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2016

Pai AA, Baharian G, Page Sabourin A, Brinkworth JF, Nedelec Y, Foley JW, Grenier JC, Siddle KJ, Dumaine A, Yotova V, Johnson Z, Landford RE, Bruge CB, Barreiro LB, (2016) Widespread Shortening of 3' Untranslated Regions and Increased Exon Inclusion Are Evolutionarily Conserved Features of Innate Immune Responses to Infection. PLoS Genet 12(9): e1006338. doi:10.1371/journal.pgen.1006338

Martinez FJ, Pratt GA, Van Nostrand EL, BatraR, 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 F, Ares M, Burge CB, Taylor JP, Rigo F, Yeo GW, (2016) Protein-RNA Networks Regulated by Normal and ALS-Associated Mutant HNRNPA2B1 in the Nervous System Neuron 92, 1–16 http://dx.doi.org/10.1016/j.neuron.2016.09.050

Taliaferro JM, Lambert NJ, Sudmant PH, Dominguez D, Merkin JJ, Alexis MS, Bazile C, Burge CB (2016). RNA sequence context effects measured in vitro predict in vivo protein binding and regulation. Mol Cell 2016 Oct 20;64(2):294-306. doi: 10.1016/j.molcel.2016.08.035. Epub 2016 Oct 6.

Gould G, Paggi J, Yuchun G, Phizicky D, Zinshteyn B, Wang ET, Gilbert W, Gifford D, Burge CB. (2016). Identification of new branch points and unconventional introns in saccharomyces cerevisiae. Published in Advance, RNA 2016. 10.1261/rna.057216.116

Taliaferro JM, Vidaki M, Oliveira R, Olson S, Zhan L, Saxena T, Wang ET, Graveley BR, Gertler FB, Swanson MS, Burge CB. (2016). Distal alternative last exons localize mRNAs to neural projections. Mol. Cell 62, 1-13. doi: 10.1016/j.molcel.2016.01.020. Epub 2016 Feb 18.

2015

Sudmant PH, Alexis MS, Burge CB. (2015). Meta-analysis of RNA-seq expression data across species, tissues and studies. Genome Biol. 16, 287.

Wang ET, Ward AJ, Cherone J, Wang TT, Giudice J, Treacy D, Freese P, Lambert NJ, Saxena T, Cooper TA, Burge CB. (2015). Antagonistic regulation of mRNA expression and splicing by CELF and MBNL proteins. Genome Res. 25, 858-71.

Lambert NJ, Robertson AD, Burge CB. (2015). RNA Bind-n-Seq: measuring the binding affinity landscape of RNA-binding proteins. Methods Enzymol. 558, 465-93.

Merkin JJ, Chen P, Alexis MS Hautaniemi SK, Burge CB (2015). Origins and impacts of new mammalian exons. Cell Reports 10, 1-14. (Open Access)

Katz Y, Wang ET, Silterra J, Schwartz S, Wong B, Thorvaldsdottir H, Robinson JT, Mesirov JP, Airoldi EM, Burge CB (2015). Quantitative visualization of alternative exon expression from RNA-seq data. Bioinformatics. pii: btv034 (Pub ahead of print)

2014

Katz Y, Li F, Lambert N, Sokol E, Tam WL, Cheng A, Airoldi E, Lengner C, Gupta P, Yu Z, Jaenisch R, Burge C. (2014). Musashi proteins are post-transcriptional regulators of the epithelial-luminal cell state eLife 2014;10.7554/eLife.03915

Taliaferro JM, Wang ET, Burge CB (2014). Genomic analysis of mRNA localization. RNA Biol 11, 1040-50. (Review).

Cheng AW, Shi J, Wong P, Luo KL, Trepman P, Wang ET, Choi H, Burge CB, Lodish HF (2014). Muscleblind-like 1 (Mbnl1) regulates pre-mRNA alternative splicing during terminal erythropoiesis. Blood 124:598-610.

Aijö T, Butty V, Chen Z, Salo V, Tripathi S, Burge CB, Lahesmaa R, Lähdesmäki H. (2014). Methods for time series analysis of RNA-seq data with application to human Th17 cell differentiation. Bioinformatics 30, 1113-1120.

Shalgi R, Hurt JA, Lindquist S, Burge CB. (2014). Widespread Inhibition of Posttranscriptional Splicing Shapes the Cellular Transcriptome following Heat Shock. Cell Reports 7, 1362-70.

Lambert N, Robertson A, Jangi M, McGeary S, Sharp PA, Burge CB. (2014). RNA Bind-n-Seq: Quantitative Assessment of the Sequence and Structural Binding Specificity of RNA Binding Proteins. Mol. Cell 54, 887-900.

