BIOINFORMATICS SEMINAR SERIES: SPRING 2011

BIOINFORMATICS SEMINAR SERIES: SPRING 2011 STATISTICAL BIOINFORMATICS SEMINAR SERIES
STAT 598B is a 1 credit seminar course (public is welcome)
4:30pm on Tuesdays in HORT 117
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
Fall 2010 seminar series speakers

Tuesday, January 11, 2011, 4:30pm, HORT 117: NO SEMINAR
Tuesday, January 18, 2011, 4:30pm, HORT 117: 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 25, 2011, 4:30pm, HORT 117: Sanvesh Srivastava , Department of Statistics, Purdue University; "Workflow for a Statistical Data Analysis Project"; Associated reading:; [1] Galili, T. 2010. Managing a statistical analysis project -guidelines and best practices, R-statistics blog.
[2] Smith, D.M. 2010. A workflow in R, Revolution Analytics Blog.
[3] Healy, K. 2011. Choosing Your Workflow Applications.
Tuesday, February 1, 2011, 4:30pm, HORT 117: Rebecca 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.)"; 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, February 8, 2011, 4:30pm, HORT 117: Danni Yu , Department of Statistics, Purdue University; "Noise reduction in genome-wide perturbation screens using linear mixed-effect models"; Associated reading:; Malo, N. et al. 2006. Statistical practice in high-throughput screening data analysis. Nature Biotechnology 24:167-175.
Tuesday, February 15, 2011, 4:30pm, HORT 117: Sael Lee, Department of Biology/Computer Science, Purdue University; "Predicting Protein Function by Surface Comparison"; Associated reading:; 1. Sael, Lee, Bin Li, David La, Yi Fang, Karthik Ramani, and Raif Rustamov, Kih. "Fast protein tertiary structure retrieval based on global surface shape similarity." Proteins: Structure, Function, and Bioinformatics 72, no. 4 (2008): 1259-1273.

2. Sael, Lee, and Daisuke Kihara. "Binding Ligand Prediction for Proteins Using Partial Matching of Local Surface Patches." International Journal of Molecular Sciences 11, no. 12 (December 2010): 5009-5026.
Tuesday, February 22, 2011, 4:30pm, HORT 117: Vitara Pungpapong, Department of Statistics, Purdue University; "A Fast and Efficient Approach for Genomic Selection"; Associated reading:; 1. Meuwissen, T.H.E., Hayes, B.J., and Goddard, M.E. (2001). Prediction of total genetic value using genome-wide dense marker maps. Genetics, 157: 1819-1829.

2. Zhang, D., Lin, Y., and Zhang, M. (2009). Penalized orthogonal-components regression for large p small n data. Electronic Journal of Statistics, 3: 781-796.
Tuesday, March 1, 2011, 4:30pm, HORT 117: Yunlong Liu, Department of Medical and Molecular Genetics, Center for Computational Biology and Bioinformatics Center for Medical Genomics, Indiana University School of Medicine, Indianapolis, IN; "Statistical modeling in non-coding RNA mediated regulatory network"; Associated reading:; 1. Wang G, Wang Y, Shen C, Huang YW, Huang K, Huang TH, Nephew KP, Li L, Liu Y. 2010. RNA polymerase II binding patterns reveal genomic regions involved in microRNA gene regulation. PLoS One. Nov 2;5(11):e13798.

