storeylab.github.io/index.xml at master · StoreyLab/storeylab.github.io · GitHub

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    <title>Storey Lab on John Storey Lab | Princeton University</title>
    <link>https://storeylab.org/</link>
    <description>Recent content in Storey Lab on John Storey Lab | Princeton University</description>
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      <title>Research</title>
      <link>https://storeylab.org/patterns/research/</link>
      <pubDate>Mon, 01 Jan 0001 00:00:00 +0000</pubDate>
      <guid>https://storeylab.org/patterns/research/</guid>
      <description>&lt;!-- raw HTML omitted --&gt;&#xA;&lt;p&gt;&lt;img src=&#34;https://storeylab.org/images/research.gif#center&#34; alt=&#34;Images of published research figures&#34;&gt;&lt;/p&gt;&#xA;&lt;!-- raw HTML omitted --&gt;&#xA;&lt;!-- raw HTML omitted --&gt;&#xA;&lt;p&gt;The Storey Lab&amp;rsquo;s current research efforts are in the following areas:&lt;/p&gt;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Extending fundamental population genetics models and quantities &amp;mdash; such as allele frequencies, Hardy-Weinberg equilibrium, &#xA;&lt;em&gt;F&lt;/em&gt;&lt;sub&gt;ST&lt;/sub&gt;, admixture, ancestry, and kinship &amp;mdash; to genome-wide genotype data making minimal assumptions about population structure&lt;/li&gt;&#xA;&lt;li&gt;Improving the accuracy and applicability of the polygenic trait model in population-based studies for determining the genetic basis of complex traits, including association studies, genome-wide heritability, and polygenic risk scores&lt;/li&gt;&#xA;&lt;li&gt;Developing causal inference methods and study designs for population-based genetics studies of complex traits&lt;/li&gt;&#xA;&lt;li&gt;Latent variable decompositions of high-dimensional data, with an&#xA;emphasis on admixture, population structure, and exponential family distributions&lt;/li&gt;&#xA;&lt;li&gt;Latent variable modeling in the context of high-dimensional significance testing &amp;mdash; such as surrogate variable analysis and cross-dimensional inference&lt;/li&gt;&#xA;&lt;li&gt;Signficance testing on high-dimensional regression models&lt;/li&gt;&#xA;&lt;li&gt;Models and estimators for false discovery rates and q-values&lt;/li&gt;&#xA;&lt;/ul&gt;</description>
    </item>
    <item>
      <title>Publications</title>
      <link>https://storeylab.org/patterns/publications/</link>
      <pubDate>Mon, 01 Jan 0001 00:00:00 +0000</pubDate>
      <guid>https://storeylab.org/patterns/publications/</guid>
      <description>&lt;ol&gt;&#xA;&lt;li&gt;Tang, Y., I. Cabreros, and J. D. Storey (2026). &amp;ldquo;Identifying causal genotype-phenotype relationships for population-sampled parent-child trios&amp;rdquo;. &lt;em&gt;Genetic Epidemiology&lt;/em&gt; 50: e70027. &lt;a href=&#34;https://doi.org/10.1002/gepi.70027&#34;&gt;https://doi.org/10.1002/gepi.70027&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;Chen, D. and J. D. Storey (2025). &amp;ldquo;Coancestry superposed on admixed populations yields measures of relatedness at individual-level resolution&amp;rdquo;. &lt;em&gt;PLoS Computational Biology&lt;/em&gt; 21(12): e1013848. &lt;a href=&#34;https://doi.org/10.1371/journal.pcbi.1013848&#34;&gt;https://doi.org/10.1371/journal.pcbi.1013848&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;Tang, Y., and J. D. Storey (2025). &amp;ldquo;A generalized test of genotype-phenotype causality in population-sampled nuclear families&amp;rdquo;. &lt;em&gt;bioRxiv&lt;/em&gt; doi:10.64898/2025.12.29.696865. &lt;a href=&#34;https://doi.org/10.64898/2025.12.29.696865&#34;&gt;https://doi.org/10.64898/2025.12.29.696865&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;Storey, J. D. (2025). &amp;ldquo;False discovery rate&amp;rdquo;. In: &lt;em&gt;International Encyclopedia of Statistical Science&lt;/em&gt;, 2nd ed. Ed. by M. Lovric. Springer Berlin, Heidelberg. &lt;a href=&#34;https://link.springer.com/rwe/10.1007/978-3-662-69359-9_229&#34;&gt;https://link.springer.com/rwe/10.1007/978-3-662-69359-9_229&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;Chen, D. and J. D. Storey (2024). &amp;ldquo;Coancestry superposed on admixed populations yields measures of relatedness at individual-level resolution&amp;rdquo;. &lt;em&gt;bioRxiv&lt;/em&gt; doi:10.1101/2024.12.29.630632. &lt;a href=&#34;https://doi.org/10.1101/2024.12.29.630632&#34;&gt;https://doi.org/10.1101/2024.12.29.630632&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;Tang, Y., I. Cabreros, and J. D. Storey (2024). &amp;ldquo;Identifying causal genotype-phenotype relationships for population-sampled parent-child trios&amp;rdquo;. &lt;em&gt;bioRxiv&lt;/em&gt; doi:10.1101/2024.12.10.627752. &lt;a href=&#34;https://doi.org/10.1101/2024.12.10.627752&#34;&gt;https://doi.org/10.1101/2024.12.10.627752&lt;/a&gt;.&lt;/li&gt;&#xA;&lt;li&gt;Ochoa, A. and J. D. Storey (2021). &amp;ldquo;Estimating &#xA;&lt;em&gt;F&lt;/em&gt;&lt;sub&gt;ST&lt;/sub&gt; and kinship for arbitrary population structures&amp;rdquo;. &lt;em&gt;PLoS Genetics&lt;/em&gt; 17.1: e1009241. &lt;a href=&#34;https://doi.org/10.1371/journal.pgen.1009241&#34;&gt;https://doi.org/10.1371/journal.pgen.1009241&lt;/a&gt;.&lt;/li&gt;&#xA;&lt;li&gt;Graim, K. and et al. (2021). &amp;ldquo;Modeling molecular development of breast cancer in canine mammary tumors&amp;rdquo;. &lt;em&gt;Genome Research&lt;/em&gt; 31: 337-347. &lt;a href=&#34;https://doi.org/10.1101/gr.256388.119&#34;&gt;https://doi.org/10.1101/gr.256388.119&lt;/a&gt;.&lt;/li&gt;&#xA;&lt;li&gt;Bass, A. J. and J. D. Storey (2021). &amp;ldquo;The optimal discovery procedure for significance analysis of general gene expression studies&amp;rdquo;. &lt;em&gt;Bioinformatics&lt;/em&gt; 37.3, pp. 367-374. &lt;a href=&#34;https://doi.org/10.1093/bioinformatics/btaa707&#34;&gt;https://doi.org/10.1093/bioinformatics/btaa707&lt;/a&gt;.