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Items: 1 to 50 of 113

1.

Numerous recursive sites contribute to accuracy of splicing in long introns in flies.

Pai AA, Paggi JM, Yan P, Adelman K, Burge CB.

PLoS Genet. 2018 Aug 27;14(8):e1007588. doi: 10.1371/journal.pgen.1007588. eCollection 2018 Aug.

2.

Sequence, Structure, and Context Preferences of Human RNA Binding Proteins.

Dominguez D, Freese P, Alexis MS, Su A, Hochman M, Palden T, Bazile C, Lambert NJ, Van Nostrand EL, Pratt GA, Yeo GW, Graveley BR, Burge CB.

Mol Cell. 2018 Jun 7;70(5):854-867.e9. doi: 10.1016/j.molcel.2018.05.001. Epub 2018 Jun 7.

3.

Alternative RNA splicing in the endothelium mediated in part by Rbfox2 regulates the arterial response to low flow.

Murphy PA, Butty VL, Boutz PL, Begum S, Kimble AL, Sharp PA, Burge CB, Hynes RO.

Elife. 2018 Jan 2;7. pii: e29494. doi: 10.7554/eLife.29494.

4.

The kinetics of pre-mRNA splicing in the Drosophila genome and the influence of gene architecture.

Pai AA, Henriques T, McCue K, Burkholder A, Adelman K, Burge CB.

Elife. 2017 Dec 27;6. pii: e32537. doi: 10.7554/eLife.32537.

5.

A Requirement for Mena, an Actin Regulator, in Local mRNA Translation in Developing Neurons.

Vidaki M, Drees F, Saxena T, Lanslots E, Taliaferro MJ, Tatarakis A, Burge CB, Wang ET, Gertler FB.

Neuron. 2017 Aug 2;95(3):608-622.e5. doi: 10.1016/j.neuron.2017.06.048. Epub 2017 Jul 20.

6.

Protein-RNA Networks Regulated by Normal and ALS-Associated Mutant HNRNPA2B1 in the Nervous System.

Martinez FJ, Pratt GA, Van Nostrand EL, Batra R, Huelga SC, Kapeli K, Freese P, Chun SJ, Ling K, Gelboin-Burkhart C, Fijany L, Wang HC, Nussbacher JK, Broski SM, Kim HJ, Lardelli R, Sundararaman B, Donohue JP, Javaherian A, Lykke-Andersen J, Finkbeiner S, Bennett CF, Ares M Jr, Burge CB, Taylor JP, Rigo F, Yeo GW.

Neuron. 2016 Nov 23;92(4):780-795. doi: 10.1016/j.neuron.2016.09.050. Epub 2016 Oct 20.

7.

RNA Sequence Context Effects Measured In Vitro Predict In Vivo Protein Binding and Regulation.

Taliaferro JM, Lambert NJ, Sudmant PH, Dominguez D, Merkin JJ, Alexis MS, Bazile C, Burge CB.

Mol Cell. 2016 Oct 20;64(2):294-306. doi: 10.1016/j.molcel.2016.08.035. Epub 2016 Oct 6.

8.

Widespread Shortening of 3' Untranslated Regions and Increased Exon Inclusion Are Evolutionarily Conserved Features of Innate Immune Responses to Infection.

Pai AA, Baharian G, Pagé Sabourin A, Brinkworth JF, Nédélec Y, Foley JW, Grenier JC, Siddle KJ, Dumaine A, Yotova V, Johnson ZP, Lanford RE, Burge CB, Barreiro LB.

PLoS Genet. 2016 Sep 30;12(9):e1006338. doi: 10.1371/journal.pgen.1006338. eCollection 2016 Sep.

9.

Identification of new branch points and unconventional introns in Saccharomyces cerevisiae.

Gould GM, Paggi JM, Guo Y, Phizicky DV, Zinshteyn B, Wang ET, Gilbert WV, Gifford DK, Burge CB.

RNA. 2016 Oct;22(10):1522-34. doi: 10.1261/rna.057216.116. Epub 2016 Jul 29.

10.

Distinct and shared functions of ALS-associated proteins TDP-43, FUS and TAF15 revealed by multisystem analyses.

Kapeli K, Pratt GA, Vu AQ, Hutt KR, Martinez FJ, Sundararaman B, Batra R, Freese P, Lambert NJ, Huelga SC, Chun SJ, Liang TY, Chang J, Donohue JP, Shiue L, Zhang J, Zhu H, Cambi F, Kasarskis E, Hoon S, Ares M Jr, Burge CB, Ravits J, Rigo F, Yeo GW.

