Journal Club (Fall 2005)
Thursdays, 12 noon-1pm
239 Gortner Lab
Credit available as BInf 5480.
To change dates, swap with another presenter and tell Lynda Ellis.
Two or more people are presenting at most sessions!
First one starts at 12 sharp; second at 12:30pm.
If you are scheduled first, and will have problems arriving at 12 noon, swap with the second speaker and let Lynda know.
| Sept 8 |
Lynda Ellis, Larry Wackett, Arkady Kodursky, Kevin Messner |
Organizational Meeting Finding Bioinformatics Articles |
| Sept 15 | Lynda Ellis, Flora Fan, Daniel Feldman, Michael Heuer, Bill Long, Nyalleng Moorosi, Germana Paterlini, Dave Roe, Libby Shoop, Carlos Sosa |
ISMB05 Conference Report http://www.iscb.org/ismb2005/ |
| Sept 22 |
Michael Heuer |
Yuan GC, Liu YJ, Dion MF, Slack MD, Wu LF, Altschuler SJ, Rando OJ.
(2005) Genome-scale identification of nucleosome positions in S. cerevisiae. Science. 2005 Jul 22;309(5734):626-30. http://www.sciencemag.org/cgi/content/full/309/5734/626 http://tc.liblink.umn.edu/sfx_local?sid=Entrez:PubMed&id=pmid:15961632 |
| Sept 29 |
Dave Roe Martin Maiers |
Pegg SC, Brown S, Ojha S, Huang CC, Ferrin TE, Babbitt PC
(2005) "Representing structure-function relationships in mechanistically diverse enzyme superfamilies" Pac Symp Biocomput. 2005: 358-69. http://helix-web.stanford.edu/psb05/abstracts/p358.html http://sfld.rbvi.ucsf.edu/ Martin MP, Gao X, Lee JH, Nelson GW, Detels R, Goedert JJ, Buchbinder S, Hoots K, Vlahov D, Trowsdale J, Wilson M, O'Brien SJ, Carrington M (2002) "Epistatic interaction between KIR3DS1 and HLA-B delays the progression to AIDS." Nature Genetics 31:429-434. http://www.nature.com/ng/journal/v31/n4/abs/ng934.html http://tc.liblink.umn.edu/sfx_local?sid=Entrez:PubMed&id=pmid:12134147 |
| Oct 6 |
Tim Kunau Jun Li |
Phillip Lord, Sean Bechhofer, Mark D. Wilkinson, Gary Schiltz, Damian
Gessler, Duncan Hull, Carole Goble and Lincoln Stein (2004) "Applying Semantic Web Services to Bioinformatics: Experiences Gained, Lessons Learnt." Lecture Notes in Computer Science 3298:350. http://www.springerlink.com/openurl.asp?genre=article&issn=0302-9743&volume=3298&spage=350 Eran Segal, Nir Friedman, Naftali Kaminski, Aviv Regev & Daphne Koller (2005) "From signatures to models: understanding cancer using microarrays" Nature Genetics 37:S38-S45. http://www.nature.com/ng/journal/v37/n6s/abs/ng1561.html http://tc.liblink.umn.edu/sfx_local?sid=Entrez:PubMed&id=pmid:15920529 |
| Oct 13 |
Steve Cannon Zheng Jin Tu |
Pan X, Stein L, Brendel V. (2005) "SynBrowse: a synteny browser for comparative sequence analysis." Bioinformatics. 2005 Sep 1;21(17):3461-8. http://bioinformatics.oxfordjournals.org/cgi/content/abstract/21/17/3461 http://tc.liblink.umn.edu/sfx_local?sid=Entrez:PubMed&id=pmid:15994196 http://www.gmod.org/ Kersey P. J., Duarte, J., Williams, A., Karavidopoulou Y., Birney, E. and Apweiler R. (2004) "The International Protein Index: An integrated database for proteomics experiments." Proteomics 4:1985-1988. http://www3.interscience.wiley.com/cgi-bin/abstract/108562573/ABSTRACT http://tc.liblink.umn.edu/sfx_local?sid=Entrez:PubMed&id=pmid:15221759 |
| Oct 20 |
Jim Auer Wayne Xu |
Vucetic S, Obradovic Z, Vacic V, Radivojac P, Peng K, Iakoucheva LM,
Cortese MS, Lawson JD, Brown CJ, Sikes JG, Newton CD, Dunker AK.
