BIOINFORMATICS SEMINAR SERIES: FALL 2007 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
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    • FALL 2007 Schedule:

    Tuesday, August 21, 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, August 28, 2007, 4:30pm, Mechanical Engineering (ME) 161
    No Seminar

    Tuesday, September 4, 2007, 4:30pm, Mechanical Engineering (ME) 161
    Dr. Anthony Fiumera, Department of Biological Sciences, SUNY Binghamton University, NY
    "Reproductive success and the genetic basis for natural variation in sexually selected traits"

    Associated reading:
    1. Fiumera, Dumont, Clark. 2007. Associations Between Sperm Competition and Natural Variation in Male Reproductive Genes on the Third Chromosome. of Drosophila melanogaster. Genetics online.

    2. Jones et al. 2007. Estimating Differential Reproductive Success from Nests of Related Individuals, with Application to a Study of the Mottled Sculpin, Cottus bairdi. Genetics online.

    Tuesday, September 11, 2007, 4:30pm, Mechanical Engineering (ME) 161
    Dr. Yuan (Alan) Qi, Department of Computer Science, Department of Statistics, and Department of Biology (courtesy), Purdue University
    "Bayesian Machine Learning for Deciphering Gene Regulation"

    Associated reading:
    1. High-resolution Computational Models of Genome Binding Events, Y. Qi, A. Rolfe, K. D. MacIsaac, G. K. Gerber, D. Pokholok, J. Zeitlinger, T. Danford, R. D. Dowell, E. Fraenkel, T. S. Jaakkola, R. A. Young and D. K. Gifford, Nature Biotechnology, vol. 24, 963-970, August, 2006.

    2. Semi-supervised Analysis of Gene Expression Profiles for Lineage-specific Development in the Caenorhabditis Elegans Embryo, Yuan Qi, Patrycja E. Missiuro, Ashish Kapoor, Craig P. Hunter, Tommi S. Jaakkola, David K. Gifford and Hui Ge, Bioinformatics, vol. 22, no. 14, e417-e423, 2006.


    Tuesday, September 18, 2007, 4:30pm, Mechanical Engineering (ME) 161
    Dr. Jessica Schlueter, Postdoctoral Research Associate, Department of Agronomy, Purdue University
    "Identification and Analysis of Genome Duplication in Soybean"

    Associated reading:
    Schlueter, J.A., J-Y Lin, S.D. Schlueter, I.F. Vasylenko-Sanders, S. Deshpande, J. Yi, M. Siegfried, B.A. Roe, R.T. Nelson, B.E. Scheffler, S.A. Jackson and R.C. Shoemaker. 2007. Genome duplication in soybean and the implications for whole genome sequencing. BMC Genomics in press.

    Figures and Supplemental Material for Schlueter et al. manuscript

    Tuesday, September 25, 2007, 4:30pm, Mechanical Engineering (ME) 161
    Dr. RW Doerge, Department of Statistics, Department of Agronomy, Purdue University
    "Part 1: How to find, apply, and interview for a job (academic, industry, etc.)"

    Associated reading (direct links provided):
    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 2, 2007, 4:30pm, Mechanical Engineering (ME) 161
    Dr. Min Zhang, Department of Statistics, Purdue University
    "Bayesian Approach for Identifying Molecular Signatures"

    Associated reading:
    M. Zhang and D. Zhang. 2007. Bayesian profiling of molecular signatures to predict event times. Theor Biol Med Model. 2007; 4:3.

    Tuesday, October 9, 2007, 4:30pm, Mechanical Engineering (ME) 161
    Fall Break: No Seminar. ,

    Tuesday, October 16, 2007, 4:30pm, Mechanical Engineering (ME) 161
    Dr. Ivan Baxter , Senior Research Associate, Bindley Bioscience Center, Purdue University
    "Mapping and Modeling the Arabidopsis Ionome"

    Associated reading:
    1. Rus A, Baxter I, Muthukumar B, Gustin J, Lahner B, et al. (2006) Natural Variants of AtHKT1 Enhance Na+ Accumulation in Two Wild Populations of Arabidopsis. PLoS Genet 2(12): e210.

    2. Baxter et al. (2007) Purdue Ionomics Information Management System. An Integrated Functional Genomics Platform. Plant Physiology 143:600-611.

    3. Zhao K, Aranzana MJ, Kim S, Lister C, Shindo C, et al. (2007) An Arabidopsis Example of Association Mapping in Structured Samples. PLoS Genet 3(1): e4.

    Tuesday, October 23, 2007, 4:30pm, Mechanical Engineering (ME) 161
    Ph.D. Candidate, Mr. Riyan Cheng , Department of Statistics, Purdue University
    "Statistical Methods for Mapping Multiple Complex Traits"

    Associated reading:
    Jiang and Zeng (1995). Multiple trait analysis of genetic mapping for quantitative trait loci. Genetics 140: 1111-1127.

    Tuesday, October 30, 2007, 4:30pm, Mechanical Engineering (ME) 161
    No Seminar

    Tuesday, November 6, 2007, 4:30pm, Mechanical Engineering (ME) 161
    Dr. Tian Zheng , Department of Statistics, Columbia University
    "Studying co-regulation and inter-regulation of genes via eQTL mapping"

    Associated reading:
    Morley et al. 2004. Genetic analysis of genome-wide variation in human gene expression. Nature. 43:743-747.

    NOTE: DATE AND LOCATION CHANGE:=> Tuesday, November 13, 2007, will be held November 15, 2007 4:30pm, MATH 175
    All registered students expected to atttend, please let RWD know if you will not attend
    Dr. Kim Siegmund, Department of Preventive Medicine University of Southern California
    "DNA methylation patterns tell a tale of cancer stem cells"

    Associated reading:
    Paul Marjoram* and Simon Tavare. 2006. Modern computational approaches for analysing molecular genetic variation data. Nature Reviews Genetics. 7:759-770.

    Tuesday, November 20, 2007, 4:30pm, Mechanical Engineering (ME) 161
    Thanksgiving Break: No Seminar.

    Tuesday, November 27, 2007, 4:30pm, Mechanical Engineering (ME) 161
    Dr. Shannon Schlueter, Department of Computer and Information Technology, Purdue University
    "Computational Genomics: Developing Workflow Systems for Data Processing and Management"

    Associated reading:
    Schlueter SD, Wilkerson MD, Dong Q, Brendel V. xGDB: open-source computational infrastructure for the integrated evaluation and analysis of genome features. Genome Biol. 2006;7(11):R111.

    Wilkerson MD, Schlueter SD, Brendel V. yrGATE: a web-based gene-structure annotation tool for the identification and dissemination of eukaryotic genes. Genome Biol. 2006;7(7):R58.

    Duncan Hull, Katy Wolstencroft, Robert Stevens, Carole Goble, Mathew R. Pocock, Peter Li and Tom Oinn Taverna: a tool for building and running workflows of services Nucleic Acids Research 2006 34(Web Server issue):W729-W732; doi:10.1093/nar/gkl320

    Tuesday, December 4, 2007, 4:30pm, Mechanical Engineering (ME) 161
    Dr. RW Doerge , Department of Statistics and Department of Agronomy, Purdue University
    "Part 2: The job interview and what to do when you get an offer (academic, industry, etc.)"

    Open forum to discuss career choices, academic careers, and everything more...

    Tuesday, December 11, 2007
    No Seminar. We are finished for the semester. See you for the Bioinformatics Seminar in 2008!!! (Tuesdays 4:30pm)

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