JASON RAFE MILLER

Summary

Affiliation: J. Craig Venter Institute
Country: USA

Publications

  1. ncbi Assembly algorithms for next-generation sequencing data
    Jason R Miller
    J Craig Venter Institute, Rockville, MD 20850 3343, USA
    Genomics 95:315-27. 2010
  2. ncbi A comparison of whole-genome shotgun-derived mouse chromosome 16 and the human genome
    Richard J Mural
    Celera Genomics, 45 West Gude Drive, Rockville, MD 20850, USA
    Science 296:1661-71. 2002
  3. ncbi Whole-genome shotgun assembly and comparison of human genome assemblies
    Sorin Istrail
    Applied Biosystems, 45 West Gude Drive, Rockville, MD 20850, USA
    Proc Natl Acad Sci U S A 101:1916-21. 2004
  4. ncbi Genome sequence of Aedes aegypti, a major arbovirus vector
    Vishvanath Nene
    Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD 20850, USA
    Science 316:1718-23. 2007
  5. ncbi New assembly, reannotation and analysis of the Entamoeba histolytica genome reveal new genomic features and protein content information
    Hernan A Lorenzi
    J Craig Venter Institute, Rockville, Maryland, United States of America
    PLoS Negl Trop Dis 4:e716. 2010
  6. ncbi A vertebrate case study of the quality of assemblies derived from next-generation sequences
    Liang Ye
    The Genome Center, Washington University School of Medicine, Campus Box 8501, 4444 Forest Park Avenue, St Louis, MO 63108, USA
    Genome Biol 12:R31. 2011
  7. ncbi An algorithm for automated closure during assembly
    Sergey Koren
    The J Craig Venter Institute, 9712 Medical Center Drive, Rockville MD 20850, USA
    BMC Bioinformatics 11:457. 2010
  8. ncbi Aggressive assembly of pyrosequencing reads with mates
    Jason R Miller
    The J Craig Venter Institute, 9712 Medical Center Drive, Rockville MD 20850, USA
    Bioinformatics 24:2818-24. 2008

Research Grants

  1. Continued Development of the Celera Whole Genome Shotgun Assembler
    JASON RAFE MILLER; Fiscal Year: 2010

Collaborators

Detail Information

Publications8

  1. ncbi Assembly algorithms for next-generation sequencing data
    Jason R Miller
    J Craig Venter Institute, Rockville, MD 20850 3343, USA
    Genomics 95:315-27. 2010
    ..More generally, it compares the two standard methods known as the de Bruijn graph approach and the overlap/layout/consensus approach to assembly...
  2. ncbi A comparison of whole-genome shotgun-derived mouse chromosome 16 and the human genome
    Richard J Mural
    Celera Genomics, 45 West Gude Drive, Rockville, MD 20850, USA
    Science 296:1661-71. 2002
    ....
  3. ncbi Whole-genome shotgun assembly and comparison of human genome assemblies
    Sorin Istrail
    Applied Biosystems, 45 West Gude Drive, Rockville, MD 20850, USA
    Proc Natl Acad Sci U S A 101:1916-21. 2004
    ..The Celera results provide more order and orientation, and the consortium sequence provides better coverage of exact and nearly exact repeats...
  4. ncbi Genome sequence of Aedes aegypti, a major arbovirus vector
    Vishvanath Nene
    Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD 20850, USA
    Science 316:1718-23. 2007
    ..An increase in genes encoding odorant binding, cytochrome P450, and cuticle domains relative to An. gambiae suggests that members of these protein families underpin some of the biological differences between the two mosquito species...
  5. ncbi New assembly, reannotation and analysis of the Entamoeba histolytica genome reveal new genomic features and protein content information
    Hernan A Lorenzi
    J Craig Venter Institute, Rockville, Maryland, United States of America
    PLoS Negl Trop Dis 4:e716. 2010
    ..For this reason, after five years from the initial submission of the Entamoeba histolytica draft genome publication, we have re-examined the original 23 Mb assembly and the annotation of the predicted genes...
  6. ncbi A vertebrate case study of the quality of assemblies derived from next-generation sequences
    Liang Ye
    The Genome Center, Washington University School of Medicine, Campus Box 8501, 4444 Forest Park Avenue, St Louis, MO 63108, USA
    Genome Biol 12:R31. 2011
    ..Nonetheless, these assemblies are sufficient for the identification of the majority of genes and can reveal novel sequences when compared to existing assembly references...
  7. ncbi An algorithm for automated closure during assembly
    Sergey Koren
    The J Craig Venter Institute, 9712 Medical Center Drive, Rockville MD 20850, USA
    BMC Bioinformatics 11:457. 2010
    ..Finishing reads may be incorporated by manual or automated means. One automated method uses targeted addition by local re-assembly of gap regions. An obvious alternative uses de novo assembly of all the reads...
  8. ncbi Aggressive assembly of pyrosequencing reads with mates
    Jason R Miller
    The J Craig Venter Institute, 9712 Medical Center Drive, Rockville MD 20850, USA
    Bioinformatics 24:2818-24. 2008
    ..This is true even of pyrosequencing mated and unmated read combinations. Without special modifications, assemblers tuned for homogeneous sequence data may perform poorly on hybrid data...

Research Grants2

  1. Continued Development of the Celera Whole Genome Shotgun Assembler
    JASON RAFE MILLER; Fiscal Year: 2010
    ..To enable the wider adoption of the Celera Assembler, the project will include documentation, training, end-user support, and support for integration with data sources and analysis tools. ..