(2005) "DisProt: a database of protein disorder." Bioinformatics. 2005 Jan 1;21(1):137-40. http://bioinformatics.oxfordjournals.org/cgi/content/full/21/1/137 http://tc.liblink.umn.edu/sfx_local?sid=Entrez:PubMed&id=pmid:15310560 Dyson HJ, Wright PE. (2005) "Intrinsically unstructured proteins and their functions." Nat Rev Mol Cell Biol. 2005 Mar;6(3):197-208. http://tc.liblink.umn.edu/sfx_local?sid=Entrez:PubMed&id=pmid:15738986 ========= The FANTOM Consortium (2005) "The Transcriptional Landscape of the Mammalian Genome" Science 309(5740): 1559-1563. http://www.sciencemag.org/cgi/content/full/309/5740/1559 http://tc.liblink.umn.edu/sfx_local?sid=Entrez:PubMed&id=pmid:16141072 |
| Oct 27 | Art Eschenlauer |
Jonsson P, Johansson AI, Gullberg J, Trygg J, Jiye A, Grung B,
Marklund S, Sjostrom M, Antti H, Moritz T. (2005) "High-Throughput Data Analysis for Detecting and Identifying Differences between Samples in GC/MS-Based Metabolomic Analyses" Anal. Chem. 77(17): 5635 - 5642. http://tc.liblink.umn.edu/sfx_local?sid=Entrez:PubMed&id=pmid:16131076 Kell DB. (2004) "Metabolomics and systems biology: making sense of the soup." Curr Opin Microbiol. 7(3): 296-307. http://tc.liblink.umn.edu/sfx_local?sid=Entrez:PubMed&id=pmid:15196499 |
| Nov 3 |
Getiria Onsongo Ethy Cannon |
Rakesh Nagarajan, Mushtaq Ahmed, Aditya Phatak (2004) "Database Challenges in the Integration of Biomedical Data Sets" eProceedings of the Thirtieth International Conference on Very Large Data Bases Editors: MA Nascimento, MT Ozsu, D Kossmann, RJ Miller, JA Blakeley, B Schiefer, Toronto, Canada, August 31 - September 3 2004, pp 1202-1213. http://www.isys.ucl.ac.be/vldb04/eProceedings/contents/pdf/IND7P2.PDF =========== Stefanie De Bodt, Steven Maere and Yves Van de Peer (2005) "Genome duplication and the origin of angiosperms" TRENDS in Ecology and Evolution 20:591-597. http://tc.liblink.umn.edu/sfx_local?sid=Elsevier:SD&genre=article&issn=01695347&date=2005&volume=20&issue=11&spage=591 Pfeil, BE, Schlueter, JA, Doyle, JJ (2005) "Placing Paleopolyploidy in Relation to Taxon Divergence: A Phylogenetic Analysis in Legumes using 39 Gene Families" Systematic Biology 54: 441-454. http://tc.liblink.umn.edu/sfx_local?sid=Entrez:PubMed&id=pmid:16012110 |
| Nov 10 | Zhigang Zhang |
L Tian, SA Greenberg , SW Kong, J Altschuler, IS Kohane and PJ Park
(2005) "Discovering statistically significant pathways in expression profiling studies" PNAS 102: 13544-13549. http://www.pnas.org/cgi/content/full/102/38/13544 |
| Nov 17 |
Ninad Pendse Betsy Martinez-Vaz |
Fang Zhao, Zhenyu Xuan, Lihua Liu and Michael Zhang. (2005) "TRED: a transcriptional regulatory element database and a platform for in silico gene regulation studies" Nucleic Acid Research, 2005, vol 33, Database Issue, D103-107. http://nar.oxfordjournals.org/cgi/content/full/33/suppl_1/D103 ========== Munch R, Hiller K, Grote A, Scheer M, Klein J, Schobert M, Jahn D. (2005) "Virtual Footprint and PRODORIC: an integrative framework for regulon prediction in prokaryotes." Bioinformatics. 2005 Nov 15;21(22):4187-9. http://bioinformatics.oxfordjournals.org/cgi/content/full/21/22/4187 http://tc.liblink.umn.edu/sfx_local?sid=Entrez:PubMed&id=pmid:16109747 Tompa M, Li N, Bailey TL, Church GM, De Moor B, Eskin E, Favorov AV, Frith MC, Fu Y, Kent WJ, Makeev VJ, Mironov AA, Noble WS, Pavesi G, Pesole G, Regnier M, Simonis N, Sinha S, Thijs G, van Helden J, Vandenbogaert M, Weng Z, Workman C, Ye C, Zhu Z. (2005) "Assessing computational tools for the discovery of transcription factor binding sites." Nat Biotechnol. 2005 Jan;23(1):137-44. http://www.nature.com/nbt/journal/v23/n1/abs/nbt1053.html http://tc.liblink.umn.edu/sfx_local?sid=Entrez:PubMed&id=pmid:15637633 |
| Nov 24 | No Journal Club | ***Thanksgiving*** |
| Dec 1 |
Kyeong Jeong Dipen Sangurdekar |
Tu BP, Kudlicki A, Rowicka M, McKnight SL. (2005) Logic of the yeast metabolic cycle: temporal compartmentalization of cellular processes. Science. 2005 Nov 18; 310(5751):1152-8. http://www.sciencemag.org/cgi/content/full/310/5751/1152 http://tc.liblink.umn.edu/sfx_local?sid=Entrez:PubMed&id=pmid:16254148 Shim Choi S, Li W, Lahn BT. (2005) Robust signals of coevolution of interacting residues in mammalian proteomes identified by phylogeny-aided structural analysis. Nat Genet. 37: 1367 - 1371. http://www.nature.com/ng/journal/v37/n12/full/ng1685.html http://tc.liblink.umn.edu/sfx_local?sid=Entrez:PubMed&id=pmid:16282975 |
| Dec 8 | Kevin Messner |
DNA: Curing Cancer, PBS video |