Complete List of Publications

Spies, N., Burge, C.B., Bartel, D.P. 2013. 3' UTR-isoform choice has limited influence on the stability and translational efficiency of most mRNAs in mouse fibroblasts. Genome Res. (Advance Online Article)

Almada, A.E., Wu, X., Kriz, A.J., Burge, C.B., and Sharp, P.A. 2013. Promoter directionality is controlled by U1 snRNP and polyadenylation signals. Nature AOP.

Han, H., Irimia, M., Ross, P.J., Sung, H.K., Alipanahi, B., David, L., Golipour, A., Gabut, M., Michael, I.P., Nachman, E.N., Wang, E., Trcka, D., Thompson, T., O'Hanlon, D., Slobodeniuc, V., Barbosa-Morais, N.L., Burge, C.B., Moffat, J., Frey, B.J., Nagy, A., Ellis, J., Wrana, J.L., and Blencowe, B.J. (2013) MBNL proteins repress ES-cell-specific alternative splicing and reprogramming. Nature 498, 241-245.

Hurt, J.A., Robertson, D.A., and Burge, C.B. (2013) Global analyses of UPF1 binding and function reveals expanded scope of nonsense-mediated mRNA decay. Genome Res. [AOP].

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

Klattenhoff, C.A., Scheuermann, J.C., Surface, L.E., Bradley, R.K., Fields, P.A., Steinhauser, M.L., Ding. H., Butty, V.L., Torrey, L., Haas, S., Abo, R., Tabebordbar, M., Lee, R.T., Burge, C.B., and Boyer, L.A. (2013). Braveheart, a Long Noncoding RNA Required for CardiovascularLineage Commitment. Cell 152, 1-14.

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

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

Wang, Y., Xiao, X., Zhang, J., Choudhury, R., Robertson, A., Li, K., Ma, M., Burge, C.B., and Wang, Z. (2012). A complex network of factors with overlapping affinities represses splicing through intronic elements. NSMB 20, 36-45, 2013. (Epub 2012 Dec 16).

Lin, C.Y., Lovén, J., Rahl, P.B., Paranal, R.M., Burge, C.B., Bradner, J.E., Lee, T.I., and Young, R.A. (2012). Transcriptional Amplification in Tumor Cells with Elevated c-Myc. Cell 151, 56-67.

Wang, E.T., Cody, N.A., Jog, S., Biancollela, M., Wang, T.T., Treacy, D.J., Luo, S., Schroth, G.P., Housman, D.E., Reddy, S., Lécuyer, E., and Burge, C.B. (2012).Transcriptome-wide regulation of pre-mRNA splicing and mRNA localization by muscleblind proteins. Cell 150, 710-724. PMCID: PMC3428802.

Anderson, E.S., Lin, C.H., Xiao, X., Stoilov, P., Burge, C.B., and Black, D.L. (2012). The cardiotonic steroid digitoxin regulates alternative splicing through depletion of the splicing factors SRSF3 and TRA2B. RNA 18, 1041-9. Open Access

Janas, M.M., Wang, E.T., Love, T., Harris, A.S., Stevenson, K., Semmelmann, K., Shaffer, J.M., Chen, P., Doench, J.G., Yerramilli, S.V.B.K., Neuberg, D., Iliopoulos, D., Housman, D.E., Burge, C.B. and Novina, C.D. (2012). Reduced expression of ribosomal proteins relieves microRNA-mediated repression. Mol. Cell 46, 171-186 .

Bradley, R. K., Merkin, J., Lambert, N.J. and Burge, C. B. (2012). Alternative Splicing of RNA Triplets is Often Regulated and Accelerates Proteome Evolution. PLoS Biol. 10, e1001229. Open Access

Zheng, G. X. Y., Ravia, A., Gould, G. M., Burge, C. B. and Sharp, P. A. (2011). Genome-Wide Impact of A Recently Expanded MicroRNA Cluster in Mouse. PNAS USA 108, 15804-9.

Shapiro, I.M., Cheng, A.W., Flytzanis, N.C., Balsamo, M., Condeelis, J.S., Oktay, M.H., Burge, C.B., Gertler, F.B. (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, R.C., Luo, S., Khrebtukova, I., Silva, D., Li, R., Zhan, L., Schroth, G.P., Burge, C.B. (2011). Direct visualization of DNA affinity landscapes using a sequencing instrument. Nature Biotech 29, 659-664.

