2008
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, 1643-7. ABSTRACT. Download PDF
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. Science 310, 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. RNA 9, 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
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