Michael C Zody

Summary

Affiliation: Massachusetts Institute of Technology
Country: USA

Publications

  1. pmc DNA sequence of human chromosome 17 and analysis of rearrangement in the human lineage
    Michael C Zody
    Broad Institute of MIT and Harvard, 7 Cambridge Center, Massachusetts 02142, USA
    Nature 440:1045-9. 2006
  2. ncbi request reprint Genome of the marsupial Monodelphis domestica reveals innovation in non-coding sequences
    Tarjei S Mikkelsen
    Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, Massachusetts 02142, USA
    Nature 447:167-77. 2007
  3. ncbi request reprint Analysis of the DNA sequence and duplication history of human chromosome 15
    Michael C Zody
    Broad Institute of MIT and Harvard, 320 Charles Street, Cambridge, Massachusetts 02141, USA
    Nature 440:671-5. 2006
  4. ncbi request reprint Genome sequence, comparative analysis and haplotype structure of the domestic dog
    Kerstin Lindblad-Toh
    Broad Institute of Harvard and MIT, 320 Charles Street, Cambridge, Massachusetts 02141, USA
    Nature 438:803-19. 2005
  5. ncbi request reprint DNA sequence and analysis of human chromosome 18
    Chad Nusbaum
    Broad Institute of MIT and Harvard, 320 Charles Street, Cambridge, Massachusetts 02141, USA
    Nature 437:551-5. 2005
  6. pmc Highly sensitive and specific detection of rare variants in mixed viral populations from massively parallel sequence data
    Alexander R Macalalad
    Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
    PLoS Comput Biol 8:e1002417. 2012
  7. ncbi request reprint DNA sequence and analysis of human chromosome 8
    Chad Nusbaum
    Broad Institute of MIT and Harvard, 320 Charles St, Cambridge, Massachusetts 02141, USA
    Nature 439:331-5. 2006
  8. pmc De novo assembly of highly diverse viral populations
    Xiao Yang
    The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
    BMC Genomics 13:475. 2012
  9. pmc A high-resolution map of human evolutionary constraint using 29 mammals
    Kerstin Lindblad-Toh
    Broad Institute of Harvard and Massachusetts Institute of Technology, 7 Cambridge Center, Cambridge, Massachusetts 02142, USA
    Nature 478:476-82. 2011
  10. ncbi request reprint Efficient mapping of mendelian traits in dogs through genome-wide association
    Elinor K Karlsson
    Broad Institute of Harvard and Massachusetts Institute of Technology MIT, 7 Cambridge Center, Cambridge, Massachusetts 02142, USA
    Nat Genet 39:1321-8. 2007