Nat Commun. 2016 Jul 5;7:12143. doi: 10.1038/ncomms12143.

11.

Enhanced CLIP Uncovers IMP Protein-RNA Targets in Human Pluripotent Stem Cells Important for Cell Adhesion and Survival.

Conway AE, Van Nostrand EL, Pratt GA, Aigner S, Wilbert ML, Sundararaman B, Freese P, Lambert NJ, Sathe S, Liang TY, Essex A, Landais S, Burge CB, Jones DL, Yeo GW.

Cell Rep. 2016 Apr 19;15(3):666-679. doi: 10.1016/j.celrep.2016.03.052. Epub 2016 Apr 7.

12.

Distal Alternative Last Exons Localize mRNAs to Neural Projections.

Taliaferro JM, Vidaki M, Oliveira R, Olson S, Zhan L, Saxena T, Wang ET, Graveley BR, Gertler FB, Swanson MS, Burge CB.

Mol Cell. 2016 Mar 17;61(6):821-33. doi: 10.1016/j.molcel.2016.01.020. Epub 2016 Feb 18.

13.

Meta-analysis of RNA-seq expression data across species, tissues and studies.

Sudmant PH, Alexis MS, Burge CB.

Genome Biol. 2015 Dec 22;16:287. doi: 10.1186/s13059-015-0853-4.

14.

Interactome analysis brings splicing into focus.

Dominguez D, Burge CB.

Genome Biol. 2015 Jul 7;16:135. doi: 10.1186/s13059-015-0707-0.

15.

RNA Bind-n-Seq: Measuring the Binding Affinity Landscape of RNA-Binding Proteins.

Lambert NJ, Robertson AD, Burge CB.

Methods Enzymol. 2015;558:465-93. doi: 10.1016/bs.mie.2015.02.007. Epub 2015 May 12.

16.

Antagonistic regulation of mRNA expression and splicing by CELF and MBNL proteins.

Wang ET, Ward AJ, Cherone JM, Giudice J, Wang TT, Treacy DJ, Lambert NJ, Freese P, Saxena T, Cooper TA, Burge CB.

Genome Res. 2015 Jun;25(6):858-71. doi: 10.1101/gr.184390.114. Epub 2015 Apr 16.

17.

Can serial PEF measurements separate occupational asthma from allergic alveolitis?

Burge PS, Moore VC, Burge CB, Vellore AD, Robertson AS, Robertson W.

Occup Med (Lond). 2015 Apr;65(3):251-5. doi: 10.1093/occmed/kqv013.

PMID:
25825508
18.

Origins and impacts of new mammalian exons.

Merkin JJ, Chen P, Alexis MS, Hautaniemi SK, Burge CB.

Cell Rep. 2015 Mar 31;10(12):1992-2005. doi: 10.1016/j.celrep.2015.02.058. Epub 2015 Mar 19.

19.

Quantitative visualization of alternative exon expression from RNA-seq data.

Katz Y, Wang ET, Silterra J, Schwartz S, Wong B, Thorvaldsdóttir H, Robinson JT, Mesirov JP, Airoldi EM, Burge CB.

Bioinformatics. 2015 Jul 15;31(14):2400-2. doi: 10.1093/bioinformatics/btv034. Epub 2015 Jan 22.

20.

Genomic analysis of RNA localization.

Taliaferro JM, Wang ET, Burge CB.

RNA Biol. 2014;11(8):1040-50. doi: 10.4161/rna.32146. Review.

21.

Musashi proteins are post-transcriptional regulators of the epithelial-luminal cell state.

Katz Y, Li F, Lambert NJ, Sokol ES, Tam WL, Cheng AW, Airoldi EM, Lengner CJ, Gupta PB, Yu Z, Jaenisch R, Burge CB.

Elife. 2014 Nov 7;3:e03915. doi: 10.7554/eLife.03915.

22.

Methods for time series analysis of RNA-seq data with application to human Th17 cell differentiation.

Äijö T, Butty V, Chen Z, Salo V, Tripathi S, Burge CB, Lahesmaa R, Lähdesmäki H.

Bioinformatics. 2014 Jun 15;30(12):i113-20. doi: 10.1093/bioinformatics/btu274.

23.

Muscleblind-like 1 (Mbnl1) regulates pre-mRNA alternative splicing during terminal erythropoiesis.

Cheng AW, Shi J, Wong P, Luo KL, Trepman P, Wang ET, Choi H, Burge CB, Lodish HF.

