Publications

2024

Harris SE, Alexis MS, Giri G, Cavazos Jr FF, Hu Y, Murn J, Aleman MA, Burge CB, Dominguez D (2024). Understanding species-specific and conserved RNA-protein interactions in vivo and in vitro. Nature Communications 15:8400. PMCID: PMC11436793..

Jacobs H, Gorissen B, Guez J, Kanai M, Finucane H, Karczewski K, Burge CB. Widespread naturally variable human exons aid genetic interpretation https://biorxiv.org/cgi/content/short/2024.09.09.612029v1

McGurk MP, McWatters DC, Burge CB. KATMAP: Inferring splicing factor activity and regulatory targets from knockdown data bioRxiv 2024.06.25.600605; https://www.biorxiv.org/content/10.1101/2024.06.25.600605v1

Vanoye CG, Abramova TV, DeKeyser JM, Ghabra NF, Oudin MJ, Burge CB, Helbig I, Thompson CH, George AL Jr. Molecular and cellular context influences SCN8A variant function. JCI Insight. 2024 May 21;9(12):e177530. doi: 10.1172/jci.insight.177530. PMID: 38771640. PMCID: PMC11383174.

Kenny CJ, McGurk MP, Schuler S, Cordero A, Laubinger S, Burge CB. (2024) LUC7 proteins define two major classes of 5’ splice sites in animals and plants. Nature Communications (accepted in principle) https://www.biorxiv.org/content/10.1101/2022.12.07.519539v2

McCue K, Burge CB. (2024) An interpretable model of pre-mRNA splicing for animal and plant genes. Science Advances 10(19):eadn1547. PMID 38718117. PMCID PMC11078188.

Gupta K, Yang C, McCue K, Bastani O, Sharp PA, Burge CB, Solar-Lezama A. (2024) Improved modeling of RNA-binding protein motifs in an interpretable neural model of RNA splicing. Genome Biology 25(1):23. PMID 38229106. PMCID: PMC10790492.

Findlay SD, Romo L, Burge CB (2024). Quantifying negative selection in human 3’ UTRs uncovers constrained targets of RNA-binding proteins Nature Communications 15:85 PMID: 38168060. PMCID PMC10762232

Romo L, Findlay SD, Burge CB. (2024) Regulatory features aid interpretation of 3'UTR Variants. Am J Hum Genet S0002-9297(23)00449-4. PMID 38237594. PMCID: in process.

2023

Vanoye CG, Abramova TV, DeKeyser JM, Ghabra N, Oudin M, Burge CB, Helbig I, Thompson CH, George Jr AL. Molecular and Cellular Context Influences SCN8A Variant Function bioRxiv 2023.11.11.566702; doi: https://doi.org/10.1101/2023.11.11.566702

Feng Q, Krick K, Chu J, Burge CB. Splicing quality control mediated by DHX15 and its G-patch activator SUGP1. Cell Rep. 2023 Oct 31;42(10):113223. doi: 10.1016/j.celrep.2023.113223. Epub 2023 Oct 8. PMID: 37805921.

2022

Le TT, Payne SL, Buckwald MN, Hayes LA, Parker SR, Burge CB, Oudin MJ. Sensory nerves enhance triple-negative breast cancer invasion and metastasis via the axon guidance molecule PlexinB3. NPJ Breast Cancer. 2022 Nov 4;8(1):116. doi: 10.1038/s41523-022-00485-z. PMID: 36333352; PMCID: PMC9636220.

Kenny, CJ, McGurk MP, Burge CB (2022). Human LUC7 proteins impact splicing of two major subclasses of 5’ splice sites bioRxiv 2022.12.07.519539

Feng Q, Krick K, Chu J, Burge B (2022). Splicing quality control mediated by DHX15 and its G-patch activator, SUGP1bioRxiv 2022.11.14.516533

Jens M, McGurk M, Budschuh R, Burge CB (2022). RBPamp: Quantitative Modeling of Protein-RNA Interactions in vitro Predicts in vivo Binding bioRxiv 2022.11.08.515616

Fiszbein A, McGurk M, Calvo-Roitberg E, Kim G, Burge CB, Pai AA (2022). Widespread occurrence of hybrid internal-terminal exons in human transcriptomes Sci Adv. (2022) 8(3):eabk1752

2021

Jourdain AA, Begg BE, Mick E, Hardik S, Calvo ES, Skinner OS, Sharma R, Blue SM, Yeo GW, Burge CB, Mootha VK (2021) Loss of LUCJL2 and U1 snRNP subunits shifts energy metabolism from glycolysis to OXPHOS Molecular Cell Free Share Link through June 2, 2021