&lt;/li&gt;&#xA;&lt;li&gt;Chen, X., D. G. Robinson, and J. D. Storey (2021). &amp;ldquo;The functional false discovery rate with applications to genomics&amp;rdquo;. &lt;em&gt;Biostatistics&lt;/em&gt; 22.1, pp. 68-81. &lt;a href=&#34;https://dx.doi.org/10.1093/biostatistics/kxz010&#34;&gt;https://dx.doi.org/10.1093/biostatistics/kxz010&lt;/a&gt;.&lt;/li&gt;&#xA;&lt;li&gt;Bass, A. J., D. G. Robinson, and J. D. Storey (2019). &amp;ldquo;Determining sufficient sequencing depth in RNA-Seq differential expression studies&amp;rdquo;. &lt;em&gt;bioRxiv&lt;/em&gt; doi:10.1101/635623. &lt;a href=&#34;https://dx.doi.org/10.1101/635623&#34;&gt;https://dx.doi.org/10.1101/635623&lt;/a&gt;.&lt;/li&gt;&#xA;&lt;li&gt;Bass, A. J. and J. D. Storey (2019). &amp;ldquo;The optimal discovery procedure for significance analysis of general gene expression studies&amp;rdquo;. &lt;em&gt;bioRxiv&lt;/em&gt; doi:10.1101/571992. &lt;a href=&#34;https://dx.doi.org/10.1101/571992&#34;&gt;https://dx.doi.org/10.1101/571992&lt;/a&gt;.&lt;/li&gt;&#xA;&lt;li&gt;Ochoa, A. and J. D. Storey (2019). &amp;ldquo;New kinship and &#xA;&lt;em&gt;F&lt;/em&gt;&lt;sub&gt;ST&lt;/sub&gt; estimates reveal higher levels of differentiation in the global human population&amp;rdquo;. &lt;em&gt;bioRxiv&lt;/em&gt; doi:10.1101/653279. &lt;a href=&#34;https://dx.doi.org/10.1101/653279&#34;&gt;https://dx.doi.org/10.1101/653279&lt;/a&gt;.&lt;/li&gt;&#xA;&lt;li&gt;Ochoa, A. and J. D. Storey (2019). &amp;ldquo;&#xA;&lt;em&gt;F&lt;/em&gt;&lt;sub&gt;ST&lt;/sub&gt; and kinship for arbitrary population structures II: Method-of-moments estimators&amp;rdquo;. &lt;em&gt;bioRxiv&lt;/em&gt; doi:10.1101/083923. &lt;a href=&#34;https://dx.doi.org/10.1101/083923&#34;&gt;https://dx.doi.org/10.1101/083923&lt;/a&gt;.&lt;/li&gt;&#xA;&lt;li&gt;Ochoa, A. and J. D. Storey (2019). &amp;ldquo;&#xA;&lt;em&gt;F&lt;/em&gt;&lt;sub&gt;ST&lt;/sub&gt; and kinship for arbitrary population structures I: Generalized definitions&amp;rdquo;. &lt;em&gt;bioRxiv&lt;/em&gt; doi:10.1101/083915. &lt;a href=&#34;https://dx.doi.org/10.1101/083915&#34;&gt;https://dx.doi.org/10.1101/083915&lt;/a&gt;.&lt;/li&gt;&#xA;&lt;li&gt;Cabreros, I. and J. D. Storey (2019). &amp;ldquo;A likelihood-free estimator of population structure bridging admixture models and principal components analysis&amp;rdquo;. &lt;em&gt;Genetics&lt;/em&gt; 212.4, pp. 1009-1029. &lt;a href=&#34;https://dx.doi.org/10.1534/genetics.119.302159&#34;&gt;https://dx.doi.org/10.1534/genetics.119.302159&lt;/a&gt;.&lt;/li&gt;&#xA;&lt;li&gt;Hao, W. and J. D. Storey (2019). &amp;ldquo;Extending tests of Hardy-Weinberg equilibrium to structured populations&amp;rdquo;. &lt;em&gt;Genetics&lt;/em&gt; 213.3, pp. 759-770. &lt;a href=&#34;https://dx.doi.org/10.1534/genetics.119.302370&#34;&gt;https://dx.doi.org/10.1534/genetics.119.302370&lt;/a&gt;.&lt;/li&gt;&#xA;&lt;li&gt;Cabreros, I. and J. D. Storey (2019). &amp;ldquo;Causal models on probability spaces&amp;rdquo;. &lt;em&gt;arXiv&lt;/em&gt; 1907.01672. &lt;a href=&#34;https://arxiv.org/abs/1907.01672&#34;&gt;https://arxiv.org/abs/1907.01672&lt;/a&gt;.&lt;/li&gt;&#xA;&lt;li&gt;Cabreros, I. and J. D. Storey (2019). &amp;ldquo;A likelihood-free estimator of population structure bridging admixture models and principal components analysis&amp;rdquo;. &lt;em&gt;bioRxiv&lt;/em&gt; doi:10.1101/240812. &lt;a href=&#34;https://dx.doi.org/10.1101/240812&#34;&gt;https://dx.doi.org/10.1101/240812&lt;/a&gt;.&lt;/li&gt;&#xA;&lt;li&gt;Painter, H. J., N. C. Chung, A. Sebastian, I. Albert, J. D. Storey, and M. Llinás (2018). &amp;ldquo;Genome-wide real-time in vivo transcriptional dynamics during Plasmodium falciparum blood-stage development&amp;rdquo;. &lt;em&gt;Nature Communications&lt;/em&gt; 9.1, p. 2656. &lt;a href=&#34;http://dx.doi.org/10.1038/s41467-018-04966-3&#34;&gt;http://dx.doi.org/10.1038/s41467-018-04966-3&lt;/a&gt;.&lt;/li&gt;&#xA;&lt;li&gt;Painter, H. J., N. C. Chung, A. Sebastian, I. Albert, J. D. Storey, and M. Llinás (2018). &amp;ldquo;Genome-wide real-time in vivo transcriptional dynamics during Plasmodium falciparum blood-stage development&amp;rdquo;. &lt;em&gt;bioRiv&lt;/em&gt; doi:10.1101/265975. &lt;a href=&#34;http://dx.doi.org/10.1101/265975&#34;&gt;http://dx.doi.org/10.1101/265975&lt;/a&gt;.&lt;/li&gt;&#xA;&lt;li&gt;Hao, W. and J. D. Storey (2017). &amp;ldquo;Extending tests of Hardy-Weinberg equilibrium to structured populations&amp;rdquo;. &lt;em&gt;bioRxiv&lt;/em&gt; doi:10.1101/240804. &lt;a href=&#34;https://dx.doi.org/10.1101/240804&#34;&gt;https://dx.doi.org/10.1101/240804&lt;/a&gt;.&lt;/li&gt;&#xA;&lt;li&gt;Cabreros, I. and J. D. Storey (2017). &amp;ldquo;A nonparametric estimator of population structure unifying admixture models and principal components analysis&amp;rdquo;. &lt;em&gt;bioRxiv&lt;/em&gt; doi:10.1101/240812. &lt;a href=&#34;https://dx.doi.org/10.1101/240812&#34;&gt;https://dx.doi.org/10.1101/240812&lt;/a&gt;.&lt;/li&gt;&#xA;&lt;li&gt;Chen, X., D. G. Robinson, and J. D. Storey (2017). &amp;ldquo;The functional false discovery rate with applications to genomics&amp;rdquo;. &lt;em&gt;bioRxiv&lt;/em&gt; doi:10.1101/241133. &lt;a href=&#34;https://dx.doi.org/10.1101/241133&#34;&gt;https://dx.doi.org/10.1101/241133&lt;/a&gt;.&lt;/li&gt;&#xA;&lt;li&gt;Hackett, S. R. and J. D. Storey (2017). &amp;ldquo;Mixed membership martial arts: Data-driven analysis of winning martial arts styles&amp;rdquo;. &lt;em&gt;MIT Sloan Sports Analytics Conference&lt;/em&gt;. &lt;a href=&#34;http://www.sloansportsconference.com/wp-content/uploads/2017/02/1575.pdf&#34;&gt;http://www.sloansportsconference.com/wp-content/uploads/2017/02/1575.pdf&lt;/a&gt;.