BIOINFORMATICS SEMINAR SERIES: FALL 2009

BIOINFORMATICS SEMINAR SERIES: FALL 2009 STATISTICAL BIOINFORMATICS SEMINAR SERIES
STAT 598B is a 1 credit seminar course (public is welcome)
4:30pm on Tuesdays in Physics (PHYS) 112 (note: this is a new location)
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

Tuesday, January 12, 2010, 4:30pm, LILLY G432: 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 19, 2010, 4:30pm, Physics (PHYS) 112: NO SEMINAR
Tuesday, January 26, 2010, 4:30pm, Physics (PHYS) 112: Rebecca 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 Checklisti

5. Academic Job Interview Advice

6. Academic Interview Questions

7. Tricky (Industry) Interview Questions
Tuesday, February 2, 2010, 4:30pm, Physics (PHYS) 112: Randall Roper , Department of Biology, School of Science, Indiana University-Purdue University Indianapolis; "Altered mandibular development in Down syndrome linked to modified expression of non-trisomic genes"; Associated reading:; Randall J. Roper, Justin F. VanHorn, Colyn C. Cain, Roger H. Reeves. 2009. A neural crest deficit in Down syndrome mice is associated with deficient mitotic response to Sonic hedgehog. Mechanisms of Developmen 126:212-219.
Tuesday, February 9, 2010, 4:30pm, Physics (PHYS) 112: Jim Fleet and Min Cui, Department of Foods and Nutrition, Purdue University; "The genomics of vitamin D-mediated prostate cancer prevention"; Associated reading:; Ji, H. et al., (2008) An integrated software system for analyzing ChIP-chip and ChIP-seq data. Nature Biotechnology 26:1293.

Kovalenko, PL et al., (2010) 1,25 dihydroxyvitamin D-mediated orchestration of anticancer, transcript-level effects in the immortalized, non-transformed prostate epithelial cell line, RWPE1. BMC Genomics 11:26 (Available on-line). Ji, H. et al., (2008) An integrated software system for analyzing ChIP-chip and ChIP-seq data. Nature Biotechnology 26:1293 (attached)
Tuesday, February 16, 2010, 4:30pm, Physics (PHYS) 112: Xiao-Feng Wang, Department of Quantitative Health Sciences /Biostatistics Cleveland Clinic Foundation; School of Medicine Case Western Reserve University; "Measurement error models with applications to biomedical sciences"; Associated reading:; Xiao-Feng Wang, Zhaozhi Fan, Bin Wang. 2010. Estimating smooth distribution function in the presence of heteroscedastic measurement errors. Computational Statistics and Data Analysis 54:25-36.
Tuesday, February 23, 2010, 4:30pm, Physics (PHYS) 112: Bill Muir, Department of Animal Science, Purdue University; "Finding Genes of Interest: A mixture model approach for the analysis of small exploratory microarray experiments"; Associated reading:; Muir, W.M., G.J.M. Rosa, B.R. Pittendrigh, S. Xu, S.D. Rider, M. Fountain and J. Ogas 2008. A mixture model approach for the analysis of small exploratory microarray experiments. J. Computational Statistics and Data Analysis. doi:10.1016/j.csda.2008.06.011
Tuesday, March 2, 2010, 4:30pm, Physics (PHYS) 112: My-Hanh Thi Nguyen , Regional Applications Consultant (Bioinformatics), Roche Applied Science; "Long-Read Sequencing with the GS FLX System: Data Processing and Analysis"; Associated reading:; 1. Nitrate-responsive miR393/AFB3 regulatory module controls root system architecture in Arabidopsis thaliana; E. A. Vidal et al, 2009.; 2. MicroRNA and tasiRNA diversity in mature pollen of Arabidopsis Thaliana; R. Grant-Downton et al, 2009.; 3. Complete Khoisan and Bantu genomes from southern Africa; S. C. Schuster et al, 2010.
Tuesday, March 9, 2010, 4:30pm, Physics (PHYS) 112: No Seminar
Tuesday, March 16, 2010, 4:30pm, Physics (PHYS) 112: Spring Break. No Seminar
Tuesday, March 23, 2010, 4:30pm, Physics (PHYS) 112: Rebecca W. Doerge , Department of Statistics, 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, March 30, 2010, 4:30pm, Physics (PHYS) 112: Steve Qin , Department of Biostatistics, University of Michigan; "Detection and Refinement of Transcription Factor Binding Sites Using Hybrid Monte Carlo Method"; Associated reading:; Hu M, Yu J, Taylor, JMG, Chinnaiyan AM, Qin ZS. (2010) On the Detection and Refinement of Transcription Factor Binding Sites Using ChIP-Seq Data. Nucleic Acids Res. Jan 6. [Epub ahead of print].
Tuesday, April 6, 2010, 4:30pm, Physics (PHYS) 112: Gayla Olbricht , Department of Statistics, Purdue University; "A Hidden Markov Model with Genomic Annotation for Identifying DNA Methylation with Tiling Arrays"; Associated reading:; DNA methylation review
Suzuki, M.M., and A. Bird, (2008) DNA methylation landscapes: provocative insights from epigenomics. Nature Reviews Genetics 9: 465-476.

Example of statistical method currently being used; Ji, H., and W. H. Wong, (2005) Tilemap: Create chromosomal map of tiling array hybridizations. Bioinformatics 21: 3629-3636.
Tuesday, April 13, 2010, 4:30pm, Physics (PHYS) 112: Andrea Rau , Department of Statistics, Purdue University; "Approximate Bayesian approaches for reverse-engineering networks from time-course gene expression data"; Associated reading:; Rau et al. (2010) An empirical Bayesian method for estimating biological networks from temporal microarray data. Statistical Applica tions in Genetics and Molecular Biology 9: 1-28.; Marjoram et al. (2003) Markov chain Monte Carlo without likelihoods. Proceedings of the National Academy of Sciences 100: 15324-15328.
Tuesday, April 20, 2010, 4:30pm, Physics (PHYS) 112: Paul Auer , Department of Statistics, Purdue University; "Statistical Design and Analysis of RNA-Sequencing Data"; Associated reading:; Paul L. Auer and R.W. Doerge. 2010. Statistical Design and Analysis of RNA-Seq Data. Genetics (in press); The Bioinformatics Seminar is over for the semester. Thank you and see you FALL 2010!!!

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.