Research Topics
Species | C B BurgeSummaryAffiliation: Massachusetts Institute of Technology Country: USA Publications
Research Grants
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Detail Information
Publications
Single nucleotide polymorphism-based validation of exonic splicing enhancersWilliam G Fairbrother
Center for Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
PLoS Biol 2:E268. 2004....- Patterns of intron gain and loss in fungiCydney B Nielsen
Department of Biology, Massachusetts Institute of Technology Cambridge, Massachusetts, USA
PLoS Biol 2:e422. 2004..Contrary to standard models, we find no increased frequency of intron loss toward the 3' ends of genes. Thus, recent intron dynamics do not support a model whereby 5' intron positional bias is generated solely by 3'-biased intron loss... - Variation in alternative splicing across human tissuesGene Yeo
Department of Biology, Center for Biological and Computational Learning, Massachusetts Institute of Technology, Cambridge, MA 02319, USA
Genome Biol 5:R74. 2004..To compare AS events across human tissues, we analyzed the splicing patterns of genomically aligned expressed sequence tags (ESTs) derived from libraries of cDNAs from different tissues... 
Finding the genes in genomic DNAC B Burge
Center for Cancer Research, Massachusetts Institute of Technology, Cambridge 02139, USA
Curr Opin Struct Biol 8:346-54. 1998....- Computational inference of homologous gene structures in the human genomeR F Yeh
Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
Genome Res 11:803-16. 2001..The results show an accurate and efficient automated approach for identifying genes in higher eukaryotic genomes and provide a first-level annotation of the draft human genome... - Initial sequencing and analysis of the human genomeE S Lander
Whitehead Institute for Biomedical Research, Center for Genome Research, Cambridge, Massachusetts 02142, USA
Nature 409:860-921. 2001..We also present an initial analysis of the data, describing some of the insights that can be gleaned from the sequence... - Predictive identification of exonic splicing enhancers in human genesWilliam G Fairbrother
Department of Biology, Center for Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
Science 297:1007-13. 2002..The motifs identified enable prediction of the splicing phenotypes of exonic mutations in human genes... - RESCUE-ESE identifies candidate exonic splicing enhancers in vertebrate exonsWilliam G Fairbrother
Center for Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
Nucleic Acids Res 32:W187-90. 2004..mit.edu/burgelab/rescue-ese/) that annotates RESCUE-ESE hexamers in vertebrate exons and can be used to predict splicing phenotypes by identifying sequence changes that disrupt or alter predicted ESEs... - Gene structure prediction using an orthologous gene of known exon-intron structureStephanie Seneff
Computer Science and Artificial Intelligence Laboratory, 32 G438, Spoken Language Systems Group, Massachusetts Institute of Technology, 32 Vassar Street, Cambridge, MA 02139, USA
Appl Bioinformatics 3:81-90. 2004..For a set of 98 orthologous human-mouse pairs, we achieved 96% sensitivity and 97% specificity at the exon level on the mouse genes, given only knowledge gleaned from the annotated human genome... - Ab initio identification of functionally interacting pairs of cis-regulatory elementsBrad A Friedman
Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
Genome Res 18:1643-51. 2008..This approach can be easily generalized to problems beyond RNA splicing... - HOLLYWOOD: a comparative relational database of alternative splicingDirk Holste
Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02319, USA
Nucleic Acids Res 34:D56-62. 2006..A streamlined graphical representation of gene splicing patterns is provided, and these patterns can alternatively be layered onto existing information in the UCSC Genome Browser. The database is accessible at http://hollywood.mit.edu... - A computational analysis of sequence features involved in recognition of short intronsL P Lim
Department of Biology and Center for Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
Proc Natl Acad Sci U S A 98:11193-8. 2001.... - Identification and analysis of alternative splicing events conserved in human and mouseGene W Yeo
Department of Biology and Center for Biological and Computational Learning, Massachusetts Institute of Technology, Cambridge, MA 02319, USA
Proc Natl Acad Sci U S A 102:2850-5. 2005..Our results also imply that the vast majority of AS events represented in the human EST database are not conserved in mouse... - Systematic identification and analysis of exonic splicing silencersZefeng Wang
Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
Cell 119:831-45. 2004..ExonScan and related bioinformatic analyses suggest that these ESS motifs play important roles in suppression of pseudoexons, in splice site definition, and in AS... - Alternative isoform regulation in human tissue transcriptomesEric T Wang
Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
Nature 456:470-6. 2008.... - Biased chromatin signatures around polyadenylation sites and exonsNoah Spies
Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
Mol Cell 36:245-54. 2009..Together, these findings provide evidence for extensive functional connections between chromatin structure and RNA processing... - Most mammalian mRNAs are conserved targets of microRNAsRobin C Friedman
Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
Genome Res 19:92-105. 2009..Our expanded set of target predictions (including conserved 3'-compensatory sites), are available at the TargetScan website, which displays the P(CT) for each site and each predicted target... - Coevolutionary networks of splicing cis-regulatory elementsXinshu Xiao
Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
Proc Natl Acad Sci U S A 104:18583-8. 2007..Thus, the splicing elements defining exons coevolve in a way that preserves overall exon strength, allowing specific elements to substitute for loss or weakening of others... - Variation in sequence and organization of splicing regulatory elements in vertebrate genesGene Yeo
Departments of Biology and Brain and Cognitive Sciences, Massachusetts Institute of Technology, 77 Massachusetts Avenue 68-223, Cambridge, MA 02139-4307, USA
Proc Natl Acad Sci U S A 101:15700-5. 2004.... - The microRNAs of Caenorhabditis elegansLee P Lim
