James P Noonan

Summary

Affiliation: Yale University
Country: USA

Publications

  1. doi request reprint Evolution of Gene Regulation in Humans
    Steven K Reilly
    Department of Genetics, Yale School of Medicine, New Haven, Connecticut 06510 email
    Annu Rev Genomics Hum Genet 17:45-67. 2016
  2. doi request reprint Regulatory DNAs and the evolution of human development
    James P Noonan
    Department of Genetics and Kavli Institute for Neuroscience, Yale University School of Medicine, New Haven, CT 06510, USA
    Curr Opin Genet Dev 19:557-64. 2009
  3. doi request reprint Genomics of long-range regulatory elements
    James P Noonan
    Department of Genetics, Yale University School of Medicine, New Haven, CT 06510, USA
    Annu Rev Genomics Hum Genet 11:1-23. 2010
  4. pmc Neanderthal genomics and the evolution of modern humans
    James P Noonan
    Department of Genetics, Yale University School of Medicine, New Haven, Connecticut 06520, USA
    Genome Res 20:547-53. 2010
  5. pmc The genomic landscape of cohesin-associated chromatin interactions
    Laura E Demare
    Department of Genetics, Yale University School of Medicine, New Haven, Connecticut 06510, USA
    Genome Res 23:1224-34. 2013
  6. pmc Evolutionary genomics. Evolutionary changes in promoter and enhancer activity during human corticogenesis
    Steven K Reilly
    Department of Genetics, Yale School of Medicine, New Haven, CT 06510, USA
    Science 347:1155-9. 2015
  7. pmc The evolution of lineage-specific regulatory activities in the human embryonic limb
    Justin Cotney
    Department of Genetics, Yale University School of Medicine, New Haven, CT 06520, USA
    Cell 154:185-96. 2013
  8. pmc The autism-associated chromatin modifier CHD8 regulates other autism risk genes during human neurodevelopment
    Justin Cotney
    1 Department of Genetics, Yale School of Medicine, 333 Cedar Street, New Haven, Connecticut 06510, USA 2 Kavli Institute for Neuroscience, Yale School of Medicine, PO Box 208001, New Haven, Connecticut 06520, USA
    Nat Commun 6:6404. 2015
  9. pmc RNA-Seq profiling of spinal cord motor neurons from a presymptomatic SOD1 ALS mouse
    Urmi Bandyopadhyay
    Department of Genetics, Yale University School of Medicine, New Haven, Connecticut, United States of America
    PLoS ONE 8:e53575. 2013
  10. doi request reprint Gene regulation and the origins of human biological uniqueness
    Samuel J Sholtis
    Department of Genetics, Yale University School of Medicine, New Haven, CT 06520, USA
    Trends Genet 26:110-8. 2010

