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Items: 1 to 20 of 33


Basset: Learning the regulatory code of the accessible genome with deep convolutional neural networks.

Kelley DR, Snoek J, Rinn J.

Genome Res. 2016 May 3. pii: gr.200535.115. [Epub ahead of print]


Widespread RNA binding by chromatin-associated proteins.

G Hendrickson D, Kelley DR, Tenen D, Bernstein B, Rinn JL.

Genome Biol. 2016 Feb 16;17:28. doi: 10.1186/s13059-016-0878-3.


Lysine Residues Are Not Required for Proteasome-Mediated Proteolysis of the Auxin/Indole Acidic Acid Protein IAA1.

Gilkerson J, Kelley DR, Tam R, Estelle M, Callis J.

Plant Physiol. 2015 Jun;168(2):708-20. doi: 10.1104/pp.15.00402. Epub 2015 Apr 17.


Transposable elements modulate human RNA abundance and splicing via specific RNA-protein interactions.

Kelley DR, Hendrickson DG, Tenen D, Rinn JL.

Genome Biol. 2014 Dec 3;15(12):537. doi: 10.1186/s13059-014-0537-5.


Topological organization of multichromosomal regions by the long intergenic noncoding RNA Firre.

Hacisuleyman E, Goff LA, 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.

Nat Struct Mol Biol. 2014 Feb;21(2):198-206. doi: 10.1038/nsmb.2764. Epub 2014 Jan 26.


Transcriptional and epigenetic dynamics during specification of human embryonic stem cells.

Gifford CA, 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.

Cell. 2013 May 23;153(5):1149-63. doi: 10.1016/j.cell.2013.04.037. Epub 2013 May 9.


Long noncoding RNAs regulate adipogenesis.

Sun L, Goff LA, 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.

Proc Natl Acad Sci U S A. 2013 Feb 26;110(9):3387-92. doi: 10.1073/pnas.1222643110. Epub 2013 Feb 11.


Mis-assembled "segmental duplications" in two versions of the Bos taurus genome.

Zimin AV, Kelley DR, Roberts M, Marçais G, Salzberg SL, Yorke JA.

PLoS One. 2012;7(8):e42680. doi: 10.1371/journal.pone.0042680. Epub 2012 Aug 3.


Ubiquitin-mediated control of plant hormone signaling.

Kelley DR, Estelle M.

Plant Physiol. 2012 Sep;160(1):47-55. doi: 10.1104/pp.112.200527. Epub 2012 Jun 21. No abstract available.


Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks.

Trapnell C, Roberts A, Goff L, Pertea G, Kim D, Kelley DR, Pimentel H, Salzberg SL, Rinn JL, Pachter L.

Nat Protoc. 2012 Mar 1;7(3):562-78. doi: 10.1038/nprot.2012.016. Erratum in: Nat Protoc. 2014 Oct;9(10):2513.


ETTIN (ARF3) physically interacts with KANADI proteins to form a functional complex essential for integument development and polarity determination in Arabidopsis.

Kelley DR, Arreola A, Gallagher TL, Gasser CS.

Development. 2012 Mar;139(6):1105-9. doi: 10.1242/dev.067918. Epub 2012 Feb 1.


Gene prediction with Glimmer for metagenomic sequences augmented by classification and clustering.

Kelley DR, Liu B, Delcher AL, Pop M, Salzberg SL.

Nucleic Acids Res. 2012 Jan;40(1):e9. doi: 10.1093/nar/gkr1067. Epub 2011 Nov 18.


Assemblathon 1: a competitive assessment of de novo short read assembly methods.

Earl D, Bradnam K, St John J, Darling A, Lin D, Fass J, Yu HO, Buffalo V, Zerbino DR, Diekhans M, Nguyen N, Ariyaratne PN, Sung WK, Ning Z, Haimel M, Simpson JT, Fonseca NA, Birol İ, Docking TR, Ho IY, Rokhsar DS, Chikhi R, Lavenier D, Chapuis G, Naquin D, Maillet N, Schatz MC, Kelley DR, Phillippy AM, Koren S, Yang SP, Wu W, Chou WC, Srivastava A, Shaw TI, Ruby JG, Skewes-Cox P, Betegon M, Dimon MT, Solovyev V, Seledtsov I, Kosarev P, Vorobyev D, Ramirez-Gonzalez R, Leggett R, MacLean D, Xia F, Luo R, Li Z, Xie Y, Liu B, Gnerre S, MacCallum I, Przybylski D, Ribeiro FJ, Yin S, Sharpe T, Hall G, Kersey PJ, Durbin R, Jackman SD, Chapman JA, Huang X, DeRisi JL, Caccamo M, Li Y, Jaffe DB, Green RE, Haussler D, Korf I, Paten B.

Genome Res. 2011 Dec;21(12):2224-41. doi: 10.1101/gr.126599.111. Epub 2011 Sep 16.


Extracting between-pathway models from E-MAP interactions using expected graph compression.

Kelley DR, Kingsford C.

J Comput Biol. 2011 Mar;18(3):379-90. doi: 10.1089/cmb.2010.0268.


Quake: quality-aware detection and correction of sequencing errors.

Kelley DR, Schatz MC, Salzberg SL.

Genome Biol. 2010;11(11):R116. doi: 10.1186/gb-2010-11-11-r116. Epub 2010 Nov 29.


Clustering metagenomic sequences with interpolated Markov models.

Kelley DR, Salzberg SL.

BMC Bioinformatics. 2010 Nov 2;11:544. doi: 10.1186/1471-2105-11-544.


Investigating the function of CAF1 deadenylases during plant stress responses.

Walley JW, Kelley DR, Savchenko T, Dehesh K.

Plant Signal Behav. 2010 Jul;5(7):802-5. Epub 2010 Jul 1. Review.


Detection and correction of false segmental duplications caused by genome mis-assembly.

Kelley DR, Salzberg SL.

Genome Biol. 2010;11(3):R28. doi: 10.1186/gb-2010-11-3-r28. Epub 2010 Mar 10.


Ovule development: genetic trends and evolutionary considerations.

Kelley DR, Gasser CS.

Sex Plant Reprod. 2009 Dec;22(4):229-34. doi: 10.1007/s00497-009-0107-2. Epub 2009 Aug 9. Review.


Arabidopsis deadenylases AtCAF1a and AtCAF1b play overlapping and distinct roles in mediating environmental stress responses.

Walley JW, Kelley DR, Nestorova G, Hirschberg DL, Dehesh K.

Plant Physiol. 2010 Feb;152(2):866-75. doi: 10.1104/pp.109.149005. Epub 2009 Dec 2.

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