BIOINFORMATICS SEMINAR SERIES: FALL 2009 STATISTICAL BIOINFORMATICS SEMINAR SERIES STAT 598B is a 1 credit seminar course (public is welcome) 4:30pm on Tuesdays in HORT 117 Past Seminars (scroll down for current) FALL SPRING Fall 2000 seminar series speakers Spring 2001 seminar series speakers Fall 2001 seminar series speakers Spring 2002 seminar series speakers Fall 2002 seminar series speakers Spring 2003 seminar series speakers Fall 2003 seminar series speakers Spring 2004 seminar series speakers Fall 2004 seminar series speakers Spring 2005 seminar series speakers Fall 2005 seminar series speakers Spring 2006 seminar series speakers Fall 2006 seminar series speakers Spring 2007 seminar series speakers Fall 2007 seminar series speakers Spring 2008 seminar series speakers Fall 2008 seminar series speakers Spring 2009 seminar series speakers FALL 2009 Schedule: Tuesday, August 25, 2009, 4:30pm, HORT 117 RW Doerge, Department of Statistics and Department of Agronomy, Purdue University "This is an organizational meeting. All registered students must attend. If you need a registration form signed, please bring it to class." Tuesday, September 1, 2009, 4:30pm, HORT 117 Rick Westerman, Bioinformatics Specialist, Genomics Facility, Purdue University "Second generation sequencing: An overview plus some case studies" Associated reading: Next-generation DNA sequencing methods. Elaine R. Mardis. Annual Review of Genomics and Human Genetics. 2008. 9:387-402. Tuesday, September 8, 2009, 4:30pm, HORT 117 Paul Livermore Auer, Department of Statistics, Purdue University "Statistical issues in next-generation sequencing --An overview and case study" Associated reading: Wang, Z., M. Gerstein and M. Snyder, 2009 RNA-Seq: a revolutionary tool for transcriptomics. Nature Reviews Genetics 10: 57-63. Tuesday, September 15, 2009, 4:30pm, HORT 117 Scott Jackson, Department of Agronomy, Purdue University "Dealing with duplicated genes in plant genomes" Associated reading: Lex E. Flagel and Jonathan F. Wendel. 2009. Gene duplication and evolutionary novelty in plants. New Phytologist. Tuesday, September 22, 2009, 4:30pm, HORT 117 No Seminar Tuesday, September 29, 2009, 4:30pm, HORT 117 Matthew Palakal, Associate Dean for Research and Graduate Program in the School of Informatics and Professor of Computer Science in the School of Science at Indiana University Purdue University, Indianapolis "Bibliomics, Literature Mining, and Biomarker Discovery" Associated reading: M. Palakal, T. Sebastian and D. L. Stocum. Discovering implicit protein-protein interactions in the Cell Cycle using bioinformatics approaches, Journal of Biomedical Science, 15(3): 317-331, 2008. Tuesday, October 6, 2009, 4:30pm, HORT 117 No Seminar Tuesday, October 13, 2009, 4:30pm, HORT 117 No Seminar. Fall Break Tuesday, October 20, 2009, 4:30pm, HORT 117 Michelle Lacey, Department of Mathematics, Tulane University, New Orleans, LA "Statistical Modeling of Methylation Patterns in Ovarian Carcinomas" Associated reading: Lacey, Michelle R. and Ehrlich, Melanie (2009) "Modeling Dependence in Methylation Patterns with Application to Ovarian Carcinomas," Statistical Applications in Genetics and Molecular Biology: Vol. 8 : Iss. 1, Article 40. DOI: 10.2202/1544-6115.1489 Tuesday, October 27, 2009, 4:30pm, HORT 117 George Casella, Department of Statistics, University of Florida, Gainesville, FA " From R. A. Fisher to Microarrays: Why 70 year old theory is relevant today" Associated reading: Kerr and Churchill. 2001. Statistical design and the analysis of gene expression microarray data. Genet. Res., Camb. (2001), 77, pp. 123-128. Tuesday, November 3, 2009, 4:30pm, HORT 117 John Marioni, Department of Human Genetics, University of Chicago "Using RNA-seq to understand variation in the human transcriptome" Associated reading: Degner J.F., Marioni J.C., Pai A.A., Pickrell J.K., Nkadori E., Gilad Y., Pritchard J.K. Effect of read-mapping biases on detecting allele-specific expression from RNA-sequencing data. Bioinformatics 2009 (advance access online). ********************************CANCELLED***************************** Tuesday, November 10, 2009, 4:30pm, HORT 117 Alexander E. Lipka, Department of Statistics, Purdue University "Associating Single Nucleotide Polymorphisms (SNPs) with Binary Traits" Associated reading: Balding DJ. 2006. "A Tutorial on Statistical Methods for Population Association Studies," Nature Reviews Genetics. Vol. 7 Iss. 10:781-791. ************************************************************* Three Lecture Series (Nov. 17; Dec. 1; Dec. 8): Technology, Analysis, and Goals in the Ionomics of Arabidopsis Tuesday, November 17, 2009, 4:30pm, HORT 117 John M.C. Danku, Department of Horticulture & Landscape Architecture (Salt Lab), Purdue University "High-throughput analytical technology for the ionomics of model organisms" Associated reading: David E. Salt, Ivan Baxter and Brett Lahner. Ionomics and the Study of the Plant Ionome. Annu. Rev. Plant Biol. 2008, 59,709-733. Tuesday, November 24, 2009 No Seminar Tuesday, December 1, 2009, 4:30pm, HORT 117 Tilman Achberger, Department of Statistics, Purdue University "Ionomic QTL analysis in Arabidopsis thaliana" Associated reading: Artak Ghandilyan, et al. A strong effect of growth medium and organ type on the identification of QTLs for phytate and mineral concentrations in three Arabidopsis thaliana RIL populations. Journal of Experimental Botany. 2009, Vol. 60, No. 5, p. 1409-1425. Tuesday, December 8, 2009, 4:30pm, HORT 117 David Salt, Department of Horticulture & Landscape Architecture, Purdue University "Biologiocal Significance of Natural Ionomic Variation in Arabidopsis thaliana" Associated reading: Salt DE, Baxter I, Lahner B. Ionomics and the study of the plant ionome. Annu Rev Plant Biol. 2008;59:709-33. Review. PubMed PMID: 18251712. The Bioinformatics Seminar is over for the semester. Thank you and see you SPRING 2010!!! Please contact firstname.lastname@example.org if there is a speaker (including yourself) you would like to invite for this series, or if you would like to be added to the weekly email list.