BIOINFORMATICS SEMINAR SERIES: FALL 2008 ST598B is a 1 credit seminar course (public is welcome) that meets at 4:30pm on Tuesdays in Mechanical Engineering (ME) 161.

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

FALL SPRING
  • Fall 2000 seminar series speakers
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  • Spring 2001 seminar series speakers
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  • Spring 2008 seminar series speakers

    • FALL 2008 Schedule:

    Tuesday, August 26, 2008, 4:30pm, Mechanical Engineering (ME) 161
    Dr. 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 2, 2008, 4:30pm, Mechanical Engineering (ME) 161
    Dr. Alan Willse, Crop Biometrics Group, Monsanto Company, St. Louis, MO
    "Statistics and quantitative genetics in commercial plant biotechnology and breeding R&D"

    Tuesday, September 9, 2008, 4:30pm, Mechanical Engineering (ME) 161
    Dr. Dabao Zhang, Department of Statistics, Purdue University
    "On Preprocessing and Analyzing GCGC-MS Data "

    Associated reading:
    Dabao Zhang, Xiaodong Huang, Fred E. Regnier, Min Zhang. 2008. Two-Dimensional Correlation Optimized Warping Algorithm for Aligning GCGC-MS Data.

    Tuesday, September 16, 2008, 4:30pm, Mechanical Engineering (ME) 161
    Dr. Jun Xie, Department of Statistics, Purdue University
    "Group variable selection methods for data with interdependent structures"

    Associated reading:
    Zeng and Xie. 2008. Regularization and variable selection for data with interdependent structures.

    Tuesday, September 23, 2008, 4:30pm, Mechanical Engineering (ME) 161
    CANCELLED
    Dr. Peter Waddell, Department of Biological Sciences, Purdue University, and Allan Wilson Institute for Molecular Ecology and Evolution, Massey University, New Zealand
    "Molecular Divergence Time Estimation"

    Associated reading:
    WADDELL, P.J., AND D. PENNY. (1996). Evolutionary trees of apes and humans from DNA sequences. In: "Handbook of Symbolic Evolution", pp 53 -73. Ed. A.J. Lock and C.R. Peters. Clarendon Press, Oxford.

    KITAZOE, Y., H. KISHINO, P.J. WADDELL, N. NAKAJIMA, T. OKABAYASHI, T. WATABE, AND Y. OKUHARA. (2007). Robust time estimation reconciles views of the antiquity of placental mammals. PLoS ONE. 2007 2:e384.

    WADDELL, P.J. (2007). Comparing a menagarie of molecular divergence time models. arXiv 0712:4332

    Tuesday, September 30, 2008, 4:30pm, Mechanical Engineering (ME) 161
    Dr. RW Doerge, Department of Statistics, Purdue University
    "Part 1: Beginning a Job Search: Academic, Industry, Government..."

    Associated reading:
    1. Applying for a Job (U.S. Department of Labor)

    2a. (Cover letter information; Craig's List)
    2b. (Academic cover letter information)

    3. (Information on applying for academic jobs)


    Tuesday, October 7, 2008, 4:30pm, Mechanical Engineering (ME) 161
    Dr. Hongmei Jiang, Department of Statistics, Northwestern University, Evanston, IL
    "Gene set analysis for microarray gene expression data"

    Associated reading:
    1. Discovering statistically significant pathways in expression profiling studies. 2005. PNAS.

    2. Analyzing gene expression data in terms of gene sets: methodological issues. 2007. Bioinformatics.


    Tuesday, October 14, 2008, 4:30pm, Mechanical Engineering (ME) 161
    NO SEMINAR: Fall Break

    Tuesday, October 21, 2008, 4:30pm, Mechanical Engineering (ME) 161
    Mr. Rick Westerman, Bioinformatics Specialist, Genomics Facility, Purdue University
    "Second generation sequencing: An overview plus potential benefits and pitfalls"

    Associated reading:
    1. Next-Generation Sequencing: The Race is on. Cell 132, March 7, 2008. Andreas von Bubnoff.