&lt;/li&gt;&#xA;&lt;li&gt;Ochoa, A. and J. D. Storey (2016). &amp;ldquo;&#xA;&lt;em&gt;F&lt;/em&gt;&lt;sub&gt;ST&lt;/sub&gt; and kinship for arbitrary population structures II: Method of moments estimators&amp;rdquo;. &lt;em&gt;bioRxiv&lt;/em&gt; doi:10.1101/083923. &lt;a href=&#34;https://dx.doi.org/10.1101/083923&#34;&gt;https://dx.doi.org/10.1101/083923&lt;/a&gt;.&lt;/li&gt;&#xA;&lt;li&gt;Ochoa, A. and J. D. Storey (2016). &amp;ldquo;&#xA;&lt;em&gt;F&lt;/em&gt;&lt;sub&gt;ST&lt;/sub&gt; and kinship for arbitrary population structures I: Generalized definitions&amp;rdquo;. &lt;em&gt;bioRxiv&lt;/em&gt; doi:10.1101/083915. &lt;a href=&#34;https://dx.doi.org/10.1101/083915&#34;&gt;https://dx.doi.org/10.1101/083915&lt;/a&gt;.&lt;/li&gt;&#xA;&lt;li&gt;Gopalan, P., W. Hao, D. M. Blei, and J. D. Storey (2016). &amp;ldquo;Scaling probabilistic models of genetic variation to millions of humans&amp;rdquo;. &lt;em&gt;Nature Genetics&lt;/em&gt; 48.12, pp. 1587-1590. &lt;a href=&#34;https://dx.doi.org/10.1038/ng.3710&#34;&gt;https://dx.doi.org/10.1038/ng.3710&lt;/a&gt;.&lt;/li&gt;&#xA;&lt;li&gt;Hackett, S. R., V. R. T. Zanotelli, W. Xu, J. Goya, J. O. Park, D. H. Perlman, et al. (2016). &amp;ldquo;Systems-level analysis of mechanisms regulating yeast metabolic flux&amp;rdquo;. &lt;em&gt;Science&lt;/em&gt; 354.6311, pp. aaf2786-aaf2786. &lt;a href=&#34;https://dx.doi.org/10.1126/science.aaf2786&#34;&gt;https://dx.doi.org/10.1126/science.aaf2786&lt;/a&gt;.&lt;/li&gt;&#xA;&lt;li&gt;Hao, W., M. Song, and J. D. Storey (2015). &amp;ldquo;Probabilistic models of genetic variation in structured populations applied to global human studies&amp;rdquo;. &lt;em&gt;Bioinformatics&lt;/em&gt; 32.5, pp. 713-721. &lt;a href=&#34;https://dx.doi.org/10.1093/bioinformatics/btv641&#34;&gt;https://dx.doi.org/10.1093/bioinformatics/btv641&lt;/a&gt;.&lt;/li&gt;&#xA;&lt;li&gt;Song, M., W. Hao, and J. D. Storey (2015). &amp;ldquo;Testing for genetic associations in arbitrarily structured populations&amp;rdquo;. &lt;em&gt;Nature Genetics&lt;/em&gt; 47.5, pp. 550-554. &lt;a href=&#34;https://dx.doi.org/10.1038/ng.3244&#34;&gt;https://dx.doi.org/10.1038/ng.3244&lt;/a&gt;.&lt;/li&gt;&#xA;&lt;li&gt;Robinson, D. G., J. Y. Wang, and J. D. Storey (2015). &amp;ldquo;A nested parallel experiment demonstrates differences in intensity-dependence between RNA-seq and microarrays&amp;rdquo;. &lt;em&gt;Nucleic Acids Research&lt;/em&gt;, p. gkv636. &lt;a href=&#34;https://dx.doi.org/10.1093/nar/gkv636&#34;&gt;https://dx.doi.org/10.1093/nar/gkv636&lt;/a&gt;.&lt;/li&gt;&#xA;&lt;li&gt;Ochoa, A., J. D. Storey, M. Llinás, and M. Singh (2015). &amp;ldquo;Beyond the E-Value: Stratified statistics for protein domain prediction&amp;rdquo;. &lt;em&gt;PLOS Computational Biology&lt;/em&gt; 11.11, p. e1004509. &lt;a href=&#34;https://dx.doi.org/10.1371/journal.pcbi.1004509&#34;&gt;https://dx.doi.org/10.1371/journal.pcbi.1004509&lt;/a&gt;.&lt;/li&gt;&#xA;&lt;li&gt;Gopalan, P., W. Hao, D. M. Blei, and J. D. Storey (2015). &amp;ldquo;Scaling probabilistic models of genetic variation to millions of humans&amp;rdquo;. &lt;em&gt;bioRxiv&lt;/em&gt; doi:10.1101/013227. &lt;a href=&#34;https://dx.doi.org/10.1101/013227&#34;&gt;https://dx.doi.org/10.1101/013227&lt;/a&gt;.&lt;/li&gt;&#xA;&lt;li&gt;Chen, X. and J. D. Storey (2015). &amp;ldquo;Consistent estimation of low-dimensional latent structure in high-dimensional data&amp;rdquo;. &lt;em&gt;arXiv&lt;/em&gt; 1510.03497. &lt;a href=&#34;https://arxiv.org/abs/1510.03497&#34;&gt;https://arxiv.org/abs/1510.03497&lt;/a&gt;.&lt;/li&gt;&#xA;&lt;li&gt;Song, M., W. Hao, and J. D. Storey (2015). &amp;ldquo;Testing for genetic associations in arbitrarily structured populations&amp;rdquo;. &lt;em&gt;bioRxiv&lt;/em&gt; doi:10.1101/012682. &lt;a href=&#34;https://dx.doi.org/10.1101/012682&#34;&gt;https://dx.doi.org/10.1101/012682&lt;/a&gt;.&lt;/li&gt;&#xA;&lt;li&gt;Robinson, D. G. and J. D. Storey (2014). &amp;ldquo;subSeq: Determining appropriate sequencing depth through efficient read subsampling&amp;rdquo;. &lt;em&gt;Bioinformatics&lt;/em&gt; 30.23, pp. 3424-3426. &lt;a href=&#34;https://dx.doi.org/10.1093/bioinformatics/btu552&#34;&gt;https://dx.doi.org/10.1093/bioinformatics/btu552&lt;/a&gt;.&lt;/li&gt;&#xA;&lt;li&gt;Chung, N. C. and J. D. Storey (2014). &amp;ldquo;Statistical significance of variables driving systematic variation in high-dimensional data&amp;rdquo;. &lt;em&gt;Bioinformatics&lt;/em&gt; 31.4, pp. 545-554. &lt;a href=&#34;https://dx.doi.org/10.1093/bioinformatics/btu674&#34;&gt;https://dx.doi.org/10.1093/bioinformatics/btu674&lt;/a&gt;.&lt;/li&gt;&#xA;&lt;li&gt;Marstrand, T. T. and J. D. Storey (2014). &amp;ldquo;Identifying and mapping cell-type-specific chromatin programming of gene expression&amp;rdquo;. &lt;em&gt;Proceedings of the National Academy of Sciences&lt;/em&gt; 111.6, pp. E645-E654. &lt;a href=&#34;https://dx.doi.org/10.1073/pnas.1312523111&#34;&gt;https://dx.doi.org/10.1073/pnas.1312523111&lt;/a&gt;.&lt;/li&gt;&#xA;&lt;li&gt;Kim, J., N. Ghasemzadeh, D. J. Eapen, N. Chung, J. D. Storey, A. A. Quyyumi, et al. (2014). &amp;ldquo;Gene expression profiles associated with acute myocardial infarction and risk of cardiovascular death&amp;rdquo;. &lt;em&gt;Genome Medicine&lt;/em&gt; 6.5, p. 40. &lt;a href=&#34;https://dx.doi.org/10.1186/gm560&#34;&gt;https://dx.doi.org/10.1186/gm560&lt;/a&gt;.&lt;/li&gt;&#xA;&lt;li&gt;Ochoa, A., J. D. Storey, M. Llinás, and M. Singh (2014). &amp;ldquo;Beyond the E-value: Stratified statistics for protein domain prediction&amp;rdquo;. &lt;em&gt;arXiv&lt;/em&gt; 1409.6384. &lt;a href=&#34;https://arxiv.org/abs/1409.6384&#34;&gt;https://arxiv.org/abs/1409.6384&lt;/a&gt;.&lt;/li&gt;&#xA;&lt;li&gt;Robinson, D. G., J. Wang, and J. D. Storey (2014). &amp;ldquo;A nested parallel experiment demonstrates differences in intensity-dependence between RNA-seq and microarrays&amp;rdquo;. &lt;em&gt;bioRxiv&lt;/em&gt; doi:10.1101/013342. &lt;a href=&#34;https://dx.doi.org/10.1101/013342&#34;&gt;https://dx.doi.org/10.1101/013342&lt;/a&gt;.