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
Jan 21 Lynda Ellis
Peter Kirlew
Organizational Meeting
Finding Bioinformatics Articles
Jan 28 Zeke McKinney  Koomen JM, Haura EB, Bepler G, Sutphen R, Remily-Wood ER, Benson K, Hussein M, Hazlehurst LA, Yeatman TJ, Hildreth LT, Sellers TA, Jacobsen PB, Fenstermacher DA, Dalton WS. (2008)
"Proteomic contributions to personalized cancer care."
Mol Cell Proteomics. 2008 Oct;7(10):1780-94.
http://www.mcponline.org/cgi/content/full/7/10/1780
http://tc.liblink.umn.edu/sfx_local?sid=Entrez:PubMed&id=pmid:18664563  
Feb 4 Wayne Xu
Wei Pan 
Alessio Farcomeni (2008)
"A review of modern multiple hypothesis testing, with particular attention to the false discovery proportion"
Statistical Methods in Medical Research, 17(4), 347-388 (2008).
http://smm.sagepub.com/cgi/content/refs/17/4/347

Sandrine Dudoit, Juliet Popper Shaffer and Jennifer C. Boldrick (2003)
"Multiple Hypothesis Testing in Microarray Experiments"
Statistical Science, 2003, 18(1), 71-103. http://www.stat.berkeley.edu/~sandrine/Docs/Papers/StatSci2003Final.pdf  
Feb 11 Nicholas McCarty  Mark Newman (2008)
"The Physics of Networks"
Physics Today, November 2008, 33-38.
http://www.math.umn.edu/~othmer/5445/networks_physics.pdf  
Feb 18 Tamara Schmidt-Hegge   Ritchie M. and Motsinger A. (December 2005).
"Multifactor dimensionality reduction for detecting gene-gene and gene-environment interactions in pharmacogenomics studies."
Pharmacogenomics, 6(8): 823-834.
http://www.futuremedicine.com/doi/abs/10.2217/14622416.6.8.823
http://tc.liblink.umn.edu/sfx_local?sid=Entrez:PubMed&id=pmid:16296945  
Feb 25
*330 Diehl Hall
Chimezie Ononenyi  Lin H, Wang H, Ding H, Chen YL, Li QZ (2009).
"Prediction of Subcellular Localization of Apoptosis Protein Using Chou's Pseudo Amino Acid Composition."
Acta Biotheor. 2009 Jan 24.
http://www.springerlink.com/content/r1h327077n510606/
http://tc.liblink.umn.edu/sfx_local?sid=Entrez:PubMed&id=pmid:19169652  
Mar 4
Vic Bloomfield
 
Tran LM, Rizk ML, Liao JC. (2008)
"Ensemble modeling of metabolic networks."
Biophys J. 2008 Dec 15;95(12):5606-17
http://dx.doi.org/doi:10.1529/biophysj.108.135442
http://tc.liblink.umn.edu/sfx_local?sid=Entrez:PubMed&id=pmid:18820235 
Mar 11 Getiria Onsango  Du P, Stolovitzky G, Horvatovich P, Bischoff R, Lim J, Suits F. (2008)
"A noise model for mass spectrometry based proteomics."
Bioinformatics 24:1070-1077.
http://bioinformatics.oxfordjournals.org/cgi/content/full/24/8/1070  
Mar 25 Zheng Jin Tu




Jeff Gao 
Kunin V, Copeland A, Lapidus A, Mavromatis K, and Hugenholtz P. (2008)
"A Bioinformatician's Guide to Metagenomics"
Microbiology and Molecular Biology Reviews 72(4):557-578.
http://mmbr.asm.org/cgi/content/full/72/4/557?view=long&pmid=19052320

