Complete List of Publications

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

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 .

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.