2. Wang G, Wang Y, Teng M, Zhang D, Li L, Liu Y. 2010. Signal transducers and activators of transcription-1 (STAT1) regulates microRNA transcription in interferon gamma-stimulated HeLa cells. PLoS One. Jul 26;5(7):e11794.
Tuesday, March 8, 2011, 4:30pm, HORT 117: Veavi Chang, Department of Statistics, Purdue University; "Statistical framework for protein quantification with Selected Reaction Monitoring (SRM) experiments"; Associated reading:; P. Picotti, B. Bodenmiller, L.N. Mller, B. Domon and R. Aebersold. Full dynamic range proteome analysis of S. cerevisiae by targeted proteomics. (2009) Cell, 138(4):795-806, 2009.
Tuesday, March 15, 2011, 4:30pm, HORT 117: SPRING BREAK. No seminar.
Tuesday, March 22, 2011, 4:30pm, HORT 117: Hyonho Chun, Department of Statistics, Purdue University; "Joint estimation of multiple Gaussian graphical models by nonconvex penalty functions with an application to genomic data"; Associated reading:; Jian Guo, Elizaveta Levina, George Michailidis and Ji Zhu. 2011. Joint estimation of multiple graphical models. Biometrika (2011) 98 (1): 1-15.
Tuesday, March 29, 2011, 4:30pm, HORT 117: Ji-Ping Wang, Department of Statistics, Northwestern Univeristy, Evanston, IL; "Bayesian approach for deconvolution of sparsely convolved nucleosome signals in yeast"; Associated reading:; 1. Segal et al. 2006. A genomic code for nucleosome positioning link. Nature 442:772-778.

2. Wang et al. 2008. Preferentially quantized linker DNA lengths in Saccharomyces cerevisiae. PLoS Comput Biol 4(9): e1000175. doi:10.1371/journal.pcbi.1000175

3. Xi et al. 2010. Predicting nucleosome positioning using a duration Hidden Markov Model. BMC Bioinformatics 2010, 11:346
Tuesday, April 5, 2011, 4:30pm, HORT 117: Yanzhu Lin, Department of Statistics, Purdue University; "Fitting High-Dimensional Generalized Linear Models via Supervised Dimension Reduction"; Associated reading:; Dabao Zhang, Yanzhu Lin, Min Zhang. 2009. Penalized orthogonal-components regression for large p small n data. Electronic Journal of Statistics. Vol. 3 (2009) 781-796.
Tuesday, April 12, 2011, 4:30pm, HORT 117: Mehmet Koyutürk, T. & D. Schroeder Assistant Professor of Computer Science & Engineering, Department of Electrical Engineering and Computer Science, Center for Proteomics and Bioinformatics; Case Western Reserve University, Clevland, OH; "Integrative -omics for the Systems Biology of Complex Phenotypes"; Associated reading:; Salim A. Chowdhury, Rod K. Nibbe, Mark R. Chance, and Mehmet Koyuturk. 2010. Subnetwork State Functions Define Dysregulated Subnetworks in Cancer. B. Berger (Ed.): RECOMB 2010, LNBI 6044, pp. 80-95. Springer-Verlag Berlin Heidelberg.
Tuesday, April 19, 2011, 4:30pm, HORT 117: Lauren McIntyre Department of Molecular Genetics and Microbiology, University of Florida; "Widespread allelic imbalance in Drosophila hybrid heads"; Associated reading:; Rita M. Graze, Lauren M. McIntyre, Bradley J. Main, Marta L. Wayne, and Sergey V. Nuzhdin. 2009. Regulatory Divergence in Drosophila melanogaster and D. simulans, a Genomewide Analysis of Allele-Specific Expression. Genetics. 183: 547-561.; Website: all data and code.
Tuesday, April 26, 2011, 4:30pm, HORT 117: Tilman Achberger, Department of Statistics, Purdue University; "Selecting Proper Degrees of Sparsity for Sparse CCA with Applications to Analyzing Multiple Data Sets in QTL Mapping"; Associated reading:; 1. Parkhomenko, E., D. Tritchler, and J. Beyene (2009). Sparse canonical correlation analysis with application to genomic data integration. Statistical Applications in Genetics and Molecular Biology 8 (1), Article 1.

2. Buescher, E., T. Achberger, I. Amusan, A. Giannini, C. Ochsenfeld, A. Rus, B. Lahner, O. Hoekenga, E. Yakubova, J. F. Harper, M. L. Guerinot, M. Zhang, D. E. Salt, and I. R. Baxter (2010). Natural genetic variation in selected populations of Arabidopsis thaliana is associated with ionomic differences. PLoS ONE 5 (6), e11081.
Tuesday, May 3, 2011, 4:30pm, HORT 117: No Seminar.; The Bioinformatics Seminar is over for the semester. Thank you and see you Fall 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.