Blood. 2014 Jul 24;124(4):598-610. doi: 10.1182/blood-2013-12-542209. Epub 2014 May 28.

24.

Widespread inhibition of posttranscriptional splicing shapes the cellular transcriptome following heat shock.

Shalgi R, Hurt JA, Lindquist S, Burge CB.

Cell Rep. 2014 Jun 12;7(5):1362-1370. doi: 10.1016/j.celrep.2014.04.044. Epub 2014 May 22.

25.

RNA Bind-n-Seq: quantitative assessment of the sequence and structural binding specificity of RNA binding proteins.

Lambert N, Robertson A, Jangi M, McGeary S, Sharp PA, Burge CB.

Mol Cell. 2014 Jun 5;54(5):887-900. doi: 10.1016/j.molcel.2014.04.016. Epub 2014 May 15.

26.

Alternative splicing regulates vesicular trafficking genes in cardiomyocytes during postnatal heart development.

Giudice J, Xia Z, Wang ET, Scavuzzo MA, Ward AJ, Kalsotra A, Wang W, Wehrens XH, Burge CB, Li W, Cooper TA.

Nat Commun. 2014 Apr 22;5:3603. doi: 10.1038/ncomms4603.

27.

MicroRNA target finding by comparative genomics.

Friedman RC, Burge CB.

Methods Mol Biol. 2014;1097:457-76. doi: 10.1007/978-1-62703-709-9_21. Review.

PMID:
24639172
28.

3' UTR-isoform choice has limited influence on the stability and translational efficiency of most mRNAs in mouse fibroblasts.

Spies N, Burge CB, Bartel DP.

Genome Res. 2013 Dec;23(12):2078-90. doi: 10.1101/gr.156919.113. Epub 2013 Sep 26.

29.

Promoter directionality is controlled by U1 snRNP and polyadenylation signals.

Almada AE, Wu X, Kriz AJ, Burge CB, Sharp PA.

Nature. 2013 Jul 18;499(7458):360-3. doi: 10.1038/nature12349. Epub 2013 Jun 23.

30.

Global analyses of UPF1 binding and function reveal expanded scope of nonsense-mediated mRNA decay.

Hurt JA, Robertson AD, Burge CB.

Genome Res. 2013 Oct;23(10):1636-50. doi: 10.1101/gr.157354.113. Epub 2013 Jun 13.

31.

MBNL proteins repress ES-cell-specific alternative splicing and reprogramming.

Han H, Irimia M, Ross PJ, Sung HK, Alipanahi B, David L, Golipour A, Gabut M, Michael IP, Nachman EN, Wang E, Trcka D, Thompson T, O'Hanlon D, Slobodeniuc V, Barbosa-Morais NL, Burge CB, Moffat J, Frey BJ, Nagy A, Ellis J, Wrana JL, Blencowe BJ.

Nature. 2013 Jun 13;498(7453):241-5. doi: 10.1038/nature12270. Epub 2013 Jun 5.

32.

SR proteins collaborate with 7SK and promoter-associated nascent RNA to release paused polymerase.

Ji X, Zhou Y, Pandit S, Huang J, Li H, Lin CY, Xiao R, Burge CB, Fu XD.

Cell. 2013 May 9;153(4):855-68. doi: 10.1016/j.cell.2013.04.028.

33.

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.

34.

Widespread regulation of translation by elongation pausing in heat shock.

Shalgi R, Hurt JA, Krykbaeva I, Taipale M, Lindquist S, Burge CB.

Mol Cell. 2013 Feb 7;49(3):439-52. doi: 10.1016/j.molcel.2012.11.028. Epub 2013 Jan 3.

35.

Evolutionary dynamics of gene and isoform regulation in Mammalian tissues.

Merkin J, Russell C, Chen P, Burge CB.

Science. 2012 Dec 21;338(6114):1593-9. doi: 10.1126/science.1228186.

36.

A complex network of factors with overlapping affinities represses splicing through intronic elements.

Wang Y, Xiao X, Zhang J, Choudhury R, Robertson A, Li K, Ma M, Burge CB, Wang Z.

Nat Struct Mol Biol. 2013 Jan;20(1):36-45. doi: 10.1038/nsmb.2459. Epub 2012 Dec 16.

37.

Revisiting global gene expression analysis.

Lovén J, Orlando DA, Sigova AA, Lin CY, Rahl PB, Burge CB, Levens DL, Lee TI, Young RA.

Cell. 2012 Oct 26;151(3):476-82. doi: 10.1016/j.cell.2012.10.012. Review.

