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Results: 18

1.

Genome-wide RNAi screens in human brain tumor isolates reveal a novel viability requirement for PHF5A.

Hubert CG, Bradley RK, Ding Y, Toledo CM, Herman J, Skutt-Kakaria K, Girard EJ, Davison J, Berndt J, Corrin P, Hardcastle J, Basom R, Delrow JJ, Webb T, Pollard SM, Lee J, Olson JM, Paddison PJ.

Genes Dev. 2013 May 1;27(9):1032-45. doi: 10.1101/gad.212548.112.

PMID:
23651857
[PubMed - indexed for MEDLINE]
Free PMC Article
2.

Massive mitochondrial gene transfer in a parasitic flowering plant clade.

Xi Z, Wang Y, Bradley RK, Sugumaran M, Marx CJ, Rest JS, Davis CC.

PLoS Genet. 2013;9(2):e1003265. doi: 10.1371/journal.pgen.1003265. Epub 2013 Feb 14.

PMID:
23459037
[PubMed - indexed for MEDLINE]
Free PMC Article
3.

Braveheart, a long noncoding RNA required for cardiovascular lineage commitment.

Klattenhoff CA, Scheuermann JC, Surface LE, Bradley RK, Fields PA, Steinhauser ML, Ding H, Butty VL, Torrey L, Haas S, Abo R, Tabebordbar M, Lee RT, Burge CB, Boyer LA.

Cell. 2013 Jan 31;152(3):570-83. doi: 10.1016/j.cell.2013.01.003. Epub 2013 Jan 24.

PMID:
23352431
[PubMed - indexed for MEDLINE]
Free PMC Article
4.

Horizontal transfer of expressed genes in a parasitic flowering plant.

Xi Z, Bradley RK, Wurdack KJ, Wong K, Sugumaran M, Bomblies K, Rest JS, Davis CC.

BMC Genomics. 2012 Jun 8;13:227.

PMID:
22681756
[PubMed - indexed for MEDLINE]
Free PMC Article
5.

The TAGteam motif facilitates binding of 21 sequence-specific transcription factors in the Drosophila embryo.

Satija R, Bradley RK.

Genome Res. 2012 Apr;22(4):656-65. doi: 10.1101/gr.130682.111. Epub 2012 Jan 13.

PMID:
22247430
[PubMed - indexed for MEDLINE]
Free PMC Article
6.

Alternative splicing of RNA triplets is often regulated and accelerates proteome evolution.

Bradley RK, Merkin J, Lambert NJ, Burge CB.

PLoS Biol. 2012 Jan;10(1):e1001229. doi: 10.1371/journal.pbio.1001229. Epub 2012 Jan 3.

PMID:
22235189
[PubMed - indexed for MEDLINE]
Free PMC Article
7.

Binding site turnover produces pervasive quantitative changes in transcription factor binding between closely related Drosophila species.

Bradley RK, Li XY, Trapnell C, Davidson S, Pachter L, Chu HC, Tonkin LA, Biggin MD, Eisen MB.

PLoS Biol. 2010 Mar 23;8(3):e1000343. doi: 10.1371/journal.pbio.1000343.

PMID:
20351773
[PubMed - indexed for MEDLINE]
Free PMC Article
8.

Evolutionary triplet models of structured RNA.

Bradley RK, Holmes I.

PLoS Comput Biol. 2009 Aug;5(8):e1000483. doi: 10.1371/journal.pcbi.1000483. Epub 2009 Aug 28.

PMID:
19714212
[PubMed - indexed for MEDLINE]
Free PMC Article
9.

Evolutionary modeling and prediction of non-coding RNAs in Drosophila.

Bradley RK, Uzilov AV, Skinner ME, Bendaña YR, Barquist L, Holmes I.

PLoS One. 2009 Aug 11;4(8):e6478. doi: 10.1371/journal.pone.0006478.

PMID:
19668382
[PubMed - indexed for MEDLINE]
Free PMC Article
10.

Fast statistical alignment.

Bradley RK, Roberts A, Smoot M, Juvekar S, Do J, Dewey C, Holmes I, Pachter L.

PLoS Comput Biol. 2009 May;5(5):e1000392. doi: 10.1371/journal.pcbi.1000392. Epub 2009 May 29.

PMID:
19478997
[PubMed - indexed for MEDLINE]
Free PMC Article
11.

Tools for simulating evolution of aligned genomic regions with integrated parameter estimation.

Varadarajan A, Bradley RK, Holmes IH.

Genome Biol. 2008 Oct 8;9(10):R147. doi: 10.1186/gb-2008-9-10-r147.

