C B Burge

Summary

Affiliation: Massachusetts Institute of Technology
Country: USA

Publications

  1. pmc Single nucleotide polymorphism-based validation of exonic splicing enhancers
    William G Fairbrother
    Center for Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
    PLoS Biol 2:E268. 2004
  2. pmc Patterns of intron gain and loss in fungi
    Cydney B Nielsen
    Department of Biology, Massachusetts Institute of Technology Cambridge, Massachusetts, USA
    PLoS Biol 2:e422. 2004
  3. pmc Variation in alternative splicing across human tissues
    Gene Yeo
    Department of Biology, Center for Biological and Computational Learning, Massachusetts Institute of Technology, Cambridge, MA 02319, USA
    Genome Biol 5:R74. 2004
  4. ncbi request reprint Finding the genes in genomic DNA
    C B Burge
    Center for Cancer Research, Massachusetts Institute of Technology, Cambridge 02139, USA
    Curr Opin Struct Biol 8:346-54. 1998
  5. ncbi request reprint Initial sequencing and analysis of the human genome
    E S Lander
    Whitehead Institute for Biomedical Research, Center for Genome Research, Cambridge, Massachusetts 02142, USA
    Nature 409:860-921. 2001
  6. ncbi request reprint Predictive identification of exonic splicing enhancers in human genes
    William G Fairbrother
    Department of Biology, Center for Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
    Science 297:1007-13. 2002
  7. pmc Ab initio identification of functionally interacting pairs of cis-regulatory elements
    Brad A Friedman
    Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
    Genome Res 18:1643-51. 2008
  8. pmc HOLLYWOOD: a comparative relational database of alternative splicing
    Dirk Holste
    Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02319, USA
    Nucleic Acids Res 34:D56-62. 2006
  9. ncbi request reprint Gene structure prediction using an orthologous gene of known exon-intron structure
    Stephanie 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
  10. pmc RESCUE-ESE identifies candidate exonic splicing enhancers in vertebrate exons
    William G Fairbrother
    Center for Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
    Nucleic Acids Res 32:W187-90. 2004

Detail Information

Publications34

  1. pmc Single nucleotide polymorphism-based validation of exonic splicing enhancers
    William G Fairbrother
    Center for Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
    PLoS Biol 2:E268. 2004
    ....
  2. pmc Patterns of intron gain and loss in fungi
    Cydney 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...
  3. pmc Variation in alternative splicing across human tissues
    Gene 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...
  4. ncbi request reprint Finding the genes in genomic DNA
    C B Burge
    Center for Cancer Research, Massachusetts Institute of Technology, Cambridge 02139, USA
    Curr Opin Struct Biol 8:346-54. 1998
    ....
  5. ncbi request reprint Initial sequencing and analysis of the human genome
    E 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...
  6. ncbi request reprint Predictive identification of exonic splicing enhancers in human genes
    William 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...
  7. pmc Ab initio identification of functionally interacting pairs of cis-regulatory elements
    Brad 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...
  8. pmc HOLLYWOOD: a comparative relational database of alternative splicing
    Dirk 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...
  9. ncbi request reprint Gene structure prediction using an orthologous gene of known exon-intron structure
    Stephanie 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...
  10. pmc RESCUE-ESE identifies candidate exonic splicing enhancers in vertebrate exons
    William 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...
  11. pmc A computational analysis of sequence features involved in recognition of short introns
    L 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
    ....
  12. pmc Alternative isoform regulation in human tissue transcriptomes
    Eric T Wang
    Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
    Nature 456:470-6. 2008
    ....
  13. ncbi request reprint Systematic identification and analysis of exonic splicing silencers
    Zefeng 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...
  14. pmc Identification and analysis of alternative splicing events conserved in human and mouse
    Gene 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...
  15. pmc Biased chromatin signatures around polyadenylation sites and exons
    Noah 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...
  16. pmc Variation in sequence and organization of splicing regulatory elements in vertebrate genes
    Gene 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
    ....
  17. pmc Most mammalian mRNAs are conserved targets of microRNAs
    Robin 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...
  18. pmc The microRNAs of Caenorhabditis elegans
    Lee 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...
  19. pmc Coevolutionary networks of splicing cis-regulatory elements
    Xinshu 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...
  20. pmc Computational inference of homologous gene structures in the human genome
    R 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...
  21. pmc Splice site strength-dependent activity and genetic buffering by poly-G runs
    Xinshu 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...
  22. pmc General and specific functions of exonic splicing silencers in splicing control
    Zefeng 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...
  23. ncbi request reprint The widespread impact of mammalian MicroRNAs on mRNA repression and evolution
    Kyle 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
    ....
  24. ncbi request reprint Maximum entropy modeling of short sequence motifs with applications to RNA splicing signals
    Gene 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...
  25. ncbi request reprint Prediction of mammalian microRNA targets
    Benjamin 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...
  26. ncbi request reprint Vertebrate microRNA genes
    Lee P Lim
    Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
    Science 299:1540. 2003
  27. pmc Widespread selection for local RNA secondary structure in coding regions of bacterial genes
    Luba 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...
  28. pmc Patterns of flanking sequence conservation and a characteristic upstream motif for microRNA gene identification
    Uwe 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...
  29. ncbi request reprint Linking C5 deficiency to an exonic splicing enhancer mutation
    Nicole 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...
  30. pmc Inference of splicing regulatory activities by sequence neighborhood analysis
    Michael 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...
  31. ncbi request reprint Weak definition of IKBKAP exon 20 leads to aberrant splicing in familial dysautonomia
    El Cherif Ibrahim
    Department of Cell Biology, Harvard Medical School, Boston, Massachusetts 02115, USA
    Hum Mutat 28:41-53. 2007
    ....
  32. pmc A combinatorial code for splicing silencing: UAGG and GGGG motifs
    Kyoungha Han
    Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
    PLoS Biol 3:e158. 2005
    ....
  33. pmc Splicing regulation: from a parts list of regulatory elements to an integrated splicing code
    Zefeng 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...
  34. ncbi request reprint Prediction of plant microRNA targets
    Matthew 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 Grants14

  1. Computational and Experimental Analysis of Vertebrate RNA Splicing
    Christopher 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. ..
  2. Identification and Function of Sequence-specific Splicing Regulators
    Christopher B Burge; Fiscal Year: 2010
    ....
  3. Computational and Experimental Analysis of Vertebrate RNA Splicing
    Christopher 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. ..
  4. Identification and Function of Sequence-specific Splicing Regulators
    Christopher Burge; Fiscal Year: 2009
    ....
  5. Computational and Experimental Analysis of Vertebrate RNA Splicing
    Christopher 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. ..
  6. Computational Analysis of Vertebrate RNA Splicing
    Christopher Burge; Fiscal Year: 2006
    ..abstract_text> ..
  7. Computational and Experimental Analysis of Vertebrate RNA Splicing
    Christopher 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. ..