38.

Transcriptional amplification in tumor cells with elevated c-Myc.

Lin CY, Lovén J, Rahl PB, Paranal RM, Burge CB, Bradner JE, Lee TI, Young RA.

Cell. 2012 Sep 28;151(1):56-67. doi: 10.1016/j.cell.2012.08.026.

39.

Transcriptome-wide regulation of pre-mRNA splicing and mRNA localization by muscleblind proteins.

Wang ET, Cody NA, Jog S, Biancolella M, Wang TT, Treacy DJ, Luo S, Schroth GP, Housman DE, Reddy S, Lécuyer E, Burge CB.

Cell. 2012 Aug 17;150(4):710-24. doi: 10.1016/j.cell.2012.06.041.

40.

An outbreak of occupational asthma due to chromium and cobalt.

Walters GI, Moore VC, Robertson AS, Burge CB, Vellore AD, Burge PS.

Occup Med (Lond). 2012 Oct;62(7):533-40. doi: 10.1093/occmed/kqs111. Epub 2012 Jul 23.

PMID:
22826555
41.

Shift work effects on serial PEF measurements for occupational asthma.

Moore VC, Jaakkola MS, Burge CB, Pantin CF, Robertson AS, Burge PS.

Occup Med (Lond). 2012 Oct;62(7):525-32. doi: 10.1093/occmed/kqs097. Epub 2012 Jul 9.

PMID:
22778240
42.

Reduced expression of ribosomal proteins relieves microRNA-mediated repression.

Janas MM, Wang E, Love T, Harris AS, Stevenson K, Semmelmann K, Shaffer JM, Chen PH, Doench JG, Yerramilli SV, Neuberg DS, Iliopoulos D, Housman DE, Burge CB, Novina CD.

Mol Cell. 2012 Apr 27;46(2):171-86. doi: 10.1016/j.molcel.2012.04.008.

43.

The cardiotonic steroid digitoxin regulates alternative splicing through depletion of the splicing factors SRSF3 and TRA2B.

Anderson ES, Lin CH, Xiao X, Stoilov P, Burge CB, Black DL.

RNA. 2012 May;18(5):1041-9. doi: 10.1261/rna.032912.112. Epub 2012 Mar 28.

44.

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.

45.

Genome-wide impact of a recently expanded microRNA cluster in mouse.

Zheng GX, Ravi A, Gould GM, Burge CB, Sharp PA.

Proc Natl Acad Sci U S A. 2011 Sep 20;108(38):15804-9. doi: 10.1073/pnas.1112772108. Epub 2011 Sep 12.

46.

An EMT-driven alternative splicing program occurs in human breast cancer and modulates cellular phenotype.

Shapiro IM, Cheng AW, Flytzanis NC, Balsamo M, Condeelis JS, Oktay MH, Burge CB, Gertler FB.

PLoS Genet. 2011 Aug;7(8):e1002218. doi: 10.1371/journal.pgen.1002218. Epub 2011 Aug 18.

47.

Direct measurement of DNA affinity landscapes on a high-throughput sequencing instrument.

Nutiu R, Friedman RC, Luo S, Khrebtukova I, Silva D, Li R, Zhang L, Schroth GP, Burge CB.

Nat Biotechnol. 2011 Jun 26;29(7):659-64. doi: 10.1038/nbt.1882.

48.

Hepatitis C virus infection and hepatic stellate cell activation downregulate miR-29: miR-29 overexpression reduces hepatitis C viral abundance in culture.

Bandyopadhyay S, Friedman RC, Marquez RT, Keck K, Kong B, Icardi MS, Brown KE, Burge CB, Schmidt WN, Wang Y, McCaffrey AP.

J Infect Dis. 2011 Jun 15;203(12):1753-62. doi: 10.1093/infdis/jir186.

49.

A latent pro-survival function for the mir-290-295 cluster in mouse embryonic stem cells.

Zheng GX, Ravi A, Calabrese JM, Medeiros LA, Kirak O, Dennis LM, Jaenisch R, Burge CB, Sharp PA.

PLoS Genet. 2011 May;7(5):e1002054. doi: 10.1371/journal.pgen.1002054. Epub 2011 May 5.

50.

Analysis and design of RNA sequencing experiments for identifying isoform regulation.

Katz Y, Wang ET, Airoldi EM, Burge CB.

Nat Methods. 2010 Dec;7(12):1009-15. doi: 10.1038/nmeth.1528. Epub 2010 Nov 7.

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