BIOINFORMATICS SEMINAR SERIES: FALL 2012
STATISTICAL BIOINFORMATICS SEMINAR SERIES
STAT 598B is a 1 credit seminar course (public is welcome)
4:30pm on Tuesdays in LILY G126

Past Seminars (scroll down for current)
FALL SPRING
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  • Spring 2012 seminar series speakers
  • Fall 2012 Schedule:

    Tuesday, August 21, 2012, 4:30pm, LILY G126
    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, 2012, 4:00pm, MRGN 121 (Discovery Park)
    Jian-Kang Zhu, Department of Horticulture & Landscape Architecture and Department of Biochemistry, Purdue University
    "Active DNA demethylation in Arabidopsis"

    Tuesday, September 4, 2012, 4:30pm, LILY G126
    Sarath Chandra Janga, School of Informatics Indiana University & Purdue University Indianapolis (IUPUI), Center for Computational Biology & Bioinformatics, Indiana University School of Medicine, Indianapolis, IN
    "Exploiting network-based approaches for understanding the dynamic and evolutionary constraints imposed on regulatory systems"

    Associated reading:
    Goodarzi H, Najafabadi HS, Oikonomou P, Greco TM, Fish L, Salavati R, Cristea IM, Tavazoie S. 2012. Systematic discovery of structural elements governing stability of mammalian messenger RNAs. Nature. Apr 8;485(7397):264-8. doi: 10.1038/nature11013.

    Tuesday,September 11, 2012, 4:30pm, LILY G126
    Lang Li, Center for Computational Biology, Indiana University School of Medicine, Indianapolis, IN
    "Drug Interaction Research: A Translational Bioinformatics Spectrum"

    Associated reading:
    Duke et al. 2012. "Literature Based Drug Interaction Prediction with Clinical Assessment Using Electronic Medical Records: Novel Myopathy Associated Drug Interactions". PLoS Comput Biol 8(8): e1002614. doi:10.1371/journal.pcbi.1002614.

    Tuesday, September 18, 2012, 4:30pm, LILY G126
    Michael Schatz, Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY
    "De novo assembly of complex genomes"

    Associated reading:
    S. Koren, M.C. Schatz, et al. 2012. Hybrid error correction and de novo assembly of single-molecule sequencing reads. Nature Biotechnology. doi:10.1038/nbt.2280.

    Tuesday, September 25, 2012, 4:30pm, LILY G126
    No Seminar

    Tuesday,October 2, 2012, 4:30pm, LILY G126
    Munni Begum, Department of Mathematical Sciences, Ball State University, Muncie, IN
    "Network motif identification and structure detection in biological databases using graphical models"

    Associated reading:
    Zachary M. Saul* and Vladimir Filkov. 2007. Exploring biological network structure using exponential random graph models. Bioinformatics. Vol. 23 no. 19 2007, pages 2604-2611.

    Tuesday, October 9, 2012, 4:30pm, LILY G126
    No Seminar. Fall Break.

    Tuesday, October 16, 2012, 4:30pm, LILY G126
    Thomas R. Gingeras, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY
    "Lessons Learned from Complex Genomes"

    Learn about ENCODE (Encyclopedia of DNA Elements): http://www.nature.com/encode/#/threads

    Associated reading:
    1. Djebali et al. 2012. Landscape of transcription in human cells. Nature. doi:10.1038/nature11233.

    2. Thurman et al. 2012. The accessible chromatin landscape of the human genome. doi:10.1038/nature11232.

    Tuesday, October 23, 2012, 4:30pm, LILY G126
    Vishwanath Iyer, Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, TX
    "Genomic views of transcriptional and post-transcriptional gene regulation"

    Associated reading:
    1. Lee et al. 2012. Cell-type specific and combinatorial usage of diverse transcription factors revealed by genome-wide binding studies in multiple human cells. Genome Res. 22: 9-24.

    2. Thurman et al. 2012. The accessible chromatin landscape of the human genome. Nature 489; doi:10.1038/nature11232.

    Tuesday, October 30, 2012, 4:30pm, LILY G126
    Kyle Bemis, Department of Statistics, Purdue University
    "Efficient Processing and Spatial Segmentation with Automated Feature Selection for DESI Imagin Mass Spectrometry"

    Associated reading:
    Alexandrov, T., and Kobarg, J. H. 2011. Efficient spatial segmentation of large imaging mass spectrometry datasets with spatially aware clustering. Bioinformatics, 27(13), i230i238. doi:10.1093/bioinformatics/btr246

    Tuesday, November 6, 2012, 4:30pm, LILY G126
    Joseph M.K. Irudayaraj, Department of Biological Engineering, Purdue University
    "Single Molecule and single particle technologies in biology"

    Associated reading:
    1. Kyuwan Lee, Vladimir P. Drachev, and Joseph Irudayaraj. 2011. DNA-Gold Nanoparticle Reversible Networks Grown on Cell Surface Marker Sites: Application in Diagnostics. ACS Nano. 2011 Mar 22;5(3):2109-17. Epub 2011 Feb 11.

    2. Lan Sun and Joseph Irudayaraj. 2009. Quantitative Surface-Enhanced Raman for Gene Expression Estimation. Biophysical Journal Volume 96:4709-4716.

    3. Jiji Chen, Andrew Miller, Ann L. Kirchmaier and Joseph M. K. Irudayaraj. 2012. Single Molecule Tools Elucidate H2A.Z Nucleosome Composition.JCS online publication date 5 March 2012.

    Tuesday, November 13, 2012, 4:30pm, LILY G126
    Paul Livermore Auer, Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA.
    "Associating Rare-Genetic Variants with Complex Traits"

    Associated reading:
    Jennifer Asimit and Eleftheria Zeggini. 2012. Rare Variant Association Analysis Methods for Complex Traits. www.annualreviews.org

    Tuesday, November 20, 2012, 4:30pm, LILY G126
    No Seminar.

    Tuesday, November 27, 2012, 4:30pm, LILY G126
    Malgorzata Bogdan, Departments of Mathematics and Computer Science, Wroclaw University of Technology and Jan Dlugosz University, Czestochowa, Poland

    "Model selection approach for genome wide association studies in admixed populations"


    Associated reading:
    1. Bogdan M, Frommlet F, Biecek P, Cheng R, Ghosh JK, Doerge RW (2008). Extending the Modified Bayesian Information Criterion (mBIC) to dense markers and multiple interval mapping. Biometrics 64: 1162--1169.

    2. Frommlet F, Ruhaltinger F, Twarg P, Bogdan M (2012) A model selection approach to genome wide association studies, Computational Statistics and Data Analysis, 56: 1038-1051.

    3. Redden DT, Divers J, Vaughan LK, Tiwari HK, Beasley TM, Fernandez JR, Kimberly RP, Feng R, Padilla MA, Liu N, Miller MB, Allison DB (2006) Regional admixture mapping and structured association testing: conceptual unification and an extensible general linear model. PLoS Genet 2:e137.

    4. Tang H, Siegmund DO, Johnson NA, Romieu I, London SJ (2010) Joint testing of genotype and ancestry association in admixed families. Genet Epidemiol 34: 783-791.

    Tuesday, December 4 2012, 4:30pm, LILY G126
    No Seminar. We are done for the semester. Thank you.

    Please contact doerge@purdue.edu 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.