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Christopher B. Burge - Publications

Affiliations: 
Biology Massachusetts Institute of Technology, Cambridge, MA, United States 
Area:
genomics, RNA splicing, and microRNA regulation in vertebrates and invertebrates
Website:
http://genes.mit.edu/burgelab/cburge.html
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140 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
2024 Romo L, Findlay SD, Burge CB. Regulatory features aid interpretation of 3'UTR variants. American Journal of Human Genetics. PMID 38237594 DOI: 10.1016/j.ajhg.2023.12.017  0.332
2024 Gupta K, Yang C, McCue K, Bastani O, Sharp PA, Burge CB, Solar-Lezama A. Improved modeling of RNA-binding protein motifs in an interpretable neural model of RNA splicing. Genome Biology. 25: 23. PMID 38229106 DOI: 10.1186/s13059-023-03162-x  0.649
2024 Findlay SD, Romo L, Burge CB. Quantifying negative selection in human 3' UTRs uncovers constrained targets of RNA-binding proteins. Nature Communications. 15: 85. PMID 38168060 DOI: 10.1038/s41467-023-44456-9  0.355
2023 Feng Q, Krick K, Chu J, Burge CB. Splicing quality control mediated by DHX15 and its G-patch activator SUGP1. Cell Reports. 42: 113223. PMID 37805921 DOI: 10.1016/j.celrep.2023.113223  0.674
2023 Romo L, Findlay SD, Burge CB. Regulatory features aid interpretation of 3'UTR Variants. Biorxiv : the Preprint Server For Biology. PMID 37577470 DOI: 10.1101/2023.08.01.551549  0.334
2022 Benoit Bouvrette LP, Wang X, Boulais J, Kong J, Syed EU, Blue SM, Zhan L, Olson S, Stanton R, Wei X, Yee B, Van Nostrand EL, Fu XD, Burge CB, Graveley BR, et al. RBP Image Database: A resource for the systematic characterization of the subcellular distribution properties of human RNA binding proteins. Nucleic Acids Research. PMID 36321651 DOI: 10.1093/nar/gkac971  0.565
2022 Moore JE, Purcaro MJ, Pratt HE, Epstein CB, Shoresh N, Adrian J, Kawli T, Davis CA, Dobin A, Kaul R, Halow J, Van Nostrand EL, Freese P, Gorkin DU, Shen Y, ... ... Burge CB, et al. Author Correction: Expanded encyclopaedias of DNA elements in the human and mouse genomes. Nature. PMID 35474001 DOI: 10.1038/s41586-021-04226-3  0.437
2021 Jourdain AA, Begg BE, Mick E, Shah H, Calvo SE, Skinner OS, Sharma R, Blue SM, Yeo GW, Burge CB, Mootha VK. Loss of LUC7L2 and U1 snRNP subunits shifts energy metabolism from glycolysis to OXPHOS. Molecular Cell. PMID 33852893 DOI: 10.1016/j.molcel.2021.02.033  0.496
2021 Van Nostrand EL, Freese P, Pratt GA, Wang X, Wei X, Xiao R, Blue SM, Chen JY, Cody NAL, Dominguez D, Olson S, Sundararaman B, Zhan L, Bazile C, Bouvrette LPB, ... ... Burge CB, et al. Author Correction: A large-scale binding and functional map of human RNA-binding proteins. Nature. PMID 33402748 DOI: 10.1038/s41586-020-03067-w  0.741
2020 Begg BE, Jens M, Wang PY, Minor CM, Burge CB. Concentration-dependent splicing is enabled by Rbfox motifs of intermediate affinity. Nature Structural & Molecular Biology. PMID 32807990 DOI: 10.1038/S41594-020-0475-8  0.48
2020 Moore JE, Purcaro MJ, Pratt HE, Epstein CB, Shoresh N, Adrian J, Kawli T, Davis CA, Dobin A, Kaul R, Halow J, Van Nostrand EL, Freese P, Gorkin DU, ... ... Burge CB, et al. Expanded encyclopaedias of DNA elements in the human and mouse genomes. Nature. 583: 699-710. PMID 32728249 DOI: 10.1038/S41586-020-2493-4  0.626
2020 Van Nostrand EL, Freese P, Pratt GA, Wang X, Wei X, Xiao R, Blue SM, Chen JY, Cody NAL, Dominguez D, Olson S, Sundararaman B, Zhan L, Bazile C, Bouvrette LPB, ... ... Burge CB, et al. A large-scale binding and functional map of human RNA-binding proteins. Nature. 583: 711-719. PMID 32728246 DOI: 10.1038/S41586-020-2077-3  0.801
2019 Fiszbein A, Krick KS, Begg BE, Burge CB. Exon-Mediated Activation of Transcription Starts. Cell. 179: 1551-1565.e17. PMID 31787377 DOI: 10.1016/J.Cell.2019.11.002  0.476
2019 Cherone JM, Jorgji V, Burge CB. Cotargeting among microRNAs in the brain. Genome Research. 29: 1791-1804. PMID 31649056 DOI: 10.1101/Gr.249201.119  0.333
