Cross-species regulatory sequence activity prediction von Kelley, David R.

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The genetic and biochemical determinants of mRNA degradation rates in mammals von Agarwal, Vikram, Kelley, David R

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Effective gene expression prediction from sequence by integrating long-range interactions von Avsec, Žiga, Agarwal, Vikram, Visentin, Daniel, Ledsam, Joseph R., Grabska-Barwinska, Agnieszka, Taylor, Kyle R., Assael, Yannis, Jumper, John, Kohli, Pushmeet, Kelley, David R.

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Transcriptional and Epigenetic Dynamics during Specification of Human Embryonic Stem Cells von Gifford, Casey A., Ziller, Michael J., Gu, Hongcang, Trapnell, Cole, Donaghey, Julie, Tsankov, Alexander, Shalek, Alex K., Kelley, David R., Shishkin, Alexander A., Issner, Robbyn, Zhang, Xiaolan, Coyne, Michael, Fostel, Jennifer L., Holmes, Laurie, Meldrim, Jim, Guttman, Mitchell, Epstein, Charles, Park, Hongkun, Kohlbacher, Oliver, Rinn, John, Gnirke, Andreas, Lander, Eric S., Bernstein, Bradley E., Meissner, Alexander

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Quake: quality-aware detection and correction of sequencing errors von Kelley, David R, Schatz, Michael C, Salzberg, Steven L

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Murine single-cell RNA-seq reveals cell-identity- and tissue-specific trajectories of aging von Kimmel, Jacob C, Penland, Lolita, Rubinstein, Nimrod D, Hendrickson, David G, Kelley, David R, Rosenthal, Adam Z

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Topological organization of multichromosomal regions by the long intergenic noncoding RNA Firre von Hacisuleyman, Ezgi, Goff, Loyal A, Trapnell, Cole, Williams, Adam, Henao-Mejia, Jorge, Sun, Lei, McClanahan, Patrick, Hendrickson, David G, Sauvageau, Martin, Kelley, David R, Morse, Michael, Engreitz, Jesse, Lander, Eric S, Guttman, Mitch, Lodish, Harvey F, Flavell, Richard, Raj, Arjun, Rinn, John L

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The landscape of alternative polyadenylation in single cells of the developing mouse embryo von Agarwal, Vikram, Lopez-Darwin, Sereno, Kelley, David R., Shendure, Jay

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Long noncoding RNAs regulate adipogenesis von Sun, Lei, Goff, Loyal A., Trapnell, Cole, Alexander, Ryan, Lo, Kinyui Alice, Hacisuleyman, Ezgi, Sauvageau, Martin, Tazon-Vega, Barbara, Kelley, David R., Hendrickson, David G., Yuan, Bingbing, Kellis, Manolis, Lodish, Harvey F., Rinn, John L.

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Genetic determinants and epigenetic effects of pioneer-factor occupancy von Donaghey, Julie, Thakurela, Sudhir, Charlton, Jocelyn, Chen, Jennifer S., Smith, Zachary D., Gu, Hongcang, Pop, Ramona, Clement, Kendell, Stamenova, Elena K., Karnik, Rahul, Kelley, David R., Gifford, Casey A., Cacchiarelli, Davide, Rinn, John L., Gnirke, Andreas, Ziller, Michael J., Meissner, Alexander

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scBasset: sequence-based modeling of single-cell ATAC-seq using convolutional neural networks von Yuan, Han, Kelley, David R.

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Evaluating the informativeness of deep learning annotations for human complex diseases von Dey, Kushal K., van de Geijn, Bryce, Kim, Samuel Sungil, Hormozdiari, Farhad, Kelley, David R., Price, Alkes L.

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Basset: learning the regulatory code of the accessible genome with deep convolutional neural networks von Kelley, David R, Snoek, Jasper, Rinn, John L

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Recurrent noncoding regulatory mutations in pancreatic ductal adenocarcinoma von Feigin, Michael E, Garvin, Tyler, Bailey, Peter, Waddell, Nicola, Chang, David K, Kelley, David R, Shuai, Shimin, Gallinger, Steven, McPherson, John D, Grimmond, Sean M, Khurana, Ekta, Stein, Lincoln D, Biankin, Andrew V, Schatz, Michael C, Tuveson, David A

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Clustering metagenomic sequences with interpolated Markov models von Kelley, David R, Salzberg, Steven L

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Novel insights from a multiomics dissection of the Hayflick limit von Chan, Michelle, Yuan, Han, Soifer, Ilya, Maile, Tobias M, Wang, Rebecca Y, Ireland, Andrea, O'Brien, Jonathon J, Goudeau, Jérôme, Chan, Leanne J G, Vijay, Twaritha, Freund, Adam, Kenyon, Cynthia, Bennett, Bryson D, McAllister, Fiona E, Kelley, David R, Roy, Margaret, Cohen, Robert L, Levinson, Arthur D, Botstein, David, Hendrickson, David G

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Predicting 3D genome folding from DNA sequence with Akita von Fudenberg, Geoff, Kelley, David R., Pollard, Katherine S.

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Detecting genome-wide directional effects of transcription factor binding on polygenic disease risk von Reshef, Yakir A., Finucane, Hilary K., Kelley, David R., Gusev, Alexander, Kotliar, Dylan, Ulirsch, Jacob C., Hormozdiari, Farhad, Nasser, Joseph, O’Connor, Luke, van de Geijn, Bryce, Loh, Po-Ru, Grossman, Sharon R., Bhatia, Gaurav, Gazal, Steven, Palamara, Pier Francesco, Pinello, Luca, Patterson, Nick, Adams, Ryan P., Price, Alkes L

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Semisupervised adversarial neural networks for single-cell classification von Kimmel, Jacob C., Kelley, David R.

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Sequential regulatory activity prediction across chromosomes with convolutional neural networks von Kelley, David R, Reshef, Yakir A, Bileschi, Maxwell, Belanger, David, McLean, Cory Y, Snoek, Jasper

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