Is it time to change the reference genome? von Ballouz, Sara, Dobin, Alexander, Gillis, Jesse A

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"Guilt by association" is the exception rather than the rule in gene networks von Gillis, Jesse, Pavlidis, Paul

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Predictability of human differential gene expression von Crow, Megan, Lim, Nathaniel, Ballouz, Sara, Pavlidis, Paul, Gillis, Jesse

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The impact of multifunctional genes on "guilt by association" analysis von Gillis, Jesse, Pavlidis, Paul

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Transcriptional Architecture of Synaptic Communication Delineates GABAergic Neuron Identity von Paul, Anirban, Crow, Megan, Raudales, Ricardo, He, Miao, Gillis, Jesse, Huang, Z. Josh

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Characterizing the replicability of cell types defined by single cell RNA-sequencing data using MetaNeighbor von Crow, Megan, Paul, Anirban, Ballouz, Sara, Huang, Z. Josh, Gillis, Jesse

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EGAD: ultra-fast functional analysis of gene networks von Ballouz, Sara, Weber, Melanie, Pavlidis, Paul, Gillis, Jesse

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A global high-density chromatin interaction network reveals functional long-range and trans-chromosomal relationships von Lohia, Ruchi, Fox, Nathan, Gillis, Jesse

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High-Throughput Mapping of Long-Range Neuronal Projection Using In Situ Sequencing von Chen, Xiaoyin, Sun, Yu-Chi, Zhan, Huiqing, Kebschull, Justus M., Fischer, Stephan, Matho, Katherine, Huang, Z. Josh, Gillis, Jesse, Zador, Anthony M.

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Population variability in X-chromosome inactivation across 10 mammalian species von Werner, Jonathan M., Hover, John, Gillis, Jesse

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Ligand Similarity Complements Sequence, Physical Interaction, and Co-Expression for Gene Function Prediction von O'Meara, Matthew J, Ballouz, Sara, Shoichet, Brian K, Gillis, Jesse

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Characterizing the state of the art in the computational assignment of gene function: lessons from the first critical assessment of functional annotation (CAFA) von Gillis, Jesse, Pavlidis, Paul

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How many markers are needed to robustly determine a cell's type? von Fischer, Stephan, Gillis, Jesse

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Co-expression of calcium and hERG potassium channels reduces the incidence of proarrhythmic events von Ballouz, Sara, Mangala, Melissa M, Perry, Matthew D, Heitmann, Stewart, Gillis, Jesse A, Hill, Adam P, Vandenberg, Jamie I

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Gene function analysis in complex data sets using ErmineJ von Pavlidis, Paul, Gillis, Jesse, Mistry, Meeta

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Intraductal Transplantation Models of Human Pancreatic Ductal Adenocarcinoma Reveal Progressive Transition of Molecular Subtypes von Miyabayashi, Koji, Baker, Lindsey A., Deschenes, Astrid, Traub, Benno, Caligiuri, Giuseppina, Plenker, Dennis, Alagesan, Brinda, Belleau, Pascal, Li, Siran, Kendall, Jude, Jang, Gun Ho, Kawaguchi, Risa Karakida, Somerville, Tim D. D., Tiriac, Herve, Hwang, Chang-Il, Burkhart, Richard A., Roberts, Nicholas J., Wood, Laura D., Hruban, Ralph H., Gillis, Jesse, Krasnitz, Alexander, Vakoc, Christopher R., Wigler, Michael, Notta, Faiyaz, Gallinger, Steven, Park, Youngkyu, Tuveson, David A.

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AuPairWise: A Method to Estimate RNA-Seq Replicability through Co-expression von Ballouz, Sara, Gillis, Jesse

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A Genome-wide RNAi Screen Draws a Genetic Framework for Transposon Control and Primary piRNA Biogenesis in Drosophila von Muerdter, Felix, Guzzardo, Paloma M., Gillis, Jesse, Luo, Yicheng, Yu, Yang, Chen, Caifu, Fekete, Richard, Hannon, Gregory J.

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Prevalent and dynamic binding of the cell cycle checkpoint kinase Rad53 to gene promoters von Sheu, Yi-Jun, Kawaguchi, Risa Karakida, Gillis, Jesse, Stillman, Bruce

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Strength of functional signature correlates with effect size in autism von Ballouz, Sara, Gillis, Jesse

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