Ochoa, Alejandro, John D Storey, Manuel Llinás, and Mona Singh. (2015) 2015. “Beyond the E-Value: Stratified Statistics for Protein Domain Prediction.”. PLoS Comput Biol 11 (11): e1004509.

Hackett, Sean R, Vito R T Zanotelli, Wenxin Xu, Jonathan Goya, Junyoung O Park, David H Perlman, Patrick A Gibney, David Botstein, John D Storey, and Joshua D Rabinowitz. (2016) 2016. “Systems-Level Analysis of Mechanisms Regulating Yeast Metabolic Flux.”. Science 354 (6311). doi:10.1126/science.aaf2786.

Gresham, David, Viktor M Boer, Amy A Caudy, Naomi Ziv, Nathan J Brandt, John D Storey, and David Botstein. (2011) 2011. “System-Level Analysis of Genes and Functions Affecting Survival During Nutrient Starvation in Saccharomyces Cerevisiae.”. Genetics 187 (1): 299-317.

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.

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).

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.

Chen, Lin S, and John D Storey. (2008) 2008. “Eigen-R2 for Dissecting Variation in High-Dimensional Studies.”. Bioinformatics 24 (19): 2260-2.

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.

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.

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.