&lt;/li&gt;&#xA;&lt;li&gt;Robinson, D. G., W. Chen, J. D. Storey, and D. Gresham (2013). &amp;ldquo;Design and analysis of bar-seq experiments&amp;rdquo;. &lt;em&gt;G3: Genes | Genomes | Genetics&lt;/em&gt; 4.1, pp. 11-18. &lt;a href=&#34;https://dx.doi.org/10.1534/g3.113.008565&#34;&gt;https://dx.doi.org/10.1534/g3.113.008565&lt;/a&gt;.&lt;/li&gt;&#xA;&lt;li&gt;Jaffe, A. E., J. D. Storey, H. Ji, and J. T. Leek (2013). &amp;ldquo;Gene set bagging for estimating the probability a statistically significant result will replicate&amp;rdquo;. &lt;em&gt;BMC Bioinformatics&lt;/em&gt; 14.1, p. 360. &lt;a href=&#34;https://dx.doi.org/10.1186/1471-2105-14-360&#34;&gt;https://dx.doi.org/10.1186/1471-2105-14-360&lt;/a&gt;.&lt;/li&gt;&#xA;&lt;li&gt;Jaffe, A. E., J. D. Storey, H. Ji, and J. T. Leek (2013). &amp;ldquo;Gene set bagging for estimating replicability of gene set analyses&amp;rdquo;. &lt;em&gt;arXiv&lt;/em&gt; 1301.3933. &lt;a href=&#34;https://arxiv.org/abs/1301.3933&#34;&gt;https://arxiv.org/abs/1301.3933&lt;/a&gt;.&lt;/li&gt;&#xA;&lt;li&gt;Hao, W., M. Song, and J. D. Storey (2013). &amp;ldquo;Probabilistic models of genetic variation in structured populations applied to global human studies&amp;rdquo;. &lt;em&gt;arXiv&lt;/em&gt; 1312.2041. &lt;a href=&#34;https://arxiv.org/abs/1312.2041&#34;&gt;https://arxiv.org/abs/1312.2041&lt;/a&gt;.&lt;/li&gt;&#xA;&lt;li&gt;Chung, N. C. and J. D. Storey (2013). &amp;ldquo;Statistical significance of variables driving systematic variation&amp;rdquo;. &lt;em&gt;arXiv&lt;/em&gt; 1308.6013. &lt;a href=&#34;https://arxiv.org/abs/1308.6013&#34;&gt;https://arxiv.org/abs/1308.6013&lt;/a&gt;.&lt;/li&gt;&#xA;&lt;li&gt;Leek, J. T., W. E. Johnson, H. S. Parker, A. E. Jaffe, and J. D. Storey (2012). &amp;ldquo;The sva package for removing batch effects and other unwanted variation in high-throughput experiments&amp;rdquo;. &lt;em&gt;Bioinformatics&lt;/em&gt; 28.6, pp. 882-883. &lt;a href=&#34;https://dx.doi.org/10.1093/bioinformatics/bts034&#34;&gt;https://dx.doi.org/10.1093/bioinformatics/bts034&lt;/a&gt;.&lt;/li&gt;&#xA;&lt;li&gt;Desai, K. H. and J. D. Storey (2012). &amp;ldquo;Cross-dimensional inference of dependent high-dimensional data&amp;rdquo;. &lt;em&gt;Journal of the American Statistical Association&lt;/em&gt; 107.497, pp. 135-151. &lt;a href=&#34;https://dx.doi.org/10.1080/01621459.2011.645777&#34;&gt;https://dx.doi.org/10.1080/01621459.2011.645777&lt;/a&gt;.&lt;/li&gt;&#xA;&lt;li&gt;Marstrand, T. T. and J. D. Storey (2011). &amp;ldquo;Identifying and mapping cell-type specific chromatin programming of gene expression&amp;rdquo;. &lt;em&gt;arXiv&lt;/em&gt; 1210.3313. &lt;a href=&#34;https://arxiv.org/abs/1210.3313&#34;&gt;https://arxiv.org/abs/1210.3313&lt;/a&gt;.&lt;/li&gt;&#xA;&lt;li&gt;Xu, W., J. Seok, M. N. Mindrinos, A. C. Schweitzer, H. Jiang, J. Wilhelmy, et al. (2011). &amp;ldquo;Human transcriptome array for high-throughput clinical studies&amp;rdquo;. &lt;em&gt;Proceedings of the National Academy of Sciences&lt;/em&gt; 108.9, pp. 3707-3712. &lt;a href=&#34;https://dx.doi.org/10.1073/pnas.1019753108&#34;&gt;https://dx.doi.org/10.1073/pnas.1019753108&lt;/a&gt;.&lt;/li&gt;&#xA;&lt;li&gt;Xiao, W., M. N. Mindrinos, J. Seok, J. Cuschieri, A. G. Cuenca, H. Gao, et al. (2011). &amp;ldquo;A genomic storm in critically injured humans&amp;rdquo;. &lt;em&gt;The Journal of Experimental Medicine&lt;/em&gt; 208.13, pp. 2581-2590. &lt;a href=&#34;https://dx.doi.org/10.1084/jem.20111354&#34;&gt;https://dx.doi.org/10.1084/jem.20111354&lt;/a&gt;.&lt;/li&gt;&#xA;&lt;li&gt;Storey, J. D. (2011). &amp;ldquo;False discovery rate&amp;rdquo;. In: &lt;em&gt;International Encyclopedia of Statistical Science&lt;/em&gt;. Ed. by M. Lovric. Springer Nature, pp. 504-508. &lt;a href=&#34;https://dx.doi.org/10.1007/978-3-642-04898-2_248&#34;&gt;https://dx.doi.org/10.1007/978-3-642-04898-2_248&lt;/a&gt;.&lt;/li&gt;&#xA;&lt;li&gt;Leek, J. T. and J. D. Storey (2011). &amp;ldquo;The joint null criterion for multiple hypothesis tests&amp;rdquo;. &lt;em&gt;Statistical Applications in Genetics and Molecular Biology&lt;/em&gt; 10.1, pp. 2361-2373. &lt;a href=&#34;https://dx.doi.org/10.2202/1544-6115.1673&#34;&gt;https://dx.doi.org/10.2202/1544-6115.1673&lt;/a&gt;.&lt;/li&gt;&#xA;&lt;li&gt;Kanodia, J. S., Y. Kim, R. Tomer, Z. Khan, K. Chung, J. D. Storey, et al. (2011). &amp;ldquo;A computational statistics approach for estimating the spatial range of morphogen gradients&amp;rdquo;. &lt;em&gt;Development&lt;/em&gt; 138.22, pp. 4867-4874. &lt;a href=&#34;https://dx.doi.org/10.1242/dev.071571&#34;&gt;https://dx.doi.org/10.1242/dev.071571&lt;/a&gt;.&lt;/li&gt;&#xA;&lt;li&gt;Desai, K. H., C. S. Tan, J. T. Leek, R. V. Maier, R. G. Tompkins, and J. D. Storey (2011). &amp;ldquo;Dissecting inflammatory complications in critically injured patients by within-patient gene expression changes: A longitudinal clinical genomics study&amp;rdquo;. &lt;em&gt;PLoS Medicine&lt;/em&gt; 8.9, p. e1001093. &lt;a href=&#34;https://dx.doi.org/10.1371/journal.pmed.1001093&#34;&gt;https://dx.doi.org/10.1371/journal.pmed.1001093&lt;/a&gt;.&lt;/li&gt;&#xA;&lt;li&gt;Woo, S., J. T. Leek, and J. D. Storey (2010). &amp;ldquo;A computationally efficient modular optimal discovery procedure&amp;rdquo;. &lt;em&gt;Bioinformatics&lt;/em&gt; 27.4, pp. 509-515. &lt;a href=&#34;https://dx.doi.org/10.1093/bioinformatics/btq701&#34;&gt;https://dx.doi.org/10.1093/bioinformatics/btq701&lt;/a&gt;.&lt;/li&gt;&#xA;&lt;li&gt;Gresham, D., V. M. Boer, A. Caudy, N. Ziv, N. J. Brandt, J. D. Storey, et al. (2010). &amp;ldquo;System-level analysis of genes and functions affecting survival during nutrient starvation in Saccharomyces cerevisiae&amp;rdquo;. &lt;em&gt;Genetics&lt;/em&gt; 187.1, pp. 299-317. &lt;a href=&#34;https://dx.doi.org/10.1534/genetics.110.120766&#34;&gt;https://dx.doi.org/10.1534/genetics.110.120766&lt;/a&gt;.