2020

Van Nostrand EL, Freese P, Pratt GA, Wang X, Wei X, Xiao R, Blue SM, Chen J, Cody NAL, Dominguez D, Olson S, Sundararaman B, Zhan L, Bazile C, Bouvrette LPB, Bergalet J, Duff MO, Garcia KE, Gelboin-Burkhart C, Hochman M, Lambert NJ, Li H, McGurk MP, Nguyen TB, Palden T, Rabano I, Sathe S, Stanton R, Su A, Wang R, Yee BA, Zhou B, Louie AL, Aigner S, Fu X, Lécuyer E, Burge CB, Graveley BR, Yeo GW (2020). A large-scale binding and functional map of human RNA-binding proteins Nature 583, 711-719

ENCODE Project Consortium; 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, He Y, Mackiewicz M, Pauli-Behn F, Williams BA, Mortazavi A, Keller CA, Zhang X, Elhajjajy SI, Huey J, Dickel DE, Snetkova V, Wei X, Wang X, Rivera-Mulia JC, Rozowsky J, Zhang J, Chhetri SB, Zhang J, ictorsen A, White KP, Visel A, Yeo GW, Burge CB, Lécuyer E, Gilbert DM, Dekker J, Rinn J, Mendenhall EM, Ecker JR, Kellis M, Klein RJ, Noble RS, Kundaje A, Guigó R, Farnham PJ, Cherry JM, Myers RM, Ren B, Graveley BR, Gerstein MB, Pennacchio LA, Snyder MP, Bernstein BE, Wold B, Hardison RC, Gingeras TR, Stamatoyannopoulos JA , Weng Z, (2020) Expanded encyclopaedias of DNA elements in the human and mouse genomes Nature 583, 699-710.

Begg BE, Jens M, Wang PY and Burge CB (2019). Concentration-dependent splicing is enabled by Rbfox motifs of intermediate affinity. Nature Struct. Mol. Biol. (in press)

2019

Fiszbein A, Krick K, Begg BE and Burge CB (2019). Exon-mediated activation of transcription starts. Cell 179, 1551-1565.

Cherone JM, Jorgji V and Burge CB (2019). Cotargeting among microRNAs in the brain. Genome Research 29, 1791-1804.

Kröger C, Afeyan A, Mraz J, et al. Acquisition of a hybrid E/M state is essential for tumorigenicity of basal breast cancer cells. Proc Natl Acad Sci USA. 2019;116(15):7353-7362.

Xiao R, Chen JY, Liang Z, et al. Pervasive Chromatin-RNA Binding Protein Interactions Enable RNA-Based Regulation of Transcription. Cell. 2019;178(1):107-121.e18.

Wang ET, Treacy D, Eichinger K, et al. Transcriptome alterations in myotonic dystrophy skeletal muscle and heart. Hum Mol Genet. 2019;28(8):1312-1321. doi: 10.1093/hmg/ddy432

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. Allele-specific binding of RNA-binding proteins reveals functional genetic variants in the RNA. Nat Commun. 2019 Mar 22;10(1):1338. doi: 10.1038/s41467-019-09292-w.

Gonen N, Sabath N, Burge CB, Shalgi R. Widespread PERK-dependent repression of ER targets in response to ER stress. Sci Rep. 2019 Mar 13;9(1):4330. doi: 10.1038/s41598-019-38705-5.

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 Res. 2019 Feb 12. pii: canres.1604.2018. doi: 10.1158/0008-5472.CAN-18-1604.

2018

Sudmant P, Lee H, Dominguez D, Heiman M, Burge CB (2018) Widespread Accumulation of Ribosome Associated Isolated 3' UTRs in Neuronal Cell Populations of the Aging Brain. Cell Reports. Volume 25 Issue 9, 27 November 2018, Pages 2447-2456. e4

Pai AA, Paggi JM, Yan P, Adelman K, and Burge CB. Numerous recursive sites contribute to accuracy of splicing in long introns in flies. PLoS Genet 14(8): e1007588.

Dominguez D, Freese P, Maria Alexis M, Su A, Hochman M, Palden T, Bazile C, Lambert NJ, Van Nostrand EL, Pratt GA, Yeo GW, Graveley BR, and Burge CB (2018). Sequence, Structure, and Context Preferences of Human RNA Binding Proteins. Mol. Cell 70, 854-867.

