Yuan H, Kelley DR. scBasset: Sequence-based modeling of single cell ATAC-seq using convolutional neural networks. bioRxiv (2021). [link]

Chan M, Yuan H, Soifer I, Maile TM, Wang RY, Ireland A, O’Brien J, Goudeau J, Chan L, Vijay T, Freund A, Kenyon C, Bennett B, McAllister F, Kelley DR, Roy M, Cohen RL, Levinson AD, Botstein D, Hendrickson DG. Revisiting the Hayflick Limit: Insights from an Integrated Analysis of Changing Transcripts, Proteins, Metabolites and Chromatin. bioRxiv (2021). [link]

Avsec Z, Agarwal V, Visentin D, Ledsam JR, Grabska-Barwinska A, Taylor KR, Assael Y, Jumper J, Kohli P, Kelley DR. Effective gene expression prediction from sequence by integrating long-range interactions. bioRxiv (2021). [link]

Agarwal V, Lopez-Darwin S, Kelley DR, Shendure J. The landscape of alternative polyadenylation in single cells of the developing mouse embryo. Nature Communications 12:5101 (2021). [link]

Wang QS, Kelley DR, Ulirsch J, Kanai M, Sadhuka S, Cui R, Albors C, Cheng N, Okada Y, Aguet F, Ardlie KG, MacArthur DG, Finucane HK. Leveraging supervised learning for functionally informed fine-mapping of cis-eQTLs identifies an additional 20,913 putative causal eQTLs. Nature Communications 12:1 (2021). [link]

Kimmel JC, Hendrickson DG, Kelley DR. Differentiation reveals latent features of aging and an energy barrier in murine myogenesis. Cell Reports 35:4 (2021). [link]

Kimmel JC, Kelley DR. scNym: Semi-supervised adversarial neural networks for single cell classification. Genome Research [online ahead of print] (2021). [link]

Fudenberg G*, Kelley DR*, Pollard KS. Predicting 3D genome folding from DNA sequence. Nature Methods 17:11 (2020). [link]

Dey KK, Van de Geijn B, Kim SS, Hormozdiari F, Kelley DR, Price A. Evaluating the informativeness of deep learning annotations for human complex diseases. Nature Communications 11:1 (2020). [link]

Kelley DR. Cross-species regulatory sequence activity prediction. PLoS Computational Biology 16(7) (2020). [link]

Bernstein N, Fong N, Lam I, Roy M, Hendrickson DG, Kelley DR. Solo: doublet identification via semi-supervised deep learning. Cell Systems 11(1) (2020). [link]

Kimmel JC, Penland L, Rubinstein ND, Hendrickson DG, Kelley DR*, Rosenthal AZ*. Murine single-cell RNA-seq reveals cell-identity-and tissue-specific trajectories of aging. Genome Research 29:12 (2019). [link]

Reshef YA, Finucane HK, Kelley DR, Gusev A, Kotliar D, Ulirsch JC, Hormozdiari F, O'Connor L, Geijn B, Loh P, Grossman S, Bhatia G, Gazal S, Palamara PF, Pinello L, Patterson N, Adams R, Price A. Detecting genome-wide directional effects of transcription factor binding on polygenic disease risk. Nature Genetics 50(10) (2018) [link]

Kelley DR, Reshef YA, Bileschi M, Belanger D, McLean CY, Snoek J. Sequential regulatory activity prediction across chromosomes with convolutional neural networks. Genome Research 28(5) (2018). [link]

Donaghey J, Thakurela S, Charlton J, Chen JS, Smith ZD, Gu H, Pop R, Clement K, Stamenova EK, Karnik R, Kelley DR, Gifford CA, Cacchiarelli D, Rinn JL, Gnirke A, Ziller MJ, Meissner A. Genetic determinants and epigenetic effects of pioneer-factor occupancy. Nature Genetics 50(2) (2018). [link]

Delas MJ, Sabin LR, Dolzhenko E, Knott SR, MAravilla EM, Jackson BT, Wild SA, Kovacevic T, Stork EM, Zhou M, Erard N, Lee E, Kelley DR, Roth M, Barbosa IA, Zuber J, Rinn JL, Smith AD, Hannon GJ. lncRNA requirements for mouse acute myeloid leukemia and normal differentiation. eLIFE (2017). [link]

