2020 | 2019 | 2018 | 2017 | 2016 | 2015 | 2014 | 2013 | 2012 | 2010 | 2009 | 2008 | 2007 | 2006


(click image for PDF, or title for journal link)

2020

Transgenic mice expressing tunable levels of DUX4 develop characteristic facioscapulohumeral muscular dystrophy-like pathophysiology ranging in severity
Jones TI, Chew G-L, Barraza-Flores P, Schreier S, Ramirez M, Wuebbles RD, Burkin DJ, Bradley RK, Jones PL
Skeletal Muscle 10:8 (2020)
Recurrent SRSF2 mutations in MDS affect both splicing and NMD
Rahman MA, Lin K-T, Bradley RK, Abdel-Wahab O, Krainer AR
Genes & Development 34:1–15 (2020)
Rare and private spliceosomal gene mutations drive partial, complete, and dual phenocopies of hotspot alterations
Pangallo J, Kiladjian J-J, Cassinat B, Renneville A, Taylor J, Polaski JT, North K, Abdel-Wahab O, Bradley RK
Blood doi:10.1182/blood.2019002894 (2020)


Featured in Blood.

RNA isoform screens uncover the essentiality and tumor suppressor activity of ultraconserved poison exons
Thomas JD, Polaski JT*, Feng Q*, De Neef EJ, Hoppe ER, McSharry MV, Pangallo J, Gabel AM, Belleville AE, Watson J, Nkinsi NT, Berger AH, Bradley RK
Nature Genetics 52:84–94 (2020) *equal contribution


Featured in Yahoo! News, FierceBiotech, GeekWire, and Fred Hutch News.

2019

Spliceosomal disruption of the non-canonical BAF complex in cancer
Inoue D*, Chew G-L*, Liu B, Michel BC, Pangallo J, D’Avino AR, Hitchman T, North K, Lee SC-W, Bitner L, Block A, Moore AR, Yoshimi A, Escobar-Hoyos L, Cho H, Penson A, Lu SX, Taylor J, Chen Y, Kadoch C, Abdel-Wahab O, Bradley RK
Nature 574:432–436 (2019) *co-first authors; co-corresponding authors
Coordinated alterations in RNA splicing and epigenetic regulation drive leukaemogenesis
Yoshimi A, Lin K-T, Wiseman DH, Rahman MA, Pastore A, Wang B, Lee SC-W, Micol J-B, Zhang XJ, de Botton S, Penard-Lacronique V, Stein EM, Cho H, Miles RE, Inoue D, Albrecht TR, Somervaille TCP, Batta K, Amaral F, Simeoni F, Wilks DP, Cargo C, Intlekofer AM, Levine RL, Dvinge H, Bradley RK, Wagner EJ, Krainer AR, Abdel-Wahab O
Nature 574:273–277 (2019)
RNA components of the spliceosome regulate tissue- and cancer-specific alternative splicing
Dvinge H, Guenthoer J, Porter PL, Bradley RK
Genome Research 29:1591–1604 (2019) co-corresponding authors
DUX4 suppresses MHC class I to promote cancer immune evasion and resistance to checkpoint blockade
Chew G-L*, Campbell A*, De Neef E, Sutliff NA, Shadle SC, Tapscott SJ, Bradley RK
Developmental Cell 50:658–671.e7 (2019) *co-first authors; co-corresponding authors


Featured in Nature Reviews Cancer, FierceBiotech, GeekWire, and Fred Hutch News.

The splicing factor U2AF1 contributes to cancer progression through a noncanonical role in translation regulation
Palangat M, Anastasakis DG, Fei DL, Lindblad KE, Bradley RK, Hourigan CS, Hafner M, Larson DR
Genes & Development 33:1–16 (2019)
Quantitative proteomics reveals key roles for post-transcriptional gene regulation in the molecular pathology of FSHD
Jagannathan S, Ogata Y, Gafken PR, Tapscott SJ, Bradley RK
eLife 8:e41740 (2019) co-corresponding authors

2018

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
Molecular Cell 72:496–509 (2018)
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, and Varmus H
PNAS doi:10.1073/pnas.1812669115 (2018)
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 34:225–241 (2018) *co-first authors; co-corresponding authors


Featured in Cancer Discovery.

Dissecting the contributions of cooperating gene mutations to cancer phenotypes and drug responses with patient-derived iPSCs
Chang C-J, 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 10:1610–1624 (2018)
Most human introns are recognized via multiple and tissue-specific branchpoints
Pineda JMB, Bradley RK
Genes & Development 32:577–591 (2018)

2017

Congenital myotonic dystrophy—an RNA-mediated disease across a developmental continuum
Jagannathan S, Bradley RK
Genes & Development 31:1067–1068 (2017)
The RNA surveillance factor UPF1 represses myogenesis via its E3 ubiquitin ligase activity
Feng Q, Jagannathan S, Bradley RK
Molecular Cell 67:239–251 (2017)


Featured in Bioessays.

