Journal Club (Spring 2011)
Wednesdays, 12 noon-1pm
330B Diehl Hall
Unless stated otherwise (*)
1cr S/N 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 19 | Lynda Ellis Peter Kirlew |
Organizational Meeting Finding Bioinformatics Articles |
| Jan 26 | Jeff Gao | Jin G, Zhou X, Cui K, Zhang XS, Chen L, Wong ST. (2009) "Cross-platform method for identifying candidate network biomarkers for prostate cancer." IET Syst Biol. 2009 Nov;3(6):505-12. http://ieeexplore.ieee.org/xpl/freeabs_all.jsp?arnumber=5344680 http://ieeexplore.ieee.org/stamp/stamp.jsp?tp=&arnumber=5344680 Gupta R, Agrawal S, Rao N, Tian Z, Kuang R, Kumar V. (2010) "Integrative Biomarker Discovery for Breast Cancer Metastasis from Gene Expression and Protein Interaction Data Using Error-tolerant Pattern Mining." Proceedings of the ISCA 2nd International Conference on Bioinformatics and Computational Biology (BICoB), 171-177. http://www-users.cs.umn.edu/~kumar/dmbio/BICOB2010.pdf http://www.informatik.uni-trier.de/~ley/db/conf/bicob/bicob2010.html |
| Feb 2 | Yixin Chen | Meyer SU, Pfaffl MW, Ulbrich SE. (2010) "Normalization strategies for microRNA profiling experiments: a 'normal' way to a hidden layer of complexity?" Biotechnol Lett. 2010 Dec;32(12):1777-88. http://www.springerlink.com/content/r263226j26w6m638/ |
| Feb 9 | Thanh Le | Xi R, Kim TM, Park PJ. (2010) "Detecting structural variations in the human genome using next generation sequencing." Brief Funct Genomics. 2010 Dec;9(5-6):405-15. http://bfg.oxfordjournals.org/content/9/5-6/405.full |
| Feb 16 | Yetcli Huerta | Kalas M, Puntervoll P, Joseph A, Bartaseviciūte E, Töpfer A, Venkataraman P, Pettifer S, Bryne JC, Ison J, Blanchet C, Rapacki K, Jonassen I. (2010) "BioXSD: the common data-exchange format for everyday bioinformatics web services." Bioinformatics. 2010 Sep 15;26(18):i540-6. http://bioinformatics.oxfordjournals.org/content/26/18/i540.long http://www.bioxsd.org/ |
| Feb 23 | Tongbin Li | Xiao F, Zuo Z, Cai G, Kang S, Gao X, Li T. (2009) "miRecords: an integrated resource for microRNA-target interactions." Nucleic Acids Res. 2009 Jan;37(Database issue):D105-10. http://nar.oxfordjournals.org/content/37/suppl_1/D105.long http://mirecords.biolead.org/ |
| Mar 2 | Zheng Jin Tu |
Zhong M, Niu W, Lu ZJ, Sarov M, Murray JI, Janette J, Raha D, Sheaffer KL, Lam
HY, Preston E, Slightham C, Hillier LW, Brock T, Agarwal A, Auerbach R, Hyman AA,
Gerstein M, Mango SE, Kim SK, Waterston RH, Reinke V, Snyder M. (2010) "Genome-wide identification of binding sites defines distinct functions for Caenorhabditis elegans PHA-4/FOXA in development and environmental response." PLoS Genet. 2010 Feb 19;6(2):e1000848. http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1000848 Niu W, Lu ZJ, Zhong M, Sarov M, Murray JI, Brdlik CM, Janette J, Chen C, Alves P, Preston E, Slightham C, Jiang L, Hyman AA, Kim SK, Waterston RH, Gerstein M, Snyder M, Reinke V. (2011) "Diverse transcription factor binding features revealed by genome-wide ChIP-seq in C. elegans." Genome Res. 2011 Feb;21(2):245-54. http://genome.cshlp.org/content/21/2/245.long |
| Mar 9 |
Lynda Ellis |
Helbling DE, Hollender J, Kohler HP, Singer H, Fenner K. (2010) "High-throughput identification of microbial transformation products of organic micropollutants." Environ Sci Technol. 2010 Sep 1;44(17):6621-7. http://pubs.acs.org/doi/full/10.1021/es100970m http://tc.liblink.umn.edu/sfx_local?sid=Entrez:PubMed&id=pmid:20799730 http://pubs.acs.org/doi/abs/10.1021/es200415t |