Collaborators

Detail Information

Publications17

  1. doi request reprint Evolution of Gene Regulation in Humans
    Steven K Reilly
    Department of Genetics, Yale School of Medicine, New Haven, Connecticut 06510 email
    Annu Rev Genomics Hum Genet 17:45-67. 2016
    ..Finally, we highlight two novel strategies to model human-specific regulatory functions in vivo: primate induced pluripotent stem cells and the generation of humanized mice by genome editing. ..
  2. doi request reprint Regulatory DNAs and the evolution of human development
    James P Noonan
    Department of Genetics and Kavli Institute for Neuroscience, Yale University School of Medicine, New Haven, CT 06510, USA
    Curr Opin Genet Dev 19:557-64. 2009
    ....
  3. doi request reprint Genomics of long-range regulatory elements
    James P Noonan
    Department of Genetics, Yale University School of Medicine, New Haven, CT 06510, USA
    Annu Rev Genomics Hum Genet 11:1-23. 2010
    ..We discuss the advantages and limitations of sequence conservation as a predictor of regulatory function and present complementary emerging technologies now being applied to annotate regulatory elements in vertebrate genomes...
  4. pmc Neanderthal genomics and the evolution of modern humans
    James P Noonan
    Department of Genetics, Yale University School of Medicine, New Haven, Connecticut 06520, USA
    Genome Res 20:547-53. 2010
    ..A reconstructed Neanderthal genome sequence could be integrated into human-primate genome comparisons to help reveal the evolutionary genetic events that produced modern humans...
  5. pmc The genomic landscape of cohesin-associated chromatin interactions
    Laura E Demare
    Department of Genetics, Yale University School of Medicine, New Haven, Connecticut 06510, USA
    Genome Res 23:1224-34. 2013
    ..Our results reveal the diversity of cohesin-associated interactions in the genome and highlight their role in establishing the regulatory architecture of development. ..
  6. pmc Evolutionary genomics. Evolutionary changes in promoter and enhancer activity during human corticogenesis
    Steven K Reilly
    Department of Genetics, Yale School of Medicine, New Haven, CT 06510, USA
    Science 347:1155-9. 2015
    ..Our results reveal coordinated patterns of potential regulatory changes associated with conserved developmental processes during corticogenesis, providing insight into human cortical evolution. ..
  7. pmc The evolution of lineage-specific regulatory activities in the human embryonic limb
    Justin Cotney
    Department of Genetics, Yale University School of Medicine, New Haven, CT 06520, USA
    Cell 154:185-96. 2013
    ..Gains at promoters and enhancers in the human limb are associated with increased gene expression, suggesting they include molecular drivers of human morphological evolution. ..
  8. pmc The autism-associated chromatin modifier CHD8 regulates other autism risk genes during human neurodevelopment
    Justin Cotney
    1 Department of Genetics, Yale School of Medicine, 333 Cedar Street, New Haven, Connecticut 06510, USA 2 Kavli Institute for Neuroscience, Yale School of Medicine, PO Box 208001, New Haven, Connecticut 06520, USA
    Nat Commun 6:6404. 2015
    ..Integration of CHD8-binding data into ASD risk models improves detection of risk genes. These results suggest loss of CHD8 contributes to ASD by perturbing an ancient gene regulatory network during human brain development. ..
  9. pmc RNA-Seq profiling of spinal cord motor neurons from a presymptomatic SOD1 ALS mouse
    Urmi Bandyopadhyay
    Department of Genetics, Yale University School of Medicine, New Haven, Connecticut, United States of America
    PLoS ONE 8:e53575. 2013
    ....
  10. doi request reprint Gene regulation and the origins of human biological uniqueness
    Samuel J Sholtis
    Department of Genetics, Yale University School of Medicine, New Haven, CT 06520, USA
    Trends Genet 26:110-8. 2010
    ..Although the evolutionary interpretation of these events is a subject of considerable debate, the technical and analytical means are now at hand to identify the set of evolutionary genetic events that shaped our species...
  11. pmc Coelacanth genome sequence reveals the evolutionary history of vertebrate genes
    James P Noonan
    Department of Genetics, Stanford University School of Medicine, Stanford, California 94305 5120, USA
    Genome Res 14:2397-405. 2004
    ..Our results indicate that coelacanth provides the ideal outgroup sequence against which tetrapod genomes can be measured. We therefore present L. menadoensis as a candidate for whole-genome sequencing...
  12. 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...
  13. pmc Origin and evolution of developmental enhancers in the mammalian neocortex
    Deena Emera
    Department of Genetics, Yale School of Medicine, New Haven, CT
    Proc Natl Acad Sci U S A 113:E2617-26. 2016
    ..Many proto-enhancers are likely lost, but some may serve as nucleation points for complex enhancers to evolve...
  14. pmc Coexpression networks implicate human midfetal deep cortical projection neurons in the pathogenesis of autism
    A Jeremy Willsey
    Department of Genetics, Yale School of Medicine, New Haven, CT 06510, USA Department of Psychiatry, University of California, San Francisco, San Francisco, CA 94143, USA
    Cell 155:997-1007. 2013
    ..This approach informs when, where, and in what cell types mutations in these specific genes may be productively studied to clarify ASD pathophysiology. ..
  15. pmc Genomic analysis of non-NF2 meningiomas reveals mutations in TRAF7, KLF4, AKT1, and SMO
    Victoria E Clark
    Department of Neurosurgery, Yale Program in Brain Tumor Research, Yale School of Medicine, New Haven, CT 06510, USA
    Science 339:1077-80. 2013
    ..Collectively, these findings identify distinct meningioma subtypes, suggesting avenues for targeted therapeutics...
  16. pmc Chromatin state signatures associated with tissue-specific gene expression and enhancer activity in the embryonic limb
    Justin Cotney
    Department of Genetics, Yale University School of Medicine, New Haven, CT 06520, USA
    Genome Res 22:1069-80. 2012
    ..Our results establish histone modification profiling as a tool for developmental enhancer discovery, and suggest that enhancers maintain an open chromatin state in multiple embryonic tissues independent of their activity level...
  17. pmc Gene conversion and the evolution of protocadherin gene cluster diversity
    James P Noonan
    Department of Genetics, Stanford University School of Medicine, Stanford, California 94305 5120, USA
    Genome Res 14:354-66. 2004
    ..We propose that the combination of lineage-specific duplication, restricted gene conversion, and adaptive variation in diversified ectodomains drives vertebrate protocadherin cluster evolution...