2016

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 Genetics 12(10):e1006384 (2016) co-corresponding authors
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 36:1440–1450 (2016)
Model systems of DUX4 expression recapitulate the transcriptional profile of FSHD cells
Jagannathan S*, Shadle S*, Resnick R, Snider L, Tawil RN, van der Maarel SM, Bradley RK, Tapscott SJ
Human Molecular Genetics 25:4419–4431 (2016) *co-first authors; co-senior authors
RNA splicing factors as oncoproteins and tumour suppressors
Dvinge H*, Kim E*, Abdel-Wahab O, Bradley RK
Nature Reviews Cancer 16:413–430 (2016) *co-first authors; co-senior authors
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
Nature Medicine 22:672–678 (2016) *co-first authors; co-senior authors


Featured in F1000 and Cancer Discovery.

Spliceosomal gene mutations in myelodysplasia: molecular links to clonal abnormalities of hematopoiesis
Inoue D, Bradley RK, Abdel-Wahab O
Genes & Development 30:989–1001 (2016)

2015

The molecular taxonomy of primary prostate cancer
The Cancer Genome Atlas Research Network
Cell 163:1011–1025 (2015)
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 10.18632/oncotarget.6296 (2015)
Integrative clinical genomics of advanced prostate cancer
Robinson D, Van Allen EM, et al
Cell 161:1215–1228 (2015)
SRSF2 mutations contribute to myelodysplasia by mutant-specific effects on exon recognition
Kim E*, Ilagan JO*, Liang Y*, Daubner GM*, Lee SC-W, Ramakrishnan A, Li Y, Chung YR, Micol J-B, Murphy M, Cho H, Kim M-K, Zebari AS, Aumann S, Park CY, Buonamici S, Smith PG, Deeg HJ, Lobry C, Aifantis I, Modis Y, Allain FH-T, Halene S, Bradley RK, Abdel-Wahab O
Cancer Cell 27:617–630 (2015) *co-first authors; co-senior authors


Featured in Nature Reviews Cancer, Cancer Cell, and Fred Hutch News.

Widespread intron retention diversifies most cancer transcriptomes
Dvinge H, Bradley RK
Genome Medicine 7:45 (2015)
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 4:e04996 (2015) co-senior authors


Featured in F1000.

2014

Sample processing obscures cancer-specific alterations in leukemic transcriptomes
Dvinge H, Ries RE, Ilagan JO, Stirewalt DL, Meshinchi S, Bradley RK
PNAS 111:16802–16807 (2014)


Featured in F1000 and Fred Hutch News.

U2AF1 mutations alter splice site recognition in hematological malignancies
Ilagan JO*, Ramakrishnan A*, Hayes B, Murphy ME, Zebari AS, Bradley P, Bradley RK
Genome Research doi:10.1101/gr.181016.114 (2014) *co-first authors

2013

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 & Development 27(9):1032–1045 (2013) *co-first authors


Featured in Cancer Discovery.

Massive mitochondrial gene transfer in a parasitic flowering plant
Xi Z, Yuguo W, Bradley RK, Sugumaran M, Marx CJ, Rest JS, Davis CC
PLoS Genetics 9(2):e1003265 (2013)
Braveheart, a long non-coding RNA required for cardiovascular lineage commitment
Klattenhoff C, 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 152(3):570–583 (2013)

2012

Horizontal transfer of expressed genes in a parasitic flowering plant
Xi Z, Bradley RK, Wurdack KJ, Wong KM, Sugumaran M, Bomblies K, Rest JS, Davis CC
BMC Genomics 13:227 (2012)


Featured in The Economist and Scientific American.

Alternative splicing of RNA triplets is often regulated and accelerates proteome evolution
Bradley RK, Merkin JM, Lambert N, Burge CB
PLoS Biology 10:e1001229 (2012)


Featured in Molecular Cell and Genome Biology.

2010

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 Biology 8:e1000343 (2010) *co-first authors


Featured in PLoS Biology.

2009

Evolutionary triplet models of structured RNA
Bradley RK, Holmes I
PLoS Computational Biology 5(8):e1000483 (2009)
Evolutionary modeling and prediction of non-coding RNAs in Drosophila
Bradley RK, Uzilov AV, Skinner ME, Bendana YR, Barquist L, Holmes I
PLoS One 4(8):e6478 (2009)
Fast Statistical Alignment
Bradley RK, Roberts A, Smoot M, Juvekar S, Do J, Dewey C, Holmes I, Pachter L
PLoS Computational Biology 5:e1000392 (2009)

2008

Tools for simulating evolution of aligned genomic regions with integrated parameter estimation
Varadarajan A, Bradley RK, Holmes I
Genome Biology 9:R147 (2008)
Specific alignment of structured RNA: stochastic grammars and sequence annealing
Bradley RK, Pachter L, Holmes I
Bioinformatics 24:2677–2683 (2008)

2007

Evolution of genes and genomes on the Drosophila phylogeny
Drosophila 12 Genomes Consortium
Nature 450:203–218 (2007)
Transducers: an emerging probabilistic framework for modeling indels on trees
Bradley RK, Holmes I
Bioinformatics 23:3258–3262 (2007)

2006

Xrate: a fast prototyping, training and annotation tool for phylo-grammars
Klosterman PS, Uzilov AV, Bendana YR, Bradley RK, Chao S, Kosiol C, Goldman N, Holmes I
BMC Bioinformatics 7:428 (2006)