Journal Club (Spring 2005)
Wednesdays, 12 noon-1pm
748 Mayo Building
Credit available as BInf 5480.
To change dates, swap with another presenter and tell Lynda Ellis.
| Jan 19 |
Lynda Ellis |
Organizational Meeting |
| Jan 26 | Lynda Ellis |
Carlis, J.V. (2002) "Pitfalls and paths to success in
interdisciplinary scientific database research" IEEE Engineering in Medicine and Biology Magazine 21(6): 117-122. http://tc.liblink.umn.edu/sfx_local?sid=sfx:e_collection&issn=0739-5175&pid=serviceType=getFullTxt and type in year 2002, volume 21, issue 6. Once at the issue, look for start page 117. |
| Feb 2 |
John Carlis Lynda Ellis Cargill 105 |
"What everybody knows but nobody says can hurt interdisciplinary
research" "Databases for Microbes and Man" |
| Feb 9 | Mike Heuer |
Su AI, Wiltshire T, Batalov S, Lapp H, Ching KA, Block D, Zhang
J, Soden R, Hayakawa M, Kreiman G, Cooke MP, Walker JR, Hogenesch JB. (2004) "A gene atlas of the mouse and human protein-encoding transcriptomes." Proc Natl Acad Sci U S A. 2004 Apr 20;101(16):6062-7. http://www.pnas.org/cgi/content/full/101/16/6062 http://symatlas.gnf.org/SymAtlas/ |
| Feb 16 | Tim Kunau |
Jonathan Bard, Seung Y Rhee and Michael Ashburner (2005) "An ontology for cell types" Genome Biology 2005, 6:R21 http://genomebiology.com/2005/6/2/R21 http://obo.sourceforge.net |
| Feb 23 |
Pepe Jose Barbe |
J. Angulo and J. Serra (2003) "Automatic analysis of DNA microarray images using mathematical morphology." Bioinformatics 19: 553-562. http://bioinformatics.oupjournals.org/cgi/content/abstract/19/5/553 |
| Mar 2 | Charlie Paule |
C. Lottaz, C. Iseli, C.V. Jongeneel and P. Bucher (2003) "Modeling sequencing errors by combining Hidden Markov Models" Bioinformatics 19(s2): ii103-ii112. http://bioinformatics.oupjournals.org/cgi/content/abstract/19/suppl_2/ii103
Background material: |
| Mar 9 | Lee Parsons |
Pedrioli PG, Eng JK, Hubley R, Vogelzang M, Deutsch EW, Raught B,
Pratt B, Nilsson E, Angeletti RH, Apweiler R, Cheung K, Costello CE, Hermjakob H, Huang S, Julian RK, Kapp E, McComb ME, Oliver SG, Omenn G, Paton NW, Simpson R, Smith R, Taylor CF, Zhu W, Aebersold R. "A common open representation of mass spectrometry data and its application to proteomics research." Nat Biotechnol. 2004 Nov;22(11):1459-66. http://tc.liblink.umn.edu/sfx_local?sid=Entrez:PubMed&id=pmid:15529173 |
| Mar 16 | No Journal Club |
*** Spring Break *** |
| Mar 23 | Jim Auer |
E. Manduchi, G. R. Grant, H. He, J. Liu, M. D. Mailman, A. D.
Pizarro, P. L. Whetzel, and C. J. Stoeckert, Jr "RAD and the RAD Study-Annotator: an approach to collection, organization and exchange of all relevant information for high-throughput gene expression studies" Bioinformatics 2004 20: 452-459. http://bioinformatics.oupjournals.org/cgi/content/abstract/20/4/452 |
| Mar 30 | Dave Roe |
Button WG, Judson PN, Long A, Vessey JD. "Using absolute and relative reasoning in the prediction of the potential metabolism of xenobiotics." J Chem Inf Comput Sci. 2003 Sep-Oct;43(5):1371-7. http://tc.liblink.umn.edu/sfx_local?sid=Entrez:PubMed&id=pmid:14502469
Background material: |
| Apr 6 | Huzefa Rangwala |
Leslie CS, Eskin E, Cohen A, Weston J, Noble WS. "Mismatch String Kernels for Discriminative Protein Classification" Bioinformatics. 2004 Mar 1;20(4):467-76. http://bioinformatics.oupjournals.org/cgi/content/abstract/20/4/467 |
| Apr 13 | Martin Maiers |
N.A. Rosenberg, J.K. Pritchard, J.L. Weber, H.M. Cann, K.K. Kidd,
L.A. Zhivotovsky and M.W. Feldman "The genetic structure of human populations." Science 2002, 298: 2381-2385. http://www.sciencemag.org/cgi/content/full/298/5602/2381
Background material: |
| Apr 20 | Carlos P. Sosa |
Mott R, Schultz J, Bork P, Ponting CP. "Predicting protein cellular localization using a domain projection method." Genome Res. 2002 Aug;12(8):1168-74. http://www.genome.org/cgi/content/full/12/8/1168 |
| Apr 27 | Shalini Kumar |
Devulder G, Perriere G, Bety F, Flandrois JP BIBI, a Bioinformatics Bacterial Identification Tool. J Clin Microbiol. 2003 Apr;41(4): 1785-1787. http://www.pubmedcentral.gov/articlerender.fcgi?tool=pmcentrez&artid=153906 http://pbil.univ-lyon1.fr/bibi/ |
| May 3 | Kevin Messner |
DNA: Playing God, PBS video |