BIOINFORMATICS SEMINAR SERIES: FALL 2006 ST598B is a 1 credit seminar course (public is welcome) that meets at 4:30pm on Tuesdays in Krannert (KRAN) G016.

If you would like your name added to the weekly mailing of this seminar announcement, please send an e-mail request to RW Doerge: doerge@purdue.edu


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  • Spring 2006 seminar series speakers

    FALL 2006 Schedule:

    Tuesday, August 22, 2006, 4:30pm, Krannert (KRAN) G016
    Dr. RW Doerge, Departments of Statistics and Agronomy,
    "This is an organizational meeting. All registered students must attend. If you need a registration form signed, please bring it to class."

    Tuesday, August 29, 2006, 4:30pm, Krannert (KRAN) G016
    Dr. William Muir , Department of Animal Sciences, Purdue University
    "Comparison of the FDR, pFDR, and SAM for power and error rates for analysis of microarray experiments"
    Associated reading:
    "Statistical significance for genomewide studies"
    "Significance analysis of microarrays applied to the ionizing radiation response"
    "Controlling the false discovery rate: A pratical and powerful a pproach to multiple testing"
    "SAS code for pFDR"
    "SAS code for FDR"
    "Storey link to additional reso urces"
    "Link to Stanford SAM software"

    Tuesday, September 5, 2006, 4:30pm, Krannert (KRAN) G016
    No Seminar

    Tuesday, September 12, 2006, 4:30pm, Krannert (KRAN) G016
    Dr. RW Doerge , Departments of Statistics and Agronomy, Purdue University
    "Part 1: Functional Genomics of Quantitative Traits: Expression Level Polymorphisms of QTLs Affecting Disease Resistance Pathways in Arabidopsis"
    Associated reading (pdf):
    R.W. Doerge, Z-B. Zeng and B.S. Weir. 1997. Statistical issues in the search for genes affecting quantitative traits in experimental populations. Statistical Science. 12(3):195-219.

    Tuesday, September 19, 2006, 4:30pm, Krannert (KRAN) G016
    Dr. RW Doerge , Departments of Statistics and Agronomy, Purdue University
    "Part 2: Functional Genomics of Quantitative Traits: Expression Level Polymorphisms of QTLs Affecting Disease Resistance Pathways in Arabidopsis"
    Associated reading (pdf):
    This is a postscript file, please open accordingly, or go to Nature Genetics Reviews (via Purdue online journals):
    R.W. Doerge. 2002. Mapping and analysis of quantitative trait loci in experimental populations. Nature Reviews Genetics 3:43-52.


    Tuesday, September 26, 2006, 4:30pm, Krannert (KRAN) G016
    Dr. Olga Vitek , Departments of Statistics and Computer Science, Purdue University
    "Inferential Approaches to Peptide Sequence Identification and Quantitative Protein Profiling in Mass Spectrometry-Based Proteomics"
    Associated reading (pdf):
    J. Listgarten, A. Emili "Statistical and Computational Methods for Comparative Proteomic Profiling Using Liquid Chromatography-Tandem Mass Spectrometry", Molecular and Cellular Proteomics 4:419:434, 2005.

    A. Nesvizhskii, R. Aebersold "Analysis, statistical validation and dissemination of large-scale proteomics datasets generated by tandem MS", Drug Discovery Today 9:173-181, 2004.

    Tuesday, October 3, 2006, 4:30pm, Krannert (KRAN) G016
    Showcase of Potential Ph.D. Research Topics , Department of Statistics Professors (Ghosh, D. Zhang, M. Zhang, Wu, Vitek, Xie)
    "Each professor will present potential Ph.D. research topic(s) in which they are willing to work with a current Ph.D. Statistics student."

    Tuesday, October 10, 2006, 4:30pm, Krannert (KRAN) G016
    Fall Break. No Seminar.

    Tuesday, October 17, 2006, 4:30pm, Krannert (KRAN) G016
    Ms. Leah Wetherill, Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN ,
    "Finding Genes Associated with Alcoholism: If Only It Were That Easy"
    Associated reading (pdf):
    Martin ER, Monks SA, Warren LL, Kaplan NL (2000) A test for linkage and association in general pedigrees: the pedigree disequilibrium test. Am J Hum Genet 67:146-154.

    Martin ER, Bass MP, Kaplan NL (2001) Letter to the Editor: Correcting for a potential bias in the pedigree disequilibrium test. Am J Hum Genet 68:1065-1067.

