Robert K. Bradley - Publications

Affiliations: 
2009-2011 Biology Massachusetts Institute of Technology, Cambridge, MA, United States 
 2011- Computational Biology Fred Hutchinson Cancer Research Center, Seattle, WA, United States 
Website:
http://bradleybiology.org/

74 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2022 North K, Benbarche S, Liu B, Pangallo J, Chen S, Stahl M, Bewersdorf JP, Stanley RF, Erickson C, Cho H, Pineda JMB, Thomas JD, Polaski JT, Belleville AE, Gabel AM, ... ... Bradley RK, et al. Synthetic introns enable splicing factor mutation-dependent targeting of cancer cells. Nature Biotechnology. PMID 35241838 DOI: 10.1038/s41587-022-01224-2  0.811
2021 Clough CA, Pangallo J, Sarchi M, Ilagan JO, North K, Bergantinos R, Stolla MC, Naru J, Nugent P, Kim E, Stirewalt DL, Subramaniam AR, Abdel-Wahab O, Abkowitz JL, Bradley RK, et al. Coordinated mis-splicing of TMEM14C and ABCB7 causes ring sideroblast formation in SF3B1-mutant myelodysplastic syndrome. Blood. PMID 34861039 DOI: 10.1182/blood.2021012652  0.758
2021 Beauchamp EM, Leventhal M, Bernard E, Hoppe ER, Todisco G, Creignou M, Gallì A, Castellano CA, McConkey M, Tarun A, Wong W, Schenone M, Stanclift C, Tanenbaum B, Malolepsza E, ... ... Bradley RK, et al. is mutated in clonal hematopoiesis and myelodysplastic syndromes and impacts RNA splicing. Blood Cancer Discovery. 2: 500-517. PMID 34568833 DOI: 10.1158/2643-3230.BCD-20-0224  0.37
2021 Lu SX, De Neef E, Thomas JD, Sabio E, Rousseau B, Gigoux M, Knorr DA, Greenbaum B, Elhanati Y, Hogg SJ, Chow A, Ghosh A, Xie A, Zamarin D, Cui D, ... ... Bradley RK, et al. Pharmacologic modulation of RNA splicing enhances anti-tumor immunity. Cell. PMID 34171309 DOI: 10.1016/j.cell.2021.05.038  0.54
2021 Inoue D, Polaski JT, Taylor J, Castel P, Chen S, Kobayashi S, Hogg SJ, Hayashi Y, Pineda JMB, El Marabti E, Erickson C, Knorr K, Fukumoto M, Yamazaki H, Tanaka A, ... ... Bradley RK, et al. Minor intron retention drives clonal hematopoietic disorders and diverse cancer predisposition. Nature Genetics. PMID 33846634 DOI: 10.1038/s41588-021-00828-9  0.735
2021 Chew GL, Bleakley M, Bradley RK, Malik HS, Henikoff S, Molaro A, Sarthy J. Short H2A histone variants are expressed in cancer. Nature Communications. 12: 490. PMID 33473122 DOI: 10.1038/s41467-020-20707-x  0.568
2021 Polaski JT, Udy DB, Escobar-Hoyos LF, Askan G, D Leach SD, Ventura A, Kannan R, Bradley RK. The origins and consequences of variants in pancreatic adenosquamous carcinoma. Elife. 10. PMID 33404013 DOI: 10.7554/eLife.62209  0.335
2020 Taylor J, Mi X, North KD, Binder M, Penson A, Lasho TL, Knorr K, Haddadin M, Liu B, Pangallo J, Benbarche S, Wiseman DH, Tefferi A, Halene S, Liang Y, ... ... Bradley RK, et al. Single-cell genomics reveals the genetic and molecular bases for escape from mutational epistasis in myeloid neoplasms. Blood. PMID 32640014 DOI: 10.1182/Blood.2020006868  0.802
2020 Escobar-Hoyos LF, Penson A, Kannan R, Cho H, Pan CH, Singh RK, Apken LH, Hobbs GA, Luo R, Lecomte N, Babu S, Pan FC, Alonso-Curbelo D, Morris JP, Askan G, ... ... Bradley RK, et al. Altered RNA Splicing by Mutant p53 Activates Oncogenic RAS Signaling in Pancreatic Cancer. Cancer Cell. PMID 32559497 DOI: 10.1016/J.Ccell.2020.05.010  0.443