Nigel C, Son D, Ai K, Reiko M G, Mike C, Yoshio T, Quoc-Hung N, Dinh D, Asanee K, Koichi T, Mika S and Kiyosu T (2008).
"BioCaster: detecting public health rumors with a Web-based text mining system"
Bioinformatics 24: 2940-2941.
http://bioinformatics.oxfordjournals.org/cgi/content/full/24/24/2940  
Apr 1 John Garbe  Jenkinson AM, Albrecht M, Birney E, Blankenburg H, Down T, Finn RD, Hermjakob H, Hubbard TJ, Jimenez RC, Jones P, Kähäri A, Kulesha E, Macías JR, Reeves GA, Prlic A. (2008)
"Integrating biological data - the Distributed Annotation System."
BMC Bioinformatics 2008, 9(Suppl 8):S3
http://www.biomedcentral.com/1471-2105/9/S8/S3

Finn RD, Stalker JW, Jackson DK, Kulesha E, Clements J, Pettett R (2007).
"ProServer: a simple, extensible Perl DAS server."
Bioinformatics. 2007 Jun 15;23(12):1568-70.
http://bioinformatics.oxfordjournals.org/cgi/content/full/23/12/1568  
Apr 8 Mike Hardy   Watkins J (2009)
"Convergence time to the Ewens sampling formula in the infinite alleles Moran Model"
J Math Biol. 2009 Mar 15. [Epub ahead of print]
http://www.springerlink.com/content/v6244m25114kw433/
http://tc.liblink.umn.edu/sfx_local?sid=Entrez:PubMed&id=pmid:19288263  
Apr 15 Dimitrije Jevremovic 
Trinh CT, Wlaschin A, Srienc F. (2009)
"Elementary mode analysis: a useful metabolic pathway analysis tool for characterizing cellular metabolism."
Appl Microbiol Biotechnol. 2009 Jan;81(5):813-26
http://dx.doi.org/10.1007/s00253-008-1770-1
http://tc.liblink.umn.edu/sfx_local?sid=Entrez:PubMed&id=pmid:19015845

Trinh CT, Unrean P, Srienc F. (2008)
"Minimal Escherichia coli cell for the most efficient production of ethanol from hexoses and pentoses."
Appl Environ Microbiol. 2008 Jun;74(12):3634-43
http://aem.asm.org/cgi/content/full/74/12/3634?view=long&pmid=18424547 
Apr 22 HoJung Yoon





Fang Han 
John Hardy and Andrew Singleton (2009)
"Genomewide Association Studies and Human Disease."
Published online at www.nejm.org April 15, 2009 (10.1056/NEJMra0808700)
http://dx.doi.org/10.1056/NEJMra0808700
http://content.nejm.org/cgi/content/full/NEJMra0808700

Sam T. Roweis, Lawrence K. Saul (2000)
"Nonlinear Dimensionality Reduction by Locally Linear Embedding"
Science. 2000 Dec 22;290(5500):2323-6.
http://www.sciencemag.org/cgi/content/abstract/290/5500/2323

Joshua B. Tenenbaum, Vin de Silva, John C. Langford (2000)
"A Global Geometric Framework for Nonlinear Dimensionality Reduction"
Science. 2000 Dec 22;290(5500):2319-23.
http://www.sciencemag.org/cgi/content/abstract/290/5500/2319

Bernhard Schölkopf, Alexander Smola, Klaus-Robert Müller (1998)
"Nonlinear Component Analysis as a Kernel Eigenvalue Problem"
Neural Computation 10: 1299-1319. http://www.mitpressjournals.org/doi/abs/10.1162/089976698300017467  
Apr 29 Peter Kirlew  Smedley D, Haider S, Ballester B, Holland R, London D, Thorisson G, Kasprzyk A. (2009)
"BioMart - biological queries made easy."
BMC Genomics 2009, 10:22.
http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=19144180  
May 6 Peter Kirlew  Shotgun Sequencing: Howard Hughes Medical Institute
http://www.hhmi.org/biointeractive/media/DNAi_shotgun_seq-lg.wmv

Claire Fraser-Ligget, Institute for Genome Sciences, University of Maryland School of Medicine.
"Microbial Communities in Health and Disease"
Keynote presentation, ISMB 2008 conference
http://www.iscb.org/iscb-conferences/247-ismb2008-talks
 

Past Journal Clubs