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Items: 43

1.

Quantitative proteomics reveals key roles for post-transcriptional gene regulation in the molecular pathology of facioscapulohumeral muscular dystrophy.

Jagannathan S, Ogata Y, Gafken PR, Tapscott SJ, Bradley RK.

Elife. 2019 Jan 15;8. pii: e41740. doi: 10.7554/eLife.41740.

2.

Exon Junction Complex Shapes the Transcriptome by Repressing Recursive Splicing.

Blazquez L, Emmett W, Faraway R, Pineda JMB, Bajew S, Gohr A, Haberman N, Sibley CR, Bradley RK, Irimia M, Ule J.

Mol Cell. 2018 Nov 1;72(3):496-509.e9. doi: 10.1016/j.molcel.2018.09.033.

3.

Impaired hematopoiesis and leukemia development in mice with a conditional knock-in allele of a mutant splicing factor gene U2af1.

Fei DL, Zhen T, Durham B, Ferrarone J, Zhang T, Garrett L, Yoshimi A, Abdel-Wahab O, Bradley RK, Liu P, Varmus H.

Proc Natl Acad Sci U S A. 2018 Oct 30;115(44):E10437-E10446. doi: 10.1073/pnas.1812669115. Epub 2018 Oct 15.

4.

Synthetic Lethal and Convergent Biological Effects of Cancer-Associated Spliceosomal Gene Mutations.

Lee SC, North K, Kim E, Jang E, Obeng E, Lu SX, Liu B, Inoue D, Yoshimi A, Ki M, Yeo M, Zhang XJ, Kim MK, Cho H, Chung YR, Taylor J, Durham BH, Kim YJ, Pastore A, Monette S, Palacino J, Seiler M, Buonamici S, Smith PG, Ebert BL, Bradley RK, Abdel-Wahab O.

Cancer Cell. 2018 Aug 13;34(2):225-241.e8. doi: 10.1016/j.ccell.2018.07.003.

PMID:
30107174
5.

Dissecting the Contributions of Cooperating Gene Mutations to Cancer Phenotypes and Drug Responses with Patient-Derived iPSCs.

Chang CJ, Kotini AG, Olszewska M, Georgomanoli M, Teruya-Feldstein J, Sperber H, Sanchez R, DeVita R, Martins TJ, Abdel-Wahab O, Bradley RK, Papapetrou EP.

Stem Cell Reports. 2018 May 8;10(5):1610-1624. doi: 10.1016/j.stemcr.2018.03.020. Epub 2018 Apr 19.

6.

Most human introns are recognized via multiple and tissue-specific branchpoints.

Pineda JMB, Bradley RK.

Genes Dev. 2018 Apr 1;32(7-8):577-591. doi: 10.1101/gad.312058.118. Epub 2018 Apr 17.

7.

Congenital myotonic dystrophy-an RNA-mediated disease across a developmental continuum.

Jagannathan S, Bradley RK.

Genes Dev. 2017 Jun 1;31(11):1067-1068. doi: 10.1101/gad.302893.117.

8.

The RNA Surveillance Factor UPF1 Represses Myogenesis via Its E3 Ubiquitin Ligase Activity.

Feng Q, Jagannathan S, Bradley RK.

Mol Cell. 2017 Jul 20;67(2):239-251.e6. doi: 10.1016/j.molcel.2017.05.034. Epub 2017 Jun 29.

9.

Model systems of DUX4 expression recapitulate the transcriptional profile of FSHD cells.

Jagannathan S, Shadle SC, Resnick R, Snider L, Tawil RN, van der Maarel SM, Bradley RK, Tapscott SJ.

Hum Mol Genet. 2016 Oct 15;25(20):4419-4431. doi: 10.1093/hmg/ddw271.

10.

Wild-Type U2AF1 Antagonizes the Splicing Program Characteristic of U2AF1-Mutant Tumors and Is Required for Cell Survival.

Fei DL, Motowski H, Chatrikhi R, Prasad S, Yu J, Gao S, Kielkopf CL, Bradley RK, Varmus H.

PLoS Genet. 2016 Oct 24;12(10):e1006384. doi: 10.1371/journal.pgen.1006384. eCollection 2016 Oct.

11.

Systematic and functional characterization of novel androgen receptor variants arising from alternative splicing in the ligand-binding domain.

