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Items: 1 to 50 of 178

1.

Pervasive Chromatin-RNA Binding Protein Interactions Enable RNA-Based Regulation of Transcription.

Xiao R, Chen JY, Liang Z, Luo D, Chen G, Lu ZJ, Chen Y, Zhou B, Li H, Du X, Yang Y, San M, Wei X, Liu W, Lécuyer E, Graveley BR, Yeo GW, Burge CB, Zhang MQ, Zhou Y, Fu XD.

Cell. 2019 Jun 27;178(1):107-121.e18. doi: 10.1016/j.cell.2019.06.001.

PMID:
31251911
2.

Acquisition of a hybrid E/M state is essential for tumorigenicity of basal breast cancer cells.

Kröger C, Afeyan A, Mraz J, Eaton EN, Reinhardt F, Khodor YL, Thiru P, Bierie B, Ye X, Burge CB, Weinberg RA.

Proc Natl Acad Sci U S A. 2019 Apr 9;116(15):7353-7362. doi: 10.1073/pnas.1812876116. Epub 2019 Mar 25. Erratum in: Proc Natl Acad Sci U S A. 2019 Jun 4;116(23):11553-11554.

3.

Allele-specific binding of RNA-binding proteins reveals functional genetic variants in the RNA.

Yang EW, Bahn JH, Hsiao EY, Tan BX, Sun Y, Fu T, Zhou B, Van Nostrand EL, Pratt GA, Freese P, Wei X, Quinones-Valdez G, Urban AE, Graveley BR, Burge CB, Yeo GW, Xiao X.

Nat Commun. 2019 Mar 22;10(1):1338. doi: 10.1038/s41467-019-09292-w.

4.

Widespread PERK-dependent repression of ER targets in response to ER stress.

Gonen N, Sabath N, Burge CB, Shalgi R.

Sci Rep. 2019 Mar 13;9(1):4330. doi: 10.1038/s41598-019-38705-5.

5.

Acidification of Tumor at Stromal Boundaries Drives Transcriptome Alterations Associated with Aggressive Phenotypes.

Rohani N, Hao L, Alexis MS, Joughin BA, Krismer K, Moufarrej MN, Soltis AR, Lauffenburger DA, Yaffe MB, Burge CB, Bhatia SN, Gertler FB.

Cancer Res. 2019 Apr 15;79(8):1952-1966. doi: 10.1158/0008-5472.CAN-18-1604. Epub 2019 Feb 12.

PMID:
30755444
6.

Transcriptome alterations in myotonic dystrophy skeletal muscle and heart.

Wang ET, Treacy D, Eichinger K, Struck A, Estabrook J, Olafson H, Wang TT, Bhatt K, Westbrook T, Sedehizadeh S, Ward A, Day J, Brook D, Berglund JA, Cooper T, Housman D, Thornton C, Burge C.

Hum Mol Genet. 2019 Apr 15;28(8):1312-1321. doi: 10.1093/hmg/ddy432.

PMID:
30561649
7.

Widespread Accumulation of Ribosome-Associated Isolated 3' UTRs in Neuronal Cell Populations of the Aging Brain.

Sudmant PH, Lee H, Dominguez D, Heiman M, Burge CB.

Cell Rep. 2018 Nov 27;25(9):2447-2456.e4. doi: 10.1016/j.celrep.2018.10.094.

8.

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.

9.

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.

10.

Oysters and eelgrass: potential partners in a high pCO2 ocean.

Groner ML, Burge CA, Cox R, Rivlin ND, Turner M, Van Alstyne KL, Wyllie-Echeverria S, Bucci J, Staudigel P, Friedman CS.

Ecology. 2018 Aug;99(8):1802-1814. doi: 10.1002/ecy.2393. Epub 2018 Jul 2.

PMID:
29800484
11.

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.

12.

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.

13.

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.

14.

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.

15.

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.

16.

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.

17.

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.

18.

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.

19.

The Use of Filter-feeders to Manage Disease in a Changing World.

Burge CA, Closek CJ, Friedman CS, Groner ML, Jenkins CM, Shore-Maggio A, Welsh JE.

Integr Comp Biol. 2016 Oct;56(4):573-87. doi: 10.1093/icb/icw048. Epub 2016 Jul 1. Review.

PMID:
27371383
20.

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.

21.

Plant characteristics associated with widespread variation in eelgrass wasting disease.

