BIOINFORMATICS SEMINAR SERIES: SPRING 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
    		•
  • 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 Schedule:

    Tuesday, January 8, 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, January 15, 2008, 4:30pm, Mechanical Engineering (ME) 161
    Dr. Olga Vitek, Department of Statistics and Department of Computer Science, Purdue University
    "False discovery rates in database-based identification of tandem mass spectra"

    Associated reading:
    Alexey I. Nesvizhskii, Olga Vitek and Ruedi Aebersold. 2007. Analysis and validation of proteomic data generated by tandem mass spectrometry. Nature Methods. 4(10):787-797.

    Tuesday, January 22, 2008, 4:30pm, Mechanical Engineering (ME) 161
    No Seminar

    Tuesday, January 29, 2008, 4:30pm, Mechanical Engineering (ME) 161
    Dr. Rebecca Doerge, Department of Statistics, Department of Agronomy, Purdue University
    "An Open Discussion about Academic Interviews, Careers and Life"

    Tuesday, February 5, 2008, 4:30pm, Mechanical Engineering (ME) 161
    Dr. Nathan Price, Department of Chemical and Biomolecular Engineering, Institute for Genomic Biology, University of Illinois, Urbana-Champaign, IL
    "Systems Biology in Medicine: Applications to Anemia, Diabetes, and Cancer"

    Associated reading:
    Nathan D. Price, Jonathan Trent, Adel K. El-Naggar, David Cogdell, Ellen Taylor, Kelly K. Hunt, Raphael E. Pollock, Leroy Hood, Ilya Shmulevich, and Wei Zhang. 2007. Highly accurate two-gene classifier for differentiating gastrointestinal stromal tumors and leiomyosarcomas. Proceedings of the National Academy of Sciences. USA. 104(9):3414-3419.

    Nathan D. Price, Lucas B. Edelman, Inyoul Lee, Hyuntae Yoo, Daehee Hwang, George Carlson, David J. Galas, James R. Heath, and Leroy Hood. 2008. Systems Biology and the Emergence of Systems Medicine. Prepared for Genomic and Personalized Medicine: From Principles to Practice (Ginsburg, G. and Willard, H., editors). Elsevier, in press.

    Tuesday, February 12, 2008, 4:30pm, Mechanical Engineering (ME) 161
    Dr. Yuzhen Ye, School of Informatics, Indiana University, Bloomington, IN
    "Flexible Structure Alignment"

    Associated reading:
    Yuzhen Ye and Adam Godzik. 2005. Multiple flexible structure alignment using partial order graphs. Bioinformatics, 21(10):2362-2369

    Tuesday, February 19, 2008, 4:30pm, Mechanical Engineering (ME) 161
    Dr. Bruce Walsh, Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ
    "Who's your great-great-great granddaddy? Using molecular markers to estimate genealogical dates"

    Associated reading:
    Walsh, B. 2001. Estimating the time to the MRCA for the Y chromosome or mtDNA for a pair of individuals. Genetics 158:897-912.

    A recent Forensic application:
    Walsh, B., Alan J. Redd and Michael F. Hammer. Joint match probabilities for Y chromosomal and autosomal markers. Forensic Science International 174: 234-238.

    Tuesday, February 26, 2008, 4:30pm, Mechanical Engineering (ME) 161
    Dr. Matt Vaughn, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY
    "Advancing epigenomic profiling using next-generation sequencing technologies"

    Associated reading:
    M. Vaughn, M. Tanurdzic, Z. Lippman, H. Jiang, R. Carrasquillo, V. Colot, R.W. Doerge and R.A. Martienssen. 2007. Epigenetic variation in Arabidopsis thaliana. Public Library of Science (PLoS) Biology. 5(7): e174.

    Tuesday, March 4, 2008, 4:30pm, Mechanical Engineering (ME) 161
    Dr. T.M. Murali, Department of Computer Science, Virginia Tech., Blacksburg, VA
    "Network Legos: Building Blocks of Cellular Wiring Diagrams"

    Associated Reading:
    T. M. Murali and Corban G. Rivera. Network Legos: Building Blocks of Cellular Wiring Diagrams. Proceedings of the Eleventh Annual International Conference on Research in Computational Molecular Biology (RECOMB), volume 4453 of Lecture Notes in Computer Science, pp. 47-61, 2007.

    Tuesday, March 11, 2008
    SPRING BREAK: NO SEMINAR

    Tuesday, March 18, 2008, 4:30pm, Mechanical Engineering (ME) 161
    Dr. Denise Scholtens, Department of Preventive Medicine, Northwestern University
    "Statistical Modeling of Graph Theoretic Data in Systems Biology"

    Associated Reading:
    Scholtens D, Chiang T, Huber W, Gentleman R. 2007. Estimating node degree in bait-prey graphs. Bioinformatics. 2008 Jan 15;24(2):218-24. Epub 2007 Nov 19.
    Chiang T, Scholtens D, Sarkar D, Gentleman R, Huber W. 2007. Coverage and error models of protein-protein interaction data by directed graph analysis. Genome Biol. 2007;8(9):R186.

    Tuesday, March 25, 2008, 4:30pm, Mechanical Engineering (ME) 161
    Dr. Predrag Radivojac, School of Informatics, Indiana University, Bloomington, IN
    "Methods for protein identification and quantification from tandem mass spectrometry data""

    Associated Reading:
    Tang H, Arnold RJ, Alves P, Xun Z, Clemmer DE, Novotny MV, Reilly JP, Radivojac P. A computational approach toward label-free protein quantification using predicted peptide detectability.: Bioinformatics. 2006 Jul 15;22(14):e481-8.

    Alves et al. Advancement in protein inference from shotgun proteomics using peptide detectability. Pacific Symposium on Biocomputing 12:409-420(2007).

    Tuesday, April 1, 2008, 4:30pm, Mechanical Engineering (ME) 161
    Dr. Lan Zhu, Department of Statistics, Oklahoma State University
    "Single nucleotide polymorphisms refine QTL intervals for hip joint laxity in dogs"

    Associated Reading:
    Todhunter et al. Quantitative trait loci for hip dysplasia in a crossbreed canine pedigree. Mammalian Genome.Volume 16, 720730 (2005)

    Tuesday, April 8, 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, April 15, 2008, 4:30pm, Mechanical Engineering (ME) 161
    Ms. Lingling An , Department of Statistics, Purdue Univsersity
    "Dynamic Clustering of Time Series Gene Expression"

    Tuesday, April 22, 2008, 4:30pm, Mechanical Engineering (ME) 161
    NO SEMINAR. Have a nice summer, see you Fall Semester.



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