PMID:
18840304
[PubMed - indexed for MEDLINE]
Free PMC Article
12.

Specific alignment of structured RNA: stochastic grammars and sequence annealing.

Bradley RK, Pachter L, Holmes I.

Bioinformatics. 2008 Dec 1;24(23):2677-83. doi: 10.1093/bioinformatics/btn495. Epub 2008 Sep 16.

PMID:
18796475
[PubMed - indexed for MEDLINE]
Free PMC Article
13.

Evolution of genes and genomes on the Drosophila phylogeny.

Drosophila 12 Genomes Consortium, Clark AG, Eisen MB, Smith DR, Bergman CM, Oliver B, Markow TA, Kaufman TC, Kellis M, Gelbart W, Iyer VN, Pollard DA, Sackton TB, Larracuente AM, Singh ND, Abad JP, Abt DN, Adryan B, Aguade M, Akashi H, Anderson WW, Aquadro CF, Ardell DH, Arguello R, Artieri CG, Barbash DA, Barker D, Barsanti P, Batterham P, Batzoglou S, Begun D, Bhutkar A, Blanco E, Bosak SA, Bradley RK, Brand AD, Brent MR, Brooks AN, Brown RH, Butlin RK, Caggese C, Calvi BR, Bernardo de Carvalho A, Caspi A, Castrezana S, Celniker SE, Chang JL, Chapple C, Chatterji S, Chinwalla A, Civetta A, Clifton SW, Comeron JM, Costello JC, Coyne JA, Daub J, David RG, Delcher AL, Delehaunty K, Do CB, Ebling H, Edwards K, Eickbush T, Evans JD, Filipski A, Findeiss S, Freyhult E, Fulton L, Fulton R, Garcia AC, Gardiner A, Garfield DA, Garvin BE, Gibson G, Gilbert D, Gnerre S, Godfrey J, Good R, Gotea V, Gravely B, Greenberg AJ, Griffiths-Jones S, Gross S, Guigo R, Gustafson EA, Haerty W, Hahn MW, Halligan DL, Halpern AL, Halter GM, Han MV, Heger A, Hillier L, Hinrichs AS, Holmes I, Hoskins RA, Hubisz MJ, Hultmark D, Huntley MA, Jaffe DB, Jagadeeshan S, Jeck WR, Johnson J, Jones CD, Jordan WC, Karpen GH, Kataoka E, Keightley PD, Kheradpour P, Kirkness EF, Koerich LB, Kristiansen K, Kudrna D, Kulathinal RJ, Kumar S, Kwok R, Lander E, Langley CH, Lapoint R, Lazzaro BP, Lee SJ, Levesque L, Li R, Lin CF, Lin MF, Lindblad-Toh K, Llopart A, Long M, Low L, Lozovsky E, Lu J, Luo M, Machado CA, Makalowski W, Marzo M, Matsuda M, Matzkin L, McAllister B, McBride CS, McKernan B, McKernan K, Mendez-Lago M, Minx P, Mollenhauer MU, Montooth K, Mount SM, Mu X, Myers E, Negre B, Newfeld S, Nielsen R, Noor MA, O'Grady P, Pachter L, Papaceit M, Parisi MJ, Parisi M, Parts L, Pedersen JS, Pesole G, Phillippy AM, Ponting CP, Pop M, Porcelli D, Powell JR, Prohaska S, Pruitt K, Puig M, Quesneville H, Ram KR, Rand D, Rasmussen MD, Reed LK, Reenan R, Reily A, Remington KA, Rieger TT, Ritchie MG, Robin C, Rogers YH, Rohde C, Rozas J, Rubenfield MJ, Ruiz A, Russo S, Salzberg SL, Sanchez-Gracia A, Saranga DJ, Sato H, Schaeffer SW, Schatz MC, Schlenke T, Schwartz R, Segarra C, Singh RS, Sirot L, Sirota M, Sisneros NB, Smith CD, Smith TF, Spieth J, Stage DE, Stark A, Stephan W, Strausberg RL, Strempel S, Sturgill D, Sutton G, Sutton GG, Tao W, Teichmann S, Tobari YN, Tomimura Y, Tsolas JM, Valente VL, Venter E, Venter JC, Vicario S, Vieira FG, Vilella AJ, Villasante A, Walenz B, Wang J, Wasserman M, Watts T, Wilson D, Wilson RK, Wing RA, Wolfner MF, Wong A, Wong GK, Wu CI, Wu G, Yamamoto D, Yang HP, Yang SP, Yorke JA, Yoshida K, Zdobnov E, Zhang P, Zhang Y, Zimin AV, Baldwin J, Abdouelleil A, Abdulkadir J, Abebe A, Abera B, Abreu J, Acer SC, Aftuck L, Alexander A, An P, Anderson E, Anderson S, Arachi H, Azer M, Bachantsang P, Barry A, Bayul T, Berlin A, Bessette D, Bloom T, Blye J, Boguslavskiy L, Bonnet C, Boukhgalter B, Bourzgui I, Brown A, Cahill P, Channer S, Cheshatsang Y, Chuda L, Citroen M, Collymore A, Cooke P, Costello M, D'Aco K, Daza R, De Haan G, DeGray S, DeMaso C, Dhargay N, Dooley K, Dooley E, Doricent M, Dorje P, Dorjee K, Dupes A, Elong R, Falk J, Farina A, Faro S, Ferguson D, Fisher S, Foley CD, Franke A, Friedrich D, Gadbois L, Gearin G, Gearin CR, Giannoukos G, Goode T, Graham J, Grandbois E, Grewal S, Gyaltsen K, Hafez N, Hagos B, Hall J, Henson C, Hollinger A, Honan T, Huard MD, Hughes L, Hurhula B, Husby ME, Kamat A, Kanga B, Kashin S, Khazanovich D, Kisner P, Lance K, Lara M, Lee W, Lennon N, Letendre F, LeVine R, Lipovsky A, Liu X, Liu J, Liu S, Lokyitsang T, Lokyitsang Y, Lubonja R, Lui A, MacDonald P, Magnisalis V, Maru K, Matthews C, McCusker W, McDonough S, Mehta T, Meldrim J, Meneus L, Mihai O, Mihalev A, Mihova T, Mittelman R, Mlenga V, Montmayeur A, Mulrain L, Navidi A, Naylor J, Negash T, Nguyen T, Nguyen N, Nicol R, Norbu C, Norbu N, Novod N, O'Neill B, Osman S, Markiewicz E, Oyono OL, Patti C, Phunkhang P, Pierre F, Priest M, Raghuraman S, Rege F, Reyes R, Rise C, Rogov P, Ross K, Ryan E, Settipalli S, Shea T, Sherpa N, Shi L, Shih D, Sparrow T, Spaulding J, Stalker J, Stange-Thomann N, Stavropoulos S, Stone C, Strader C, Tesfaye S, Thomson T, Thoulutsang Y, Thoulutsang D, Topham K, Topping I, Tsamla T, Vassiliev H, Vo A, Wangchuk T, Wangdi T, Weiand M, Wilkinson J, Wilson A, Yadav S, Young G, Yu Q, Zembek L, Zhong D, Zimmer A, Zwirko Z, Jaffe DB, Alvarez P, Brockman W, Butler J, Chin C, Gnerre S, Grabherr M, Kleber M, Mauceli E, MacCallum I.