&lt;/li&gt;&#xA;&lt;li&gt;Mecham, B. H., P. S. Nelson, and J. D. Storey (2010). &amp;ldquo;Supervised normalization of microarrays&amp;rdquo;. &lt;em&gt;Bioinformatics&lt;/em&gt; 26.10, pp. 1308-1315. &lt;a href=&#34;https://dx.doi.org/10.1093/bioinformatics/btq118&#34;&gt;https://dx.doi.org/10.1093/bioinformatics/btq118&lt;/a&gt;.&lt;/li&gt;&#xA;&lt;li&gt;Kruglyak, L. and J. D. Storey (2009). &amp;ldquo;Cause and express&amp;rdquo;. &lt;em&gt;Nature Biotechnology&lt;/em&gt; 27.6, pp. 544-545. &lt;a href=&#34;https://dx.doi.org/10.1038/nbt0609-544&#34;&gt;https://dx.doi.org/10.1038/nbt0609-544&lt;/a&gt;.&lt;/li&gt;&#xA;&lt;li&gt;Kall, L., J. D. Storey, and W. S. Noble (2009). &amp;ldquo;QVALITY: Non-parametric estimation of q-values and posterior error probabilities&amp;rdquo;. &lt;em&gt;Bioinformatics&lt;/em&gt; 25.7, pp. 964-966. &lt;a href=&#34;https://dx.doi.org/10.1093/bioinformatics/btp021&#34;&gt;https://dx.doi.org/10.1093/bioinformatics/btp021&lt;/a&gt;.&lt;/li&gt;&#xA;&lt;li&gt;Schadt, E. E., C. Molony, E. Chudin, K. Hao, X. Yang, P. Y. Lum, et al. (2008). &amp;ldquo;Mapping the genetic architecture of gene expression in human liver&amp;rdquo;. &lt;em&gt;PLoS Biology&lt;/em&gt; 6.5. Ed. by G. Abecassis, p. e107. &lt;a href=&#34;https://dx.doi.org/10.1371/journal.pbio.0060107&#34;&gt;https://dx.doi.org/10.1371/journal.pbio.0060107&lt;/a&gt;.&lt;/li&gt;&#xA;&lt;li&gt;Leek, J. T. and J. D. Storey (2008). &amp;ldquo;A general framework for multiple testing dependence&amp;rdquo;. &lt;em&gt;Proceedings of the National Academy of Sciences&lt;/em&gt; 105.48, pp. 18718-18723. &lt;a href=&#34;https://dx.doi.org/10.1073/pnas.0808709105&#34;&gt;https://dx.doi.org/10.1073/pnas.0808709105&lt;/a&gt;.&lt;/li&gt;&#xA;&lt;li&gt;Kall, L., J. D. Storey, and W. S. Noble (2008). &amp;ldquo;Non-parametric estimation of posterior error probabilities associated with peptides identified by tandem mass spectrometry&amp;rdquo;. &lt;em&gt;Bioinformatics&lt;/em&gt; 24.16, pp. i42-i48. &lt;a href=&#34;https://dx.doi.org/10.1093/bioinformatics/btn294&#34;&gt;https://dx.doi.org/10.1093/bioinformatics/btn294&lt;/a&gt;.&lt;/li&gt;&#xA;&lt;li&gt;Käll, L., J. D. Storey, M. J. MacCoss, and W. S. Noble (2008). &amp;ldquo;Posterior error probabilities and false discovery rates: two sides of the same coin&amp;rdquo;. &lt;em&gt;Journal of Proteome Research&lt;/em&gt; 7.1, pp. 40-44. &lt;a href=&#34;https://dx.doi.org/10.1021/pr700739d&#34;&gt;https://dx.doi.org/10.1021/pr700739d&lt;/a&gt;.&lt;/li&gt;&#xA;&lt;li&gt;Käll, L., J. D. Storey, M. J. MacCoss, and W. S. Noble (2008). &amp;ldquo;Assigning significance to peptides identified by tandem mass spectrometry using decoy databases&amp;rdquo;. &lt;em&gt;Journal of Proteome Research&lt;/em&gt; 7.1, pp. 29-34. &lt;a href=&#34;https://dx.doi.org/10.1021/pr700600n&#34;&gt;https://dx.doi.org/10.1021/pr700600n&lt;/a&gt;.&lt;/li&gt;&#xA;&lt;li&gt;Idaghdour, Y., J. D. Storey, S. J. Jadallah, and G. Gibson (2008). &amp;ldquo;A genome-wide gene expression signature of environmental geography in leukocytes of Moroccan Amazighs&amp;rdquo;. &lt;em&gt;PLoS Genetics&lt;/em&gt; 4.4. Ed. by G. Barsh, p. e1000052. &lt;a href=&#34;https://dx.doi.org/10.1371/journal.pgen.1000052&#34;&gt;https://dx.doi.org/10.1371/journal.pgen.1000052&lt;/a&gt;.&lt;/li&gt;&#xA;&lt;li&gt;Hao, K., E. E. Schadt, and J. D. Storey (2008). &amp;ldquo;Calibrating the performance of SNP arrays for whole-genome association studies&amp;rdquo;. &lt;em&gt;PLoS Genetics&lt;/em&gt; 4.6. Ed. by G. R. Abecasis, p. e1000109. &lt;a href=&#34;https://dx.doi.org/10.1371/journal.pgen.1000109&#34;&gt;https://dx.doi.org/10.1371/journal.pgen.1000109&lt;/a&gt;.&lt;/li&gt;&#xA;&lt;li&gt;Chen, L. S. and J. D. Storey (2008). &amp;ldquo;Eigen-$R^2$ for dissecting variation in high-dimensional studies&amp;rdquo;. &lt;em&gt;Bioinformatics&lt;/em&gt; 24.19, pp. 2260-2262. &lt;a href=&#34;https://dx.doi.org/10.1093/bioinformatics/btn411&#34;&gt;https://dx.doi.org/10.1093/bioinformatics/btn411&lt;/a&gt;.&lt;/li&gt;&#xA;&lt;li&gt;Biswas, S., J. D. Storey, and J. M. Akey (2008). &amp;ldquo;Mapping gene expression quantitative trait loci by singular value decomposition and independent component analysis&amp;rdquo;. &lt;em&gt;BMC Bioinformatics&lt;/em&gt; 9.1, p. 244. &lt;a href=&#34;https://dx.doi.org/10.1186/1471-2105-9-244&#34;&gt;https://dx.doi.org/10.1186/1471-2105-9-244&lt;/a&gt;.&lt;/li&gt;&#xA;&lt;li&gt;Storey, J. D., J. Madeoy, J. L. Strout, M. Wurfel, J. Ronald, and J. M. Akey (2007). &amp;ldquo;Gene-Expression Variation Within and Among Human Populations&amp;rdquo;. &lt;em&gt;The American Journal of Human Genetics&lt;/em&gt; 80.3, pp. 502-509. &lt;a href=&#34;https://dx.doi.org/10.1086/512017&#34;&gt;https://dx.doi.org/10.1086/512017&lt;/a&gt;.&lt;/li&gt;&#xA;&lt;li&gt;Storey, J. D. (2007). &amp;ldquo;The optimal discovery procedure: a new approach to simultaneous significance testing&amp;rdquo;. &lt;em&gt;Journal of the Royal Statistical Society: Series B (Statistical Methodology)&lt;/em&gt; 69.3, pp. 347-368. &lt;a href=&#34;https://dx.doi.org/10.1111/j.1467-9868.2007.005592.x&#34;&gt;https://dx.doi.org/10.1111/j.1467-9868.2007.005592.x&lt;/a&gt;.&lt;/li&gt;&#xA;&lt;li&gt;Leek, J. T. and J. D. Storey (2007). &amp;ldquo;Capturing heterogeneity in gene expression studies by surrogate variable analysis&amp;rdquo;. &lt;em&gt;PLoS Genetics&lt;/em&gt; 3.9, p. e161. &lt;a href=&#34;https://dx.doi.org/10.1371/journal.pgen.0030161&#34;&gt;https://dx.doi.org/10.1371/journal.pgen.0030161&lt;/a&gt;.