2020 Jones TI, Chew GL, Barraza-Flores P, Schreier S, Ramirez M, Wuebbles RD, Burkin DJ, Bradley RK, Jones PL. Transgenic mice expressing tunable levels of DUX4 develop characteristic facioscapulohumeral muscular dystrophy-like pathophysiology ranging in severity. Skeletal Muscle. 10: 8. PMID 32278354 DOI: 10.1186/S13395-020-00227-4  0.565
2020 Rahman MA, Lin KT, Bradley RK, Abdel-Wahab O, Krainer AR. Recurrent SRSF2 mutations in MDS affect both splicing and NMD. Genes & Development. PMID 32001512 DOI: 10.1101/Gad.332270.119  0.501
2020 Pangallo J, Kiladjian JJ, Cassinat B, Renneville A, Taylor J, Polaski JT, North KD, Abdel-Wahab O, Bradley RK. Rare and private spliceosomal gene mutations drive partial, complete, and dual phenocopies of hotspot alterations. Blood. PMID 31961934 DOI: 10.1182/Blood.2019002894  0.797
2020 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. RNA isoform screens uncover the essentiality and tumor-suppressor activity of ultraconserved poison exons. Nature Genetics. PMID 31911676 DOI: 10.1038/S41588-019-0555-Z  0.796
2019 Inoue D, Chew GL, Liu B, Michel BC, Pangallo J, D'Avino AR, Hitchman T, North K, Lee SC, Bitner L, Block A, Moore AR, Yoshimi A, Escobar-Hoyos L, Cho H, ... ... Bradley RK, et al. Spliceosomal disruption of the non-canonical BAF complex in cancer. Nature. PMID 31597964 DOI: 10.1038/S41586-019-1646-9  0.813
2019 Yoshimi A, Lin KT, Wiseman DH, Rahman MA, Pastore A, Wang B, Lee SC, Micol JB, Zhang XJ, de Botton S, Penard-Lacronique V, Stein EM, Cho H, Miles RE, Inoue D, ... ... Bradley RK, et al. Coordinated alterations in RNA splicing and epigenetic regulation drive leukaemogenesis. Nature. PMID 31578525 DOI: 10.1038/S41586-019-1618-0  0.785
2019 Dvinge H, Guenthoer J, Porter PL, Bradley RK. RNA components of the spliceosome regulate tissue- and cancer-specific alternative splicing. Genome Research. PMID 31434678 DOI: 10.1101/Gr.246678.118  0.769
2019 Chew GL, Campbell AE, De Neef E, Sutliff NA, Shadle SC, Tapscott SJ, Bradley RK. DUX4 Suppresses MHC Class I to Promote Cancer Immune Evasion and Resistance to Checkpoint Blockade. Developmental Cell. PMID 31327741 DOI: 10.1016/J.Devcel.2019.06.011  0.7
2019 Palangat M, Anastasakis DG, Fei DL, Lindblad KE, Bradley R, Hourigan CS, Hafner M, Larson DR. The splicing factor U2AF1 contributes to cancer progression through a noncanonical role in translation regulation. Genes & Development. PMID 30842218 DOI: 10.1101/Gad.319590.118  0.473
2019 Jagannathan S, Ogata Y, Gafken PR, Tapscott SJ, Bradley RK. Quantitative proteomics reveals key roles for post-transcriptional gene regulation in the molecular pathology of FSHD. Elife. 8. PMID 30644821 DOI: 10.7554/Elife.41740  0.703
2019 Pufall MA, Fang M, Bradley RK, Guo-Liang C, Lanier R, Tasian SK. Glucocorticoids Regulate the Splicing Factor MBNL1, a Potential Control Point for B-Cell Specification Blood. 134: 2478-2478. DOI: 10.1182/Blood-2019-131322  0.346
2019 Clough C, Busch S, Pangallo J, Bradley RK, Doulatov S. Probing Aberrant Splicing in a Novel Model of SF3B1-Mutant Myelodysplastic Syndromes Blood. 134: 1706-1706. DOI: 10.1182/Blood-2019-129176  0.423
2019 Inoue D, Guo-Liang C, Liu B, Lee SC, Michel BC, Pangallo J, D'Avino AR, North K, Bitner LE, Xiao M, Kobayashi S, Yoshimi A, Cho H, Lu SX, Taylor J, ... ... Bradley RK, et al. Spliceosomal Disruption of the Non-Canonical SWI/SNF Chromatin Remodeling Complex in SF3B1 Mutant Leukemias Blood. 134: 637-637. DOI: 10.1182/Blood-2019-124616  0.493