Giudice J, Xia Z, Wang ET, Scavuzzo MA, Ward AJ, Kalsotra A, Wang W, Wehrens XH, Burge CB, Li W, Cooper TA. (2014). Alternative splicing regulates vesicular trafficking genes in cardiomyocytes during postnatal heart development. Nature Commun. 5:3603.

Friedman RC, Burge CB. MicroRNA target finding by comparative genomics. (2014). Methods Mol Biol 1097, 457-76. (Review).

2013

Spies N, Burge CB, Bartel DP. (2013). 3' UTR-isoform choice has limited influence on the stability and translational efficiency of most mRNAs in mouse fibroblasts. Genome Res. 23, 2078-90.

Almada AE, Wu X, Kriz AJ, Burge CB, Sharp PA. (2013). Promoter directionality is controlled by U1 snRNP and polyadenylation signals. Nature 499, 360-3.

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. (2013). MBNL proteins repress ES-cell-specific alternative splicing and reprogramming. Nature 498, 241-45.

Hurt JA, Robertson DA, Burge CB. (2013). Global analyses of UPF1 binding and function reveals expanded scope of nonsense-mediated mRNA decay. Genome Res. 23, 1636-50.

Ji, X, Zhou, Y, Pandit, S, Huang, J, Li, H, Lin, CY., Xiao, ., Burge, CB, and Fu, X-D. (2013). SR Proteins Collaborate with 7SK and Promoter-Associated Nascent RNA to Release Paused Polymerase. Cell 153, 855-868.

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, and Boyer LA. (2013). Braveheart, a Long Noncoding RNA Required for CardiovascularLineage Commitment. Cell 152, 1-14.

Shalgi R, Hurt JA, Krykbaeva I, Taipale M, Lindquist S, Burge CB. (2013). Widespread regulation of translation by elongation pausing in heat shock. Mol. Cell 49, 439-452.

Wang Y, Xiao X, Zhang J, Choudhury R, Robertson A, Li K, Ma M, Burge CB, Wang Z. (2013). A complex network of factors with overlapping affinities represses splicing through intronic elements. NSMB 20, 36-45.

 

2012

Merkin J, Russell C, Chen P, Burge CB. (2012). Evolutionary dynamics of gene and isoform regulation in mammalian tissues. Science 338, 1593-9. Abstract Reprint Full Text

Loven J, Orlando DA, Sigova AA, Lin CY, Rahl PB, Burge CB, Levens DL, Lee TI, Young RA. (2012). Revisiting global gene expression analysis. Cell 151, 476-482. (Primer).

Lin CY, Lovén J, Rahl PB, Paranal RM, Burge CB, Bradner JE, Lee TI, Young RA. (2012). Transcriptional Amplification in Tumor Cells with Elevated c-Myc. Cell 151, 56-67.

Wang ET, Cody NA, Jog S, Biancollela M, Wang TT, Treacy DJ, Luo S, Schroth GP, Housman DE, Reddy S, Lécuyer E, Burge CB. (2012). Transcriptome-wide regulation of pre-mRNA splicing and mRNA localization by muscleblind proteins. Cell 150, 710-724. PMCID: PMC3428802

Anderson, ES, Lin, CH, Xiao, X, Stoilov, P, Burge, CB, Black, DL. (2012). The cardiotonic steroid digitoxin regulates alternative splicing through depletion of the splicing factors SRSF3 and TRA2B. RNA 18, 1041-9. Open Access

Janas, MM, Wang, ET, Love, T, Harris, AS, Stevenson, K, Semmelmann, K, Shaffer, JM, Chen, P, Doench, JG, Yerramilli, SVBK, Neuberg, D, Iliopoulos, D, Housman, DE, Burge, CB, Novina, CD. (2012). Reduced expression of ribosomal proteins relieves microRNA-mediated repression. Mol. Cell 46, 171-186 .

Bradley, RK, Merkin, J, Lambert, NJ, Burge, CB. (2012). Alternative Splicing of RNA Triplets is Often Regulated and Accelerates Proteome Evolution. PLoS Biol. 10, e1001229. Open Access

 

2011

Zheng, G X.Y, Ravi, A., Gould, GM, Burge, CB, Sharp, PA. (2011). Genome-Wide Impact of A Recently Expanded MicroRNA Cluster in Mouse. PNAS USA 108, 15804-9.

