J C Mullikin

Summary

Affiliation: Wellcome Trust Genome Campus
Country: UK

Publications

  1. pmc The phusion assembler
    James C Mullikin
    Informatics Department, The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
    Genome Res 13:81-90. 2003
  2. ncbi request reprint The DNA sequence and analysis of human chromosome 6
    A J Mungall
    The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
    Nature 425:805-11. 2003
  3. pmc The DNA sequence of the human X chromosome
    Mark T Ross
    The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
    Nature 434:325-37. 2005
  4. ncbi request reprint The DNA sequence and comparative analysis of human chromosome 20
    P Deloukas
    The Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
    Nature 414:865-71. 2001
  5. pmc SSAHA: a fast search method for large DNA databases
    Z Ning
    Informatics Division, The Sanger Centre, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
    Genome Res 11:1725-9. 2001
  6. ncbi request reprint Complex haplotypes, copy number polymorphisms and coding variation in two recently divergent mouse strains
    David J Adams
    The Wellcome Trust Sanger Institute, Hinxton, Cambs, CB10 1SA, UK
    Nat Genet 37:532-6. 2005
  7. pmc An initial strategy for the systematic identification of functional elements in the human genome by low-redundancy comparative sequencing
    Elliott H Margulies
    Genome Technology Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
    Proc Natl Acad Sci U S A 102:4795-800. 2005
  8. pmc The genome sequence of Caenorhabditis briggsae: a platform for comparative genomics
    Lincoln D Stein
    Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, USA
    PLoS Biol 1:E45. 2003
  9. pmc An intermediate grade of finished genomic sequence suitable for comparative analyses
    Robert W Blakesley
    NIH Intramural Sequencing Center, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
    Genome Res 14:2235-44. 2004
  10. ncbi request reprint Initial sequencing and comparative analysis of the mouse genome
    Robert H Waterston
    Genome Sequencing Center, Washington University School of Medicine, Campus Box 8501, 4444 Forest Park Avenue, St Louis, Missouri 63108, USA
    Nature 420:520-62. 2002

