| Year |
Citation |
Score |
| 2024 |
Harris SE, Alexis MS, Giri G, Cavazos FF, Hu Y, Murn J, Aleman MM, Burge CB, Dominguez D. Understanding species-specific and conserved RNA-protein interactions in vivo and in vitro. Nature Communications. 15: 8400. PMID 39333159 DOI: 10.1038/s41467-024-52231-7 |
0.404 |
|
| 2024 |
McCue K, Burge CB. An interpretable model of pre-mRNA splicing for animal and plant genes. Science Advances. 10: eadn1547. PMID 38718117 DOI: 10.1126/sciadv.adn1547 |
0.345 |
|
| 2024 |
Harris SE, Alexis MS, Giri G, Cavazos FF, Murn J, Aleman MM, Burge CB, Dominguez D. Understanding species-specific and conserved RNA-protein interactions and . Biorxiv : the Preprint Server For Biology. PMID 38352439 DOI: 10.1101/2024.01.29.577729 |
0.403 |
|
| 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 |
0.669 |
|
| 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 |
0.559 |
|
| 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 |
0.431 |
|
| 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 |
0.49 |
|
| 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 |
0.739 |
|
| 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 |
0.622 |
|
| 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 |
0.799 |
|
| 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 |
0.659 |
|
| 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 |
0.755 |
|
| 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 |
0.66 |
|
| 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 |
0.796 |
|
| 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 |
0.605 |
|
| 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 |
0.6 |
|
| 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 |
0.419 |
|
| 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 |
0.56 |
|
| 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 |
0.815 |
|
| 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 |
0.405 |
|
| 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 |
0.669 |
|
| 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 |
0.626 |
|
| 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 |
0.738 |
|
| 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 |
0.806 |
|
| 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 |
0.347 |
|
| 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 |
0.675 |
|
| 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 |
0.646 |
|
| 2014 |
Taliaferro JM, Wang ET, Burge CB. Genomic analysis of RNA localization. Rna Biology. 11: 1040-50. PMID 25483039 DOI: 10.4161/Rna.32146 |
0.814 |
|
| 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 |
0.422 |
|
| 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 |
0.629 |
|
| 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 |
0.687 |
|
| 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 |
0.623 |
|
| 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 |
0.63 |
|
| 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 |
0.813 |
|
| 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 |
0.72 |
|
| 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 |
0.744 |
|
| 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 |
0.765 |
|
| 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 |
0.733 |
|
| 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 |
0.663 |
|
| 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 |
0.684 |
|
| 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 |
0.782 |
|
| 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 |
0.678 |
|
| 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 |
0.61 |
|
| 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 |
0.629 |
|
| 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 |
0.793 |
|
| 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 |
0.608 |
|
| 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 |
0.637 |
|
| 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 |
0.661 |
|
| 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 |
0.454 |
|
| 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 |
0.401 |
|
| 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 |
0.697 |
|
| 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 |
0.459 |
|
| 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 |
0.743 |
|
| 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 |
0.649 |
|
| 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 |
0.602 |
|
| 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 |
0.649 |
|
| 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 |
0.745 |
|
| 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 |
0.743 |
|
| 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 |
0.594 |
|
| 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 |
0.674 |
|
| 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 |
0.647 |
|
| 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 |
0.708 |
|
| 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 |
0.597 |
|
| 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 |
0.604 |
|
| 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 |
0.726 |
|
| 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 |
0.653 |
|
| 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 |
0.575 |
|
| 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 |
0.601 |
|
| 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 |
0.74 |
|
| 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 |
0.582 |
|
| 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 |
0.746 |
|
| 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 |
0.552 |
|
| 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 |
0.594 |
|
| 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 |
0.597 |
|
| 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 |
0.608 |
|
| 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 |
0.685 |
|
| 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 |
0.606 |
|
| 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 |
0.681 |
|
| 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 |
0.77 |
|
| 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 |
0.723 |
|
| 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 |
0.543 |
|
| 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 |
0.53 |
|
| 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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