Zheng, G.X.Y., Ravi, A., Calabrese, J.M., Medeiros, L.A., Kirak, O., Dennis, L., Jaenisch, R., Burge, C.B., Sharp, P.A. (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, R.C., Marquez, R.T., 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(12), 1753-1762.

Bland, C.S., Wang, E.T., Vu, A., David, M.P., Castle, J.C., Johnson, J.M., Burge, C.B., Cooper, T.A.. (2010).Global regulation of alternative splicing during myogenic differentiation.
Nucleic Acids Res. 38, 7651-64.

Katz, Y., Wang, E.T., Airoldi, E.M., Burge, C.B. (2010). Analysis and design of RNA sequencing experiments for identifying isoform regulation. Nature Methods 7, 1009-1015 .

Rahl, P.B., Lin, C.Y., Seila, A.C., Flynn, R.A., McCuine, S., Burge, C.B., Sharp, P.A., Young, R.A. (2010). cMyc regulates transcriptional pause release. Cell 141, 432-445.

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

Spies, N., Nielsen, C.B., Padgett, R.A., Burge, C.B. (2009). Biased chromatin signatures around polyadenylation sites and exons. Mol Cell 36, 245-254. Full Text

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

Friedman, R.C., Farh, K.K., Burge, C.B., Bartel, D.P. (2009). Most mammalian mRNAs are conserved targets of microRNAs. Genome Res. 19, 92-105. Open Access.

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

Wang, E.T., Sandberg, R., Luo, S., Khrebtukova, I., Zhang, L., Mayr, C., Kingsmore, S.F., Schroth, G.P., Burge, C.B. (2008). Alternative Isoform Regulation in Human Tissue Transcriptomes. Nature 456, 470-476. Full Text

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

Sandberg, R., Neilson, J.R., Sarma, A., Sharp, P.A., Burge, C.B. (2008). Proliferating cells express mRNAs with shortened 3' untranslated regions and fewer microRNA target sites. Science 320, 1643-1647. Abstract  Full Text

Wang, Z. and Burge, C.B. (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, M.M., Vinther, J., Andersen, J.S., Feig, C., Xu, J., Burge, C.B. and Peter, M.E. (2008). Identification of let-7 regulated oncofetal genes. Cancer Res. 68, 2587-2591.

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

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

Giorgi, C., Yeo, G.W., Stone, M.E., Katz, D.B., Burge, C., Turrigiano, G. and Moore, M.J. (2007). The EJC Factor eIF4AIII Modulates Synaptic Strength and Neuronal Protein Expression. Cell 130, 179-191.

Neilson, J.R., Zheng, G.X.Y., Burge, C.B. and Sharp, P.A. (2007). Dynamic regulation of miRNA expression in ordered stages of cellular development. Genes Dev. 21, 578-589.

Ruvinsky, I., Ohler, U., Burge, C.B. and Ruvkun, G. (2007). Detection of broadly expressed neuronal genes in C. elegans. Dev. Biol. 30, 617-626.

Ibrahim, E.C., Hims, M.M., Shomron, N., Burge, C.B., Slaugenhaupt, S.A. and Reed, R. (2007). Weak Definition of IKBKAP exon 20 leads to aberrant splicing in familial dysautonomia. Hum Mutat. 28, 41-53.

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

Engels, R., Yu, T., Burge, C., Mesirov, J.P., Decaprio, D. and Galagan, J.E. (2006). Combo: a whole genome comparative browser. Bioinformatics 22, 1782-1783.

Wang, Z., Xiao, X., Van Nostrand, E. and Burge, C.B. (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, 1101-1106.

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

Farh, K. K., Grimson, A., Jan, C., Lewis, B. P., Johnston, W. K., Lim, L. P., Burge, C. B. and Bartel, D. P. (2005). The widespread impact of mammalian microRNAs on mRNA repression and evolution. Science 310, 1817-1821.