2019 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, ... ... Burge CB, et al. Pervasive Chromatin-RNA Binding Protein Interactions Enable RNA-Based Regulation of Transcription. Cell. 178: 107-121.e18. PMID 31251911 DOI: 10.1016/J.Cell.2019.06.001  0.662
2019 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, et al. Allele-specific binding of RNA-binding proteins reveals functional genetic variants in the RNA. Nature Communications. 10: 1338. PMID 30902979 DOI: 10.1038/S41467-019-09292-W  0.758
2019 Gonen N, Sabath N, Burge CB, Shalgi R. Widespread PERK-dependent repression of ER targets in response to ER stress. Scientific Reports. 9: 4330. PMID 30867432 DOI: 10.1038/S41598-019-38705-5  0.338
2019 Rohani N, Hao L, Alexis MS, Joughin BA, Krismer K, Moufarrej MN, Soltis AR, Lauffenburger DA, Yaffe MB, Burge CB, Bhatia SN, Gertler FB. Acidification of tumor at stromal boundaries drives transcriptome alterations associated with aggressive phenotypes. Cancer Research. PMID 30755444 DOI: 10.1158/0008-5472.Can-18-1604  0.336
2018 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, ... ... Burge C, et al. Transcriptome alterations in myotonic dystrophy skeletal muscle and heart. Human Molecular Genetics. PMID 30561649 DOI: 10.1093/Hmg/Ddy432  0.663
2018 Sudmant PH, Lee H, Dominguez D, Heiman M, Burge CB. Widespread Accumulation of Ribosome-Associated Isolated 3' UTRs in Neuronal Cell Populations of the Aging Brain. Cell Reports. 25: 2447-2456.e4. PMID 30485811 DOI: 10.1016/J.Celrep.2018.10.094  0.698
2018 Pai AA, Paggi JM, Yan P, Adelman K, Burge CB. Numerous recursive sites contribute to accuracy of splicing in long introns in flies. Plos Genetics. 14: e1007588. PMID 30148878 DOI: 10.1371/Journal.Pgen.1007588  0.507
2018 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. Sequence, Structure, and Context Preferences of Human RNA Binding Proteins. Molecular Cell. 70: 854-867.e9. PMID 29883606 DOI: 10.1016/J.Molcel.2018.05.001  0.797
2018 Murphy PA, Butty VL, Boutz PL, Begum S, Kimble AL, Sharp PA, Burge CB, Hynes RO. Alternative RNA splicing in the endothelium mediated in part by Rbfox2 regulates the arterial response to low flow. Elife. 7. PMID 29293084 DOI: 10.7554/Elife.29494  0.606
2017 Pai AA, Henriques T, McCue K, Burkholder A, Adelman K, Burge CB. The kinetics of pre-mRNA splicing in the Drosophila genome and the influence of gene architecture. Elife. 6. PMID 29280736 DOI: 10.7554/Elife.32537  0.489
2017 Vidaki M, Drees F, Saxena T, Lanslots E, Taliaferro MJ, Tatarakis A, Burge CB, Wang ET, Gertler FB. A Requirement for Mena, an Actin Regulator, in Local mRNA Translation in Developing Neurons. Neuron. PMID 28735747 DOI: 10.1016/J.Neuron.2017.06.048  0.606
2017 Pai AA, Henriques T, McCue K, Burkholder A, Adelman K, Burge CB. Author response: The kinetics of pre-mRNA splicing in the Drosophila genome and the influence of gene architecture Elife. DOI: 10.7554/Elife.32537.022  0.384
2017 Khodor YL, Froese J, Gertler F, Weinberg RA, Burge CB. Abstract 863: Neuronal splicing regulatory factors are upregulated in models of epithelial-mesenchymal transition Cancer Research. 77: 863-863. DOI: 10.1158/1538-7445.Am2017-863  0.42
2016 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, ... ... Burge CB, et al. Protein-RNA Networks Regulated by Normal and ALS-Associated Mutant HNRNPA2B1 in the Nervous System. Neuron. PMID 27773581 DOI: 10.1016/J.Neuron.2016.09.050  0.564
2016 Taliaferro JM, Lambert NJ, Sudmant PH, Dominguez D, Merkin JJ, Alexis MS, Bazile CA, Burge CB. RNA Sequence Context Effects Measured In Vitro Predict In Vivo Protein Binding and Regulation. Molecular Cell. PMID 27720642 DOI: 10.1016/J.Molcel.2016.08.035  0.816
2016 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. Widespread Shortening of 3' Untranslated Regions and Increased Exon Inclusion Are Evolutionarily Conserved Features of Innate Immune Responses to Infection. Plos Genetics. 12: e1006338. PMID 27690314 DOI: 10.1371/Journal.Pgen.1006338  0.406
2016 Gould GM, Paggi JM, Guo Y, Phizicky DV, Zinshteyn B, Wang ET, Gilbert WV, Gifford DK, Burge CB. Identification of new branch points and unconventional introns in Saccharomyces cerevisiae. Rna (New York, N.Y.). PMID 27473169 DOI: 10.1261/Rna.057216.116  0.673
