BIOINFORMATICS SEMINAR SERIES: FALL 2013

BIOINFORMATICS SEMINAR SERIES: FALL 2013 STATISTICAL BIOINFORMATICS SEMINAR SERIES
STAT 598B is a 1 credit seminar course (public is welcome)
4:30pm on Tuesdays in Rawls (RAWL) Hall 1086
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	Spring 2011 seminar series speakers
Fall 2011 seminar series speakers	Spring 2012 seminar series speakers
Fall 2012 seminar series speakers	Spring 2013 seminar series speakers

Tuesday, August 20, 2013; 4:30pm, RAWL (Rawls Hall) 1086: 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 27, 2013; 4:30pm, RAWL (Rawls Hall) 1086: RW Doerge , Department of Statistics and Department of Statistics, Purdue University; "Common Themes in Statistical Bioinformatics"; Associated reading:
1. P.L. Auer and R.W. Doerge. 2010. Statistical Design and Analysis of RNA Sequencing Data. Genetics. 185: 405-416.

2. Paul L. Auer, Sanvesh Srivastava and R.W. Doerge. 2012. Differential expressionçthe next generation and beyond. Briefings in Functional Genomics. 11 (1): 57-62.
Tuesday, September 3, 2013; 4:30pm, RAWL (Rawls Hall) 1086: No Seminar
Tuesday, September 10, 2013; 4:30pm, RAWL (Rawls Hall) 1086: Charles Addo-Quaye, Department of Horticulture and Landscape Architecture, Purdue University; "Mutation Detection for Gene Function Discovery"; Associated reading:
Nielsen, R., Paul, J. S., Albrechtsen, A. & Song, Y. S. Genotype and SNP calling from next-generation sequencing data. Nature reviews. Genetics 12, 443-51 (2011).
Tuesday, September 17, 2013; 4:30pm, RAWL (Rawls Hall) 1086: Speaker Cancellation. No seminar.
Tuesday, September 24, 2013; 4:30pm, RAWL (Rawls Hall) 1086: Alex Lipka, Postdoctoral Associate, institute for Genomic Diversity, Cornell University; "Utilizing the Genomic Association and Prediction Integrated Tool (GAPIT) R package to facilitate analysis of diverse association panels"; Associated reading:
1. Lipka, A.E., F. Tian, Q. Wang, J. Peiffer, M. Li et al., 2012 GAPIT: genome association and prediction integrated tool. Bioinformatics. 28: 2397-2399.

2. Zhang, Z., E. Ersoz, C.Q. Lai, R.J. Todhunter, H.K. Tiwari et al., 2010 Mixed linear model approach adapted for genome-wide association studies. Nat. Genet. 42: 355-360.

3. Yu, J., G. Pressoir, W.H. Briggs, I. Vroh Bi, M. Yamasaki et al., 2006 A unified mixed-model method for association mapping that accounts for multiple levels of relatedness. Nat. Genet. 38: 203-208.
Tuesday, October 1, 2013; 4:30pm, RAWL (Rawls Hall) 1086: Bill Muir, Department of Animal Science, Purdue University; "Use of Allele Specific Expression (ASE) to fine map putative QTL associated with disease"; Associated reading:
1. MacEachern S., WM Muir, SD Crosby, and HH Cheng 2012. Genome-wide identification and quantification of cis-and trans-regulated genes responding to Marek's disease virus infection via analysis of allele-specific expression. Frontiers in Genetics. 2:1-11.

2. PJ Wittkopp, BK Haerum and AG Clark. Models of regulatory divergence. Evolutionary changes in cis and trans gene regulation Nature 430, 85-88(1 July 2004) doi:10.1038/nature02698
Tuesday, October 8, 2013; 4:30pm, RAWL (Rawls Hall) 1086: No Seminar. Fall Break
Tuesday, October 15, 2013; 4:30pm, RAWL (Rawls Hall) 1086: Molly Hammell, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY; "Mobile Genomics: Controlling Transposons in Germline and Somatic Tissues"; Associated reading:
Nikolay V. Rozhkov, Molly Hammell and Gregory J. Hannon. 2013. Multiple roles for Piwi in silencing Drosophila transposons. Genes and Development 27:400-412.
Tuesday, October 22, 2013; 4:30pm, RAWL (Rawls Hall) 1086: Can Yang , Department of Biostatistics & Psychiatry, Yale School of Public Health & Medicine; "Low-Rank Approximation and Its Applications in Bioinformatics"; Associated reading:
1. Accounting for non-genetic factors by low-rank representation and sparse regression for eQTL mapping. 2013. Can Yang, Lin Wang, Shuqin Zhang, and Hongyu Zhao. Bioinformatics. Vol. 29 no. 8, pages 1026-1034.

2. Moving Object Detection by Detecting Contiguous Outliers in the Low-Rank Representation. 2013. Xiaowei Zhou, Can Yang, and Weichuan Yu. IEEE TRANSACTIONS ON PATTERN ANALYSIS AND MACHINE INTELLIGENCE, VOL. 35, NO. 3.

3. Automatic Mitral Leaflet Tracking in Echocardiography by Outlier Detection in the Low-rank Representation. 2012. Xiaowei Zhou, Can Yang, Weichuan Yu. 978-1-4673-1228-8/12/$31.00 Š2012 IEEE.

4. Multisample aCGH Data Analysis via Total Variation and Spectral Regularization. 2013. Xiaowei Zhou, Can Yang, Xiang Wan, Hongyu Zhao, and Weichuan Yu. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS, VOL. 10, NO. 1.
Tuesday, October 29, 2013; 4:30pm, RAWL (Rawls Hall) 1086: Yingqi Zhao , Department of Biostatistics, University of Wisconsin, Madison; "Challenges and New Statistical Learning Methods for Discovering Optimal Treatment Strategies"
Tuesday, November 5, 2013; 4:30pm, RAWL (Rawls Hall) 1086: Nora Bello, Department of Statistics, Kansas State University; "Heterogeneous pleiotropy in whole genome selection models"; Associated reading:
de Los Campos G, Hickey JM, Pong-Wong R, Daetwyler HD, Calus MP. Whole-genome regression and prediction methods applied to plant and animal breeding. Genetics. 2013 Feb;193(2):327-45. doi: 10.1534/genetics.112.143313
Tuesday, November 12, 2013; 4:30pm, RAWL (Rawls Hall) 1086: Olga Vitek, Department of Statistics and Department of Computer Science, Purdue University; "Protein significance analysis in quantitative targeted and data-independent mass spectrometry-based proteomics"; Associated reading:
Lukas Kall and Olga Vitek. 2011. Computational Mass Spectrometry-Based Proteomics.PLoS Computational Biology. 7:12.
Tuesday, November 19, 2013; 4:30pm, RAWL (Rawls Hall) 1086: Ali Shojaie, Department of Biostatistics, University of Washington; "Inferring Regulatory Networks by Combining Perturbation Screens and Steady State Gene Expression Profiles"; Associated reading:
1. Ali Shojaie, Alexandra Jauhiainen, Michael Kallitsis, and George Michailidis. Inferring Regulatory Networks by Combining Perturbation Screens and Steady State Gene Expression Profiles. Arxiv.

2. Supporting Information for above manuscript.
Tuesday, November 26, 2013; 4:30pm, RAWL (Rawls Hall) 1086: No Seminar. Happy Thanksgiving.
Tuesday, December 3, 2013; 4:30pm, Mechanical Engineering (ME) 1130: No Seminar. Dead week... good luck on finals!,; We are done for the semester. Thank you. See you Spring 2014 Semester...

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.

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