Journal Club (Fall 2008)
Wednesdays, 12 noon-1pm
555 Diehl Hall
Unless stated otherwise
Credit available as BInf 5480.
To change dates, swap with another presenter and tell Lynda Ellis.
UM Library's BIJC Information Resources and Services
| Date | Presenter(s) | Title/Articles |
|---|---|---|
| Sept 3 | Lynda Ellis Peter Kirlew |
Organizational Meeting Finding Bioinformatics Articles |
| Sept 10 | Lynda Ellis Carlos Sosa |
Report on ISMB08 http://www.iscb.org/ismb2008/ |
| Sept 17 | Gaurav Pandey Jeff Gao |
Report on ISMB08 http://www.iscb.org/ismb2008/ |
| Sept 24 | Jeff Gao Aaron Sarver |
Report on ChemAxon 2008 USA User Group Meeting
http://www.chemaxon.com/UGM/08/ Kash JC, Tumpey TM, Proll SC, Carter V, Perwitasari O, Thomas MJ, Basler CF, Palese P, Taubenberger JK, Garcia-Sastre A, Swayne DE, Katze MG. (2006) "Genomic analysis of increased host immune and cell death responses induced by 1918 influenza virus." Nature. 443(7111):578-81. http://www.nature.com/nature/journal/v443/n7111/abs/nature05181.html http://tc.liblink.umn.edu/sfx_local?sid=Entrez:PubMed&id=pmid:17006449 |
| Oct 1 | Zeke McKinney Urvashi Mishra |
Zukoski MJ, Boult T, Iyriboz T. (2006) "A novel approach to medical image compression." Int J Bioinform Res Appl. 2(1):89-103. http://www.inderscience.com/browse/index.php?journalID=155&year=2006&vol=2&issue=1 and click on the last paper Shatkay H, Pan F, Rzhetsky A, Wilbur WJ. (2008) "Multi-dimensional classification of biomedical text: toward automated, practical provision of high-utility text to diverse users." Bioinformatics 24: 2086-2093. http://bioinformatics.oxfordjournals.org/cgi/content/full/24/18/2086 |
| Oct 8 | Tamara Schmidt-Hegge Getiria Onsongo |
G. Lerman and B. E. Shakhnovich (2007) "Defining functional distance using manifold embeddings of gene ontology annotations." Proc Natl Acad Sci U S A. 104(27):11334-9. http://www.pnas.org/content/104/27/11334.full http://www.math.umn.edu/~lerman/supp/protein_distance/ Haibe-Kains B, Desmedt C, Sotiriou C, Bontempi G (2008) "A comparative study of survival models for breast cancer prognostication based on microarray data: does a single gene beat them all?" Bioinformatics. 24(19):2200-8. http://bioinformatics.oxfordjournals.org/cgi/content/full/24/19/2200 http://www.ulb.ac.be/di/map/bhaibeka/software/survcomp/ |
| *Oct 15 239 Gortner |
Judy Berman Jeff Gao |
Centromere and neocentromere function in Candida albicans Improving the infrastructure for biodegradation pathway prediction Ellis, L.B.M., Gao, J., Fenner, K., and Wackett, LP. (2008) Nucleic Acids Research 36: W427-W432. http://nar.oxfordjournals.org/cgi/content/full/36/suppl_2/W427 http://umbbd.msi.umn.edu/predict/ |
| Oct 22 | Vic Bloomfield |
Gentleman RC, et al. (2004) "Bioconductor: open software development for computational biology and bioinformatics" Genome Biology 5:R80. http://genomebiology.com/2004/5/10/R80 http://www.bioconductor.org/ |
| Oct 29 | Zheng Jin Tu | Mihai Pop and Steven Salzberg (2007) "Bioinformatics challenges of new sequencing technology" Trends in Genetics, 24(3):142-149. http://dx.doi.org/doi:10.1016/j.tig.2007.12.006 http://tc.liblink.umn.edu/sfx_local?sid=Entrez:PubMed&id=pmid:18262676 |
| Nov 5 | Fang Han Jeff Gao |