Groner ML, Burge CA, Kim CJ, Rees E, Van Alstyne KL, Yang S, Wyllie-Echeverria S, Harvell CD.

Dis Aquat Organ. 2016 Feb 25;118(2):159-68. doi: 10.3354/dao02962.

PMID:
26912046
22.

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.

23.

Complementary approaches to diagnosing marine diseases: a union of the modern and the classic.

Burge CA, Friedman CS, Getchell R, House M, Lafferty KD, Mydlarz LD, Prager KC, Sutherland KP, Renault T, Kiryu I, Vega-Thurber R.

Philos Trans R Soc Lond B Biol Sci. 2016 Mar 5;371(1689). pii: 20150207. doi: 10.1098/rstb.2015.0207. Review.

24.

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.

25.

Up in Arms: Immune and Nervous System Response to Sea Star Wasting Disease.

Fuess LE, Eisenlord ME, Closek CJ, Tracy AM, Mauntz R, Gignoux-Wolfsohn S, Moritsch MM, Yoshioka R, Burge CA, Harvell CD, Friedman CS, Hewson I, Hershberger PK, Roberts SB.

PLoS One. 2015 Jul 15;10(7):e0133053. doi: 10.1371/journal.pone.0133053. eCollection 2015.

26.

Interactome analysis brings splicing into focus.

Dominguez D, Burge CB.

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

27.

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

Lambert NJ, Robertson AD, Burge CB.

Methods Enzymol. 2015;558:465-493. doi: 10.1016/bs.mie.2015.02.007. Epub 2015 May 12.

28.

Whole transcriptome analysis reveals changes in expression of immune-related genes during and after bleaching in a reef-building coral.

Pinzón JH, Kamel B, Burge CA, Harvell CD, Medina M, Weil E, Mydlarz LD.

R Soc Open Sci. 2015 Apr 1;2(4):140214. doi: 10.1098/rsos.140214. eCollection 2015 Apr.

29.

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.

30.

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
31.

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.

32.

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.

33.

Genomic analysis of RNA localization.

Taliaferro JM, Wang ET, Burge CB.

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

34.

Densovirus associated with sea-star wasting disease and mass mortality.

Hewson I, Button JB, Gudenkauf BM, Miner B, Newton AL, Gaydos JK, Wynne J, Groves CL, Hendler G, Murray M, Fradkin S, Breitbart M, Fahsbender E, Lafferty KD, Kilpatrick AM, Miner CM, Raimondi P, Lahner L, Friedman CS, Daniels S, Haulena M, Marliave J, Burge CA, Eisenlord ME, Harvell CD.

Proc Natl Acad Sci U S A. 2014 Dec 2;111(48):17278-83. doi: 10.1073/pnas.1416625111. Epub 2014 Nov 17.

35.

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.

36.

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.

37.

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.

38.

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.

39.

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.

40.

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.

41.

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
42.

Host demography influences the prevalence and severity of eelgrass wasting disease.

Groner ML, Burge CA, Couch CS, Kim CJ, Siegmund GF, Singhal S, Smoot SC, Jarrell A, Gaydos JK, Harvell CD, Wyllie-Echeverria S.

Dis Aquat Organ. 2014 Feb 19;108(2):165-75. doi: 10.3354/dao02709.

PMID:
24553421
43.

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.

44.

Immune response of the Caribbean sea fan, Gorgonia ventalina, exposed to an Aplanochytrium parasite as revealed by transcriptome sequencing.

Burge CA, Mouchka ME, Harvell CD, Roberts S.

Front Physiol. 2013 Jul 25;4:180. doi: 10.3389/fphys.2013.00180. eCollection 2013.

45.

Climate change influences on marine infectious diseases: implications for management and society.

Burge CA, Mark Eakin C, Friedman CS, Froelich B, Hershberger PK, Hofmann EE, Petes LE, Prager KC, Weil E, Willis BL, Ford SE, Harvell CD.

Ann Rev Mar Sci. 2014;6:249-77. doi: 10.1146/annurev-marine-010213-135029. Epub 2013 Jun 27. Review.

PMID:
23808894
46.

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.

47.

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.

48.

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.

49.

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.

50.

Special issue Oceans and Humans Health: the ecology of marine opportunists.

Burge CA, Kim CJ, Lyles JM, Harvell CD.

Microb Ecol. 2013 May;65(4):869-79. doi: 10.1007/s00248-013-0190-7. Epub 2013 Feb 19. Review.

PMID:
23420204

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