Shapiro IM, Cheng AW, Flytzanis NC, Balsamo M, Condeelis JS, Oktay MH, Burge CB and Gertler FB. (2011). An EMT-driven alternative splicing program occurs in human breast cancer and modulates cellular phenotype. PLoS Genet. 7, e1002218. Open Access

Nutiu R, Friedman RC, Luo S, Khrebtukova I, Silva D, Li R, Zhan L, Schroth GP, Burge CB. (2011). Direct visualization of DNA affinity landscapes using a sequencing instrument. Nature Biotech. 29, 659-664.

Zheng GXY, Ravi A, Calabrese JM, Medeiros LA, Kirak O, Dennis L, Jaenisch R, Burge CB, Sharp PA. (2011). A Latent Pro-survival Function for the Mir-290-295 Cluster in Mouse Embryonic Stem Cells. PLoS Genet. 7(5):e1002054. Full Text

Bandyopadhyay S, Friedman RC, Marquez RT, Keck K, Kong B, Icardi MS, Brown, KE, Burge CB, Schmidt W, Wang Y, McCaffrey AP. (2011). Hepatitis C Virus Infection and Hepatic Stellate Cell Activation Down-regulate miR-29: miR-29 Over-expression Reduces Hepatitis C Viral Abundance In Culture. J. Infectious Disease 203, 1753-1762.

 

2010

Bland CS, Wang ET, Vu A, David MP, Castle JC, Johnson JM, Burge CB, Cooper TA. (2010). Global regulation of alternative splicing during myogenic differentiation. Nucleic Acids Res. 38, 7651-64.

Katz Y, Wang ET, Airoldi EM, Burge CB. (2010). Analysis and design of RNA sequencing experiments for identifying isoform regulation. Nature Methods 7, 1009-1015 .

Rahl PB, Lin CY, Selia AC, FlynnRA, McCuine S, Burge CB, Sharp PA, Young RA. (2010). cMyc regulates transcriptional pause release. Cell 141, 432-445.

 

2009

Ramskold D, Wang ET, Burge CB, Sandberg R. (2009). An abundance of ubuquitously expressed genes revealed by tissue transcriptome sequence data. PLoS Comp Biol 5:e1000598.

Spies N, Nielsen CB, Padgett RA, Burge CB. (2009). Biased chromatin signatures around polyadenylation sites and exons. Mol Cell 36, 245-254. Full Texte Full Text at Mol Cell

Xiao X, Wang Z, Jang M, Nutiu R, Wang ET, Burge CB. (2009). Splice site strength–dependent activity and genetic buffering by poly-G runs. Nature Struct Mol Biol 16, 1094-1100.

Friedman, RC, Farh KK, Burge, CB, Bartel, DP. (2009). Most mammalian mRNAs are conserved targets of microRNAs. Genome Res. 19, 92-105. Open Access.

 

2008

Kalsotra, A, Xiao X, Ward A, Castle J, Johnson JM., Burge CB, Cooper TA. (2008). A post natal switch of CELF and MBNL proteins reprograms alternative splicing in the developing heart. PNAS 105, 20333-20338.

Wang ET, Sandberg R, Luo S, Khrebtukova I, Zhang L, Mayr C, Kingsmore SF, Schroth GP, Burge CB. (2008). Alternative Isoform Regulation in Human Tissue Transcriptomes. Nature 456, 470-476. Full Text

Friedman BA, Stadler MB, Shomron N, Ding Y, Burge CB. (2008). Ab initio identification of functionally interacting pairs of cis-regulatory elements. Genome Research 18, 1643-1651.

Sandberg R, Neilson JR, Sarma A, Sharp PA, Burge CB. (2008). Proliferating cells express mRNAs with shortened 3' untranslated regions and fewer microRNA target sites. Science 320, 1643-1647. AbstractxtFull Text

Wang Z, Burge CB. (2008). Splicing regulation: From a parts list of regulatory elements to an integrated splicing code. RNA 14, 802-813.

Boyerinas B, Park S-M, Shomron N, Hedegaard MM, Vinther J, Andersen JS, Feig C, Xu J, Burge CB, Peter, ME. (2008). Identification of let-7 regulated oncofetal genes. Cancer Res. 68, 2587-2591.

2007

Xiao X., Wang Z., Jang M. and Burge CB. (2007). Coevolutionary Networks of Splicing cis-Regulatory Elements. PNAS 104, 18583-18588.

Nielsen CB, Shomron N, Sandberg R, Hornstein E, Burge C.B. (2007). Determinants of Targeting by Endogenous and Exogenous MicroRNAs and siRNAs. RNA 13, 1894-1910.