2016 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, ... ... Burge CB, et al. Distinct and shared functions of ALS-associated proteins TDP-43, FUS and TAF15 revealed by multisystem analyses. Nature Communications. 7: 12143. PMID 27378374 DOI: 10.1038/Ncomms12143  0.63
2016 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. Enhanced CLIP Uncovers IMP Protein-RNA Targets in Human Pluripotent Stem Cells Important for Cell Adhesion and Survival. Cell Reports. PMID 27068461 DOI: 10.1016/J.Celrep.2016.03.052  0.74
2016 Taliaferro JM, Vidaki M, Oliveira R, Olson S, Zhan L, Saxena T, Wang ET, Graveley BR, Gertler FB, Swanson MS, Burge CB. Distal Alternative Last Exons Localize mRNAs to Neural Projections. Molecular Cell. PMID 26907613 DOI: 10.1016/J.Molcel.2016.01.020  0.807
2016 Khodor YL, Riquelme D, Gertler F, Burge CB. Abstract 2875: Genes associated with neuronal development, including splicing regulatory factors, increase in expression across epithelial-mesenchymal transition Cancer Research. 76: 2875-2875. DOI: 10.1158/1538-7445.Am2016-2875  0.419
2015 Sudmant PH, Alexis MS, Burge CB. Meta-analysis of RNA-seq expression data across species, tissues and studies. Genome Biology. 16: 287. PMID 26694591 DOI: 10.1186/S13059-015-0853-4  0.348
2015 Dominguez D, Burge CB. Interactome analysis brings splicing into focus. Genome Biology. 16: 135. PMID 26149273 DOI: 10.1186/S13059-015-0707-0  0.701
2015 Lambert NJ, Robertson AD, Burge CB. RNA Bind-n-Seq: Measuring the Binding Affinity Landscape of RNA-Binding Proteins. Methods in Enzymology. 558: 465-93. PMID 26068750 DOI: 10.1016/Bs.Mie.2015.02.007  0.491
2015 Wang ET, Ward AJ, Cherone JM, Giudice J, Wang TT, Treacy DJ, Lambert NJ, Freese P, Saxena T, Cooper TA, Burge CB. Antagonistic regulation of mRNA expression and splicing by CELF and MBNL proteins. Genome Research. 25: 858-71. PMID 25883322 DOI: 10.1101/Gr.184390.114  0.679
2015 Merkin JJ, Chen P, Alexis MS, Hautaniemi SK, Burge CB. Origins and impacts of new mammalian exons. Cell Reports. 10: 1992-2005. PMID 25801031 DOI: 10.1016/J.Celrep.2015.02.058  0.47
2015 Katz Y, Wang ET, Silterra J, Schwartz S, Wong B, Thorvaldsdóttir H, Robinson JT, Mesirov JP, Airoldi EM, Burge CB. Quantitative visualization of alternative exon expression from RNA-seq data. Bioinformatics (Oxford, England). 31: 2400-2. PMID 25617416 DOI: 10.1093/Bioinformatics/Btv034  0.651
2014 Taliaferro JM, Wang ET, Burge CB. Genomic analysis of RNA localization. Rna Biology. 11: 1040-50. PMID 25483039 DOI: 10.4161/Rna.32146  0.815
2014 Katz Y, Li F, Lambert NJ, Sokol ES, Tam WL, Cheng AW, Airoldi EM, Lengner CJ, Gupta PB, Yu Z, Jaenisch R, Burge CB. Musashi proteins are post-transcriptional regulators of the epithelial-luminal cell state. Elife. 3: e03915. PMID 25380226 DOI: 10.7554/Elife.03915  0.421
2014 Äijö T, Butty V, Chen Z, Salo V, Tripathi S, Burge CB, Lahesmaa R, Lähdesmäki H. Methods for time series analysis of RNA-seq data with application to human Th17 cell differentiation. Bioinformatics (Oxford, England). 30: i113-20. PMID 24931974 DOI: 10.1093/Bioinformatics/Btu274  0.423
2014 Cheng AW, Shi J, Wong P, Luo KL, Trepman P, Wang ET, Choi H, Burge CB, Lodish HF. Muscleblind-like 1 (Mbnl1) regulates pre-mRNA alternative splicing during terminal erythropoiesis. Blood. 124: 598-610. PMID 24869935 DOI: 10.1182/Blood-2013-12-542209  0.634
2014 Shalgi R, Hurt JA, Lindquist S, Burge CB. Widespread inhibition of posttranscriptional splicing shapes the cellular transcriptome following heat shock. Cell Reports. 7: 1362-70. PMID 24857664 DOI: 10.1016/J.Celrep.2014.04.044  0.405
2014 Lambert N, Robertson A, Jangi M, McGeary S, Sharp PA, Burge CB. RNA Bind-n-Seq: quantitative assessment of the sequence and structural binding specificity of RNA binding proteins. Molecular Cell. 54: 887-900. PMID 24837674 DOI: 10.1016/J.Molcel.2014.04.016  0.688