&lt;/li&gt;&#xA;&lt;li&gt;Dabney, A. R. and J. D. Storey (2007). &amp;ldquo;Optimality driven nearest centroid classification from genomic data&amp;rdquo;. &lt;em&gt;PLoS ONE&lt;/em&gt; 2.10. Ed. by J. Zhu, p. e1002. &lt;a href=&#34;https://dx.doi.org/10.1371/journal.pone.0001002&#34;&gt;https://dx.doi.org/10.1371/journal.pone.0001002&lt;/a&gt;.&lt;/li&gt;&#xA;&lt;li&gt;Dabney, A. R. and J. D. Storey (2007). &amp;ldquo;Normalization of two-channel microarrays accounting for experimental design and intensity-dependent relationships&amp;rdquo;. &lt;em&gt;Genome Biology&lt;/em&gt; 8.3, p. R44. &lt;a href=&#34;https://dx.doi.org/10.1186/gb-2007-8-3-r44&#34;&gt;https://dx.doi.org/10.1186/gb-2007-8-3-r44&lt;/a&gt;.&lt;/li&gt;&#xA;&lt;li&gt;Chen, L. S., F. Emmert-Streib, and J. D. Storey (2007). &amp;ldquo;Harnessing naturally randomized transcription to infer regulatory relationships among genes&amp;rdquo;. &lt;em&gt;Genome Biology&lt;/em&gt; 8.10, p. R219. &lt;a href=&#34;https://dx.doi.org/10.1186/gb-2007-8-10-r219&#34;&gt;https://dx.doi.org/10.1186/gb-2007-8-10-r219&lt;/a&gt;.&lt;/li&gt;&#xA;&lt;li&gt;Akey, J. M., S. Biswas, J. T. Leek, and J. D. Storey (2007). &amp;ldquo;On the design and analysis of gene expression studies in human populations&amp;rdquo;. &lt;em&gt;Nature Genetics&lt;/em&gt; 39.7, pp. 807-808. &lt;a href=&#34;https://dx.doi.org/10.1038/ng0707-807&#34;&gt;https://dx.doi.org/10.1038/ng0707-807&lt;/a&gt;.&lt;/li&gt;&#xA;&lt;li&gt;Storey, J. D., J. Y. Dai, and J. T. Leek (2006). &amp;ldquo;The optimal discovery procedure for large-scale significance testing, with applications to comparative microarray experiments&amp;rdquo;. &lt;em&gt;Biostatistics&lt;/em&gt; 8.2, pp. 414-432. &lt;a href=&#34;https://dx.doi.org/10.1093/biostatistics/kxl019&#34;&gt;https://dx.doi.org/10.1093/biostatistics/kxl019&lt;/a&gt;.&lt;/li&gt;&#xA;&lt;li&gt;Dabney, A. R. and J. D. Storey (2006). &amp;ldquo;A new approach to intensity-dependent normalization of two-channel microarrays&amp;rdquo;. &lt;em&gt;Biostatistics&lt;/em&gt; 8.1, pp. 128-139. &lt;a href=&#34;https://dx.doi.org/10.1093/biostatistics/kxj038&#34;&gt;https://dx.doi.org/10.1093/biostatistics/kxj038&lt;/a&gt;.&lt;/li&gt;&#xA;&lt;li&gt;Dabney, A. R. and J. D. Storey (2006). &amp;ldquo;A reanalysis of a published Affymetrix GeneChip control dataset&amp;rdquo;. &lt;em&gt;Genome Biology&lt;/em&gt; 7.3, p. 401. &lt;a href=&#34;https://dx.doi.org/10.1186/gb-2006-7-3-401&#34;&gt;https://dx.doi.org/10.1186/gb-2006-7-3-401&lt;/a&gt;.&lt;/li&gt;&#xA;&lt;li&gt;Chen, L. (2006). &amp;ldquo;Relaxed significance criteria for linkage analysis&amp;rdquo;. &lt;em&gt;Genetics&lt;/em&gt; 173.4, pp. 2371-2381. &lt;a href=&#34;https://dx.doi.org/10.1534/genetics.105.052506&#34;&gt;https://dx.doi.org/10.1534/genetics.105.052506&lt;/a&gt;.&lt;/li&gt;&#xA;&lt;li&gt;Leek, J. T., E. Monsen, A. R. Dabney, and J. D. Storey (2005). &amp;ldquo;Edge: extraction and analysis of differential gene expression&amp;rdquo;. &lt;em&gt;Bioinformatics&lt;/em&gt; 22.4, pp. 507-508. &lt;a href=&#34;https://dx.doi.org/10.1093/bioinformatics/btk005&#34;&gt;https://dx.doi.org/10.1093/bioinformatics/btk005&lt;/a&gt;.&lt;/li&gt;&#xA;&lt;li&gt;Storey, J. D., W. Xiao, J. T. Leek, R. G. Tompkins, and R. W. Davis (2005). &amp;ldquo;Significance analysis of time course microarray experiments&amp;rdquo;. &lt;em&gt;Proceedings of the National Academy of Sciences&lt;/em&gt; 102.36, pp. 12837-12842. &lt;a href=&#34;https://dx.doi.org/10.1073/pnas.0504609102&#34;&gt;https://dx.doi.org/10.1073/pnas.0504609102&lt;/a&gt;.&lt;/li&gt;&#xA;&lt;li&gt;Storey, J. D., J. M. Akey, and L. Kruglyak (2005). &amp;ldquo;Multiple locus linkage analysis of genomewide expression in yeast&amp;rdquo;. &lt;em&gt;PLoS Biology&lt;/em&gt; 3.8, p. e267. &lt;a href=&#34;https://dx.doi.org/10.1371/journal.pbio.0030267&#34;&gt;https://dx.doi.org/10.1371/journal.pbio.0030267&lt;/a&gt;.&lt;/li&gt;&#xA;&lt;li&gt;Brem, R. B., J. D. Storey, J. Whittle, and L. Kruglyak (2005). &amp;ldquo;Genetic interactions between polymorphisms that affect gene expression in yeast&amp;rdquo;. &lt;em&gt;Nature&lt;/em&gt; 436.7051, pp. 701-703. &lt;a href=&#34;https://dx.doi.org/10.1038/nature03865&#34;&gt;https://dx.doi.org/10.1038/nature03865&lt;/a&gt;.&lt;/li&gt;&#xA;&lt;li&gt;Storey, J. D., J. E. Taylor, and D. Siegmund (2004). &amp;ldquo;Strong control, conservative point estimation and simultaneous conservative consistency of false discovery rates: A unified approach&amp;rdquo;. &lt;em&gt;Journal of the Royal Statistical Society: Series B (Statistical Methodology)&lt;/em&gt; 66.1, pp. 187-205. &lt;a href=&#34;https://dx.doi.org/10.1111/j.1467-9868.2004.00439.x&#34;&gt;https://dx.doi.org/10.1111/j.1467-9868.2004.00439.x&lt;/a&gt;.&lt;/li&gt;&#xA;&lt;li&gt;Vaszar, L. T., T. Nishimura, J. D. Storey, G. Zhao, D. Qiu, J. L. Faul, et al. (2004). &amp;ldquo;Longitudinal transcriptional analysis of developing neointimal vascular occlusion and pulmonary hypertension in rats&amp;rdquo;. &lt;em&gt;Physiological Genomics&lt;/em&gt; 17.2, pp. 150-156. &lt;a href=&#34;https://dx.doi.org/10.1152/physiolgenomics.00198.2003&#34;&gt;https://dx.doi.org/10.1152/physiolgenomics.00198.2003&lt;/a&gt;.&lt;/li&gt;&#xA;&lt;li&gt;Storey, J. D. and R. Tibshirani (2003). &amp;ldquo;Statistical significance for genomewide studies&amp;rdquo;. &lt;em&gt;Proceedings of the National Academy of Sciences&lt;/em&gt; 100.16, pp. 9440-9445. &lt;a href=&#34;https://dx.doi.org/10.1073/pnas.1530509100&#34;&gt;https://dx.doi.org/10.1073/pnas.1530509100&lt;/a&gt;.&lt;/li&gt;&#xA;&lt;li&gt;Storey, J. D. and R. Tibshirani (2003). &amp;ldquo;Statistical methods for identifying differentially expressed genes in DNA microarrays&amp;rdquo;. In: &lt;em&gt;Functional Genomics: Methods and Protocols&lt;/em&gt;. Ed. by M. Kaufmann and C. Klinger. Springer Nature, pp. 149-158. &lt;a href=&#34;https://dx.doi.org/10.1385/1-59259-364-X:149&#34;&gt;https://dx.doi.org/10.1385/1-59259-364-X:149&lt;/a&gt;.