Giorgi C, Yeo GW, Stone ME, Katz DB, Burge C, Turrigiano G, Moore MJ. (2007). The EJC Factor eIF4AIII Modulates Synaptic Strength and Neuronal Protein Expression. Cell 130, 179-91.

Neilson, JR, Zheng, GXY., Burge, CB, Sharp, PA. (2007). Dynamic regulation of miRNA expression in ordered stages of cellular development.  Genes Dev. 21, 578-89.

Ruvinsky I, Ohler U, Burge CB, Ruvkun, G. (2007). Detection of broadly expressed neuronal genes in C. elegans. Dev. Biol. 302, 617-626.

Ibrahim EC, Hims MM, Shomron N, Burge CB, Slaugenhaupt SA, Reed R. (2007). Weak Definition of IKBKAP exon 20 leads to aberrant splicing in familial dysautonomia. Hum Mutat. 28, 41-53.

2006

Stadler M B, Shomron N, Yeo G, Schneider A, Xiao X, Burge CB. (2006). Inference of Splicing Regulatory Activities by Sequence Neighborhood Analysis. PLoS Genet. 2, e191.

Engels R, Yu T, Burge CB, Mesirov, JP, Decaprio, D, Galagan, JE. (2006). Combo: a whole genome comparative browser. Bioinformatics 22, 1782-1783.

Wang Z, Xiao X, Van Nostrand E, Burge CB. (2006). General and specific functions of exonic splicing silencers in splicing control. Mol. Cell 23, 61-70.

Yahyanejad M, Burge CB, Kardar M. (2006). Untangling influences of hydrophobicity on protein sequences and structures. Proteins 62, 1101-6.

Holste D, Huo G, Tung V, Burge CB. (2006). HOLLYWOOD: a comparative relational database of alternative splicing. Nucl. Acids Res. 34, D56-62.

2005

Farh KK, Grimson A, Jan C, Lewis BP, Johnston WK, Lim LP, Burge CB, Bartel DP (2005). The widespread impact of mammalian microRNAs on mRNA repression and evolution. Science 310, 1817-1821.

Goranov AI, Katz L, Breier AM, Burge CB, Grossman AD. (2005). A transcriptional response to replication status mediated by the conserved bacterial replication protein DnaA. PNAS 102, 12932-12937. PDF (Open Access).

Han K, Yeo G, An P, Burge CB, Grabowski PJ. (2005). A combinatorial code for splicing silencing: UAGG and GGGG motifs. PLoS Biol. 3, e158. PDF (Open Access).

Lewis BP, Burge CB, Bartel DP. (2005). Conserved seed pairing, often flanked by adenosines, indicates that thousands of human genes are microRNA targets. Cell 120, 15-20.

Ohler U, Shomron, N, Burge, CB. (2005). Recognition of unknown conserved alternatively spliced exons. PLoS Comp. Biol. 1, e15:0001-0010. PDF (Open Access).

Pfarr N, Prawitt D, Kirschfink M, Schroff C, Knuf M, Habermehl P, Mannhardt W, Zepp F, Fairbrother W, Loos M, Burge CB, Pohlenz J. (2005). Linking C5 deficiency to an exonic splicing enhancer mutation. J. Immunol. 174, 4172-4177.

Yeo G, Van Nostrand E, Holste D, Poggio T, Burge CB. (2005). Identification and analysis of alternative splicing events conserved in human and mouse. Proc. Natl. Acad. Sci. USA 102, 2850-2855. PDF (Open Access).

Padgett RA, Burge CB. (2005). Splice sites. In: Encyclopedia of Life Sciences. John Wiley & Sons, Ltd: Chichester http://www.els.net/

2004

Eng L, Coutinho G, Nahas S, Yeo G, Tanouye R, Babaei M, Dork T, Burge C, Gatti RA. (2004). Nonclassical splicing mutations in the coding and noncoding regions of the ATM gene: maximum entropy estimates of splice junction strengths. Hum. Mutat. 23, 67-76.

Fairbrother WG, Holste D, Burge CB, Sharp PA. (2004). Single nucleotide polymorphism-based validation of exonic splicing enhancers. PLoS Biol. 2(9), e268: 1-8. PDF at PLoS Biology web site.

Fairbrother, WG, Yeo G, Yeh R-F, Goldstein P, Mawson M, Sharp PA, Burge CB. (2004). RESCUE-ESE identifies candidate exonic splicing enhancers in vertebrate exons. Nucl. Acids Res. 32, W187-W190. PubMed Abstract and links to full text

Nielsen CB*, Friedman B*, Birren B, Burge CB, Galagan JE. (2004). Patterns of intron gain and loss in fungi. PLoS Biol. 2, e422. PDF (Open Access).

