Shyam Prabhakar

Summary

Affiliation: Lawrence Berkeley National Laboratory
Country: USA

Publications

  1. ncbi request reprint The DNA sequence and comparative analysis of human chromosome 5
    Jeremy Schmutz
    Stanford Human Genome Center, Department of Genetics, Stanford University School of Medicine, 975 California Ave, Palo Alto, California 94304, USA
    Nature 431:268-74. 2004
  2. pmc Close sequence comparisons are sufficient to identify human cis-regulatory elements
    Shyam Prabhakar
    Genomics Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
    Genome Res 16:855-63. 2006
  3. pmc Human-specific gain of function in a developmental enhancer
    Shyam Prabhakar
    Genomics Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
    Science 321:1346-50. 2008
  4. pmc Detection of weakly conserved ancestral mammalian regulatory sequences by primate comparisons
    Qian Fei Wang
    Genomics Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
    Genome Biol 8:R1. 2007
  5. pmc Ultraconservation identifies a small subset of extremely constrained developmental enhancers
    Axel Visel
    Genomics Division, MS 84 171, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
    Nat Genet 40:158-60. 2008
  6. ncbi request reprint Mapping cis-regulatory domains in the human genome using multi-species conservation of synteny
    Nadav Ahituv
    Genomics Division, Lawrence Berkeley National Laboratory, CA 94720, USA
    Hum Mol Genet 14:3057-63. 2005
  7. ncbi request reprint In vivo enhancer analysis of human conserved non-coding sequences
    Len A Pennacchio
    US Department of Energy Joint Genome Institute, Walnut Creek, California 94598, USA
    Nature 444:499-502. 2006
  8. pmc Primate-specific evolution of an LDLR enhancer
    Qian Fei Wang
    Genomics Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
    Genome Biol 7:R68. 2006
  9. ncbi request reprint Accelerated evolution of conserved noncoding sequences in humans
    Shyam Prabhakar
    U S Department of Energy DOE Joint Genome Institute, Walnut Creek, CA 94598, USA
    Science 314:786. 2006
  10. pmc Annotation of cis-regulatory elements by identification, subclassification, and functional assessment of multispecies conserved sequences
    Jim R Hughes
    Medical Research Council Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, Headington, Oxford OX3 9DS, United Kingdom
    Proc Natl Acad Sci U S A 102:9830-5. 2005

Collaborators

  • E M Rubin
  • LEN ALEXANDER PENNACCHIO
  • Qian Fei Wang
  • Jan Fang Cheng
  • Alan M Moses
  • David R Fitzpatrick
  • James P Noonan
  • Simon Minovitsky
  • I Dubchak
  • Brian Black
  • Evan E Eichler
  • Uffe Hellsten
  • Gary Xie
  • Norman A Doggett
  • Douglas R Higgs
  • Olivier Couronne
  • Joel Martin
  • Jeremy Schmutz
  • Axel Visel
  • Jim R Hughes
  • Nadav Ahituv
  • Chenier Caoile
  • Trevor Hawkins
  • Nancy Hammon
  • Mirian Denys
  • Susan M Lucas
  • Dave Flowers
  • Xinwei She
  • Mark Dickson
  • Wayne Huang
  • Eva Bajorek
  • Joan Yang
  • Sanjay Israni
  • Yee Man Chan
  • James Retterer
  • Daniel S Rokhsar
  • Mary Tran-Gyamfi
  • Sam Pitluck
  • Tijana Glavina
  • Nina Thayer
  • Martin Pollard
  • Yunian Lou
  • Dea Fotopulos
  • Frederick Lopez
  • Kristen Kadner
  • Ming Tsai
  • Lauren Haydu
  • Astrid Terry
  • Arthur Kobayashi
  • Eidelyn Gonzales
  • Maria Gomez
  • Lucia Ramirez
  • Michael Altherr
  • Matthew Groza
  • Duncan Scott
  • Heather Kimball
  • Laurie A Gordon
  • Igor Grigoriev
  • Andrea Aerts
  • Elbert Branscomb
  • Asaf Salamov
  • Paul Richardson
  • Julio Escobar
  • Richard M Myers
  • Jean F Challacombe
  • John C Detter
  • Steve Lowry
  • Kevin Wu
  • Nu Vo
  • David Goodstein
  • Alex Rodriguez
  • Jamie Jett
  • Anna Ustaszewska
  • Paul Predki
  • Hope Tice
  • Jenna Morgan
  • Stacey Black
  • Jane Grimwood
  • Ingrid Plajzer-Frick
  • Malak Shoukry
  • Amy Holt
  • Keith D Lewis
  • Jennifer A Akiyama
  • Veena Afzal
  • Eduardo Anguita
  • Marco De Gobbi
  • Kevin Clark
  • Pieter de Jong
  • Nicki Ventress
  • Francis Poulin