Department of Biology, Massachusetts Institute of Technology, Cambridge 02139, USA
Genes Dev 17:991-1008. 2003..Our census of the worm miRNAs and their expression patterns helps define this class of noncoding RNAs, lays the groundwork for functional studies, and provides the tools for more comprehensive analyses of miRNA genes in other species... - General and specific functions of exonic splicing silencers in splicing controlZefeng Wang
Department of Biology, Massachusetts Institute of Technology, Cambridge, 02139, USA
Mol Cell 23:61-70. 2006..Together, our findings provide a comprehensive picture of the functions of ESSs in the control of diverse types of splicing decisions... - Splice site strength-dependent activity and genetic buffering by poly-G runsXinshu Xiao
Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
Nat Struct Mol Biol 16:1094-100. 2009..Certain other splicing factors may function similarly... - Maximum entropy modeling of short sequence motifs with applications to RNA splicing signalsGene Yeo
Department of Biology, Massachusetts Institute of Technology, 77 Massachusetts Avenue Building 68-223, Cambridge, MA 02319, USA
J Comput Biol 11:377-94. 2004..Our best models out-perform previous probabilistic models in the discrimination of human 5' (donor) and 3' (acceptor) splice sites from decoys. Finally, we discuss mechanistically motivated ways of comparing models... - Prediction of mammalian microRNA targetsBenjamin P Lewis
Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
Cell 115:787-98. 2003..The predicted regulatory targets of mammalian miRNAs were enriched for genes involved in transcriptional regulation but also encompassed an unexpectedly broad range of other functions... - The widespread impact of mammalian MicroRNAs on mRNA repression and evolutionKyle Kai-How Farh
Whitehead Institute for Biomedical Research, Department of Biology, Massachusetts Institute of Technology, and Howard Hughes Medical Institute, 9 Cambridge Center, Cambridge, MA 02142, USA
Science 310:1817-21. 2005.... - Widespread selection for local RNA secondary structure in coding regions of bacterial genesLuba Katz
Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
Genome Res 13:2042-51. 2003..These results are interpreted in terms of possible roles of RNA structures in RNA processing, regulation of mRNA stability, and translational control... - Patterns of flanking sequence conservation and a characteristic upstream motif for microRNA gene identificationUwe Ohler
Department of Biology, Massachusetts Institute of Technology, Cambridge 02142, USA
RNA 10:1309-22. 2004..The improved analysis supports our previous assertion that miRNA gene identification is nearing completion in C. elegans with apparently no more than 20 miRNA genes now remaining to be identified... - Vertebrate microRNA genesLee P Lim
Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
Science 299:1540. 2003 - Splicing regulation: from a parts list of regulatory elements to an integrated splicing codeZefeng Wang
Department of Pharmacology, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
RNA 14:802-13. 2008..Here, we summarize the current state of knowledge of splicing cis-regulatory elements and their context-dependent effects on splicing, emphasizing recent global/genome-wide studies and open questions... - Inference of splicing regulatory activities by sequence neighborhood analysisMichael B Stadler
Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
PLoS Genet 2:e191. 2006..This observation indicates a high degree of selection for ESE activity in mammalian exons, with surprisingly frequent interchangeability between ESE sequences... - Weak definition of IKBKAP exon 20 leads to aberrant splicing in familial dysautonomiaEl Cherif Ibrahim
Department of Cell Biology, Harvard Medical School, Boston, Massachusetts 02115, USA
Hum Mutat 28:41-53. 2007.... - A combinatorial code for splicing silencing: UAGG and GGGG motifsKyoungha Han
Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
PLoS Biol 3:e158. 2005.... - Linking C5 deficiency to an exonic splicing enhancer mutationNicole Pfarr
Children s Hospital of Johannes Gutenberg University of Mainz, Mainz, Germany
J Immunol 174:4172-7. 2005..This apparently inconsequential sequence alteration represents a noncanonical splicing mutation altering an ESE. Our finding sheds a new light on the role of putative silent/conservative mutations in disease-associated genes... - Prediction of plant microRNA targetsMatthew W Rhoades
Whitehead Institute for Biomedical Research, 9 Cambridge Center, MA 02142, USA
Cell 110:513-20. 2002..The targeting of developmental transcription factors suggests that many plant miRNAs function during cellular differentiation to clear key regulatory transcripts from daughter cell lineages...
Research Grants
- Computational and Experimental Analysis of Vertebrate RNA SplicingChristopher Burge; Fiscal Year: 2009..The ability to accurately simulate splicing will enable improved genome annotation and will facilitate identification of specific genes, mutations and polymorphisms associated with human diseases. ..
- Identification and Function of Sequence-specific Splicing RegulatorsChristopher B Burge; Fiscal Year: 2010....
- Computational and Experimental Analysis of Vertebrate RNA SplicingChristopher B Burge; Fiscal Year: 2010..The ability to accurately simulate splicing will enable improved genome annotation and will facilitate identification of specific genes, mutations and polymorphisms associated with human diseases. ..
- Identification and Function of Sequence-specific Splicing RegulatorsChristopher Burge; Fiscal Year: 2009....
- Computational and Experimental Analysis of Vertebrate RNA SplicingChristopher Burge; Fiscal Year: 2009..The ability to accurately simulate splicing will enable improved genome annotation and will facilitate identification of specific genes, mutations and polymorphisms associated with human diseases. ..
- Computational Analysis of Vertebrate RNA SplicingChristopher Burge; Fiscal Year: 2006..abstract_text> ..
- Computational and Experimental Analysis of Vertebrate RNA SplicingChristopher B Burge; Fiscal Year: 2010..The ability to accurately simulate splicing will enable improved genome annotation and will facilitate identification of specific genes, mutations and polymorphisms associated with human diseases. ..