    Edenberg HJ, Xuei X, Chen HJ, Tian H, Flury-Wetherill L, Dick DM, Almasy L, Bierut L, Bucholz KK, Goate A, Hesselbrock V, Kuperman S, Nurnberger J, Porjesz B, Rice J, Schuckit M, Tischfield J, Beglieter H, Foroud T (2006) Association of alcohol dehydrogenase genes with alcohol dependence: a comprehensive analysis. Hum Mol Genet 15(9): 1539-1549.

    Tuesday, October 24, 2006, 4:30pm, Krannert (KRAN) G016
    Dr. Martina Muehlbach Bremer , Department of Statistics, Purdue University
    "Identifying Regulated Genes through the Correlation Structure of Time Dependent Microarray Data"

    Tuesday, October 31, 2006, 4:30pm, Krannert (KRAN) G016
    Dr. Dina St. Clair , Department of Plant Science, University of California, Davis
    "Global transcriptome variation in Arabidopsis thaliana"
    Associated reading: available online at Purdue e-journals
    1. West, M.A.L., K. Kim, D.J. Kliebenstein, H. van Leeuwen, R.W. Michelmore, R.W. Doerge, D.A. St.Clair. (2006) Global eQTL mapping reveals the complex genetic architecture of transcript level variation in Arabidopsis. Genetics (accepted pending revision).

    2. West, M.A.L., H. van Leeuwen, A. Kozik, D.J. Kliebenstein, R.W. Doerge, D.A. St.Clair, R.W. Michelmore. (2006) High-density haplotyping with microarray-based expression and single feature polymorphism markers in Arabidopsis. Genome Research 16:787-795.

    3. Kliebenstein, D.J., M.A.L. West, H. van Leeuwen, K. Kim, R.W. Doerge, R.W. Michelmore, D.A. St.Clair. (2006) Genomic survey of gene expression diversity in Arabidopsis thaliana. Genetics 172:1179-1189.

    4. Kliebenstein, D.J., M.A.L. West, H. van Leeuwen, O. Loudet, R.W. Doerge, D.A. St.Clair. (2006) Identification of QTLs controlling gene expression networks defined a priori. BMC Bioinformatics 7:308 (doi10.1186/1471-2105-7-308).

    Tuesday, November 7, 2006, 4:30pm, Krannert (KRAN) G016
    Dr. Malgorzata Bogdan , Institute of Mathematics and Computer Science; Wroclaw University of Technology, Poland
    "Locating quantitative trait loci with a modified version of BIC"
    Associated reading: GENETICS is available at Purdue e-journals.
    1. M.Bogdan, J.K.Ghosh and R.W.Doerge, Modifying the Schwarz Bayesian Information Criterion to Locate Multiple Interacting Quantitative Trait Loci, Genetics (2004) 167: 989-999.

    2. A. Baierl, M. Bogdan, A. Frommlet and A. Futschik, On Locating Multiple Interacting Quantitative Trait Loci in Intercross Designs, Genetics (2006) 173: 1693-1703.

    3. Z.-B. Zeng, J. Liu, L. F. Stam, C.-H. Kao, J. M. Mercer, and C. C. Laurie, Genetic Architecture of a Morphological Shape Difference Between Two Drosophila Species Genetics (2000) 154: 299-310.

    Tuesday, November 14, 2006, 4:30pm, Krannert (KRAN) G016
    Dr. Ivan Baxter , Senior Research Associate, Bindley Bioscience Center, Purdue University
    "From Genome to Gene: Using an "-omic" Aproach to Identify Causal Loci"
    Associated reading: GENETICS is available at Purdue e-journals.
    1. Lahner B, Gong J, Mahmoudian M, Smith EL, Abid KB, Rogers EE, Guerinot ML, Harper JF, Ward JM, McIntyre L, Schroeder JI, Salt DE (2003) Genomic scale profiling of nutrient and trace elements in Arabidopsis thaliana. Nat Biotechnol 21: 1215-1221

    2. Rus A, Baxter I, Muthukumar B, Gustin J, Lahner B, Yakubova E, Salt DE.* **(2006) Natural Variants of At*/*HKT1*/* Enhance Na^+ Accumulation in Two Wild Populations of Arabidopsis. PLOS Genetics*

    Tuesday, November 21, 2006, 4:30pm, Krannert (KRAN) G016
    No Seminar

    Tuesday, November 28, 2006, 4:30pm, Krannert (KRAN) G016
    Discussion with registered students about academics, working, the future, your worries/concerns/etc... Bring your hard questions...

    Thank you for a successful semester. There are no more seminars this semester. See you in January!


    Please contact doerge@purdue.edu if there is a speaker you would Like to invited for this series.