Detail Information

Publications11

  1. ncbi request reprint The DNA sequence and comparative analysis of human chromosome 5
    Jeremy Schmutz
    Stanford Human Genome Center, Department of Genetics, Stanford University School of Medicine, 975 California Ave, Palo Alto, California 94304, USA
    Nature 431:268-74. 2004
    ..These duplications are very recent evolutionary events and probably have a mechanistic role in human physiological variation, as deletions in these regions are the cause of debilitating disorders including spinal muscular atrophy...
  2. pmc Close sequence comparisons are sufficient to identify human cis-regulatory elements
    Shyam Prabhakar
    Genomics Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
    Genome Res 16:855-63. 2006
    ..Lastly, we determined that, in addition to strength of conservation, genomic location and/or density of surrounding conserved elements must also be considered in selecting candidate enhancers for in vivo testing at embryonic time points...
  3. pmc Human-specific gain of function in a developmental enhancer
    Shyam Prabhakar
    Genomics Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
    Science 321:1346-50. 2008
    ....
  4. pmc Detection of weakly conserved ancestral mammalian regulatory sequences by primate comparisons
    Qian Fei Wang
    Genomics Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
    Genome Biol 8:R1. 2007
    ..However, these methods fail to detect functional elements that are too weakly conserved among mammals to distinguish them from non-functional DNA...
  5. pmc Ultraconservation identifies a small subset of extremely constrained developmental enhancers
    Axel Visel
    Genomics Division, MS 84 171, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
    Nat Genet 40:158-60. 2008
    ..Developmental enhancers were equally prevalent in both populations, suggesting instead that ultraconservation identifies a small, functionally indistinct subset of similarly constrained cis-regulatory elements...
  6. ncbi request reprint Mapping cis-regulatory domains in the human genome using multi-species conservation of synteny
    Nadav Ahituv
    Genomics Division, Lawrence Berkeley National Laboratory, CA 94720, USA
    Hum Mol Genet 14:3057-63. 2005
    ..Our results provide an extensive data set characterizing the regulatory domains of genes and the conserved regulatory elements within them...
  7. ncbi request reprint In vivo enhancer analysis of human conserved non-coding sequences
    Len A Pennacchio
    US Department of Energy Joint Genome Institute, Walnut Creek, California 94598, USA
    Nature 444:499-502. 2006
    ....
  8. pmc Primate-specific evolution of an LDLR enhancer
    Qian Fei Wang
    Genomics Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
    Genome Biol 7:R68. 2006
    ..Sequence changes in regulatory regions have often been invoked to explain phenotypic divergence among species, but molecular examples of this have been difficult to obtain...
  9. ncbi request reprint Accelerated evolution of conserved noncoding sequences in humans
    Shyam Prabhakar
    U S Department of Energy DOE Joint Genome Institute, Walnut Creek, CA 94598, USA
    Science 314:786. 2006
    ..CNSs accelerated in mouse showed no bias toward neuronal cell adhesion. Our results indicate that widespread cis-regulatory changes in human evolution may have contributed to uniquely human features of brain development and function...
  10. pmc Annotation of cis-regulatory elements by identification, subclassification, and functional assessment of multispecies conserved sequences
    Jim R Hughes
    Medical Research Council Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, Headington, Oxford OX3 9DS, United Kingdom
    Proc Natl Acad Sci U S A 102:9830-5. 2005
    ..Together, these studies demonstrate an integrated approach by which to identify, subclassify, and predict the potential importance of MCSs...
  11. ncbi request reprint The sequence and analysis of duplication-rich human chromosome 16
    Joel Martin
    DOE Joint Genome Institute, 2800 Mitchell Avenue, Walnut Creek, California 94598, USA
    Nature 432:988-94. 2004
    ....