2014 Giudice J, Xia Z, Wang ET, Scavuzzo MA, Ward AJ, Kalsotra A, Wang W, Wehrens XH, Burge CB, Li W, Cooper TA. Alternative splicing regulates vesicular trafficking genes in cardiomyocytes during postnatal heart development. Nature Communications. 5: 3603. PMID 24752171 DOI: 10.1038/Ncomms4603  0.628
2014 Friedman RC, Burge CB. MicroRNA target finding by comparative genomics. Methods in Molecular Biology (Clifton, N.J.). 1097: 457-76. PMID 24639172 DOI: 10.1007/978-1-62703-709-9_21  0.36
2014 Katz Y, Li F, Lambert NJ, Sokol ES, Tam W, Cheng AW, Airoldi EM, Lengner CJ, Gupta PB, Yu Z, Jaenisch R, Burge CB. Author response: Musashi proteins are post-transcriptional regulators of the epithelial-luminal cell state Elife. DOI: 10.7554/Elife.03915.025  0.336
2013 Spies N, Burge CB, Bartel DP. 3' UTR-isoform choice has limited influence on the stability and translational efficiency of most mRNAs in mouse fibroblasts. Genome Research. 23: 2078-90. PMID 24072873 DOI: 10.1101/Gr.156919.113  0.632
2013 Almada AE, Wu X, Kriz AJ, Burge CB, Sharp PA. Promoter directionality is controlled by U1 snRNP and polyadenylation signals. Nature. 499: 360-3. PMID 23792564 DOI: 10.1038/Nature12349  0.814
2013 Hurt JA, Robertson AD, Burge CB. Global analyses of UPF1 binding and function reveal expanded scope of nonsense-mediated mRNA decay Genome Research. 23: 1636-1650. PMID 23766421 DOI: 10.1101/Gr.157354.113  0.483
2013 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, ... ... Burge CB, et al. MBNL proteins repress ES-cell-specific alternative splicing and reprogramming. Nature. 498: 241-5. PMID 23739326 DOI: 10.1038/Nature12270  0.724
2013 Ji X, Zhou Y, Pandit S, Huang J, Li H, Lin CY, Xiao R, Burge CB, Fu XD. SR proteins collaborate with 7SK and promoter-associated nascent RNA to release paused polymerase. Cell. 153: 855-68. PMID 23663783 DOI: 10.1016/J.Cell.2013.04.028  0.459
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  0.747
2013 Shalgi R, Hurt JA, Krykbaeva I, Taipale M, Lindquist S, Burge CB. Widespread Regulation of Translation by Elongation Pausing in Heat Shock Molecular Cell. 49: 439-452. PMID 23290915 DOI: 10.1016/J.Molcel.2012.11.028  0.302
2013 Wang Y, Xiao X, Zhang J, Choudhury R, Robertson A, Li K, Ma M, Burge CB, Wang Z. A complex network of factors with overlapping affinities represses splicing through intronic elements Nature Structural and Molecular Biology. 20: 36-45. PMID 23241926 DOI: 10.1038/Nsmb.2459  0.767
2012 Merkin J, Russell C, Chen P, Burge CB. Evolutionary dynamics of gene and isoform regulation in mammalian tissues Science. 338: 1593-1599. PMID 23258891 DOI: 10.1126/Science.1228186  0.475
2012 Lovén J, Orlando DA, Sigova AA, Lin CY, Rahl PB, Burge CB, Levens DL, Lee TI, Young RA. Revisiting global gene expression analysis. Cell. 151: 476-82. PMID 23101621 DOI: 10.1016/J.Cell.2012.10.012  0.333
2012 Lin CY, Lovén J, Rahl PB, Paranal RM, Burge CB, Bradner JE, Lee TI, Young RA. Transcriptional amplification in tumor cells with elevated c-Myc. Cell. 151: 56-67. PMID 23021215 DOI: 10.1016/J.Cell.2012.08.026  0.371
2012 Wang ET, Cody NA, Jog S, Biancolella M, Wang TT, Treacy DJ, Luo S, Schroth GP, Housman DE, Reddy S, Lécuyer E, Burge CB. Transcriptome-wide regulation of pre-mRNA splicing and mRNA localization by muscleblind proteins. Cell. 150: 710-24. PMID 22901804 DOI: 10.1016/J.Cell.2012.06.041  0.736
2012 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. Reduced expression of ribosomal proteins relieves microRNA-mediated repression. Molecular Cell. 46: 171-86. PMID 22541556 DOI: 10.1016/J.Molcel.2012.04.008  0.667
2012 Anderson ES, Lin CH, Xiao X, Stoilov P, Burge CB, Black DL. The cardiotonic steroid digitoxin regulates alternative splicing through depletion of the splicing factors SRSF3 and TRA2B. Rna (New York, N.Y.). 18: 1041-9. PMID 22456266 DOI: 10.1261/Rna.032912.112  0.686
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  0.785
2011 Zheng GX, Ravi A, Gould GM, Burge CB, Sharp PA. Genome-wide impact of a recently expanded microRNA cluster in mouse. Proceedings of the National Academy of Sciences of the United States of America. 108: 15804-9. PMID 21911408 DOI: 10.1073/Pnas.1112772108  0.6