2018 Fei DL, Zhen T, Durham B, Ferrarone J, Zhang T, Garrett L, Yoshimi A, Abdel-Wahab O, Bradley RK, Liu P, Varmus H. Impaired hematopoiesis and leukemia development in mice with a conditional knock-in allele of a mutant splicing factor gene . Proceedings of the National Academy of Sciences of the United States of America. PMID 30322915 DOI: 10.1073/Pnas.1812669115  0.41
2018 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, ... ... Bradley RK, et al. Synthetic Lethal and Convergent Biological Effects of Cancer-Associated Spliceosomal Gene Mutations. Cancer Cell. 34: 225-241.e8. PMID 30107174 DOI: 10.1016/J.Ccell.2018.07.003  0.496
2018 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. Dissecting the Contributions of Cooperating Gene Mutations to Cancer Phenotypes and Drug Responses with Patient-Derived iPSCs. Stem Cell Reports. PMID 29681544 DOI: 10.1016/J.Stemcr.2018.03.020  0.399
2018 Pineda JMB, Bradley RK. Most human introns are recognized via multiple and tissue-specific branchpoints. Genes & Development. PMID 29666160 DOI: 10.1101/Gad.312058.118  0.432
2018 Lee SC, North K, Chen C, Kim E, Lu SX, Ki M, Garippa R, Lowe SW, Bradley RK, Abdel-Wahab OI. Dependency of Spliceosomal Mutant MDS on Innate Immune Signaling Blood. 132: 937-937. DOI: 10.1182/Blood-2018-99-111552  0.423
2017 Jagannathan S, Bradley RK. Congenital myotonic dystrophy-an RNA-mediated disease across a developmental continuum. Genes & Development. 31: 1067-1068. PMID 28717044 DOI: 10.1101/Gad.302893.117  0.589
2017 Feng Q, Jagannathan S, Bradley RK. The RNA Surveillance Factor UPF1 Represses Myogenesis via Its E3 Ubiquitin Ligase Activity. Molecular Cell. PMID 28669802 DOI: 10.1016/J.Molcel.2017.05.034  0.731
2016 Jagannathan S, Shadle SC, Resnick R, Snider L, Tawil RN, van der Maarel SM, Bradley RK, Tapscott SJ. Model systems of DUX4 expression recapitulate the transcriptional profile of FSHD cells. Human Molecular Genetics. 25: 4419-4431. PMID 28171552 DOI: 10.1093/Hmg/Ddw271  0.662
2016 Fei DL, Motowski H, Chatrikhi R, Prasad S, Yu J, Gao S, Kielkopf CL, Bradley RK, Varmus H. Wild-Type U2AF1 Antagonizes the Splicing Program Characteristic of U2AF1-Mutant Tumors and Is Required for Cell Survival. Plos Genetics. 12: e1006384. PMID 27776121 DOI: 10.1371/Journal.Pgen.1006384  0.431
2016 Uo T, Dvinge H, Sprenger CC, Bradley RK, Nelson PS, Plymate SR. Systematic and functional characterization of novel androgen receptor variants arising from alternative splicing in the ligand-binding domain. Oncogene. PMID 27694897 DOI: 10.1038/Onc.2016.313  0.725
2016 Jagannathan S, Bradley RK. Translational plasticity facilitates the accumulation of nonsense genetic variants in the human population. Genome Research. PMID 27646533 DOI: 10.1101/Gr.205070.116  0.568
2016 Jagannathan S, Shadle S, Resnick R, Snider L, Tawil RN, van der Maarel SM, Bradley RK, Tapscott SJ. Model systems of DUX4 expression recapitulate the transcriptional profile of FSHD cells. Human Molecular Genetics. PMID 27530253 DOI: 10.1093/hmg/ddw271  0.636
2016 Dvinge H, Kim E, Abdel-Wahab O, Bradley RK. RNA splicing factors as oncoproteins and tumour suppressors. Nature Reviews. Cancer. PMID 27282250 DOI: 10.1038/Nrc.2016.51  0.792
