2016 | 2015 | 2014 | 2013 | 2012 | 2010 | 2009 | 2008 | 2007 | 2006


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

2016

Fei DL, Motowski H, Chatrikhi R, Prasad S, Yu J, Gao S, Kielkopf CL, Bradley RK, Varmus H (2016). Wild-type U2AF1 antagonizes the splicing program characteristic of U2AF1-mutant tumors and is required for cell survival. PLoS Genetics 12(10):e1006384. co-corresponding authors
Uo T, Dvinge H, Sprenger CC, Bradley RK, Nelson PS, Plymate SR (2016). Systematic and functional characterization of novel androgen receptor variants arising from alternative splicing in the ligand-binding domain. Oncogene. doi:10.1038/onc.2016.313.
Jagannathan S*, Shadle S*, Resnick R, Snider L, Tawil RN, van der Maarel SM, Bradley RK, Tapscott SJ (2016). Model systems of DUX4 expression recapitulate the transcriptional profile of FSHD cells. Human Molecular Genetics doi:10.1093/hmg/ddw271. *co-first authors; co-senior authors
Dvinge H*, Kim E*, Abdel-Wahab O, Bradley RK (2016). RNA splicing factors as oncoproteins and tumour suppressors. Nature Reviews Cancer 16:413-430. *co-first authors; co-senior authors
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 (2016). Modulation of splicing catalysis for therapeutic targeting of leukemia with mutations in genes encoding spliceosomal proteins. Nature Medicine doi:10.1038/nm.4097. *co-first authors; co-senior authors


See also: F1000 recommendation and Splicing may be therapeutically targetable in acute myeloid leukemia.

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

2015

The Cancer Genome Atlas Research Network (2015). The molecular taxonomy of primary prostate cancer. Cell 163:1011–1025.
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 (2015). Expression of androgen receptor splice variants in clinical breast cancers. Oncotarget 10.18632/oncotarget.6296.
Robinson D, Van Allen EM, et al (2015). Integrative clinical genomics of advanced prostate cancer. Cell 161:1215–1228.
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 (2015). SRSF2 mutations contribute to myelodysplasia by mutant-specific effects on exon recognition. Cancer Cell 27:617–630. *co-first authors; co-senior authors


See also: Charting the "splice" routes to MDS, Splicing the MDS genome, and Understanding molecular pathways behind marrow disorders.

Dvinge H, Bradley RK (2015). Widespread intron retention diversifies most cancer transcriptomes. Genome Medicine 7:45.
Feng Q, Snider L, Jagannathan S, Tawil R, van der Maarel SM, Tapscott SJ, Bradley RK (2015). A feedback loop between nonsense-mediated decay and the retrogene DUX4 in facioscapulohumeral muscular dystrophy. eLife 10.7554/eLife.04996. co-senior authors


See also: F1000 recommendation.

2014

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


See also: F1000 recommendation and The FedEx Factor.

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

2013

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 (2013). Genome-wide RNAi screens in human brain tumor isolates reveal a novel viability requirement for PHF5A. Genes & Development 27(9):1032-1045. *co-first authors


See also: A Spliceosome Protein Is Essential for Glioma Stem Cell Viability.

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

2012

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


See also: The Economist and Scientific American.

2010

Bradley RK*, Li XY*, Trapnell C, Davidson S, Pachter L, Chu HC, Tonkin LA, Biggin MD, Eisen MB (2010). Binding site turnover produces pervasive quantitative changes in transcription factor binding between closely related Drosophila species. PLoS Biology 8:e1000343. *co-first authors


See also: Variable Transcription Factor Binding: A Mechanism of Evolutionary Change.

2009

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

2008

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

2007

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

2006

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