John Storey Position William R. Harman '63 and Mary-Love Harman Professor in Genomics. Title Lewis-Sigler Institute for Integrative Genomics Email [email protected] Assistant Everett L. Morgan Office 270D Carl Icahn Laboratory Bio/Description Research FocusMy lab develops and applies quantitative methods in genomics. We are particularly focused on functional genomics problems involving high-dimensional data sets, such as that obtained from large-scale genotyping, gene expression monitoring, and mass spectroscopy based proteomics. Because our research deals with large amounts of noisy data, we also develop theory and methods for statistics and machine learning.This is an especially exciting time for quantitative genomics, as many studies are underway that involve multiple types of large-scale data. For example, we are working on studies involving high-throughput measurements on mRNA expression, protein expression, metabolite levels, protein-DNA binding, chromatin structure, and DNA sequences.The over-arching goal of our research is to utilize multiple sources of high-throughput genomic data to understand biological regulatory networks and the molecular basis of complex traits. This involves characterizing the "wiring diagram" of the molecular biology of the cell. The ultimate goal is to build a quantitative system for understanding how the hard-wired components of a cell, such as DNA sequence and epigenetic factors, interact with the environment to determine the dynamic molecular behavior of the cell, as manifested in variables such as RNA expression, protein expression, enzymatic activity, and eventually as complex traits.Specific problems we are working on include:Inferring causal regulatory networks from studies involving high-throughput molecular profiling (e.g., RNA and protein expression) and large-scale genotyping.Decomposing sources of gene expression variation in complex clinical and experimental settings.Understanding the genetic and epigenetic determinants of the gene expression program.Developing quantitative approaches to providing a causal "molecular dissection" of complex traits.Understanding the relationship between evolutionary forces driving natural genetic variation and its effect on variation in expression levels of gene products.Developing new theory and methods for high-dimensional statistical inference, large-scale significance testing, and machine learningComplete list of PublicationsGoogle Scholar Selected Publications Robinson, David G, and John D Storey. (2014) 2014. “SubSeq: Determining Appropriate Sequencing Depth Through Efficient Read Subsampling.”. Bioinformatics 30 (23): 3424-6. Chung, Neo Christopher, and John D Storey. (2014) 2014. “Statistical Significance of Variables Driving Systematic Variation in High-Dimensional Data.”. Bioinformatics. Kim, Jinhee, Nima Ghasemzadeh, Danny J Eapen, Neo Christopher Chung, John D Storey, Arshed A Quyyumi, and Greg Gibson. 2014. “Gene Expression Profiles Associated With Acute Myocardial Infarction and Risk of Cardiovascular Death.”. Genome Med 6 (5): 40. Marstrand, Troels T, and John D Storey. (2014) 2014. “Identifying and Mapping Cell-Type-Specific Chromatin Programming of Gene Expression.”. Proc Natl Acad Sci U S A 111 (6). Robinson, David G, Wei Chen, John D Storey, and David Gresham. (2014) 2014. “Design and Analysis of Bar-Seq Experiments.”. G3 (Bethesda) 4 (1): 11-8. Chung, Neo Christopher, and John D Storey. (2014) 2014. “Statistical Significance of Variables Driving Systematic Variation in High-Dimensional Data.”. Bioinformatics. Jaffe, Andrew, John Storey, Hongkai Ji, and Jeffrey Leek. (2013) 2013. “Gene Set Bagging for Estimating the Probability a Statistically Significant Result Will Replicate.”. BMC Bioinformatics 14: 360. doi:10.1186/1471-2105-14-360. Marstrand, Troels T, and John D Storey. (2014) 2014. “Identifying and Mapping Cell-Type-Specific Chromatin Programming of Gene Expression.”. Proc Natl Acad Sci U S A 111 (6). Leek, Jeffrey, Evan Johnson, Hilary Parker, Andrew Jaffe, and John Storey. (2012) 2012. “The Sva Package for Removing Batch Effects and Other Unwanted Variation in High-Throughput Experiments.”. Bioinformatics (Oxford, England) 28 (6): 882-3. doi:10.1093/bioinformatics/bts034. Xiao, Wenzhong, Michael Mindrinos, Junhee Seok, Joseph Cuschieri, Alex Cuenca, Hong Gao, Douglas Hayden, et al. (2011) 2011. “A Genomic Storm in Critically Injured Humans.”. The Journal of Experimental Medicine 208 (13): 2581-90. doi:10.1084/jem.20111354. View all publications Desai, Keyur H, Chuen Seng Tan, Jeffrey T Leek, Ronald Maier V, Ronald G Tompkins, John D Storey, and Inflammation and the Host Response to Injury Large-Scale Collaborative Research Program. (2011) 2011. “Dissecting Inflammatory Complications in Critically Injured Patients by Within-Patient Gene Expression Changes: A Longitudinal Clinical Genomics Study.”. PLoS Med 8 (9): e1001093. Kanodia, Jitendra S, Yoosik Kim, Raju Tomer, Zia Khan, Kwanghun Chung, John D Storey, Hang Lu, Philipp J Keller, and Stanislav Y Shvartsman. (2011) 2011. “A Computational Statistics Approach for Estimating the Spatial Range of Morphogen Gradients.”. Development 138 (22): 4867-74. Xu, Weihong, Junhee Seok, Michael Mindrinos, Anthony Schweitzer, Hui Jiang, Julie Wilhelmy, Tyson Clark, et al. (2011) 2011. “Human Transcriptome Array for High-Throughput Clinical Studies.”. Proceedings of the National Academy of Sciences of the United States of America 108 (9): 3707-12. doi:10.1073/pnas.1019753108. Woo, Sangsoon, Jeffrey Leek, and John Storey. (2011) 2011. “A Computationally Efficient Modular Optimal Discovery Procedure.”. Bioinformatics (Oxford, England) 27 (4): 509-15. doi:10.1093/bioinformatics/btq701. Program(s) NIH NHGRI Training Program QCB Graduate Program Research Area Computational Genomics Evolutionary and Population Genomics Statistical Genomics LSI Research Lab Storey Research Lab