Journal Club (Fall 2004)
Wednesdays, 12 noon-1pm
748 Mayo Building
Credit available as BInf 5480.
To change dates, swap with another presenter and tell Lynda Ellis.
| Sept 8 |
Lynda Ellis |
Organizational Meeting |
| Sept 15 |
Lynda Ellis, Loren Graget, Eric Klee, Bill Long, Carlos Sosa |
Report on ISMB04, July 31-Aug 4, 2004, Glasgow, Scotland http://www.iscb.org/ismbeccb2004/ |
| Sept 22 | Michael Heuer |
Enright AJ, Kunin V, Ouzounis CA. (2003) Protein families and TRIBES in genome sequence space. Nucleic Acids Res. 2003 Aug 1;31(15):4632-8. http://nar.oupjournals.org/cgi/content/full/31/15/4632 also see, Ouzounis CA, Coulson RM, Enright AJ, Kunin V, Pereira-Leal JB. (2003) Classification schemes for protein structure and function. Nat Rev Genet. 2003 Jul;4(7):508-19. PMID: 12838343 http://tc.liblink.umn.edu/sfx_local?sid=Entrez:PubMed&id=pmid:12838343 |
| Sept 29 | Tim Kunau |
Connectedness: mapping and linking knowledge domains Semantic Web: http://www.technologyreview.com/purchase/pdf_dl.asp?79juh=541165&hy6f0=16655 Mapping Knowledge Domains: http://www.pnas.org/cgi/reprint/0307852100v1.pdf Communities of Related Genes: http://www.hpl.hp.com/research/idl/papers/communities/communities.pdf Intellectual Turning Points: http://www.pnas.org/cgi/reprint/0307513100v1.pdf |
| Oct 6 | Zheng Jin Tu |
Seike M, Kondo T, Fujii K, Yamada T, Gemma A, Kudoh S, Hirohashi S
(2004) Proteomic signature of human cancer cells. PROTEOMICS 4: 2776-2788. http://www3.interscience.wiley.com/cgi-bin/abstract/109086922/ABSTRACT |
| Oct 13 |
Aidan Harrison Bruker Daltonics http://www.bdal.com/ |
Clinical Proteomics: Discovery - Validation - Identification |
| Oct 20 | Kyong Jin Shim |
Zheng J, Close TJ, Jiang T, Lonardi S (2004) Efficient selection of unique and popular oligos for large EST databases Bioinformatics 20: 2101-2112 http://bioinformatics.oupjournals.org/cgi/content/abstract/20/13/2101 |
| Oct 27 | Charlie Paule |
Schug J, Diskin S, Mazzarelli J, Brunk BP, and Stoeckert CJ
(2004) Predicting Gene Ontology Functions from ProDom and CDD Protein Domains Genome Research 12: 648-655 http://www.genome.org/cgi/reprint/12/4/648 Lu X, Zhai C, Gopalakrishnan V and Buchanan BG (2004) Automatic annotation of protein motif function with Gene Ontology terms BMC Bioinformatics, 5:122 http://www.biomedcentral.com/1471-2105/5/122 |
| Nov 3 |
Libby Shoop Macalester College |
Shoop E, Casaes P, Onsongo G, Lesnett L, Petursdottir EO, Donkor EK,
Tkach D, Cosimini M. (2004) Data exploration tools for the gene ontology database. Bioinformatics. 2004 Jul 22 http://bioinformatics.oupjournals.org/cgi/reprint/bth425v1.pdf |
| Nov 10 | Rajani Raja |
Johann DJ Jr, McGuigan MD, Patel AR, Tomov S, Ross S, Conrads TP, Veenstra TD, Fishman DA, Whiteley GR, Petricoin EF 3rd, Liotta LA. (2004) Clinical proteomics and biomarker discovery. Ann NY Acad Sci. 1022: 295-305 http://www.annalsnyas.org/cgi/content/abstract/1022/1/295 |
| Nov 17 | Dave Roe |
Lesley H. Greene and Victoria A. Higman (2003) Uncovering Network Systems Within Protein Structures Journal of Molecular Biology 334: 781-791 http://tc.liblink.umn.edu/sfx_local?sid=Entrez:PubMed&id=pmid:14636602 |
| Nov 24 | ***NO Journal Club*** | THANKSGIVING |
| Dec 1 | Carlos Sosa |
Kerstin M.L. Menne, Henning Hermjakob and Rolf Apweiler (2000) A comparison of signal sequence prediction methods using a test set of signal peptides Bioinformatics 16: 741-742 http://bioinformatics.oupjournals.org/cgi/content/abstract/16/8/741 Hilles K, Grote A, Scheer M, Munch R, Jahn D. (2004) PrediSi: prediction of signal peptides and their cleavage positions. Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W375-9. http://nar.oupjournals.org/cgi/content/full/32/suppl_2/W375 |
| Dec 8 | Hehuang Xie and Min Wang |
Liu M, Grigoriev A. (2004) Protein domains correlate strongly with exons in multiple eukaryotic genomes--evidence of exon shuffling? Trends Genet. 2004 Sep;20(9):399-403. http://tc.liblink.umn.edu/sfx_local?sid=Entrez:PubMed&id=pmid:15313546 Genetica, special issue on gene evolution, volume 118, issue 2-3, July 2003. http://tc.liblink.umn.edu/sfx_local?sid=sfx:e_collection&issn=0016-6707&pid=serviceType=getFullTxt and enter year "2003", volume "118", and issue "2". |
| Dec 15 | Kevin Messner |
Molecular Biology Videos http://blog.lib.umn.edu/archives/messn006/molbiolibrary/012643.html and PubMed Bookmarklet Enhanced with UM FindIt http://blog.lib.umn.edu/archives/messn006/molbiolibrary/012620.html |