&lt;/li&gt;&#xA;&lt;li&gt;Storey, J. D. and R. Tibshirani (2003). &amp;ldquo;SAM thresholding and false discovery rates for detecting differential gene expression in DNA microarrays&amp;rdquo;. In: &lt;em&gt;The Analysis of Gene Expression Data: Methods and Software&lt;/em&gt;. Ed. by G. Parmigiani, E. S. Garett, R. A. Irizarry and S. L. Zeger. Springer New York, pp. 272-290. &lt;a href=&#34;https://dx.doi.org/10.1007/b97411&#34;&gt;https://dx.doi.org/10.1007/b97411&lt;/a&gt;.&lt;/li&gt;&#xA;&lt;li&gt;Storey, J. D. (2003). &amp;ldquo;The positive false discovery rate: A Bayesian interpretation and the q-value&amp;rdquo;. &lt;em&gt;Annals of Statistics&lt;/em&gt; 31.6, pp. 2013-2035. &lt;a href=&#34;https://dx.doi.org/10.1214/aos/1074290335&#34;&gt;https://dx.doi.org/10.1214/aos/1074290335&lt;/a&gt;.&lt;/li&gt;&#xA;&lt;li&gt;Arava, Y., Y. Wang, J. D. Storey, C. L. Liu, P. O. Brown, and D. Herschlag (2003). &amp;ldquo;Genome-wide analysis of mRNA translation profiles in Saccharomyces cerevisiae&amp;rdquo;. &lt;em&gt;Proceedings of the National Academy of Sciences&lt;/em&gt; 100.7, pp. 3889-3894. &lt;a href=&#34;https://dx.doi.org/10.1073/pnas.0635171100&#34;&gt;https://dx.doi.org/10.1073/pnas.0635171100&lt;/a&gt;.&lt;/li&gt;&#xA;&lt;li&gt;Wang, Y., C. L. Liu, J. D. Storey, R. J. Tibshirani, D. Herschlag, and P. O. Brown (2002). &amp;ldquo;Precision and functional specificity in mRNA decay&amp;rdquo;. &lt;em&gt;Proceedings of the National Academy of Sciences&lt;/em&gt; 99.9, pp. 5860-5865. &lt;a href=&#34;https://dx.doi.org/10.1073/pnas.092538799&#34;&gt;https://dx.doi.org/10.1073/pnas.092538799&lt;/a&gt;.&lt;/li&gt;&#xA;&lt;li&gt;Storey, J. D. (2002). &amp;ldquo;False discovery rates: Theory and applications to DNA microarrays&amp;rdquo;. PhD Dissertation. Stanford University. &lt;a href=&#34;https://searchworks.stanford.edu/view/5417184&#34;&gt;https://searchworks.stanford.edu/view/5417184&lt;/a&gt;.&lt;/li&gt;&#xA;&lt;li&gt;Clement, K. (2002). &amp;ldquo;In vivo regulation of human skeletal muscle gene expression by thyroid hormone&amp;rdquo;. &lt;em&gt;Genome Research&lt;/em&gt; 12.2, pp. 281-291. &lt;a href=&#34;https://dx.doi.org/10.1101/gr.207702&#34;&gt;https://dx.doi.org/10.1101/gr.207702&lt;/a&gt;.&lt;/li&gt;&#xA;&lt;li&gt;Storey, J. D. (2002). &amp;ldquo;A direct approach to false discovery rates&amp;rdquo;. &lt;em&gt;Journal of the Royal Statistical Society: Series B (Statistical Methodology)&lt;/em&gt; 64.3, pp. 479-498. &lt;a href=&#34;https://dx.doi.org/10.1111/1467-9868.00346&#34;&gt;https://dx.doi.org/10.1111/1467-9868.00346&lt;/a&gt;.&lt;/li&gt;&#xA;&lt;li&gt;Efron, B., R. Tibshirani, J. D. Storey, and V. Tusher (2001). &amp;ldquo;Empirical Bayes analysis of a microarray experiment&amp;rdquo;. &lt;em&gt;Journal of the American Statistical Association&lt;/em&gt; 96.456, pp. 1151-1160. &lt;a href=&#34;https://dx.doi.org/10.1198/016214501753382129&#34;&gt;https://dx.doi.org/10.1198/016214501753382129&lt;/a&gt;.&lt;/li&gt;&#xA;&lt;li&gt;Storey, J. D. and R. Tibshirani (2001). &amp;ldquo;Estimating the positive false discovery rate under dependence, with applications to DNA microarrays&amp;rdquo;. Technical Report 2001-28. Department of Statistics, Stanford University. &lt;a href=&#34;http://storeylab.org/doc/2001-28.pdf&#34;&gt;http://storeylab.org/doc/2001-28.pdf&lt;/a&gt;.&lt;/li&gt;&#xA;&lt;li&gt;Efron, B., J. D. Storey, and R. Tibshirani (2001). &amp;ldquo;Microarrays, empirical Bayes methods, and false discovery rates&amp;rdquo;. Technical Report Bio-217. Department of Statistics, Stanford University. &lt;a href=&#34;http://storeylab.org/doc/BIO217.pdf&#34;&gt;http://storeylab.org/doc/BIO217.pdf&lt;/a&gt;.&lt;/li&gt;&#xA;&lt;li&gt;Storey, J. D. (2001). &amp;ldquo;A new approach to false discovery rates and multiple hypothesis testing&amp;rdquo;. Technical Report 2001-18. Department of Statistics, Stanford University. &lt;a href=&#34;http://storeylab.org/doc/2001-18.pdf&#34;&gt;http://storeylab.org/doc/2001-18.pdf&lt;/a&gt;.&lt;/li&gt;&#xA;&lt;li&gt;Efron, B., R. Tibshirani, J. D. Storey, and V. Tusher (2001). &amp;ldquo;Empirical Bayes analysis of a microarray experiment&amp;rdquo;. Technical Report Bio-216. Department of Statistics, Stanford University. &lt;a href=&#34;http://storeylab.org/doc/BIO216.pdf&#34;&gt;http://storeylab.org/doc/BIO216.pdf&lt;/a&gt;.&lt;/li&gt;&#xA;&lt;li&gt;Storey, J. D. (2001). &amp;ldquo;The false discovery rate: A Bayesian interpretation and the q-value&amp;rdquo;. Technical Report 2001-12. Department of Statistics, Stanford University. &lt;a href=&#34;http://storeylab.org/doc/2001-12.pdf&#34;&gt;http://storeylab.org/doc/2001-12.pdf&lt;/a&gt;.&lt;/li&gt;&#xA;&lt;li&gt;Gilbert, C. L., J. D. Kolesar, C. A. Reiter, and J. D. Storey (2001). &amp;ldquo;Function digraphs of quadratic maps modulo p&amp;rdquo;. &lt;em&gt;Fibonacci Quarterly&lt;/em&gt; 39.1, pp. 32-49.&lt;/li&gt;&#xA;&lt;li&gt;Storey, J. D. and D. Siegmund (2001). &amp;ldquo;Approximate p-values for local sequence alignments: Numerical studies&amp;rdquo;. &lt;em&gt;Journal of Computational Biology&lt;/em&gt; 8.5, pp. 549-556. &lt;a href=&#34;https://dx.doi.org/10.1089/106652701753216530&#34;&gt;https://dx.doi.org/10.1089/106652701753216530&lt;/a&gt;.&lt;/li&gt;&#xA;&lt;/ol&gt;</description>
    </item>
    <item>
      <title>Lab Members</title>
      <link>https://storeylab.org/patterns/members/</link>
      <pubDate>Mon, 01 Jan 0001 00:00:00 +0000</pubDate>
      <guid>https://storeylab.org/patterns/members/</guid>