Uo T, Dvinge H, Sprenger CC, Bradley RK, Nelson PS, Plymate SR.

Oncogene. 2017 Mar;36(10):1440-1450. doi: 10.1038/onc.2016.313. Epub 2016 Oct 3.

12.

Translational plasticity facilitates the accumulation of nonsense genetic variants in the human population.

Jagannathan S, Bradley RK.

Genome Res. 2016 Dec;26(12):1639-1650. Epub 2016 Sep 19.

13.

Is Hybridization a Source of Adaptive Venom Variation in Rattlesnakes? A Test, Using a Crotalus scutulatus × viridis Hybrid Zone in Southwestern New Mexico.

Zancolli G, Baker TG, Barlow A, Bradley RK, Calvete JJ, Carter KC, de Jager K, Owens JB, Price JF, Sanz L, Scholes-Higham A, Shier L, Wood L, Wüster CE, Wüster W.

Toxins (Basel). 2016 Jun 16;8(6). pii: E188. doi: 10.3390/toxins8060188.

14.

RNA splicing factors as oncoproteins and tumour suppressors.

Dvinge H, Kim E, Abdel-Wahab O, Bradley RK.

Nat Rev Cancer. 2016 Jul;16(7):413-30. doi: 10.1038/nrc.2016.51. Epub 2016 Jun 10. Review.

15.

Erratum: Modulation of splicing catalysis for therapeutic targeting of leukemia with mutations in genes encoding spliceosomal proteins.

Lee SC, Dvinge H, Kim E, Cho H, Micol JB, Chung YR, Durham BH, Yoshimi A, Kim YJ, Thomas M, Lobry C, Chen CW, Pastore A, Taylor J, Wang X, Krivtsov A, Armstrong SA, Palacino J, Buonamici S, Smith PG, Bradley RK, Abdel-Wahab O.

Nat Med. 2016 Jun 7;22(6):692. doi: 10.1038/nm0616-692d. No abstract available.

16.

Spliceosomal gene mutations in myelodysplasia: molecular links to clonal abnormalities of hematopoiesis.

Inoue D, Bradley RK, Abdel-Wahab O.

Genes Dev. 2016 May 1;30(9):989-1001. doi: 10.1101/gad.278424.116. Review.

17.

Modulation of splicing catalysis for therapeutic targeting of leukemia with mutations in genes encoding spliceosomal proteins.

Lee SC, Dvinge H, Kim E, Cho H, Micol JB, Chung YR, Durham BH, Yoshimi A, Kim YJ, Thomas M, Lobry C, Chen CW, Pastore A, Taylor J, Wang X, Krivtsov A, Armstrong SA, Palacino J, Buonamici S, Smith PG, Bradley RK, Abdel-Wahab O.

Nat Med. 2016 Jun;22(6):672-8. doi: 10.1038/nm.4097. Epub 2016 May 2. Erratum in: Nat Med. 2016 Jun 7;22(6):692.

18.

Expression of androgen receptor splice variants in clinical breast cancers.

Hickey TE, Irvine CM, Dvinge H, Tarulli GA, Hanson AR, Ryan NK, Pickering MA, Birrell SN, Hu DG, Mackenzie PI, Russell R, Caldas C, Raj GV, Dehm SM, Plymate SR, Bradley RK, Tilley WD, Selth LA.

Oncotarget. 2015 Dec 29;6(42):44728-44. doi: 10.18632/oncotarget.6296.

19.

Integrative Clinical Genomics of Advanced Prostate Cancer.

Robinson D, Van Allen EM, Wu YM, Schultz N, Lonigro RJ, Mosquera JM, Montgomery B, Taplin ME, Pritchard CC, Attard G, Beltran H, Abida W, Bradley RK, Vinson J, Cao X, Vats P, Kunju LP, Hussain M, Feng FY, Tomlins SA, Cooney KA, Smith DC, Brennan C, Siddiqui J, Mehra R, Chen Y, Rathkopf DE, Morris MJ, Solomon SB, Durack JC, Reuter VE, Gopalan A, Gao J, Loda M, Lis RT, Bowden M, Balk SP, Gaviola G, Sougnez C, Gupta M, Yu EY, Mostaghel EA, Cheng HH, Mulcahy H, True LD, Plymate SR, Dvinge H, Ferraldeschi R, Flohr P, Miranda S, Zafeiriou Z, Tunariu N, Mateo J, Perez-Lopez R, Demichelis F, Robinson BD, Sboner A, Schiffman M, Nanus DM, Tagawa ST, Sigaras A, Eng KW, Elemento O, Sboner A, Heath EI, Scher HI, Pienta KJ, Kantoff P, de Bono JS, Rubin MA, Nelson PS, Garraway LA, Sawyers CL, Chinnaiyan AM.

