Journal Club (Spring 2008)
Wednesdays, 12 noon-1pm
748 Mayo
(except if indicted elsewhere)
Credit available as BInf 5480.
To change dates, swap with another presenter and tell Lynda Ellis.
UM Library's BIJC Information Resources and Services
| Date | Presenter(s) | Title/Articles |
|---|---|---|
| Jan 23 | Lynda Ellis, Peter Kirlew | Organizational Meeting Finding Bioinformatics Articles |
| Jan 30 | Lynda Ellis |
Oh M, Yamada T, Hattori M, Goto S, Kanehisa M. (2007) "Systematic analysis of enzyme-catalyzed reaction patterns and prediction of microbial biodegradation pathways." J Chem Inf Model. 47(4):1702-12. http://pubs.acs.org/cgi-bin/abstract.cgi/jcisd8/2007/47/i04/abs/ci700006f.html http://tc.liblink.umn.edu/sfx_local?sid=Entrez:PubMed&id=pmid:17516640 http://www.genome.jp/kegg/reaction/ |
| Feb 6 | Getiria Onsongo, John Carlis | Draghici S, Khatri P, Tarca AL, Amin K, Done A, Voichita C, Georgescu C, Romero R. (2007) "A systems biology approach for pathway level analysis." Genome Res. 17(10):1537-45. http://www.genome.org/cgi/content/full/17/10/1537 http://tc.liblink.umn.edu/sfx_local?sid=Entrez:PubMed&id=pmid:17785539 http://vortex.cs.wayne.edu |
| Feb 13 | Daniel Feldman | Ruttenberg A, Clark T, Bug W, Samwald M, Bodenreider O, Chen H, Doherty D, Forsberg K, Gao Y, Kashyap V, Kinoshita J, Luciano J, Marshall MS, Ogbuji C, Rees J, Stephens S, Wong GT, Wu E, Zaccagnini D, Hongsermeier T, Neumann E, Herman I, Cheung KH. (2007) "Advancing translational research with the Semantic Web." BMC Bioinformatics. 8 Suppl 3:S2. http://www.biomedcentral.com/1471-2105/8/S3/S2 Bussler C (2008) "Is Semantic Web Technology Taking the Wrong Turn?" IEEE Internet Computing 12(1): 75-79. http://ieeexplore.ieee.org/search/wrapper.jsp?arnumber=4428341 |
| Feb 20 | Zheng Jin Tu | Yant SR, Wu X, Huang Y, Garrison B, Burgess SM, Kay MA. (2005) "High-resolution genome-wide mapping of transposon integration in mammals." Mol Cell Biol. 25(6):2085-94. http://mcb.asm.org/cgi/content/full/25/6/2085?view=long&pmid=15743807 |
| Feb 27 | Vic Bloomfield | Alon U. (2007) "Network motifs: theory and experimental approaches." Nat Rev Genet. 8(6):450-61. http://www.nature.com/nrg/journal/v8/n6/abs/nrg2102.html http://tc.liblink.umn.edu/sfx_local?sid=Entrez:PubMed&id=pmid:17510665 |
| Mar 5 | Huzefa Rangwala |
Rangwala H, Karypis G (2008) "fRMSDPred: Predicting local RMSD between structural fragments using sequence information" Proteins: Structure, Function, and Bioinformatics, Published Online: Feb 25 2008, DOI: 10.1002/prot.21998. http://www3.interscience.wiley.com/cgi-bin/abstract/117922761/ http://bio.dtc.umn.edu/monster/ |
| Mar 12 | Tim Kunau |
Emerging Technology (ETech) 2008 http://en.oreilly.com/et2008/public/content/news-coverage Graphing Social Patterns (GSP) 2008 http://en.oreilly.com/gspwest2008/public/content/news-coverage |
| Mar 19 | No Journal Club | *** Spring Break *** |
| Mar 26 | Sue Van Riper | Caspi R, Foerster H, Fulcher CA, Kaipa P, Krummenacker M, Latendresse M, Paley S, Rhee SY, Shearer AG, Tissier C, Walk TC, Zhang P, Karp PD. (2008) "The MetaCyc Database of metabolic pathways and enzymes and the BioCyc collection of Pathway/Genome Databases." Nucleic Acids Res. 2008 Jan;36(Database issue):D623-31. http://nar.oxfordjournals.org/cgi/content/full/36/suppl_1/D623 |
| Apr 2 | Carlos Sosa | Seiler KP, George GA, Happ MP, Bodycombe NE, Carrinski HA, Norton S, Brudz S, Sullivan JP, Muhlich J, Serrano M, Ferraiolo P, Tolliday NJ, Schreiber SL, Clemons PA. (2008) "ChemBank: a small-molecule screening and cheminformatics resource database." Nucleic Acids Res. 36(Database issue):D351-9. http://nar.oxfordjournals.org/cgi/content/full/gkm843v1 http://chembank.broad.harvard.edu/ Irwin JJ, Shoichet BK. (2005) "ZINC - a free database of commercially available compounds for virtual screening." J Chem Inf Model. 45(1):177-82. http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=15667143 http://zinc.docking.org/ |
| Apr 9 | Jeff Gao |
Luca Pireddu, Duane Szafron, Paul Lu and Russell Greiner (2006) "The Path-A metabolic pathway prediction web server" Nucleic Acids Research 2006 34(Web Server issue):W714-W719. http://nar.oxfordjournals.org/cgi/content/abstract/34/suppl_2/W714 http://path-a.cs.ualberta.ca/ Luca Pireddu, Brett Poulin, Duane Szafron, Paul Lu, and David Wishart (2005) "Pathway Analyst - Automated Metabolic Pathway Prediction" In Proc. of the IEEE 2005 Symposium on Computational Intelligence in Bioinformatics and Computational Biology: page(s) 1-8. http://ieeexplore.ieee.org/xpls/abs_all.jsp?arnumber=1594924 |
| Apr 16 | Esfan Haghverdi |
DeCaprio D, Vinson J, Pearson M, Montgomery P, Doherty M, Galagan J. (2007) "Conrad: Gene prediction using conditional random fields" Genome Research, 17(9):1389-98. http://www.genome.org/cgi/content/full/17/9/1389 http://www.broad.mit.edu/annotation/conrad/ |
| Apr 23 | Peter Kirlew |
Thomas T, Egan S, Burg, D, Ng, C, Ting, L. (2007) "Integration of genomics and proteomics into marine microbial ecology" Marine Ecology Progress Series 332, 291-299. http://www.int-res.com/abstracts/meps/v332/p291-299/ Markowitz VM,Ivanova NA, Szeto E, Palaniappan K, Chu K, Dalevi D, Chen IA, Grechkin Y, Dubchak I, Anderson I, Lykidis A, Mavromatis K, Hugenholtz P, Kyrpides NC. (2008) "IMG/M: a data management and analysis system for metagenomes" Nucleic Acids Research 36(Database issue): D534-8 http://nar.oxfordjournals.org/cgi/content/full/36/suppl_1/D534 |
| Apr 30 | Flora Danhua Fan |
Pujana MA, et al. (2007) "Network modeling links breast cancer susceptibility and centrosome dysfunction." Nat Genet. 2007 Nov;39(11):1338-49. http://www.nature.com/ng/journal/v39/n11/abs/ng.2007.2.html http://tc.liblink.umn.edu/sfx_local?sid=Entrez:PubMed&id=pmid:17922014 |
| May 7 | Peter Kirlew |
Videos, including "Human Genetic Variation" (Science, 2007) http://www.sciencemag.org/sciext/btoy2007/video/bt_video.html |