Nature. 2007 Nov 8;450(7167):203-18.

PMID:
17994087
[PubMed - indexed for MEDLINE]
14.

Transducers: an emerging probabilistic framework for modeling indels on trees.

Bradley RK, Holmes I.

Bioinformatics. 2007 Dec 1;23(23):3258-62. Epub 2007 Sep 5. No abstract available.

PMID:
17804440
[PubMed - indexed for MEDLINE]
Free Article
15.

XRate: a fast prototyping, training and annotation tool for phylo-grammars.

Klosterman PS, Uzilov AV, Bendaña YR, Bradley RK, Chao S, Kosiol C, Goldman N, Holmes I.

BMC Bioinformatics. 2006 Oct 3;7:428.

PMID:
17018148
[PubMed - indexed for MEDLINE]
Free PMC Article
16.

Guanine-rich telomeric sequences stimulate DNA polymerase activity in vitro.

Ying J, Bradley RK, Jones LB, Reddy MS, Colbert DT, Smalley RE, Hardin SH.

Biochemistry. 1999 Dec 14;38(50):16461-8.

PMID:
10600107
[PubMed - indexed for MEDLINE]
17.

Fullerene pipes

Liu J, Rinzler AG, Dai H, Hafner JH, Bradley RK, Boul PJ, Lu A, Iverson T, Shelimov K, Huffman CB, Rodriguez-Macias F, Shon YS, Lee TR, Colbert DT, Smalley RE.

Science. 1998 May 22;280(5367):1253-6.

PMID:
9596576
[PubMed - as supplied by publisher]
Free Article
18.

Four cases of spinal cord compression: the need for early diagnosis.

Bradley RK, Murch SH.

J R Nav Med Serv. 1985 Summer;71(2):92-5. No abstract available.

PMID:
4032342
[PubMed - indexed for MEDLINE]

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