BIOINFORMATICS SEMINAR SERIES: FALL 2010

BIOINFORMATICS SEMINAR SERIES: FALL 2010 STATISTICAL BIOINFORMATICS SEMINAR SERIES
STAT 598B is a 1 credit seminar course (public is welcome)
4:30pm on Tuesdays in LILLY G126
Past Seminars (scroll down for current)

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 seminar series speakers
Fall 2008 seminar series speakers	Spring 2009 seminar series speakers
Fall 2009 seminar series speakers	Spring 2010 seminar series speakers

Tuesday, August 24, 2010, 4:30pm, LILLY G126: NO SEMINAR
Tuesday, August 31, 2010, 4:30pm, LILLY 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, September 7, 2010, 4:30pm, LILLY G126: Tim Clough , Department of Statistics, Purdue University; "Statistical Issues in Mass Spectrometry-Based Proteomics"; Associated reading:; T. Clough, M. Key, I. Ott, S. Ragg, G. Schadow, and O. Vitek. "Protein quantification in label-free LC-MS experiments ". Journal of Proteome Research, 8, 5275-5284, 2009.
Tuesday, September 14, 2010, 4:30pm, LILLY G126: Malgorzata (Gosia) Bogdan, Institute of Mathematics and Computer Science, Wroclaw University of Technology, Wroclaw, Poland; "Model Selection Approach for Genome Wide Association Studies"; Associated reading:; [1] Bogdan, M., Ghosh, J.K., and Doerge, R.W. (2004). Modifying the Schwarz Bayesian Information Criterion to locate multiple interacting quantitive trait loci. Genetics, 167, 989--999.

[2] Chen, J. and Chen, Z. (2008). Extended Bayesian Information criteria for model selection with large model spaces. Biometrika, 95, 759--771.

[3] Stranger, B.E., et al. (2007). Nature Genetics, Population genomics of human gene expression. Nature Genetics, 39: 1217--1224.
Tuesday, September 21, 2010, 4:30pm, LILLY G126: Yuri Nikolsky, GeneGo, Inc., 500 Renaissance Drive, St. Joseph, MI 49085; "Functional analysis reveals the biological underpinnings of predictive genomic signatures"; Associated reading:; Shi W., Tsyganova M., Dosymbekov D., Dezso Z., Nikolskaya T. Dudoladova M. Serebryiskaya T., Guryanov A., Brennan R., Shah R., Dopazo J., Chen M., Deng Y. Shi Y., Jurman G., Furlanello G., Thomas R.S., Corton J.C.; Tong W., Shi L., Nikolsky Y. Functional analysis reveals the biological underpinnings of predictive genomic signatures. The Pharmacogenomics J., 2010, in press
Tuesday, September 28, 2010, 4:30pm, LILLY G126: Min Zhang, Department of Statistics, Purdue University; "Empirical Bayes Method for Variable Selection with Applications to Genome-Wide Association Studies"; Associated reading:; Li and Li. 2008. Network-constrained regularization and variable selection for analysis of genomic data. Bioinformatics. 24(9):1175-1182.
Tuesday, October 5, 2010, 2010, 4:30pm, LILLY G126: Alan Qi, Department of Computer Science and Department of Statistics, Purdue University; "Sparse Bayesian learning for identifying imaging biomarkers in AD prediction"; Associated reading:; 1. Sparse Bayesian learning for identifying imaging biomarkers in AD prediction. Shen, L., Qi, Y., Kim, S., Nho, K., Wan, J., Risacher, S.L., Saykin, A.J., ADNI. Proceedings of the 13th International Conference on Medical Image Computing and Computer Assisted Intervention (MICCAI), September 20-24, 2010, Beijing, China.

2. Predictive Automatic Relevance Determination by Expectation Propagation, Yuan Qi, Thomas P. Minka, Rosalind W. Picard, and Zoubin Ghahramani, in the Proceedings of Twenty-first International Conference on Machine Learning, July 4-8, 2004, Banff, Alberta, Canada.
Tuesday, October 12, 2010: FALL BREAK. NO SEMINAR
Tuesday, October 19, 2010, 4:30pm, LILLY G126: Yuliya Karpievitch , Pacific Northwest National Laboratory, Richland, WA; "Shotgun Proteomic Data Analysis and Statistical Approaches to Protein Quantitation"; Associated reading:; Karpievitch Y, Stanley J, Taverner T, Huang J, Adkins JN, Ansong C, Heffron F, Metz TO, Qian WJ, Y oon H, Smith RD, Dabney AR. "A statistical framework for protein quantitation in bottom-up MS-based proteomics." Bioinformatics. 2009 Aug 15;25(16):2028-34.

Karpievitch YV, Taverner T, Adkins JN, Callister SJ, Anderson GA, Smith RD, Dabney AR. "Normalizat ion of peak intensities in bottom-up MS-based proteomics using singular value decomposition." Bioinformatics. 2009 Oct 1;25(19):2573-80.
Tuesday, October 26, 2010, 4:30pm, LILLY G126: R.W. Doerge, Department of Statistics, Purdue University; "Part 1: Beginning a Job Search: Academic, Industry, Government..."; Associated reading:; 1. Center for Career Opportunities (CCO), Purdue University

2. Applying for a Job (U.S. Department of Labor)

3a. How to write a cover letter.
3b. How to write an academic cover letter.

4. Academic Job Application Checklist

5. Academic Job Interview Advice

6. Academic Interview Questions

7. Tricky (Industry) Interview Questions
Tuesday, November 2, 2010, 4:30pm, LILLY G126: Sijian Wang, Department of Statistics, University of Wisconsin, Madison; "Sparse Integrative Clustering of Multiple "Omic" Data Sets"; Associated reading:; Shen R, Olshen AB, Ladanyi M. Integrative Clustering of multiple genomic data types using a joint latent variable model with application to breast and lung cancer subtype analysis. Bioinformatics 2009; 25(22): 2906-12.
Tuesday, November 9, 2010, 4:30pm, LILLY G126: R.W. Doerge, Department of Statistics, Purdue University; "Continuation of (October 26, 2010) Part 1: Beginning a Job Search: Academic, Industry, Government..."
Tuesday, November 16, 2010, 4:30pm, LILLY G126: Tilman Achberger, Department of Statistics, Purdue University; "Trait Selection for Quantitative Trait Loci Mapping via Sparse Principal Component Analysis"; Associated reading:; 1. Buescher E, Achberger T, Amusan I, Giannini A, Ochsenfeld C, et al. (2010) Natural Genetic Variation in Selected Populations of Arabidopsis thaliana Is Associated with Ionomic Differences. PLoS ONE 5(6): e11081.; 2. Shen H, Huang J. Z. (2008) Sparse Principal Component Analysis via Regularized Low Rank Matrix Approximation. Journal of Multivariate Analysis 99(6): 1015 - 1034.
Tuesday, November 23, 2010: NO SEMINAR
~~Tuesday, November 30, 2010, 4:30pm, LILLY G126~~ CANCELLED (this seminar will be scheduled for early Spring semester): R.W. Doerge, Departments of Statistics and Agronomy, Purdue University; ~~"The job interview and what to do when you get an offer (academic, industry, etc.)"~~; ~~Associated reading:~~; ~~Center for Career Opportunities (CCO), Purdue University~~
Tuesday, December 7, 2010: NO SEMINAR; The Bioinformatics Seminar is over for the semester. Thank you and see you SPRING 2011!!!

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.