2016 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, ... ... Bradley RK, et al. Erratum: Modulation of splicing catalysis for therapeutic targeting of leukemia with mutations in genes encoding spliceosomal proteins. Nature Medicine. 22: 692. PMID 27270779 DOI: 10.1038/nm0616-692d  0.732
2016 Inoue D, Bradley RK, Abdel-Wahab O. Spliceosomal gene mutations in myelodysplasia: molecular links to clonal abnormalities of hematopoiesis. Genes & Development. 30: 989-1001. PMID 27151974 DOI: 10.1101/Gad.278424.116  0.453
2016 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, ... ... Bradley RK, et al. Modulation of splicing catalysis for therapeutic targeting of leukemia with mutations in genes encoding spliceosomal proteins. Nature Medicine. PMID 27135740 DOI: 10.1038/Nm.4097  0.769
2016 Cameron RC, McKinstry M, De La Garza A, Nik S, Smith PG, Buonamici S, Bradley RK, Bowman TV. A Chemical Modifier Screen in Zebrafish Mutants for the Spliceosomal Component Sf3b1reveals Genotype-Selective Vulnerabilities Blood. 128: 965-965. DOI: 10.1182/Blood.V128.22.965.965  0.43
2016 Chang C, Kotini A, Teruya-Feldstein J, Abdel-Wahab O, Bradley R, Papapetrou EP. Isogenic iPSC Models of SRSF2-Mutant Myelodysplastic Syndrome Capture Disease Phenotypes, Splicing Defects and Drug Responses Blood. 128: 962-962. DOI: 10.1182/Blood.V128.22.962.962  0.494
2016 Lee SC, Dilai K, Obeng EA, Kim E, Micol J, Yoshimi A, Willekens C, Inoue D, Saada V, Cho H, Chung YR, Palacino J, Seiler M, Buonamici S, Smith P, ... ... Bradley R, et al. Synthetic Lethal Interactions of MDS-Associated Spliceosomal Gene Mutations Identifies the Basis for Their Mutual Exclusivity Blood. 128: 961-961. DOI: 10.1182/Blood.V128.22.961.961  0.468
2016 Fei D, Motowski H, Prasad S, Yu J, Bradley R, Varmus H. Abstract 4163: Molecular and physiological effects of splicing factor mutant U2AF1 in human lung cell lines and in mice Cancer Research. 76: 4163-4163. DOI: 10.1158/1538-7445.Am2016-4163  0.423
2016 Uo T, Dvinge H, Sprenger CC, Bradley RK, Nelson PS, Plymate SR. Abstract 1819: Intrinsic determinants of constitutive activity of exon-skipping variants of androgen receptor in castration resistant prostate cancer Cancer Research. 76: 1819-1819. DOI: 10.1158/1538-7445.Am2016-1819  0.725
2015 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, et al. Integrative Clinical Genomics of Advanced Prostate Cancer. Cell. 162: 454. PMID 28843286 DOI: 10.1016/J.Cell.2015.06.053  0.708
2015 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, et al. Expression of androgen receptor splice variants in clinical breast cancers. Oncotarget. PMID 26554309 DOI: 10.18632/Oncotarget.6296  0.73
2015 Dvinge H, Bradley RK. Widespread intron retention diversifies most cancer transcriptomes. Genome Medicine. 7: 45. PMID 26113877 DOI: 10.1186/S13073-015-0168-9  0.782
2015 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, et al. Integrative clinical genomics of advanced prostate cancer. Cell. 161: 1215-28. PMID 26000489 DOI: 10.1016/J.Cell.2015.05.001  0.735
2015 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, ... ... Bradley RK, et al. SRSF2 Mutations Contribute to Myelodysplasia by Mutant-Specific Effects on Exon Recognition. Cancer Cell. 27: 617-30. PMID 25965569 DOI: 10.1016/J.Ccell.2015.04.006  0.474
