BIOINFORMATICS SEMINAR SERIES: SPRING 2012

BIOINFORMATICS SEMINAR SERIES: SPRING 2012 STATISTICAL BIOINFORMATICS SEMINAR SERIES
STAT 598B is a 1 credit seminar course (public is welcome)
4:30pm on Tuesdays in PHYS 223
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

Tuesday, January 10, 2012, 4:30pm, PHYS 223: 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 17, 2012, 4:30pm, PHYS 223: No Seminar
Tuesday, January 24, 2012, 4:30pm, PHYS 223: Jyothi Thimmapura, Bioinformatics Core Director; Cyber Center, Discovery Park, Purdue University; "Bioinformatics Core Facility at Purdue University"; Associated reading:; 1. Lewitter, F., Rebhan, M., Richter, B. and Sexton, D. 2009. The Need for Centralization of Computational Biology Resources. PLoS Comput Biol. 5(6): e1000372.
2. Lewitter, F. and Rebhan, M. 2009. Establishing a Successful Bioinformatics Core Facility Team. PLoS Comput Biol. 5(6):e1000368.
3. Richter, B. and Sexton, D. 2009. Managing and Analyzing Next-Generation Sequence Data. PLoS Comput Biol. 5(6): e1000369
Tuesday, January 31, 2012, 4:30pm, PHYS 223: Yu (Michael) Zhu, Department of Statistics, Purdue University; "Using Finite Poisson Mixture Models for RNA-Seq Data Analysis and Transcript Expression Level Quantification "; Associated reading:; Ming Hu. Yu Zhu, Jeremy M.G. Taylor, Jun S. Liu, Zhaohui S. Qui. 2011. Using Poisson mixed-effects model to quantify transcript-level gene expression in RNA-Seq. Bioinformatics. 28, 1: 63-68.
http://bioinformatics.oxfordjournals.org/content/28/1/63.short?rss=1
Tuesday, February 7, 2012, 4:30pm, PHYS 223: Brian Dilkes, Department of Horticulture and Landscape Architecture, Purdue University; "Part 1: Bioinformatics for Next Generation Genetics"; Associated reading:; 1. Author suggested YouTube video (read abstract, then video). http: //www.youtube.com/watch?v=OXc5ltzKq3Y

2. Austin et al. 2011. Next-generation mapping of Arabidopsis genes. The Plant Journal (2011) 67: 715-725.
Tuesday, February 14, 2012, 4:30pm, PHYS 223: Elizabeth Buescher, Department of Horticulture and Landscape Architecture; "Part 2: "Cloning Genes Using Next Generation Sequencing"; Associated reading:; iSHOREmap: Simultaneous Mapping and Mutation Identification by Deep Sequencing. 2009. Nature Methods 6, 550-551.
Tuesday, February 21, 2012, 4:30pm, PHYS 223: Malgorzata (Gosia) Bogdan, Malgorzata (Gosia) Bogdan, Politechnika Wroclawska, Instytut Matematyki i Informatyki, Wroclaw, Poland; "Logic regression for localizing interacting quantitative trait loci"; Associated reading:; 1. Kooperberg C. and I. Ruczinski, 2005 Identifying Interacting SNPs Using Monte Carlo Logic Regression. Genetic Epidemiology 28:157-170.
2. Ruczinski, I., C. Kooperberg, M. LeBlanc, 2003 Logic regression. J. Comput. Graphical Statist. 12(3):474-511.
3. Schwender, H. and K. Ickstadt, 2008 Identification of SNP interactions using logic regression. Biostatistics 9:187-198.
Tuesday, February 28, 2012, 4:30pm, PHYS 223: Karen Kafadar, Chair & Rudy Professor of Statistics; Department of Statistics, Indiana University, Bloomington, IN; "Gene expression in Beattles tissue"; Associated reading:; 1. K. Kafadar and T. Phang. 2003. Transformations, Background Estimation, and Process Effects in the Statistical Analysis of Microarrays, Computational Statistics & Data Analysis 44(1-2), 313-338.

2. Armin P. Moczek and Lisa M. Nagy. 2005. Diverse developmental mechanisms contribute to different levels of diversity in horned beetles. EVOLUTION & DEVELOPMENT 7:3, 175-185
Tuesday, March 6, 2012, 4:30pm, PHYS 223: No Seminar
Tuesday, March 13, 2012, 4:30pm, PHYS 223: Spring Break
Tuesday, March 20, 2012, 4:30pm, PHYS 223: Glen DePalma, Department of Statistics, Purdue University; "Disk Diffusion Breakpoint Determination for Antimicrobial Susceptibility Testing"; Associated reading:; B.A. Craig. 2000. Modeling Approach to Diameter Breakpoint Determination. Diagnostic Microbiology and Infectious Disease 36.3:193-202.
Tuesday, March 27, 2012, 4:30pm, PHYS 223: Yaomin Xu, Cleveland Clinic, Cleveland, OH; "DPT Approach: A New Strategy for Differential Analysis of Multiple Enrichment-based High-throughput Sequencing Profiles"; Associated reading:; Yaomin Xu, Bo Hu, Ae-Jin Choi, et al. 2011. Unique DNA methylome profiles in CpG island methylator phenotype colon cancers. Genome Research. doi:10.1101/gr.122788.111
Tuesday, April 3, 2012, 4:30pm, PHYS 223: Danni Yu, Department of Statistics, Purdue University; "On estimating dispersion in Negative Binomial models for RNA-seq experiments with small sample size"; Associated reading:; S. Anders and W. Huber. 2010. Differential expression analysis for sequence count data. Genome Biology 2010, 11:R106.
Tuesday, April 10, 2012, 4:30pm, PHYS 223: Mi-Youn Brusniak, Institute for Systems Biology, Seattle, WA; "Design and development of open source software for discovery and validation of biomarkers"; Associated reading:; Mi-Youn Brusniak et al. 2008. Corra: Computational framework and tools for LC-MS discovery and targeted mass spectrometry-based proteomics. BMC Bioinformatics 9:542.
Tuesday, April 17, 2012, 4:30pm, PHYS 223: Stanley Pounds, Department of Biostatistics, St. Jude Children's Research Hospital; Memphis, TN; "A Genomic Random Interval Model for Functional Analysis of Genomic Lesion Data"; Associated reading:; Zhang et al. 2012. The genetic basis of early T-cell precursor acute lymphoblastic leukaemia. Nature. 481:157-163.
Tuesday, April 24, 2012, 4:30pm, PHYS 223: No Seminar; The Bioinformatics Seminar is over for the semester. Thank you and see you Fall 2012!!!

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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.