2011 Shapiro IM, Cheng AW, Flytzanis NC, Balsamo M, Condeelis JS, Oktay MH, Burge CB, Gertler FB. An EMT-driven alternative splicing program occurs in human breast cancer and modulates cellular phenotype. Plos Genetics. 7: e1002218. PMID 21876675 DOI: 10.1371/Journal.Pgen.1002218  0.399
2011 Nutiu R, Friedman RC, Luo S, Khrebtukova I, Silva D, Li R, Zhang L, Schroth GP, Burge CB. Direct measurement of DNA affinity landscapes on a high-throughput sequencing instrument. Nature Biotechnology. 29: 659-64. PMID 21706015 DOI: 10.1038/Nbt.1882  0.375
2011 Zheng GX, Ravi A, Calabrese JM, Medeiros LA, Kirak O, Dennis LM, Jaenisch R, Burge CB, Sharp PA. A latent pro-survival function for the mir-290-295 cluster in mouse embryonic stem cells. Plos Genetics. 7: e1002054. PMID 21573140 DOI: 10.1371/Journal.Pgen.1002054  0.595
2010 Katz Y, Wang ET, Airoldi EM, Burge CB. Analysis and design of RNA sequencing experiments for identifying isoform regulation. Nature Methods. 7: 1009-15. PMID 21057496 DOI: 10.1038/Nmeth.1528  0.682
2010 Bland CS, Wang ET, Vu A, David MP, Castle JC, Johnson JM, Burge CB, Cooper TA. Global regulation of alternative splicing during myogenic differentiation Nucleic Acids Research. 38: 7651-7664. PMID 20634200 DOI: 10.1093/Nar/Gkq614  0.615
2010 Rahl PB, Lin CY, Seila AC, Flynn RA, McCuine S, Burge CB, Sharp PA, Young RA. c-Myc regulates transcriptional pause release. Cell. 141: 432-45. PMID 20434984 DOI: 10.1016/J.Cell.2010.03.030  0.796
2009 Ramsköld D, Wang ET, Burge CB, Sandberg R. An abundance of ubiquitously expressed genes revealed by tissue transcriptome sequence data Plos Computational Biology. 5. PMID 20011106 DOI: 10.1371/Journal.Pcbi.1000598  0.634
2009 Spies N, Nielsen CB, Padgett RA, Burge CB. Biased chromatin signatures around polyadenylation sites and exons. Molecular Cell. 36: 245-54. PMID 19854133 DOI: 10.1016/J.Molcel.2009.10.008  0.671
2009 Xiao X, Wang Z, Jang M, Nutiu R, Wang ET, Burge CB. Splice site strength-dependent activity and genetic buffering by poly-G runs Nature Structural and Molecular Biology. 16: 1094-1100. PMID 19749754 DOI: 10.1038/Nsmb.1661  0.795
2009 Friedman RC, Farh KK, Burge CB, Bartel DP. Most mammalian mRNAs are conserved targets of microRNAs. Genome Research. 19: 92-105. PMID 18955434 DOI: 10.1101/Gr.082701.108  0.611
2008 Kalsotra A, Xiao X, Ward AJ, Castle JC, Johnson JM, Burge CB, Cooper TA. A postnatal switch of CELF and MBNL proteins reprograms alternative splicing in the developing heart Proceedings of the National Academy of Sciences of the United States of America. 105: 20333-20338. PMID 19075228 DOI: 10.1073/Pnas.0809045105  0.641
2008 Wang ET, Sandberg R, Luo S, Khrebtukova I, Zhang L, Mayr C, Kingsmore SF, Schroth GP, Burge CB. Alternative isoform regulation in human tissue transcriptomes. Nature. 456: 470-6. PMID 18978772 DOI: 10.1038/Nature07509  0.665
2008 Friedman BA, Stadler MB, Shomron N, Ding Y, Burge CB. Ab initio identification of functionally interacting pairs of cis-regulatory elements Genome Research. 18: 1643-1651. PMID 18799692 DOI: 10.1101/Gr.080085.108  0.455
2008 Sandberg R, Neilson JR, Sarma A, Sharp PA, Burge CB. Proliferating cells express mRNAs with shortened 3' untranslated regions and fewer microRNA target sites. Science (New York, N.Y.). 320: 1643-7. PMID 18566288 DOI: 10.1126/Science.1155390  0.672
2008 Boyerinas B, Park SM, Shomron N, Hedegaard MM, Vinther J, Andersen JS, Feig C, Xu J, Burge CB, Peter ME. Identification of let-7-regulated oncofetal genes Cancer Research. 68: 2587-2591. PMID 18413726 DOI: 10.1158/0008-5472.Can-08-0264  0.402
2008 Wang Z, Burge CB. Splicing regulation: From a parts list of regulatory elements to an integrated splicing code Rna. 14: 802-813. PMID 18369186 DOI: 10.1261/Rna.876308  0.698
2008 Kimchi-Sarfaty C, Blaisdell A, Marple A, Roma I, Newell J, Dobkin A, Allen C, Friedman S, Burge C, Shomron N. Human Hepatic Stellate Cells Carry a New Splice Variant of the Human ADAMTS13 Blood. 112: 4085-4085. DOI: 10.1182/Blood.V112.11.4085.4085  0.46