Detail Information

Publications27

  1. pmc The phusion assembler
    James C Mullikin
    Informatics Department, The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
    Genome Res 13:81-90. 2003
    ..The mouse data was generated by the Mouse Genome Sequencing Consortium. The C. briggsae sequence was generated at The Wellcome Trust Sanger Institute and the Genome Sequencing Center, Washington University School of Medicine...
  2. ncbi request reprint The DNA sequence and analysis of human chromosome 6
    A J Mungall
    The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
    Nature 425:805-11. 2003
    ..Within the essential immune loci of the major histocompatibility complex, we find HLA-B to be the most polymorphic gene on chromosome 6 and in the human genome...
  3. pmc The DNA sequence of the human X chromosome
    Mark T Ross
    The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
    Nature 434:325-37. 2005
    ..Of this number, 168 have been explained by mutations in 113 X-linked genes, which in many cases were characterized with the aid of the DNA sequence...
  4. ncbi request reprint The DNA sequence and comparative analysis of human chromosome 20
    P Deloukas
    The Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
    Nature 414:865-71. 2001
    ....
  5. pmc SSAHA: a fast search method for large DNA databases
    Z Ning
    Informatics Division, The Sanger Centre, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
    Genome Res 11:1725-9. 2001
    ..The SSAHA algorithm is used for high-throughput single nucleotide polymorphism (SNP) detection and very large scale sequence assembly. Also, it provides Web-based sequence search facilities for Ensembl projects...
  6. ncbi request reprint Complex haplotypes, copy number polymorphisms and coding variation in two recently divergent mouse strains
    David J Adams
    The Wellcome Trust Sanger Institute, Hinxton, Cambs, CB10 1SA, UK
    Nat Genet 37:532-6. 2005
    ..Collectively, these genomic changes denote the level and direction of allele fixation that has occurred during inbreeding and provide a basis for defining what makes these mouse strains unique...
  7. pmc An initial strategy for the systematic identification of functional elements in the human genome by low-redundancy comparative sequencing
    Elliott H Margulies
    Genome Technology Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
    Proc Natl Acad Sci U S A 102:4795-800. 2005
    ....
  8. pmc The genome sequence of Caenorhabditis briggsae: a platform for comparative genomics
    Lincoln D Stein
    Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, USA
    PLoS Biol 1:E45. 2003
    ..elegans genome. Based on similarity to C. briggsae, we found strong evidence for 1,300 new C. elegans genes. In addition, comparisons of the two genomes will help to understand the evolutionary forces that mold nematode genomes...
  9. pmc An intermediate grade of finished genomic sequence suitable for comparative analyses
    Robert W Blakesley
    NIH Intramural Sequencing Center, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
    Genome Res 14:2235-44. 2004
    ..Our experience to date demonstrates that comparative-grade sequence finishing represents a practical and affordable option for sequence refinement en route to comparative analyses...
  10. ncbi request reprint Initial sequencing and comparative analysis of the mouse genome
    Robert H Waterston
    Genome Sequencing Center, Washington University School of Medicine, Campus Box 8501, 4444 Forest Park Avenue, St Louis, Missouri 63108, USA
    Nature 420:520-62. 2002
    ....
  11. pmc Initial sequence and comparative analysis of the cat genome
    Joan U Pontius
    Laboratory of Genomic Diversity, SAIC Frederick, Inc, NCI Frederick, Frederick, Maryland 21702, USA
    Genome Res 17:1675-89. 2007
    ..9-fold) coverage mammal genome sequence...
  12. pmc Measurement of the human allele frequency spectrum demonstrates greater genetic drift in East Asians than in Europeans
    Alon Keinan
    Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
    Nat Genet 39:1251-5. 2007
    ..Our analysis shows that East Asian and northern European ancestors shared the same population bottleneck expanding out of Africa but that both also experienced more recent genetic drift, which was greater in East Asians...
  13. pmc A second generation human haplotype map of over 3.1 million SNPs
    Kelly A Frazer
    The Scripps Research Institute, 10550 North Torrey Pines Road MEM275, La Jolla, California 92037, USA
    Nature 449:851-61. 2007
    ..Finally, we demonstrate increased differentiation at non-synonymous, compared to synonymous, SNPs, resulting from systematic differences in the strength or efficacy of natural selection between populations...
  14. pmc Genome-wide detection and characterization of positive selection in human populations
    Pardis C Sabeti
    Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02139, USA
    Nature 449:913-8. 2007
    ....
  15. pmc Revisiting the mouse mitochondrial DNA sequence
    Maria Pilar Bayona-Bafaluy
    Departamento de Bioquimica y Biologia Molecular y Celular, Universidad de Zaragoza, Miguel Servet 177, Zaragoza 50013, Spain
    Nucleic Acids Res 31:5349-55. 2003
    ..Consequently, the mtDNA of the strain used for the mouse genome project (C57BL/6J) is proposed as the new standard for the mouse mtDNA sequence...
  16. pmc Construction, alignment and analysis of twelve framework physical maps that represent the ten genome types of the genus Oryza
    Hyeran Kim
    Arizona Genomics Institute, Department of Plant Sciences, University of Arizona, Tucson, Arizona 85721, USA
    Genome Biol 9:R45. 2008
    ..sativa ssp. japonica reference genome sequence. Over 932 Mb of end sequence was analyzed for repeats, simple sequence repeats, miRNA and single nucleotide variations, providing the most extensive analysis of Oryza sequence to date...
  17. pmc Mapping and sequencing of structural variation from eight human genomes
    Jeffrey M Kidd
    Department of Genome Sciences and Howard Hughes Medical Institute, University of Washington, Seattle, Washington 98195, USA
    Nature 453:56-64. 2008
    ..These data provide the first high-resolution sequence map of human structural variation--a standard for genotyping platforms and a prelude to future individual genome sequencing projects...
  18. pmc Functional constraint and small insertions and deletions in the ENCODE regions of the human genome
    Taane G Clark
    Department of Epidemiology and Public Health, Imperial College, Norfolk Place, London, W2 1PG, UK
    Genome Biol 8:R180. 2007
    ..We relate indels to known genomic annotation features and measures of evolutionary constraint...
  19. pmc Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project
    Ewan Birney
    Nature 447:799-816. 2007
    ..Together, these studies are defining a path for pursuit of a more comprehensive characterization of human genome function...
  20. pmc Analyses of deep mammalian sequence alignments and constraint predictions for 1% of the human genome
    Elliott H Margulies
    Genome Technology Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
    Genome Res 17:760-74. 2007
    ..Together, these findings demonstrate and quantify how many genomic functional elements await basic molecular characterization...
  21. pmc Completing the map of human genetic variation
    Evan E Eichler
    Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA
    Nature 447:161-5. 2007
  22. ncbi request reprint Conserved and novel Wnt clusters in the basal eumetazoan Nematostella vectensis
    James C Sullivan
    Department of Biology, Boston University, 5 Cummington Street, Boston, MA 02215, USA
    Dev Genes Evol 217:235-9. 2007
    ..Wnt6 and Wnt10 are not expressed in a spatially or temporally contiguous manner, and Wnt5 and Wnt7 are expressed in different germ layers...
  23. pmc StellaBase: the Nematostella vectensis Genomics Database
    James C Sullivan
    Department of Biology, Boston University, 5 Cummington Street, Boston, MA 02215, USA
    Nucleic Acids Res 34:D495-9. 2006
    ..In addition, StellaBase provides a framework for the integration of additional species-specific databases into CnidBase. StellaBase is available at http://www.stellabase.org...
  24. ncbi request reprint Human genome sequence variation and the influence of gene history, mutation and recombination
    David E Reich
    Whitehead Institute MIT Center for Genome Research, One Kendall Square, Cambridge, Massachusetts 02139, USA
    Nat Genet 32:135-42. 2002
    ....
  25. pmc Identifying gene regulatory elements by genome-wide recovery of DNase hypersensitive sites
    Gregory E Crawford
    Genome Technology Branch and National Institutes of Health Intramural Sequencing Center, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
    Proc Natl Acad Sci U S A 101:992-7. 2004
    ....
  26. ncbi request reprint The mosaic structure of variation in the laboratory mouse genome
    Claire M Wade
    Whitehead Institute for Biomedical Research and Whitehead MIT Center for Genome Research, 9 Cambridge Center, Cambridge, Massachusetts 02139, USA
    Nature 420:574-8. 2002
    ..These observations have important implications for the design and interpretation of positional cloning experiments...
  27. pmc Sequences, annotation and single nucleotide polymorphism of the major histocompatibility complex in the domestic cat
    Naoya Yuhki
    Laboratory of Genomic Diversity, National Cancer Institute at Frederick, Frederick, Maryland, United States of America
    PLoS ONE 3:e2674. 2008
    ..84 Mbp (0.00411 SNP per bp), which is 2.4 times higher rate than average heterozygous region in the WGS (0.0017 SNP per bp genome), and slightly higher than the SNP rate observed in human MHC (0.00337 SNP per bp)...