Computational Biology Journal Club
Biology 270 - Fall 2009

Location: Gilman 310 Time: Monday, 12:00-1:15 Professor: Robert Gross

This journal club involves more discussion and less "presentation." The concept is to have us sitting around a table discussing the paper rather than staring at a screen during a presentation. Although we sometimes choose a specific topic to focus on for the term, for 2009 Fall, we will allow any topic that uses computational approaches to address biological problems. We intend to focus on both the theory and practice, while examining applications to biological and biomedical research. We are looking for participants with various backgrounds and interests to add unique perspectives, particularly to the practice and practicality of these methods. By having a cross section of both potential method developers and method users, we will gain a more full understanding of the what new methods bring to the table as well as what potential stumbling blocks stand in the way of their successful application.

The individual choosing the paper should prepare a short (no more than 10 minute) summary of the paper. This should include a brief discussion of the significance of the paper. It should also include a very quick summary of the methods used. The person presenting should provide more detailed information about the methods employed by the authors. The presenter should be prepared to lead the discussion. If a slide or two is needed to illustrate some of the methods (especially those from previous papers or supplementary material), this is acceptable. In general, we will try to avoid the use of slides during the discussion. Please be sure to bring a printed copy of the paper with you to the journal club.

Members of the journal club are expected to come with questions about the paper. These questions can focus on methods and discussion and interpretation of the results. We will have about 40 minutes for discussion.

previous terms: 2002F, 2002S, 2003W, 2003S, 2003F, 2004W, 2004S, 2004F, 2005W, 2005S, 2005F, 2006W, 2006S, 2006F, 2007W, 2007S, 2007F, 2008W, 2008S, 2008F, 2009W, 2009S

mutual information discussion by Chris Langmead [PDF]

mathematical symbols - definitions       algorithms - Wikipedia entries
Sep 28 no presentation organizational meeting, if needed
Oct 5 Anna Tyler "High-Betweenness Proteins in the Yeast Protein Interaction Network" by Maliackal Poulo Joy, Amy Brock, Donald E. Ingber, and Sui Huang; Journal of Biomedicine and Biotechnology (2005); 96–103 [PDF]
Oct 12 Tom Hampton "A Novel Approach to Analyze Gene Expression Data Demonstrates that the deltaF508 Mutation in CFTR Down Regulates the Antigen Presentation Pathway" by Thomas H. Hampton and Bruce A. Stanton [PDF]

note: this is a special preview version of a submitted paper. Tom would like feedback and discussion.
Oct 19 Ryan Urbanowicz "An algorithm for learning maximum entropy probability models of disease risk that efficiently searches and sparingly encodes multilocus genomic interactions" by David J. Miller, Yanxin Zhang, Guoqiang Yu, Yongmei Liu, Li Chen, Carl D. Langefeld, David Herrington and Yue Wang; Bioinformatics (2009) 25(19):2478–2485 [PDF]
Oct 26 Juliette Madan "Quantifying environmental adaptation of metabolic pathways in metagenomics" by Tara A. Gianoulisa, Jeroen Raesb, Prianka V. Patelc, Robert Bjornsond, Jan O. Korbelc, Ivica Letunicb, Takuji Yamadab, Alberto Paccanaroe, Lars J. Jensenb, Michael Snyderc, Peer Borkb, and Mark B. Gerstein; PNAS (2009) 106(5):1374–1379 [PDF]
Nov 2 Krissy Pattin "Using biological networks to search for interacting loci in genome-wide association studies" by Mathieu Emily, Thomas Mailund, Jotun Hein, Leif Schauser and Mikkel Heide Schierup; European Journal of Human Genetics (2009), 1–10 [advanced online publication, PDF]
Nov 9 Bob Gross "GR-Aligner: an algorithm for aligning pairwise genomic sequences containing rearrangement events" by Te-Chin Chu, Tsunglin Liu, D. T. Lee, Greg C. Lee and Arthur Chun-Chieh Shih; Bioinformatics (2009) 25(17):2188–2193 [PDF]
Nov 16 Viktor Martyanov "Relationship between gene co-expression and sharing of transcription factor binding sites in Drosophila melanogaster" by Antonio Marco, Charlotte Konikoff, Timothy L. Karr and Sudhir Kumar; Bioinformatics (2009) 25(19): 2473–2477 [PDF]
Nov 23 Jason Moore "Integrating Statistics and Visualization for Exploratory Power: From Long-Term Case Studies to Design Guidelines" by Adam Perer and Ben Shneiderman; IEEE Computer Graphics and Applications May/June (2009) p39 [PDF]

ALSO: read this Wikipedia page as background. Our discussion will focus on how you show that a visual analytics approach is truly useful for the discovery of new knowledge in scientific data.
Nov 30 Qinxin Pan "A Statistical Model of Protein Sequence Similarity and Function Similarity Reveals Overly-Specific Function Predictions" by Brenton Louie, Roger Higdon, Eugene Kolker; PLoS One (2009) 4(10):e75 [PDF]