      <description>&lt;h3 id=&#34;john-d-storey&#34;&gt;John D. Storey&lt;/h3&gt;&#xA;&lt;!-- raw HTML omitted --&gt;&#xA;&lt;p&gt;&lt;img src=&#34;https://storeylab.org/images/storey.jpg#floatleft&#34; alt=&#34;Photo of John D. Storey&#34;&gt;&lt;/p&gt;&#xA;&lt;!-- raw HTML omitted --&gt;&#xA;&lt;!-- raw HTML omitted --&gt;&#xA;&lt;p&gt;John is the William R. Harman &amp;lsquo;63 and Mary-Love Harman Professor in Genomics, primarly appointed in the &lt;a href=&#34;https://lsi.princeton.edu&#34;&gt;Lewis-Sigler Institute for Integrative Genomics&lt;/a&gt; at &lt;a href=&#34;https://www.princeton.edu&#34;&gt;Princeton University&lt;/a&gt;. He has associated faculty appointments in Applied and Computational Mathematics, the Center for Statistics and Machine Learning, Computer Science, Molecular Biology, Operations Research and Financial Engineering, and the Princeton Institute for Computational Science and Engineering (PICSciE). He is the director (with Josh Akey) of the NHGRI Quantitative and Computational Biology Graduate Training Program at Princeton University. For more information, check out a &lt;a href=&#34;https://storeylab.org/storeybio/&#34;&gt;brief biography&lt;/a&gt;, his &lt;a href=&#34;https://jdstorey.org/&#34;&gt;personal website&lt;/a&gt;, and his &lt;a href=&#34;https://github.com/jdstorey&#34;&gt;GitHub&lt;/a&gt;, &lt;a href=&#34;https://scholar.google.com/citations?hl=en&amp;amp;user=oi4x2XIAAAAJ&amp;amp;view_op=list_works&amp;amp;pagesize=100&#34;&gt;Google Scholar&lt;/a&gt;, and &lt;a href=&#34;https://www.linkedin.com/in/jdstorey/&#34;&gt;LinkedIn&lt;/a&gt; profiles.&lt;/p&gt;</description>
    </item>
    <item>
      <title>Software</title>
      <link>https://storeylab.org/patterns/software/</link>
      <pubDate>Mon, 01 Jan 0001 00:00:00 +0000</pubDate>
      <guid>https://storeylab.org/patterns/software/</guid>
      <description>&lt;p&gt;&lt;strong&gt;biobroom.&lt;/strong&gt; This R package converts standard objects constructed by bioinformatics packages, especially those in Bioconductor, to the tidy data format.  &lt;a href=&#34;http://www.bioconductor.org/packages/release/bioc/html/biobroom.html&#34;&gt;Bioconductor&lt;/a&gt; / &lt;a href=&#34;https://github.com/StoreyLab/biobroom&#34;&gt;GitHub&lt;/a&gt;&lt;/p&gt;&#xA;&lt;p&gt;&lt;strong&gt;bnpsd.&lt;/strong&gt; This R package simulates admixed populations via simulated allele frequencies and genotypes from the BN-PSD (&amp;ldquo;Balding-Nichols Pritchard-Stephens-Donnelly&amp;rdquo;) admixture model. This model enables the simulation of complex population structures, ideal for illustrating challenges in kinship coefficient and &#xA;&lt;em&gt;F&lt;/em&gt;&lt;sub&gt;ST&lt;/sub&gt; estimation. &lt;a href=&#34;https://cran.r-project.org/web/packages/bnpsd/index.html&#34;&gt;CRAN&lt;/a&gt; / &lt;a href=&#34;https://github.com/StoreyLab/bnpsd/&#34;&gt;GitHub&lt;/a&gt;&lt;/p&gt;&#xA;&lt;p&gt;&lt;strong&gt;dnamix.&lt;/strong&gt; This Fortran program calcluates likelihood ratios as they pertain to mixed DNA samples encountered in forensic science. &lt;a href=&#34;https://github.com/StoreyLab/dnamix&#34;&gt;GitHub&lt;/a&gt;&lt;/p&gt;</description>
    </item>
    <item>
      <title>Contact &amp; Links</title>
      <link>https://storeylab.org/patterns/contact/</link>
      <pubDate>Mon, 01 Jan 0001 00:00:00 +0000</pubDate>
      <guid>https://storeylab.org/patterns/contact/</guid>
      <description>&lt;h3 id=&#34;contact&#34;&gt;Contact&lt;/h3&gt;&#xA;&lt;p&gt;Carl Icahn Labs&lt;br&gt;&#xA;Princeton University&lt;br&gt;&#xA;Princeton NJ 08544, USA&lt;/p&gt;&#xA;&lt;p&gt;JDS &lt;a href=&#34;https://mailhide.io/e/ugECs&#34;&gt;Email&lt;/a&gt;&lt;/p&gt;&#xA;&lt;p&gt;Faculty Assistant: Laura Hoffman&lt;br&gt;&#xA;Phone: +1.609.258.8607&lt;br&gt;&#xA;Email: &lt;a href=&#34;mailto:lh7396@princeton.edu&#34;&gt;lh7396@princeton.edu&lt;/a&gt;&lt;br&gt;&#xA;Office: 147 Carl Icahn Labs&lt;/p&gt;&#xA;&lt;h3 id=&#34;links&#34;&gt;Links&lt;/h3&gt;&#xA;&lt;p&gt;&lt;a href=&#34;https://github.com/StoreyLab&#34;&gt;Storey Lab GitHub&lt;/a&gt;&lt;br&gt;&#xA;JDS on &lt;a href=&#34;https://scholar.google.com/citations?hl=en&amp;amp;user=oi4x2XIAAAAJ&amp;amp;view_op=list_works&amp;amp;pagesize=100&#34;&gt;Google Scholar&lt;/a&gt;&lt;br&gt;&#xA;JDS on &lt;a href=&#34;https://orcid.org/0000-0001-5992-402X&#34;&gt;ORCID&lt;/a&gt; &lt;em&gt;may be out of date&lt;/em&gt;&lt;/p&gt;</description>
    </item>
    <item>
      <title>John D. Storey</title>
      <link>https://storeylab.org/storeybio/</link>
      <pubDate>Mon, 01 Jan 0001 00:00:00 +0000</pubDate>
      <guid>https://storeylab.org/storeybio/</guid>
      <description>&lt;h3 id=&#34;brief-biography&#34;&gt;Brief Biography&lt;/h3&gt;&#xA;&lt;p&gt;John D. Storey received his PhD in 2002 from Stanford University in statistics with a PhD minor in genetics. He then held faculty positions at the University of California, Berkeley and the University of Washington. Since 2008, he has a been a professor in the &lt;a href=&#34;https://lsi.princeton.edu&#34;&gt;Lewis-Sigler Institute for Integrative Genomics&lt;/a&gt; at &lt;a href=&#34;https://www.princeton.edu&#34;&gt;Princeton University&lt;/a&gt;. He has associated faculty appointments in Applied and Computational Mathematics, the Center for Statistics and Machine Learning, Computer Science, Molecular Biology, Operations Research and Financial Engineering, and the Princeton Institute for Computational Science and Engineering (PICSciE). His research has been concerned with developing and applying statistical methods in genomics. He has made contributions to the development and application of methods for significance testing and inference on high-dimensional data.&lt;/p&gt;</description>
    </item>
    <item>
      <title>Print version</title>
      <link>https://storeylab.org/print-version/</link>
      <pubDate>Mon, 01 Jan 0001 00:00:00 +0000</pubDate>
      <guid>https://storeylab.org/print-version/</guid>
      <description>&lt;p&gt;You don&amp;rsquo;t want to edit this file :-)&lt;/p&gt;</description>
    </item>
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