2007 Xiao X, Wang Z, Jang M, Burge CB. Coevolutionary networks of splicing cis-regulatory elements Proceedings of the National Academy of Sciences of the United States of America. 104: 18583-18588. PMID 17998536 DOI: 10.1073/Pnas.0707349104  0.745
2007 Nielsen CB, Shomron N, Sandberg R, Hornstein E, Kitzman J, Burge CB. Determinants of targeting by endogenous and exogenous microRNAs and siRNAs. Rna (New York, N.Y.). 13: 1894-910. PMID 17872505 DOI: 10.1261/Rna.768207  0.333
2007 Giorgi C, Yeo GW, Stone ME, Katz DB, Burge C, Turrigiano G, Moore MJ. The EJC factor eIF4AIII modulates synaptic strength and neuronal protein expression. Cell. 130: 179-91. PMID 17632064 DOI: 10.1016/J.Cell.2007.05.028  0.652
2007 Neilson JR, Zheng GX, Burge CB, Sharp PA. Dynamic regulation of miRNA expression in ordered stages of cellular development. Genes & Development. 21: 578-89. PMID 17344418 DOI: 10.1101/Gad.1522907  0.602
2007 Ruvinsky I, Ohler U, Burge CB, Ruvkun G. Detection of broadly expressed neuronal genes in C. elegans. Developmental Biology. 302: 617-26. PMID 17046742 DOI: 10.1016/J.Ydbio.2006.09.014  0.606
2007 Ibrahim EC, Hims MM, Shomron N, Burge CB, Slaugenhaupt SA, Reed R. Weak definition of IKBKAP exon 20 leads to aberrant splicing in familial dysautonomia. Human Mutation. 28: 41-53. PMID 16964593 DOI: 10.1002/Humu.20401  0.425
2007 Wang Z, Xiao X, Friedman B, Shomron N, Burge CB. Towards an RNA Splicing Code The Faseb Journal. 21. DOI: 10.1096/Fasebj.21.5.A147-B  0.652
2006 Stadler MB, Shomron N, Yeo GW, Schneider A, Xiao X, Burge CB. Inference of splicing regulatory activities by sequence neighborhood analysis. Plos Genetics. 2: e191. PMID 17121466 DOI: 10.1371/Journal.Pgen.0020191  0.748
2006 Wang Z, Xiao X, Van Nostrand E, Burge CB. General and Specific Functions of Exonic Splicing Silencers in Splicing Control Molecular Cell. 23: 61-70. PMID 16797197 DOI: 10.1016/J.Molcel.2006.05.018  0.745
2006 Holste D, Huo G, Tung V, Burge CB. HOLLYWOOD: a comparative relational database of alternative splicing. Nucleic Acids Research.. 34: D56-62. PMID 16381932 DOI: 10.1093/Nar/Gkj048  0.498
2006 Yahyanejad M, Burge CB, Kardar M. Untangling influences of hydrophobicity on protein sequences and structures Proteins: Structure, Function and Genetics. 62: 1101-1106. PMID 16374871 DOI: 10.1002/Prot.20775  0.306
2005 Farh KK, Grimson A, Jan C, Lewis BP, Johnston WK, Lim LP, Burge CB, Bartel DP. The widespread impact of mammalian MicroRNAs on mRNA repression and evolution. Science (New York, N.Y.). 310: 1817-21. PMID 16308420 DOI: 10.1126/Science.1121158  0.596
2005 Goranov AI, Katz L, Breier AM, Burge CB, Grossman AD. A transcriptional response to replication status mediated by the conserved bacterial replication protein DnaA. Proceedings of the National Academy of Sciences of the United States of America. 102: 12932-7. PMID 16120674 DOI: 10.1073/Pnas.0506174102  0.37
2005 Ohler U, Shomron N, Burge CB. Recognition of unknown conserved alternatively spliced exons. Plos Computational Biology. 1: 113-22. PMID 16110330 DOI: 10.1371/Journal.Pcbi.0010015  0.677
2005 Han K, Yeo G, An P, Burge CB, Grabowski PJ. A combinatorial code for splicing silencing: UAGG and GGGG motifs. Plos Biology.. 3: e158. PMID 15828859 DOI: 10.1371/Journal.Pbio.0030158  0.651
2005 Pfarr N, Prawitt D, Kirschfink M, Schroff C, Knuf M, Habermehl P, Mannhardt W, Zepp F, Fairbrother WG, Fairbrother W, Loos M, Burge CB, Pohlenz J. Linking C5 deficiency to an exonic splicing enhancer mutation. Journal of Immunology (Baltimore, Md. : 1950). 174: 4172-7. PMID 15778377 DOI: 10.4049/Jimmunol.174.7.4172  0.371
2005 Yeo GW, Van Nostrand E, Holste D, Poggio T, Burge CB. Identification and analysis of alternative splicing events conserved in human and mouse. Proceedings of the National Academy of Sciences of the United States of America. 102: 2850-5. PMID 15708978 DOI: 10.1073/Pnas.0409742102  0.71
2005 Lewis BP, Burge CB, Bartel DP. Conserved seed pairing, often flanked by adenosines, indicates that thousands of human genes are microRNA targets. Cell. 120: 15-20. PMID 15652477 DOI: 10.1016/J.Cell.2004.12.035  0.6