Tibshirani, R. (1996). "Regression shrinkage and selection via the lasso." J. Royal. Statist. Soc B., 58(1): 267-288. http://www-stat.stanford.edu/~tibs/lasso/lasso.pdf Huber W, Carey VJ, Long L, Falcon S, Gentleman R. (2007) "Graphs in molecular biology." BMC Bioinformatics. 8 Suppl 6:S8. http://www.biomedcentral.com/1471-2105/8/S6/S8 http://www.biomedcentral.com/1471-2105/8/S6/S8/additional/ |
| Nov 12 | Gaurav Pandey |
CANCELLED |
| Nov 19 | Christopher Fraser |
Altman RB, Klein TE (2007) "Biomedical informatics training at Stanford in the 21st century." Journal of Biomedical Informatics 40(1): 55-58 http://dx.doi.org/doi:10.1016/j.jbi.2006.02.005 Gerstein M, Greenbaum D, Cheung K, et al. (2007) "An interdepartmental Ph.D. program in computational biology and bioinformatics: The Yale perspective." Journal of Biomedical Informatics 40(1): 73-79 http://dx.doi.org/doi:10.1016/j.jbi.2006.02.008 Friedman CP, Altman RB, Kohane IS, et al. (2004) "Training the next generation of informaticians: The impact of "BISTI" and bioinformatics - A report from the American College of Medical Informatics." Journal of the American Medical Informatics Association. 11(3): 167-172 http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=14764617 Pevzner PA (2004) "Educating biologists in the 21st century: bioinformatics scientists versus bioinformatics technicians." Bioinformatics 20(14): 2159-2161 http://bioinformatics.oxfordjournals.org/cgi/reprint/20/14/2159 Cattley S (2004) "A review of bioinformatics degrees in Australia." Briefings in Bioinformatics 5(4): 350-354 http://bib.oxfordjournals.org/cgi/reprint/5/4/350 Doom T, Raymer M, Krane D, et al. (2003) Crossing the interdisciplinary barrier: A baccalaureate computer science option in bioinformatics." IEEE Transactions on Education 46(3): 387-393 http://ieeexplore.ieee.org/xpl/freeabs_all.jsp?isnumber=27429&arnumber=1220740 Zauhar RJ (2001) "University bioinformatics programs on the rise." Nature Biotechnology 19(3): 285-286 http://www.nature.com/nbt/journal/v19/n3/abs/nbt0301_285.html Campbell P (1999) "Don't leave the biology out of bioinformatics." Nature 401(6751): 321-321 http://www.nature.com/doifinder/10.1038/43764 MacLean M, Miles C (1999) "Swift action needed to close the skills gap in bioinformatics." Nature 401(6748): 10-10 http://www.nature.com/doifinder/10.1038/43269 Altman RB (1998) "A curriculum for bioinformatics: The time is ripe." Bioinformatics 14(7): 549-550 http://www.nature.com/doifinder/10.1038/43269 |
| Nov 26 | No Journal Club | ***Thanksgiving Break*** |
| Dec 3 | Peter Kirlew John Garbe |
Olivier Bodenreider and Robert Stevens (2006) "Bio-ontologies: current trends and future directions." Briefings in Bioinformatics 7 (3): 256-274. http://bib.oxfordjournals.org/cgi/content/full/7/3/256 Berglund AC, Sjolund E, Ostlund G, Sonnhammer ELL "InParanoid 6: eukaryotic ortholog clusters with inparalogs" Nucleic Acids Res. 36:D263-266 (2008) http://nar.oxfordjournals.org/cgi/content/full/36/suppl_1/D263 http://inparanoid.sbc.su.se/ |
| Dec 10 | Peter Kirlew | Biological Videos DNA Visualization (EBI) http://www.ebi.ac.uk/2can/evideos/ The Nuclear Pore Complex (Nature) http://www.nature.com/nature/videoarchive/cellarchitecture A Green Light for Biology - Making the Invisible Visible (VCU) http://www.pubinfo.vcu.edu/secretsofthesequence/showdetail.asp?id=20 Plant Genomes: From Evolutionary Insights to Crop Development (Science) http://www.sciencemag.org/plantgenomes/feature.html |