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Results: 1 to 20 of 29

1.

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.

PMID:
24463464
[PubMed - indexed for MEDLINE]
Free PMC Article
2.

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.

PMID:
23664763
[PubMed - indexed for MEDLINE]
Free PMC Article
3.

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.

PMID:
23401553
[PubMed - indexed for MEDLINE]
Free PMC Article
4.

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.

PMID:
22880081
[PubMed - indexed for MEDLINE]
Free PMC Article
5.

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.

PMID:
22723083
[PubMed - indexed for MEDLINE]
Free PMC Article
6.

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.

PMID:
22383036
[PubMed - indexed for MEDLINE]
Free PMC Article
7.

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.

PMID:
22296848
[PubMed - indexed for MEDLINE]
Free PMC Article
8.

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.

PMID:
22102569
[PubMed - indexed for MEDLINE]
Free PMC Article
9.

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.

PMID:
21926179
[PubMed - indexed for MEDLINE]
Free PMC Article
10.

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.

PMID:
21385041
[PubMed - indexed for MEDLINE]
11.

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.

PMID:
21114842
[PubMed - indexed for MEDLINE]
Free PMC Article
12.

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.

PMID:
21044341
[PubMed - indexed for MEDLINE]
Free PMC Article
13.

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.

PMID:
20421740
[PubMed - indexed for MEDLINE]
Free PMC Article
14.

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.

PMID:
20219098
[PubMed - indexed for MEDLINE]
Free PMC Article
15.

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.

PMID:
20033444
[PubMed - indexed for MEDLINE]
Free PMC Article
16.

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.

PMID:
19955262
[PubMed - indexed for MEDLINE]
Free PMC Article
17.

A whole-genome assembly of the domestic cow, Bos taurus.

Zimin AV, Delcher AL, Florea L, Kelley DR, Schatz MC, Puiu D, Hanrahan F, Pertea G, Van Tassell CP, Sonstegard TS, Marçais G, Roberts M, Subramanian P, Yorke JA, Salzberg SL.

Genome Biol. 2009;10(4):R42. doi: 10.1186/gb-2009-10-4-r42. Epub 2009 Apr 24.

PMID:
19393038
[PubMed - indexed for MEDLINE]
Free PMC Article
18.

Roles of polarity determinants in ovule development.

Kelley DR, Skinner DJ, Gasser CS.

Plant J. 2009 Mar;57(6):1054-64. doi: 10.1111/j.1365-313X.2008.03752.x. Epub 2008 Nov 26.

PMID:
19054366
[PubMed - indexed for MEDLINE]
Free PMC Article
19.

Medicaid DRG system being improved for Texas children.

Bellamy GR, Svadlenak SR, Peters R, Kelley DR.

Tex Hosp. 1987 Jun;43(1):14-5. No abstract available.

PMID:
10312095
[PubMed - indexed for MEDLINE]
20.

Histological parameters and pitfalls in the interpretation of bladder biopsies in bacillus Calmette-Guerin treatment of superficial bladder cancer.

Lage JM, Bauer WC, Kelley DR, Ratliff TL, Catalona WJ.

J Urol. 1986 May;135(5):916-9.

PMID:
3959240
[PubMed - indexed for MEDLINE]

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