2005 Ohler U, Shomron N, Burge CB. Recognition of unknown conserved alternatively spliced exons Plos Computational Biology. 1: 0113-0122. DOI: 10.1371/journal.pcbi.0010015  0.609
2004 Seneff S, Wang C, Burge CB. Gene structure prediction using an orthologous gene of known exon-intron structure Applied Bioinformatics. 3: 81-90. PMID 15693733 DOI: 10.2165/00822942-200403020-00002  0.379
2004 Wang Z, Rolish ME, Yeo G, Tung V, Mawson M, Burge CB. Systematic identification and analysis of exonic splicing silencers Cell. 119: 831-845. PMID 15607979 DOI: 10.1016/J.Cell.2004.11.010  0.728
2004 Nielsen CB, Friedman B, Birren B, Burge CB, Galagan JE. Patterns of intron gain and loss in fungi Plos Biology. 2. PMID 15562318 DOI: 10.1371/Journal.Pbio.0020422  0.374
2004 Yeo G, Hoon S, Venkatesh B, Burge CB. Variation in sequence and organization of splicing regulatory elements in vertebrate genes Proceedings of the National Academy of Sciences of the United States of America. 101: 15700-15705. PMID 15505203 DOI: 10.1073/Pnas.0404901101  0.657
2004 Yeo G, Holste D, Kreiman G, Burge CB. Variation in alternative splicing across human tissues. Genome Biology. 5: R74. PMID 15461793 DOI: 10.1186/Gb-2004-5-10-R74  0.58
2004 Fairbrother WG, Holste D, Burge CB, Sharp PA. Single nucleotide polymorphism-based validation of exonic splicing enhancers. Plos Biology. 2: E268. PMID 15340491 DOI: 10.1371/Journal.Pbio.0020268  0.602
2004 Ohler U, Yekta S, Lim LP, Bartel DP, Burge CB. Patterns of flanking sequence conservation and a characteristic upstream motif for microRNA gene identification. Rna (New York, N.Y.). 10: 1309-22. PMID 15317971 DOI: 10.1261/Rna.5206304  0.743
2004 Yeo G, Burge CB. Maximum entropy modeling of short sequence motifs with applications to RNA splicing signals Journal of Computational Biology. 11: 377-394. PMID 15285897 DOI: 10.1089/1066527041410418  0.586
2004 Fairbrother WG, Yeo GW, Yeh R, Goldstein P, Mawson M, Sharp PA, Burge CB. RESCUE-ESE identifies candidate exonic splicing enhancers in vertebrate exons. Nucleic Acids Research. 32: W187-90. PMID 15215377 DOI: 10.1093/Nar/Gkh393  0.748
2004 Eng L, Coutinho G, Nahas S, Yeo G, Tanouye R, Babaei M, Dörk T, Burge C, Gatti RA. Nonclassical splicing mutations in the coding and noncoding regions of the ATM Gene: maximum entropy estimates of splice junction strengths. Human Mutation. 23: 67-76. PMID 14695534 DOI: 10.1002/Humu.10295  0.557
2003 Lewis BP, Shih IH, Jones-Rhoades MW, Bartel DP, Burge CB. Prediction of mammalian microRNA targets. Cell. 115: 787-98. PMID 14697198 DOI: 10.1016/S0092-8674(03)01018-3  0.597
2003 Katz L, Burge CB. Widespread selection for local RNA secondary structure in coding regions of bacterial genes Genome Research. 13: 2042-2051. PMID 12952875 DOI: 10.1101/Gr.1257503  0.474
2003 Lim LP, Lau NC, Weinstein EG, Abdelhakim A, Yekta S, Rhoades MW, Burge CB, Bartel DP. The microRNAs of Caenorhabditis elegans. Genes & Development. 17: 991-1008. PMID 12672692 DOI: 10.1101/Gad.1074403  0.6
2003 Lim LP, Glasner ME, Yekta S, Burge CB, Bartel DP. Vertebrate microRNA genes. Science (New York, N.Y.). 299: 1540. PMID 12624257 DOI: 10.1126/Science.1080372  0.61
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. A uniform system for microRNA annotation. Rna (New York, N.Y.). 9: 277-9. PMID 12592000 DOI: 10.1261/Rna.2183803  0.686
2002 Rhoades MW, Reinhart BJ, Lim LP, Burge CB, Bartel B, Bartel DP. Prediction of plant microRNA targets. Cell. 110: 513-20. PMID 12202040 DOI: 10.1016/S0092-8674(02)00863-2  0.609
2002 Fairbrother WG, Yeh RF, Sharp PA, Burge CB. Predictive identification of exonic splicing enhancers in human genes. Science (New York, N.Y.). 297: 1007-13. PMID 12114529 DOI: 10.1126/Science.1073774  0.682
2001 Lim LP, Burge CB. A computational analysis of sequence features involved in recognition of short introns Proceedings of the National Academy of Sciences of the United States of America. 98: 11193-11198. PMID 11572975 DOI: 10.1073/Pnas.201407298  0.451
2001 Das M, Burge CB, Park E, Colinas J, Pelletier J. Assessment of the total number of human transcription units Genomics. 77: 71-78. PMID 11543635 DOI: 10.1006/Geno.2001.6620  0.385