Goranov, A. I., Katz, L., Breier, A. M., Burge, C. B. and Grossman, A. D. (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, C. B. and Grabowski, P. J. (2005). A combinatorial code for splicing silencing: UAGG and GGGG motifs. PLoS Biol. 3, e158. PDF (Open Access).

Lewis, B. P., Burge, C. B. and Bartel, D. P. (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. and Burge, C. B. (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, C. B. and 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. and Burge, C. B. (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, R. A. and Burge, C. B. (2005). Splice sites. In: Encyclopedia of Life Sciences. John Wiley & Sons, Ltd: Chichester http://www.els.net/

Eng, L., Coutinho, G., Nahas, S., Yeo, G., Tanouye, R., Babaei, M., Dork, T., Burge, C., and Gatti, R. A. (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, W. G., Holste, D., Burge, C. B. and Sharp, P. A. (2004). Single nucleotide polymorphism-based validation of exonic splicing enhancers. PLoS Biol. 2(9), e268: 1-8. PDF at PLoS Biology web site.

Fairbrother, W. G., Yeo, G., Yeh, R.-F., Goldstein, P., Mawson, M., Sharp, P. A. and Burge, C. B. (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, C. B.*, Friedman, B.*, Birren, B., Burge, C. B. and Galagan, J. E. (2004). Patterns of intron gain and loss in fungi. PLoS Biol. 2, e422. PDF at PLoS Biology web site.

Ohler, U., Yekta, S., Lim, L. P., Bartel, D. P. and Burge, C. B. (2004). Patterns of flanking sequence conservation and a characteristic upstream motif for microRNA gene identification. RNA 10, 1309-1322.

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

Yeo, G.*, Holste, D.*, Kreiman, G. and Burge, C. B. (2004). Variation in alternative splicing across human tissues. Genome Biol. 5, R74. PDF at Genome Biology web site.

Yeo, G., Hoon, S., Venkatesh, B. and Burge, C. B. (2004). Variation in sequence and organization of splicing regulatory elements in vertebrate genes. Proc. Natl. Acad. Sci. USA (PNAS Early Edition) PDF at PNAS web site.

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

Ambros, V., Bartel, B., Bartel, D. P., Burge, C. B., Carrington, J. C., Chen, X., Dreyfuss, G., Eddy, S. R., Griffiths-Jones, S., Marshall, M., Matzke, M., Ruvkun, G., and Tuschl, T. (2003). A uniform system for microRNA annotation. RNA 9, 277-279.

Arndt, P. F., Burge, C. B. and Hwa, T. (2003). DNA sequence evolution with neighbor-dependent mutation. J. Comp. Biol. 10 313-322.

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

Lewis, B. P.*, Shih, I-h.*, Jones-Rhoades, M. W., Bartel, D. P. and Burge, C. B. (2003). Prediction of mammalian microRNA targets. Cell 115, 787-798.

* These authors contributed equally.

Lim, L. P.*, Glasner, M. E.*, Yekta, S.*, Burge, C. B. and Bartel, D. P. (2003). Vertebrate MicroRNA genes. Science 299, 1540.

* These authors contributed equally.

Lim, L. P.*, Lau, N. C.*, Weinstein, E. G.*, Abdelhakim, A.*, Yekta, S., Rhoades, M. W., Burge, C. B. and Bartel, D. P. (2003). The microRNAs of Caenorhabditis elegans. Genes & Dev. 17, 977-990.

* These authors contributed equally.

Yeo, G. and Burge, C. B. (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).

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

Rhoades, M.W., Reinhart, B.J., Lim, L.P., Burge, C. B., Bartel, B., and Bartel, D.P. (2002). Prediction of plant microRNA targets. Cell 110, 513-520.

Yeh, R.-F.*, Fairbrother, W.*, Sharp, P. A. and Burge, C. B. (2002). Predictive identification of exonic splicing enhancers in human genes. Science 297, 1007-1013.

* These authors contributed equally

Yeh, R.-F., Lim, L. P. and Burge, C. B. (2001) Computational inference of homologous gene structures in the human genome. Genome Res. 11, 803-816.

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

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

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

Lim, L. P. and Burge, C. B. (2001). A computational analysis of sequence features involved in recognition of short introns. Proc. Natl. Acad. Sci. USA 98, 11193­11198.

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 coli contigs. 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.