Journal Club (Spring 2007)
Wednesdays, 12 noon-1pm
748 Mayo Building
(except if indicted elsewhere)
Credit available as BInf 5480.
To change dates, swap with another presenter and tell Lynda Ellis.
| Date | Presenter(s) | Title/Articles |
|---|---|---|
| Jan 17 | Lynda Ellis | Organizational Meeting Finding Bioinformatics Articles |
| Jan 24 | Tim Kunau | Hoffmann, R., Valencia, A. (2005) “Implementing the iHOP concept for navigation of biomedical literature.” Bioinformatics. 2005 Sep 1;21 Suppl 2:ii252-ii258. http://bioinformatics.oxfordjournals.org/cgi/reprint/21/suppl_2/ii252 http://www.ihop-net.org/UniPub/iHOP/ Good BM, Kawas EA, Kuo BY, Wilkinson MD. (2006) “iHOPerator: user-scripting a personalized bioinformatics Web, starting with the iHOP website.” BMC Bioinformatics 2006, 7:534 http://www.biomedcentral.com/1471-2105/7/534 http://bioinfo.icapture.ubc.ca/iHOPerator/ |
| Jan 31 | Dave Roe | Thompson JD, Higgins DG, Gibson TJ. (1994) "CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice." Nucleic Acids Res. 1994 Nov 11;22(22):4673-80. http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=7984417 Chenna R, Sugawara H, Koike T, Lopez R, Gibson TJ, Higgins DG, Thompson JD. (2003) "Multiple sequence alignment with the Clustal series of programs." Nucleic Acids Res. 2003 Jul 1;31(13):3497-500. http://nar.oxfordjournals.org/cgi/content/full/31/13/3497 http://www.ebi.ac.uk/clustalw/ |
| Feb 7 | Meijuan Li | Markus Friberg, Peter von Rohr and Gaston Gonnet (2005) "Scoring functions for transcription factor binding site prediction" BMC Bioinformatics 2005, 6:84 http://www.biomedcentral.com/1471-2105/6/84 |
| Feb 14 | Chunhui Li | Jahn K and Kramer S (2005) "Optimizing gSpan for Molecular Datasets" Proceedings of the Third International Workshop on Mining Graphs, Trees and Sequences (MGTS'05), October 7, 2005, Porto, Portugal. http://wwwkramer.in.tum.de/kramer/jahn_mgts05.pdf Mu F, Unkefer PJ, Unkefer CJ, Hlavacek WS. (2006) "Prediction of oxidoreductase-catalyzed reactions based on atomic properties of metabolites." Bioinformatics 2006 22(24):3082-3088 http://bioinformatics.oxfordjournals.org/cgi/content/full/22/24/3082 http://tc.liblink.umn.edu/sfx_local?sid=Entrez:PubMed&id=pmid:17060354 |
| Feb 21 | Yanji Xu | Goldberg JM, Manning G, Liu A, Fey P, Pilcher KE, Xu Y, Smith JL. (2006) "The dictyostelium kinome--analysis of the protein kinases from a simple model organism." PLoS Genet. 2006 Mar;2(3):e38 http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1420674 |
| Feb 28 | Charlie Paule | Heintzman ND,
Stuart RK, Hon G, Fu Y, Ching CW, Hawkins RD, Barrera LO, Van Calcar S, Qu C, Ching KA, Wang W, Weng Z, Green RD, Crawford GE, Ren B. "Distinct and predictive chromatin signatures of transcriptional promoters and enhancers in the human genome." Nat Genet. 2007 Feb 4 http://www.nature.com/ng/journal/v39/n3/full/ng1966.html http://tc.liblink.umn.edu/sfx_local?sid=Entrez:PubMed&id=pmid:17277777 |
| Mar 7 | Zheng Jin Tu | Duarte ND, Becker SA, Jamshidi N, Thiele I, Mo M L, Vo TD, Srivas R, Palsson BO. (2007) "Global reconstruction of the human metabolic network based on genomic and bibliomic data" Proc. Nat.l Acad. Sci. 104(6):1777-82 (2007) http://www.pnas.org/cgi/content/full/104/6/1777 http://tc.liblink.umn.edu/sfx_local?sid=Entrez:PubMed&id=pmid:17267599 |
| Mar 14 | No Journal Club | ***Spring Break*** |
| Mar 21 | Youxing Qu | Youxing Qu, Jun-tao Guo, Victor Olman, and Ying Xu (2004) "Protein structure prediction using sparse dipolar coupling data" Nucleic Acids Research, 2004, 32(2): 551-561 http://nar.oxfordjournals.org/cgi/content/full/32/2/551 |
| Mar 28 | Carol Gross | Zeldovich KB, Berezovsky IN, Shakhnovich EI (2007) "Protein and DNA Sequence Determinants of Thermophilic Adaptation." PLOS Computational Biology. Vol 3(1):e5 http://compbiol.plosjournals.org/perlserv/?request=get-document&doi=10.1371%2Fjournal.pcbi.0030005 |
| Apr 4 | Bing-Bing Wang | Zhang Z, Hesselberth JR, Fields S. (2007) "Genome-wide identification of spliced introns using a tiling microarray." Genome Research. Published online Mar 9, 2007 http://www.genome.org/cgi/content/abstract/gr.6049107v1 |
| Apr 11 | Wayne Xu | Tobias Sjöblom, et al. (2006) "The consensus coding sequences of human breast and colorectal cancers" Science 314: 268-274. http://www.sciencemag.org/cgi/content/full/314/5797/268 W Chng, LA Loeb, JH Bielas, BS Straus (2007) "Limits to the Human Cancer Genome Project?" Science 315: 762-766. http://www.sciencemag.org/cgi/content/full/315/5813/762b |
| Apr 18 | Carlos Sosa | O'Brien KP, Remm M, Sonnhammer ELL (2005) "Inparanoid: a comprehensive database of eukaryotic orthologs" Nucleic Acids Research, 33: D476-D480. http://nar.oxfordjournals.org/cgi/content/full/33/suppl_1/D476 Remm M, Storm CEV, Sonnhammer ELL (2001) "Automatic clustering of orthologs and in-paralogs from pairwise species comparisons" J. Mol. Biol. 314: 1041-1052. http://tc.liblink.umn.edu/sfx_local?sid=Entrez:PubMed&id=pmid:11743721 http://inparanoid.sbc.su.se/ |
| Apr 25 | Wade Schulz | A. G. Pedersen and H. Nielsen (1997) "Neural network prediction of translation initiation sites in eukaryotes: perspectives for EST and genome analysis." Proc Int Conf Intell Syst Mol Biol. 1997;5:226-33. http://www.cbs.dtu.dk/services/NetStart/abstract.php http://www.cbs.dtu.dk/services/NetStart/ |
| May 4 | Jim Beattie | Variations on Protein Synthesis UCSD, "Protein Synthesis: an epic on the cellular level" (1971) http://www.youtube.com/watch?v=u9dhO0iCLww Harvard, "The inner life of a cell" (2006) http://multimedia.mcb.harvard.edu/media.html NHGRI, "Our molecular selves" (April, 2007) http://www.genome.gov/25019879 |