2001 Yeh RF, Lim LP, Burge CB. Computational inference of homologous gene structures in the human genome Genome Research. 11: 803-816. PMID 11337476 DOI: 10.1101/Gr.175701  0.377
2001 Burge CB. Chipping away at the transcriptome Nature Genetics. 27: 232-234. PMID 11242095 DOI: 10.1038/85772  0.367
2001 Lander ES, Linton LM, Birren B, Nusbaum C, Zody MC, Baldwin J, Devon K, Dewar K, Doyle M, FitzHugh W, Funke R, Gage D, Harris K, Heaford A, Howland J, ... ... Burge CB, et al. Initial sequencing and analysis of the human genome. Nature. 409: 860-921. PMID 11237011 DOI: 10.1038/35057062  0.324
2001 Lander ES, Linton LM, Birren B, Nusbaum C, Zody MC, Baldwin J, Devon K, Dewar K, Doyle M, Fitzhugh W, Funke R, Gage D, Harris K, Heaford A, Howland J, ... ... Burge CB, et al. Erratum: Initial sequencing and analysis of the human genome: International Human Genome Sequencing Consortium (Nature (2001) 409 (860-921)) Nature. 412: 565-566. DOI: 10.1038/35087627  0.317
2000 Miyajima N, Burge CB, Saito T. Computational and experimental analysis identifies many novel human genes Biochemical and Biophysical Research Communications. 272: 801-807. PMID 10860834 DOI: 10.1006/Bbrc.2000.2866  0.37
1999 Burge CB, Tuschl T, Sharp PA. 20 Splicing of Precursors to mRNAs by the Spliceosomes Cold Spring Harbor Monograph Archive. 37: 525-560. DOI: 10.1101/087969589.37.525  0.771
1998 Burge CB, Padgett RA, Sharp PA. Evolutionary fates and origins of U12-type introns. Molecular Cell. 2: 773-85. PMID 9885565 DOI: 10.1016/S1097-2765(00)80292-0  0.724
1998 Burge CB, Karlin S. Finding the genes in genomic DNA. Current Opinion in Structural Biology. 8: 346-54. PMID 9666331 DOI: 10.1016/S0959-440X(98)80069-9  0.518
1998 Burge C. Chapter 8 Modeling dependencies in pre-mRNA splicing signals New Comprehensive Biochemistry. 32: 129-164. DOI: 10.1016/S0167-7306(08)60465-2  0.339
1997 Sharp PA, Burge CB. Classification of introns: U2-type or U12-type. Cell. 91: 875-9. PMID 9428511 DOI: 10.1016/S0092-8674(00)80479-1  0.544
1997 Burge C, Karlin S. Prediction of complete gene structures in human genomic DNA. Journal of Molecular Biology. 268: 78-94. PMID 9149143 DOI: 10.1006/Jmbi.1997.0951  0.568
1996 Karlin S, Burge C. Trinucleotide repeats and long homopeptides in genes and proteins associated with nervous system disease and development. Proceedings of the National Academy of Sciences of the United States of America. 93: 1560-5. PMID 8643671 DOI: 10.1073/Pnas.93.4.1560  0.531
1995 Karlin S, Burge C. Dinucleotide relative abundance extremes: a genomic signature. Trends in Genetics : Tig. 11: 283-90. PMID 7482779 DOI: 10.1016/S0168-9525(00)89076-9  0.49
1994 Cardon LR, Burge C, Clayton DA, Karlin S. Pervasive CpG suppression in animal mitochondrial genomes. Proceedings of the National Academy of Sciences of the United States of America. 91: 3799-803. PMID 8170990 DOI: 10.1073/Pnas.91.9.3799  0.46
1993 Karlin S, Blaisdell BE, Sapolsky RJ, Cardon L, Burge C. Assessments of DNA inhomogeneities in yeast chromosome III. Nucleic Acids Research. 21: 703-11. PMID 8441679 DOI: 10.1093/Nar/21.3.703  0.542
1993 Cardon LR, Burge C, Schachtel GA, Blaisdell BE, Karlin S. Comparative DNA sequence features in two long Escherichia coli contigs. Nucleic Acids Research. 21: 3875-84. PMID 8367304 DOI: 10.1093/Nar/21.16.3875  0.532
1992 Burge C, Campbell AM, Karlin S. Over- and under-representation of short oligonucleotides in DNA sequences. Proceedings of the National Academy of Sciences of the United States of America. 89: 1358-62. PMID 1741388 DOI: 10.1073/Pnas.89.4.1358  0.543
1992 Karlin S, Burge C, Campbell AM. Statistical analyses of counts and distributions of restriction sites in DNA sequences. Nucleic Acids Research. 20: 1363-70. PMID 1313968 DOI: 10.1093/Nar/20.6.1363  0.513
1991 Leung MY, Blaisdell BE, Burge C, Karlin S. An efficient algorithm for identifying matches with errors in multiple long molecular sequences. Journal of Molecular Biology. 221: 1367-78. PMID 1942056 DOI: 10.1016/0022-2836(91)90938-3  0.482
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