Murphy PA, Butty VL, Boutz PL, Begum S, Kimble AL, Sharp PA, Burge CB, Hynes RO. (2018). Alternative RNA splicing in the endothelium mediated in part by Rbfox2 regulates the arterial response to low flow. eLife e29494.

2017

Vidaki M, Drees F, Saxena T, Lanslots E, Taliaferro MJ, Tatarakis A, Burge CB, Wang ET, Gertler FB. (2017). A Requirement for Mena, an Actin Regulator, in Local mRNA Translation in Developing Neurons. Neuron 95(3):608-622.

Pai AA, Henriques T, McCue K, Burkholder A, Adelman K and Burge CB. (2017). The Kinetics of pre-mRNA splicing in the Drosphila genome and the influence of gene architecture. eLife e32537.

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, 15, 666-679, 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, Zhang J, Zhu H, Cambi F, Kasarskis E, Hoon S, Ares MJr, Burge CB, Ravits J, Rigo F, Yeo GW. Distinct and shared functions of ALS-associated proteins TDP-43, FUS and TAF15 revealed by multisystem analyses. Nature communications, 7, 12143, 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, Burge 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.

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 Text e 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. Abstract xt Full 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.Science310, 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.RNA9,277-279.

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

2000 and prior

Miyajima, N., Burge, C. B. and Saito, T. (2000) Computational and experimental analysis identifies many previously unknown human genes. Biochem. Biophys. Res. Comm. 272, 801-807.

Burge, C. B., Tuschl, T. H. and Sharp, P. A. (1999) Splicing of precursors to mRNAs by the spliceosomes. In Gesteland, R. F., Cech, T. and Atkins, J. F., eds. The RNA World, 2nd Ed., Cold Spring Harbor Laboratory Press, Plainview, NY, pp. 525-560.

Burge, C. B. and Karlin, S. (1998) Finding the genes in genomic DNA. Curr. Opin. Struct. Biol. 8, 346-354.

Burge, C. B., Padgett, R. A. and Sharp, P. A. (1998) Evolutionary fates and origins of U12-type introns. Mol. Cell 2, 773-785.

Burge, C. B. (1998) Modeling dependencies in pre-mRNA splicing signals. In Salzberg, S., Searls, D. and Kasif, S., eds. Computational Methods in Molecular Biology, Elsevier Science, Amsterdam, pp. 127-163.

Burge, C. (1997) Identification of genes in human genomic DNA. PhD thesis, Stanford University, Stanford, CA.

Burge, C. and Karlin, S. (1997) Prediction of complete gene structures in human genomic DNA. J. Mol. Biol. 268, 78 - 94.

Sharp, P. A. and Burge, C. B. (1997) Classification of introns: U2-type or U12-type. Cell 91, 875-879.

Karlin, S. and Burge, C. (1996) Trinucleotide repeats and long homopeptides in genes and proteins associated with nervous system disease and development. Proc. Natl. Acad. Sci. USA 93, 1560 - 1565.

Karlin, S. and Burge, C. (1995) Dinucleotide relative abundance extremes: a genomic signature. Trends Genet. 11, 283 - 290.

Cardon, L. R., Burge, C., Clayton, D. A. and Karlin, S. (1994) Pervasive CpG suppression in animal mitochondrial genomes. Proc. Natl. Acad. Sci. USA 91, 3799 - 3803.

Cardon, L. R., Burge, C., Schachtel, G. A., Blaisdell, B. E. and Karlin, S. (1993) Comparative DNA sequence features in two long Escherichia colicontigs. Nucl. Acids Res. 21, 3875 - 3884.

Karlin, S., Blaisdell, B. E., Sapolsky, R. J., Cardon, L. R. and Burge, C. (1993) Assessments of DNA inhomogeneities in yeast chromosome III. Nucl. Acids Res. 21, 703 - 711.

Karlin, S., Burge, C. and Campbell, A. M. (1992) Statistical analyses of counts and distributions of restriction sites in DNA sequences. Nucl. Acids Res. 20, 1363 - 1370.

Burge, C., Campbell, A. M. and Karlin, S. (1992) Over- and under-representation of short oligonucleotides in DNA sequences. Proc. Natl. Acad. Sci. USA 89, 1358 - 1362.

Burge, C., Sanders, W. and Alderman, E. L. (1991) Anatomic and machine projection angles of various radiographic imaging systems used for cardiac angiography. Cath. Cardiovasc. Diag. 22, 64 - 74.

Leung, M.-Y., Blaisdell, B. E., Burge, C. and Karlin, S. (1991) An efficient algorithm for identifying matches with errors in multiple long molecular sequences. J. Mol. Biol. 221, 1367 - 1378.