| Mar 16 |
No Journal Club | Spring Break |
| Mar 23 | Getiria Onsongo |
Eddy SR. (2009) "A new generation of homology search tools based on probabilistic inference." Genome Inform. 2009 Oct;23(1):205-11. http://eproceedings.worldscinet.com/9781848165632/9781848165632_0019.html http://hmmer.janelia.org/ |
| Mar 30 | Yuk Sham | Palpant NJ, Houang EM, Delport W, Hastings KE, Onufriev AV,
Sham YY, Metzger JM. (2010) "Pathogenic peptide deviations support a model of adaptive evolution of chordate cardiac performance by troponin mutations" Physiol Genomics 42: 287-299, 2010. http://physiolgenomics.physiology.org/content/42/2/287.abstract |
| Apr 6 | Daniel Beisang |
Ramsköld D, Wang ET, Burge CB, Sandberg R. (2009) "An abundance of ubiquitously expressed genes revealed by tissue transcriptome sequence data." PLoS Comput Biol. 2009 Dec;5(12):e1000598. http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1000598 |
| Apr 13 | Shawn Balcome |
Croft D, O'Kelly G, Wu G, Haw R, Gillespie M, Matthews L, Caudy M, Garapati P,
Gopinath G, Jassal B, Jupe S, Kalatskaya I, Mahajan S, May B, Ndegwa N, Schmidt
E, Shamovsky V, Yung C, Birney E, Hermjakob H, D'Eustachio P, Stein L. (2011) "Reactome: a database of reactions, pathways and biological processes." Nucleic Acids Res. 2011 Jan;39(Database issue):D691-7. http://nar.oxfordjournals.org/content/39/suppl_1/D691.long http://www.reactome.org/ |
| Apr 20 | Dimitrije Jevremovic |
Jevremovic D, Trinh CT, Srienc F, Boley D. (2010) "On algebraic properties of extreme pathways in metabolic networks." J Comput Biol. 2010 Feb;17(2):107-19. http://www.liebertonline.com/doi/abs/10.1089/cmb.2009.0020 http://tc.liblink.umn.edu/sfx_local?sid=Entrez:PubMed&id=pmid:20170399 Jevremovic D, Trinh CT, Srienc F, Sosa C, Boley D. (2010) "Parallelization of Nullspace Algorithm for the computation of metabolic pathways" University of Minnesota - Computer Science and Engineering Techical Report 10-028 http://www.cs.umn.edu/research/technical_reports.php?page=report&report_id=10-028 http://elmocomp.sourceforge.net/ |
| Apr 27 | Svante Pääbo Lynda Ellis |
Green RE et al. (2010) "A Draft Sequence of the Neandertal Genome" Science 328: 710-722. http://www.sciencemag.org/content/328/5979/710.full http://www.iscb.org/cms_addon/multimedia/flvmedia.php?i=704 http://www.sciencemag.org/site/special/neandertal/feature/ http://www.sciencemag.org/content/328/5979/680.full http://www.sciencemag.org/content/328/5979/683.full |
| May 4 | Peter Kirlew |
Frederick, Robert (2011) "Sequencing Cancer Genomes: Targeted Cancer Therapies" http://video.sciencemag.org/SciOriginals/850053254001/1 From: Cancer Crusade at 40. Science v331(6024) (March 2011 special issue) http://www.sciencemag.org/site/special/cancer2011/ The NIH Common Fund (2010) "To Boldly Go Where No Robot Has Gone Before" http://www.youtube.com/watch?v=vyfr5MuVNis An interview with Dr. Chris Austin, Director, NIH Chemical Genomics Center http://ncgc.nih.gov/ WellCome Trust Sanger Institute. (2010) "1000 Genomes: A New Foundation for Genetic Research." http://www.sanger.ac.uk/about/press/2010/101027-1000genomes.html http://www.1000genomes.org/ |