2015 Feng Q, Snider L, Jagannathan S, Tawil R, van der Maarel SM, Tapscott SJ, Bradley RK. A feedback loop between nonsense-mediated decay and the retrogene DUX4 in facioscapulohumeral muscular dystrophy. Elife. 4. PMID 25564732 DOI: 10.7554/Elife.04996  0.752
2015 Ilagan JO, Ramakrishnan A, Hayes B, Murphy ME, Zebari AS, Bradley P, Bradley RK. U2AF1 mutations alter splice site recognition in hematological malignancies. Genome Research. 25: 14-26. PMID 25267526 DOI: 10.1101/Gr.181016.114  0.487
2015 Lee SC, Dvinge H, Kim E, Cho H, Chung YR, Micol J, Durham B, Kim YJ, Thomas M, Lobry C, Buonamici S, Smith P, Bradley RK, Abdel-Wahab O. Therapeutic Targeting of Spliceosomal Mutant Myeloid Leukemias through Modulation of Splicing Catalysis Blood. 126: 4-4. DOI: 10.1182/Blood.V126.23.4.4  0.766
2015 Kim E, Ilagan JO, Lee S, Ramakrishnan A, Chung YR, Micol J, Murphy ME, Kim M, Zebari AS, Buonamici S, Smith P, Deeg HJ, Lobry C, Aifantis I, Bradley RK, et al. Abstract IA36:SRSF2mutations impair hematopoietic differentiation by altering exonic splicing enhancer preference. Clinical Cancer Research. 21. DOI: 10.1158/1557-3265.Hemmal14-Ia36  0.509
2015 Uo T, Dvinge H, Sprenger CC, Sun S, Bradley RK, Nelson PS, Plymate SR. Abstract 4676: In silico and in vitro analyses of androgen receptor splicing variants with a special focus on human patient samples Endocrinology. 75: 4676-4676. DOI: 10.1158/1538-7445.Am2015-4676  0.698
2015 Abeshouse A, Ahn J, Akbani R, Ally A, Amin S, Andry CD, Annala M, Aprikian A, Armenia J, Arora A, Auman JT, Balasundaram M, Balu S, Barbieri CE, Bauer T, ... ... Bradley RK, et al. The Molecular Taxonomy of Primary Prostate Cancer Cell. 163: 1011-1025. DOI: 10.1016/j.cell.2015.10.025  0.687
2014 Dvinge H, Ries RE, Ilagan JO, Stirewalt DL, Meshinchi S, Bradley RK. Sample processing obscures cancer-specific alterations in leukemic transcriptomes. Proceedings of the National Academy of Sciences of the United States of America. 111: 16802-7. PMID 25385641 DOI: 10.1182/Blood.V124.21.2201.2201  0.773
2014 Feng Q, Snider L, Jagannathan S, Tawil R, Maarel SMvd, Tapscott SJ, Bradley RK. Author response: A feedback loop between nonsense-mediated decay and the retrogene DUX4 in facioscapulohumeral muscular dystrophy Elife. DOI: 10.7554/Elife.04996.010  0.667
2014 Kim E, Ilagan JO, Lee S, Ramakrishnan A, Chung YR, Micol J, Murphy ME, Kim M, Zebari AS, Feala J, Buonamici S, Smith PG, Deeg HJ, Lobry C, Aifantis I, ... Bradley RK, et al. SRSF2 Mutations Impair Hematopoietic Differentiation By Altering Exonic Splicing Enhancer Preference Blood. 124: 824-824. DOI: 10.1182/Blood.V124.21.824.824  0.503
2014 Ilagan JO, Ramakrishnan A, Hayes B, Murphy ME, Zebari AS, Bradley P, Bradley RK. U2AF1 Mutations Cause Allele-Specific Alterations in 3' Splice Site Recognition in Myeloid Malignancies Blood. 124: 1889-1889. DOI: 10.1182/Blood.V124.21.1889.1889  0.476
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, et al. Genome-wide RNAi screens in human brain tumor isolates reveal a novel viability requirement for PHF5A. Genes & Development. 27: 1032-45. PMID 23651857 DOI: 10.1101/Gad.212548.112  0.377
2013 Xi Z, Wang Y, Bradley RK, Sugumaran M, Marx CJ, Rest JS, Davis CC. Massive mitochondrial gene transfer in a parasitic flowering plant clade. Plos Genetics. 9: e1003265. PMID 23459037 DOI: 10.1371/Journal.Pgen.1003265  0.304