Ohler U, Yekta S, Lim LP, Bartel DP, Burge CB. (2004). Patterns of flanking sequence conservation and a characteristic upstream motif for microRNA gene identification. RNA 10, 1309-1322.

Seneff S, Wang C, Burge CB. (2004). Gene structure prediction using an orthologous gene of known exon-intron structure. Appl. Bioinformatics 3, 81-90.

Wang Z, Rolish ME, Yeo G, Tung V, Mawson M, Burge CB. (2004). Systematic identification and analysis of exonic splicing silencers. Cell 119, 831-845.

Yeo G*, Holste D*, Kreiman, G, Burge CB. (2004). Variation in alternative splicing across human tissues. Genome Biol. 5, R74. PDF (Open Access).

Yeo G, Hoon S, Venkatesh B, Burge CB. (2004). Variation in sequence and organization of splicing regulatory elements in vertebrate genes. Proc. Natl. Acad. Sci. USA 101, 15700-15705. PDF (Open Access).

Yeo G, Burge CB. (2004). Maximum entropy modeling of short sequence motifs with applications to RNA splicing signals. J. Comp. Biol. 11, 377-394.

* These authors contributed equally.

2003

Ambros V, Bartel B, Bartel DP, Burge CB, Carrington JC, Chen X, Dreyfuss G, Eddy SR, Griffiths-Jones S, Marshall M, Matzke M, Ruvkun G, Tuschl T. (2003). A uniform system for microRNA annotation. RNA 9, 277-279.

Arndt PF, Burge CB, Hwa T. (2003). DNA sequence evolution with neighbor-dependent mutation. J. Comp. Biol. 10, 313-322.

Katz L, Burge CB. (2003). Widespread selection for local RNA structure in coding regions of bacterial genes. Genome Res. 13, 2042-2051.

Lewis BP*, Shih I-h*, Jones-Rhoades MW, Bartel DP, Burge CB. (2003). Prediction of mammalian microRNA targets. Cell 115, 787-798.

Lim LP*, Glasner ME*, Yekta S*, Burge CB, Bartel DP. (2003). Vertebrate microRNA genes. Science 299, 1540.

Lim LP*, Lau, NC*, Weinstein EG*, Abdelhakim A*, Yekta S, Rhoades MW, Burge CB, Bartel DP. (2003). The microRNAs of Caenorhabditis elegans. Genes & Dev. 17, 977-990.

Yeo G, Burge CB. (2003). Maximum entropy modeling of short sequence motifs with applications to RNA splicing signals. in Proceedings of the 7th Annual International Conference on Computational Molecular Biology (RECOMB03), W. Miller et al., eds., pp. 322-331 (ACM Press, New York).

* These authors contributed equally.

2002

Arndt PF, Burge CB, Hwa T. (2002). DNA sequence evolution with neighbor-dependent mutation. in Proceedings of the 6th Annual International Conference on Computational Molecular Biology (RECOMB02), G. Meyer et al., eds., ACM Press, New York, pp. 32-38.

Crollius HR, Jaillon O, Bernot A, Pelletier E, Dasilva C, Bouneau L, Burge C, Yeh R-F, Quetier F, Saurin W, Weissenbach J. (2002). Genome-wide comparisons between human and tetraodon. Ernst Schering Res. Found Workshop 36, 11-29.

Fairbrother W*, Yeh R-F*, Sharp PA, Burge CB. (2002). Predictive identification of exonic splicing enhancers in human genes. Science 297, 1007-1013. PDF at Science web site.

Rhoades MW, Reinhart BJ, Lim LP, Burge CB, Bartel B, and Bartel DP. (2002). Prediction of plant microRNA targets. Cell 110, 513-520.

* These authors contributed equally.

2001

Burge, CB. (2001). Chipping away at the transcriptome. Nature Genet. 27, 4-6.

Das M*, Burge CB*, Park E., Colinas J, Pelletier J. (2001). Assessment of the total number of human transcription units. Genomics 77, 71-78.

International Human Genome Sequencing Consortium (2001). Initial sequencing and analysis of the human genome. Nature 409, 860-921.

Lim LP, Burge CB. (2001). A computational analysis of sequence features involved in recognition of short introns. Proc. Natl. Acad. Sci. USA 98, 11193­11198.

Yeh R-F, Lim LP, Burge CB. (2001) Computational inference of homologous gene structures in the human genome. Genome Res. 11, 803-816.

* These authors contributed equally


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