Readings for Journal Club

Fall 2006 

http://www.bork.embl-heidelberg.de/Docu/literature_mining/

[Text Mining] (Oct. 25)

L. Jensen, J. Saric, P. Bork [2006] Literature mining for the biologist: From information retrieval to biological discovery, Nature Reviews Genetics 7:119-129 (Feb 2006). http://www.nature.com/nrg/journal/v7/n2/abs/nrg1768.html

T. Jenssen, A. Laegreid, J. Komorowski, E. Hovig [2001] A literature network of human genes for high-throughput analysis of gene expression, Nature Genetics 28:21-28 (May 2001). http://www.nature.com/ng/journal/v28/n1/abs/ng0501_21.html

H. Muller, E. Kenny, P. Sternberg [2004] Textpresso: An ontology-based information retrieval and extraction system for biological literature, PLoS Biology 2: e309. http://www.pubmedcentral.gov/articlerender.fcgi?artid=517822

C. Perez-Iratxeta, M. Wjst, P. Bork, M. Andrade [2005] G2D: A tool for mining genes associated to disease, BMC Genetics 6: 45. http://www.biomedcentral.com/1471-2156/6/45

[Expression Analysis] (Nov. 1) 

D. Rhodes, A. Chinnaiyan [2005] Integrative analysis of the cancer transcriptome, Nature Genetics Supplement 37:S31-S37 (Jun 2005). http://www.nature.com/ng/journal/v37/n6s/full/ng1570.html

S. Raychaudhuri, J. Chang, F. Imam, R. Altman [2003] Computational analysis of scientific literature to define and recognize gene expression clusters, Nucleic Acids Research 31(15): 4553-4560. http://nar.oxfordjournals.org/cgi/content/abstract/31/15/4553

[Pathway Analysis] (Nov. 29)

A. Rzhetsky, I. Iossifov, T. Koike, ... W. Wilbur, V. Hatzivassiloglou, C. Friedman [2004] GeneWays: A system for extracting, analyzing, visualizing, and integrating molecular pathway data, J. Biomedical Informatics, 37: 43-53. http://www.cs.nyu.edu/~parida/DIMACSworkshopJune20-2205/DIMACSworkshop/slides/AndreyRzhetsky1.pdf

S. Raychaudhuri, H. Schutze, R. Altman [2002] Using text analysis to identify functionally coherent gene groups, Genome Research 12: 1582-1590. http://www.genome.org/cgi/content/abstract/12/10/1582