2013 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. Braveheart, a long noncoding RNA required for cardiovascular lineage commitment. Cell. 152: 570-83. PMID 23352431 DOI: 10.1016/J.Cell.2013.01.003  0.708
2013 Hubert CG, Bradley RK, Ding Y, Chad TM, Skutt-Kakaria K, Girard EJ, Davison J, Berndt J, Corrin P, Basom R, Delrow JJ, Webb T, Pollard SM, Lee J, Olson JM, et al. Abstract A20: Genome-wide RNAi screens in human brain tumor isolates reveal a novel viability requirement for PHF5A Molecular Cancer Therapeutics. 12. DOI: 10.1158/1535-7163.Pms-A20  0.404
2012 Satija R, Bradley RK. The TAGteam motif facilitates binding of 21 sequence-specific transcription factors in the Drosophila embryo. Genome Research. 22: 656-65. PMID 22247430 DOI: 10.1101/Gr.130682.111  0.356
2012 Bradley RK, Merkin J, Lambert NJ, Burge CB. Alternative splicing of RNA triplets is often regulated and accelerates proteome evolution. Plos Biology. 10: e1001229. PMID 22235189 DOI: 10.1371/Journal.Pbio.1001229  0.742
2011 Friedland J, Sang J, Modi S, Bradley R, El-Hariry I, Wada Y, Proia D. P3-17-05: Beyond HER2 and Hormonal Agents: The Heat Shock Protein 90 Inhibitor Ganetespib as a Potential New Breast Cancer Therapy. Cancer Research. 71. DOI: 10.1158/0008-5472.Sabcs11-P3-17-05  0.325
2010 Bradley RK, Li XY, Trapnell C, Davidson S, Pachter L, Chu HC, Tonkin LA, Biggin MD, Eisen MB. Binding site turnover produces pervasive quantitative changes in transcription factor binding between closely related Drosophila species. Plos Biology. 8: e1000343. PMID 20351773 DOI: 10.1371/Journal.Pbio.1000343  0.564
2009 Bradley RK, Holmes I. Evolutionary triplet models of structured RNA. Plos Computational Biology. 5: e1000483. PMID 19714212 DOI: 10.1371/Journal.Pcbi.1000483  0.555
2009 Bradley RK, Uzilov AV, Skinner ME, Bendaña YR, Barquist L, Holmes I. Evolutionary modeling and prediction of non-coding RNAs in Drosophila. Plos One. 4: e6478. PMID 19668382 DOI: 10.1371/Journal.Pone.0006478  0.541
2009 Bradley RK, Roberts A, Smoot M, Juvekar S, Do J, Dewey C, Holmes I, Pachter L. Fast statistical alignment. Plos Computational Biology. 5: e1000392. PMID 19478997 DOI: 10.1371/Journal.Pcbi.1000392  0.519
2008 Varadarajan A, Bradley RK, Holmes IH. Tools for simulating evolution of aligned genomic regions with integrated parameter estimation. Genome Biology. 9: R147. PMID 18840304 DOI: 10.1186/Gb-2008-9-10-R147  0.512
2008 Bradley RK, Pachter L, Holmes I. Specific alignment of structured RNA: stochastic grammars and sequence annealing. Bioinformatics (Oxford, England). 24: 2677-83. PMID 18796475 DOI: 10.1093/Bioinformatics/Btn495  0.576
2007 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, ... ... Bradley RK, et al. Evolution of genes and genomes on the Drosophila phylogeny. Nature. 450: 203-18. PMID 17994087 DOI: 10.1038/Nature06341  0.764
2007 Bradley RK, Holmes I. Transducers: an emerging probabilistic framework for modeling indels on trees. Bioinformatics (Oxford, England). 23: 3258-62. PMID 17804440 DOI: 10.1093/Bioinformatics/Btm402  0.507
2006 Klosterman PS, Uzilov AV, Bendaña YR, Bradley RK, Chao S, Kosiol C, Goldman N, Holmes I. XRate: a fast prototyping, training and annotation tool for phylo-grammars. Bmc Bioinformatics. 7: 428. PMID 17018148 DOI: 10.1186/1471-2105-7-428  0.54
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