
challenges.
Proteins. 2006 Oct 1;65(1):15-26. Review. By Sousa SF, Fernandes PA, Ramos MJ.
Flexible protein-protein docking. Curr Opin Struct Biol. 2006 Apr;16(2):194-200. A. Bonvin Docking and scoring protein complexes: CAPRI 3rd Edition. Proteins. 2007 Oct 5. by Lensink MF, Mendez R, Wodak SJ. |
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Nov
12
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Xuefeng Zhou |
A new protein–protein docking scoring function
based on interface residue properties. Bioinformatics 2007
23(5):555-562 J. Bernauer, J.
Aze, J. Janin and A. Poupon
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Nov
19
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Nick
Lyle
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Background material on RosettaDock can be found in
these papers:
Protein–protein docking with simultaneous
optimization of rigid-body displacement and side-chain conformations. J Mol
Biol 2003;331:281–299.
Improved side-chain modeling for protein–protein
docking. Protein Sci 2005;14:1328–1339.
Improved beta-protein structure prediction by multilevel
optimization of nonlocal strand pairings and local backbone conformation.
Proteins 2006;65:922–929.
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Nov
26
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Dec
3
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Dec
10
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Martha Bulyk is the Genetics
seminar speaker on Dec 13:
Inferring condition-specific transcription
factor function from DNA binding and gene expression data
Molecular
Systems Biology 3:100
by McCord RP, Berger MF, Philippakis AA, Bulyk ML.
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Looking for a topic or paper?
List of Computational
Biology related journals
PubMed literature search at NCBI
Related Seminars:
Previous Semesters
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
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 : Monday Sept 3, 2007