Journal Club (Spring 2006)
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/Articals |
|---|---|---|
| Jan 18 | Wei Pan, Lynda Ellis | Organizational Meeting |
| Jan 25 | No Journal Club | Cancelled |
| Feb 1 | Martin Maiers |
Kesmir, C., Nussbaum, A., Schild, H., Detours V., Brunak S.
(2002) Prediction of proteasome cleavage motifs by neural networks Protein Engineering 15: 287-296. http://peds.oxfordjournals.org/cgi/content/full/15/4/287 http://www.cbs.dtu.dk/services/NetChop/ |
| Feb 8 | Koffi Adragni |
M Blangiardo, S Toti, B Giusti, R Abbate, A Magi, F Poggi,
L Rossi, F Torricelli, A Biggeri (2006) Using a calibration experiment to assess gene-specific information: full Bayesian and empirical Bayesian models for two-channel microarray data Bioinformatics 2006 22(1):50-57. http://bioinformatics.oxfordjournals.org/cgi/content/full/22/1/50 http://tc.liblink.umn.edu/sfx_local?sid=Entrez:PubMed&id=pmid:16267084 |
| Feb 15 | Dave Roe |
H. Zhou and Y. Zhou (2006) "SPEM: Improving multiple-sequence alignment with sequence profiles and predicted secondary structures" Bioinformatics 21: 3615-3621. http://bioinformatics.oxfordjournals.org/cgi/content/full/21/18/3615 http://tc.liblink.umn.edu/sfx_local?sid=Entrez:PubMed&id=pmid:16020471 http://theory.med.buffalo.edu/ |
| Feb 22 |
Yiannis Kaznessis Tim Kunau Cargill 105 |
"Model-driven Gene Network Engineering" "Developing an architecture for participation: many parts, loosely joined" |
| Mar 1 | Lynda Ellis & Carlos Sosa |
Klee, Eric W., Ellis, Lynda B.M. (2005) Evaluating Eukaryotic Secreted Protein Prediction BMC Bioinformatics, 6:256. http://www.biomedcentral.com/1471-2105/6/256 http://www.secretomes.umn.edu/ |
| Mar 8 | Zheng Jin Tu |
A Rauch, M Bellew, J Eng, M Fitzgibbon, T Holzman, P
Hussey, M Igra, B Maclean, WL Chen, A Detter, R Fang, V
Faca, P Gafken, H Zhang, J Whitaker, D States, S Hanash, A
Paulovich, MW McIntosh (2006) Computational Proteomics Analysis System (CPAS): An Extensible, Open-Source Analytic System for Evaluating and Publishing Proteomic Data and High Throughput Biological Experiments J. Proteome Res., 5: 112-121 http://pubs.acs.org/cgi-bin/sample.cgi/jprobs/2006/5/i01/html/pr0503533.html http://tc.liblink.umn.edu/sfx_local?sid=Entrez:PubMed&id=pmid:16396501 https://proteomics.fhcrc.org:443/CPAS/Project/home/home.view |
| Mar 15 | No Journal Club |
*** Spring Break *** |
| Mar 22 | Niroopshankar Ammbashankar |
Anders Bengtsson, Henrik Bengtsson (2006) Microarray image analysis: background estimation using quantile and morphological filters BMC Bioinformatics 2006, 7:96 http://www.biomedcentral.com/1471-2105/7/96 |
| Mar 29 | Tim Kunau |
Remko de Knikker, Youjun Guo, Jin-long Li, Albert KH Kwan,
Kevin Y Yip, David W Cheung and Kei-Hoi Cheung "A web services choreography scenario for interoperating bioinformatics applications" BMC Bioinformatics 2004, 5:25 http://www.biomedcentral.com/1471-2105/5/25 |
| Apr 5 | Getiria Onsongo |
Khatri P, Draghici S. "Ontological analysis of gene expression data: current tools, limitations, and open problems" Bioinformatics. 2005 Sep 15;21(18):3587-95 http://bioinformatics.oxfordjournals.org/cgi/reprint/21/18/3587 http://tc.liblink.umn.edu/sfx_local?sid=Entrez:PubMed&id=pmid:15994189 |
| Apr 12 | Michael Heuer |
Michael Meissner, Michael Schmuker and Gisbert
Schneider "Optimized Particle Swarm Optimization (OPSO) and its application to artificial neural network training" BMC Bioinformatics 2006, 7:125 http://www.biomedcentral.com/1471-2105/7/125 PsoVis, a tool for visualizing the optimization process of Particle Swarm Optimization. |
| Apr 19 | Feng Tai |
Lottaz C, Spang R. "Molecular decomposition of complex clinical phenotypes using biologically structured analysis of microarray data." Bioinformatics. 2005, 21:1971-8. http://bioinformatics.oxfordjournals.org/cgi/reprint/bti292v1 http://tc.liblink.umn.edu/sfx_local?sid=Entrez:PubMed&id=pmid:15677704 |
| Apr 26 |
Ariel Abell |
Victor Maojo, Casimir A. Kulikowski "Bioinformatics and Medical Informatics: Collaborations on the Road to Genomic Medicine?" J Am Med Inform Assoc. 2003;10:515-522 http://www.pubmedcentral.gov/articlerender.fcgi?tool=pubmed&pubmedid=12925552 |
| May 3 | Kevin Messner |
Stuart Schreiber, Harvard Departments of Chemistry and
Chemical Biology "Probing Genes and Genomes," part of the HHMI Scanning Life's Matrix: Genes, Proteins and Small Molecules DVD |