    2. Next-Generation DNA Sequencing Methods. Annual Review of Genetics and Human Genetics, 9:387-402. Elaine R Mardis.

    3. Bioinformatics challenges of new sequencing technology. Trends in Genetics. Volume 24, Issue 3, March 2008, Pages 142-149. Mihai Pop, Steven L. Salzberg.

    4. Sequencing of natural strains of Arabidopsis thaliana with short reads. Genome Research. (pre-print) Sep 25, 2008. Stephan Ossowski, et. al


    Tuesday, October 28, 2008, 4:30pm, Mechanical Engineering (ME) 161
    Dr. Peter Waddell, Department of Biological Sciences, Purdue University, and Allan Wilson Institute for Molecular Ecology and Evolution, Massey University, New Zealand
    "Molecular Divergence Time Estimation"

    Associated reading:
    WADDELL, P.J., AND D. PENNY. (1996). Evolutionary trees of apes and hu mans from DNA sequences. In: "Handbook of Symbolic Evolution", pp 53 -73. Ed. A.J. Lock and C.R. Peters. Clarendon Press, Oxford.

    KITAZOE, Y., H. KISHINO, P.J. WADDELL, N. NAKAJIMA, T. OKABAYASHI, T. WATABE, AND Y. OK UHARA. (2007). Robust time estimation reconciles views of the antiquity of placental mammals. PLoS ONE. 2007 2:e384.

    WADDELL, P.J. (2007). Comparing a menagarie of molecular divergence time models. arXiv 0712:4332


    Tuesday, November 4, 2008, 4:30pm, Mechanical Engineering (ME) 161
    NO SEMINAR

    Tuesday, November 11, 2008, 4:30pm, Mechanical Engineering (ME) 161
    Dr. Bill Muir,PULSe Molecular Evolutionary Genetics program and Department of Animal Sciences, Purdue University
    "Missing Alleles as a Metric of Biodiversity: An Example Using Commercial Poultry"

    Associated reading:
    Muir, WM., GKS Wong, Y Zhang, J Wang, MAM Groenen, RPMA Crooijmans, HJ Megens, H Zhang, R Okimoto, A Vereijken, A Jungerius, GAA Albers, C Taylor-Lawley, ME Delany, S MacEachern, and HH Cheng. 2008. Genome-Wide Assessment of World-Wide Chicken SNP Genetic Diversity Indicates Significant Absence of Rare Alleles in Commercial Breeds. Proceeds of the National Academy of Sciences. November 11, 2008 vol. 105 no. 45 17313.

    Tuesday, November 18, 2008, 4:30pm, Mechanical Engineering (ME) 161
    Dr. Shizhong Xu, Department of Botany and Plant Sciences, University of California, Riverside, CA
    "Bayesian Shrinkage Mapping of Quantitative Trait Loci"

    Associated reading:
    Xu, S. 2003. Estimating polygenic effects using markers of the entire genome. Genetics 163:789-801.

    Xu, S. 2007. An empirical Bayes method for estimating epistatic effects of quantitative trait loci. Biometrics 63:513-521.

    Yi, N. J. and S. H. Xu. 2008. Bayesian LASSO for quantitative trait loci mapping. Genetics 179:1045-1055.

    Tuesday, November 25, 2008, 4:30pm, Mechanical Engineering (ME) 161
    NO SEMINAR

    Tuesday, December 2, 2008, 4:30pm, Mechanical Engineering (ME) 161
    Dr. RW Doerge, Department of Statistics, Purdue University
    "Part 2: The job interview and what to do when you get an offer (academic, industry, etc.)"



    Tuesday, December 9, 2008, 4:30pm, Mechanical Engineering (ME) 161
    NO SEMINAR. Thank you for a great semester!

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