Cell. 2015 Jul 16;162(2):454. doi: 10.1016/j.cell.2015.06.053. Epub 2015 Jul 16. No abstract available.

20.

Widespread intron retention diversifies most cancer transcriptomes.

Dvinge H, Bradley RK.

Genome Med. 2015 May 15;7(1):45. doi: 10.1186/s13073-015-0168-9. eCollection 2015.

21.

Integrative clinical genomics of advanced prostate cancer.

Robinson D, Van Allen EM, Wu YM, Schultz N, Lonigro RJ, Mosquera JM, Montgomery B, Taplin ME, Pritchard CC, Attard G, Beltran H, Abida W, Bradley RK, Vinson J, Cao X, Vats P, Kunju LP, Hussain M, Feng FY, Tomlins SA, Cooney KA, Smith DC, Brennan C, Siddiqui J, Mehra R, Chen Y, Rathkopf DE, Morris MJ, Solomon SB, Durack JC, Reuter VE, Gopalan A, Gao J, Loda M, Lis RT, Bowden M, Balk SP, Gaviola G, Sougnez C, Gupta M, Yu EY, Mostaghel EA, Cheng HH, Mulcahy H, True LD, Plymate SR, Dvinge H, Ferraldeschi R, Flohr P, Miranda S, Zafeiriou Z, Tunariu N, Mateo J, Perez-Lopez R, Demichelis F, Robinson BD, Schiffman M, Nanus DM, Tagawa ST, Sigaras A, Eng KW, Elemento O, Sboner A, Heath EI, Scher HI, Pienta KJ, Kantoff P, de Bono JS, Rubin MA, Nelson PS, Garraway LA, Sawyers CL, Chinnaiyan AM.

Cell. 2015 May 21;161(5):1215-1228. doi: 10.1016/j.cell.2015.05.001. Erratum in: Cell. 2015 Jul 16;162(2):454.

22.

SRSF2 Mutations Contribute to Myelodysplasia by Mutant-Specific Effects on Exon Recognition.

Kim E, Ilagan JO, Liang Y, Daubner GM, Lee SC, Ramakrishnan A, Li Y, Chung YR, Micol JB, Murphy ME, Cho H, Kim MK, Zebari AS, Aumann S, Park CY, Buonamici S, Smith PG, Deeg HJ, Lobry C, Aifantis I, Modis Y, Allain FH, Halene S, Bradley RK, Abdel-Wahab O.

Cancer Cell. 2015 May 11;27(5):617-30. doi: 10.1016/j.ccell.2015.04.006.

23.

A feedback loop between nonsense-mediated decay and the retrogene DUX4 in facioscapulohumeral muscular dystrophy.

Feng Q, Snider L, Jagannathan S, Tawil R, van der Maarel SM, Tapscott SJ, Bradley RK.

Elife. 2015 Jan 7;4. doi: 10.7554/eLife.04996.

24.

Sample processing obscures cancer-specific alterations in leukemic transcriptomes.

Dvinge H, Ries RE, Ilagan JO, Stirewalt DL, Meshinchi S, Bradley RK.

Proc Natl Acad Sci U S A. 2014 Nov 25;111(47):16802-7. doi: 10.1073/pnas.1413374111. Epub 2014 Nov 10.

25.

U2AF1 mutations alter splice site recognition in hematological malignancies.

Ilagan JO, Ramakrishnan A, Hayes B, Murphy ME, Zebari AS, Bradley P, Bradley RK.

Genome Res. 2015 Jan;25(1):14-26. doi: 10.1101/gr.181016.114. Epub 2014 Sep 29.

26.

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.

27.

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.

28.

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.

29.

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.

30.

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.

31.

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.

32.

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.

33.

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.

34.

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.

35.

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.

36.

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.

37.

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.

38.

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
39.

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
40.

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.

41.

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
42.

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.

43.

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

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