Feigin ME, Garvin T, Bailey P, Waddell N, Chang DK, Kelley DR, Shuai S, Gallinger S, McPherson JD, Grimmond SM, Khurana E, Stein LD, Blankin AV, Schatz MC, Tuveson DA. Recurrent noncoding regulatory mutations in pancreatic ductal adenocarcinoma. Nature Genetics 49(6) (2017). [link]

Kelley DR, Snoek J, Rinn JL. Basset: Learning the regulatory code of the accessible genome with deep convolutional neural networks. Genome Research 26:7 (2016). [link]

Hendrickson D*, Kelley DR*, Tenen D, Bernstein, B., Rinn JL. Widespread RNA binding by chromatin-associated proteins. Genome Biology 17:28 (2016). [link]

Kelley DR, Hendrickson D, Tenen D, Rinn JL. Transposable elements modulate human RNA abundance and splicing via specific RNA-protein interactions. Genome Biology 15:537 (2014). [link]

Hacisuleyman E, Goff L, Trapnell C, Williams A, Henao-Mejia J, Sun L, McClanahan P, Hendrickson DG, Sauvageau M, Kelley DR, Morse M, Engreitz J, Lander ES, Guttman M, Lodish HF, Flavell R, Raj A, Rinn JL. Topological organization of multichromosomal regions by the long intergenic noncoding RNA Firre. Nat Struct Mol Biol (2014). [link]

Gifford C, Ziller MJ, Gu H, Trapnell C, Donaghey J, Tsankov A, Shalek AK, Kelley DR, Shishkin AA, Issner R, Zhang X, Coyne M, Fostel JL, Holmes L, Meldrim J, Guttman M, Epstein C, Park H, Kohlbacher O, Rinn J, Gnirke A, Lander ES, Bernstein BE, Meissner A. Transcriptional and epigenetic dynamics during specification of human embryonic stem cells. Cell 153:5 (2013). [link]

Sun L, Goff L, Trapnell C, Alexander R, Lo KA, Hacisuleyman E, Sauvageau M, Tazon-Vega B, Kelley DR, Hendrickson DG, Yuan B, Kellis M, Lodish HF, Rinn JL. Long noncoding RNAs regulate adipogenesis. Proc Natl Acad Sci 110:9 (2013). [link]

Kelley DR, Rinn JL. Transposable elements reveal a stem cell specific class of long noncoding RNA. Genome Biology 13:R107 (2012). [link]

Zimin AV, Kelley DR, Roberts M, Marcais G, Salzberg SL, Yorke JA. Mis-Assembled “Segmental Duplications” in Two Versions of the Bos taurus Genome. PLoS One 7:8 (2012). [link]

Trapnell C, Roberts A, Goff L, Pertea G, Kim D, Kelley DR, Pimentel H, Salzberg SL, Rinn JL, Pachter L. Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks. Nature Protocols 7:3 (2012). [link]

Kelley DR, Liu B, Delcher A, Pop M, Salzberg SL. Gene prediction with Glimmer for metagenomic sequences augmented by classification and clustering. Nucleic Acids Research 40:1 e9 (2012). [link]

Earl D, … [71 authors]. Assemblathon 1: A competitive assessment of de novo short read assembly methods. Genome Research 21:12 (2011). [link]

Kelley DR, Kingsford C. Extracting between-pathway models from E-MAP interactions using expected graph compression. Journal of Computational Biology 18:3 (2011). [link]

Kelley DR, Schatz MC, Salzberg SL. Quake: quality-aware error correction of sequencing reads. Genome Biology 11:R116 (2010). [link]

Kelley DR, Salzberg SL. Clustering metagenomic sequences with interpolated Markov models. BMC Bioinformatics 11:544 (2010). [link]

Kelley DR, Salzberg SL. Detection and correction of false segmental duplications caused by mis-assembly. Genome Biology 11:R28 (2010). [link]

Zimin AV, Delcher AL, Florea L, Kelley DR, Schatz MC, Puiu D, Hanrahan F, Pertea G, Van Tassell CP, Sonstegard TS, Marcais G, Roberts M, Subramanian P, Yorke JA, Salzberg SL. A whole-genome assembly of the domestic cow, Bos Taurus. Genome Biology 10:R42 (2009). [link]

Salzberg SL, … [35 authors]. Genome sequence and rapid evolution of the rice pathogen Xanthomonas oryzae pv. oryzae PX099A. BMC Genomics 9:204 (2008). [link]