Detail Information

Publications29

  1. pmc DNA sequence of human chromosome 17 and analysis of rearrangement in the human lineage
    Michael C Zody
    Broad Institute of MIT and Harvard, 7 Cambridge Center, Massachusetts 02142, USA
    Nature 440:1045-9. 2006
    ..Examination of the main classes of duplicated segments provides insight into the dynamics underlying expansion of chromosome-specific, low-copy repeats in the human genome...
  2. ncbi request reprint Genome of the marsupial Monodelphis domestica reveals innovation in non-coding sequences
    Tarjei S Mikkelsen
    Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, Massachusetts 02142, USA
    Nature 447:167-77. 2007
    ..A substantial proportion of these eutherian-specific CNEs arose from sequence inserted by transposable elements, pointing to transposons as a major creative force in the evolution of mammalian gene regulation...
  3. ncbi request reprint Analysis of the DNA sequence and duplication history of human chromosome 15
    Michael C Zody
    Broad Institute of MIT and Harvard, 320 Charles Street, Cambridge, Massachusetts 02141, USA
    Nature 440:671-5. 2006
    ..Finally, we demonstrate that some remaining gaps in the genome sequence are probably due to structural polymorphisms between haplotypes; this may explain a significant fraction of the gaps remaining in the human genome...
  4. ncbi request reprint Genome sequence, comparative analysis and haplotype structure of the domestic dog
    Kerstin Lindblad-Toh
    Broad Institute of Harvard and MIT, 320 Charles Street, Cambridge, Massachusetts 02141, USA
    Nature 438:803-19. 2005
    ..The current SNP map now makes it possible for genome-wide association studies to identify genes responsible for diseases and traits, with important consequences for human and companion animal health...
  5. ncbi request reprint DNA sequence and analysis of human chromosome 18
    Chad Nusbaum
    Broad Institute of MIT and Harvard, 320 Charles Street, Cambridge, Massachusetts 02141, USA
    Nature 437:551-5. 2005
    ..This has important implications for the nature and roles of non-protein-coding sequence elements...
  6. pmc Highly sensitive and specific detection of rare variants in mixed viral populations from massively parallel sequence data
    Alexander R Macalalad
    Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
    PLoS Comput Biol 8:e1002417. 2012
    ..The high sensitivity and specificity of V-Phaser enables identifying and tracking changes in low frequency variants in mixed populations such as RNA viruses...
  7. ncbi request reprint DNA sequence and analysis of human chromosome 8
    Chad Nusbaum
    Broad Institute of MIT and Harvard, 320 Charles St, Cambridge, Massachusetts 02141, USA
    Nature 439:331-5. 2006
    ..The data from chromosome 8 should allow a better understanding of both normal and disease biology and genome evolution...
  8. pmc De novo assembly of highly diverse viral populations
    Xiao Yang
    The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
    BMC Genomics 13:475. 2012
    ....
  9. pmc A high-resolution map of human evolutionary constraint using 29 mammals
    Kerstin Lindblad-Toh
    Broad Institute of Harvard and Massachusetts Institute of Technology, 7 Cambridge Center, Cambridge, Massachusetts 02142, USA
    Nature 478:476-82. 2011
    ..Overlap with disease-associated variants indicates that our findings will be relevant for studies of human biology, health and disease...
  10. ncbi request reprint Efficient mapping of mendelian traits in dogs through genome-wide association
    Elinor K Karlsson
    Broad Institute of Harvard and Massachusetts Institute of Technology MIT, 7 Cambridge Center, Cambridge, Massachusetts 02142, USA
    Nat Genet 39:1321-8. 2007
    ....
  11. pmc Identifying novel constrained elements by exploiting biased substitution patterns
    Manuel Garber
    Department of Biology, Broad Institute of MIT and Harvard, 7 Cambridge Center, MIT, Cambridge, MA 02142, USA
    Bioinformatics 25:i54-62. 2009
    ..Many methods have been developed to identify conserved sequences across species; however, existing methods only model conservation as a decrease in the rate of mutation and have ignored selection acting on the pattern of mutations...
  12. pmc V-Phaser 2: variant inference for viral populations
    Xiao Yang
    Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, MA 02142 USA
    BMC Genomics 14:674. 2013
    ..However, differentiation of true low frequency variants from sequencing errors remains challenging...
  13. pmc Complete viral RNA genome sequencing of ultra-low copy samples by sequence-independent amplification
    Christine M Malboeuf
    Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
    Nucleic Acids Res 41:e13. 2013
    ....
  14. pmc Closing gaps in the human genome using sequencing by synthesis
    Manuel Garber
    Genome Sequencing and Analysis Program, Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, MA 02142, USA
    Genome Biol 10:R60. 2009
    ..We present an approach for closing these gaps using 454 sequencing. As a proof of principle, we closed all three remaining non-structural gaps in chromosome 15...
  15. pmc Evolutionary toggling of the MAPT 17q21.31 inversion region
    Michael C Zody
    Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, Massachusetts 02142, USA
    Nat Genet 40:1076-83. 2008
    ..We show that the H2 architecture has evolved more extensive sequence homology, perhaps explaining its tendency to undergo microdeletion associated with mental retardation in European populations...
  16. ncbi request reprint Genome sequence and analysis of the Irish potato famine pathogen Phytophthora infestans
    Brian J Haas
    Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02141, USA
    Nature 461:393-8. 2009
    ..infestans genome. This probably plays a crucial part in the rapid adaptability of the pathogen to host plants and underpins its evolutionary potential...
  17. pmc Whole-genome sequence assembly for mammalian genomes: Arachne 2
    David B Jaffe
    Whitehead Institute MIT Center for Genome Research, Cambridge, Massachusetts 02141, USA
    Genome Res 13:91-6. 2003
    ..The outcome of this mouse assembly and its analysis are described in (Mouse Genome Sequencing Consortium 2002)...
  18. pmc Whole genome pyrosequencing of rare hepatitis C virus genotypes enhances subtype classification and identification of naturally occurring drug resistance variants
    Ruchi M Newman
    Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, MA 02142, USA
    J Infect Dis 208:17-31. 2013
    ..Unfortunately, the paucity of genetic data from many of these subtypes makes time-consuming primer walking the limiting step for sequencing understudied subtypes...
  19. pmc Mutations causing medullary cystic kidney disease type 1 lie in a large VNTR in MUC1 missed by massively parallel sequencing
    Andrew Kirby
    Broad Institute of Harvard and MIT, Cambridge, Massachusetts, USA
    Nat Genet 45:299-303. 2013
    ..These results provide a cautionary tale about the challenges in identifying the genes responsible for mendelian, let alone more complex, disorders through massively parallel sequencing...
  20. pmc ATHLATES: accurate typing of human leukocyte antigen through exome sequencing
    Chang Liu
    Department of Pathology and Immunology, Washington University School of Medicine, St Louis, MO 63110, USA
    Nucleic Acids Res 41:e142. 2013
    ..This novel approach should be broadly applicable to research and clinical laboratories. ..
  21. pmc Whole genome deep sequencing of HIV-1 reveals the impact of early minor variants upon immune recognition during acute infection
    Matthew R Henn
    Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
    PLoS Pathog 8:e1002529. 2012
    ....
  22. ncbi request reprint Identification of mixups among DNA sequencing plates
    Nikola Stojanovic
    Whitehead Institute, Center for Genome Research, 320 Charles Street, Cambridge MA 02141, USA
    Bioinformatics 18:1418-26. 2002
    ..The sequencing templates or sequence data generated for an assembly may become contaminated with reagents or sequences from another project, resulting in poorer quality and inaccurate assemblies...
  23. 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...
  24. ncbi request reprint Human chromosome 11 DNA sequence and analysis including novel gene identification
    Todd D Taylor
    RIKEN Genomic Sciences Center, 1 7 22 Suehiro cho, Tsurumi ku, Yokohama, Kanagawa 230 0045, Japan
    Nature 440:497-500. 2006
    ..5 million base pairs representing 99.8% coverage of the euchromatic sequence--provide scientists with a solid foundation for understanding the genetic basis of these disorders and other biological phenomena...
  25. ncbi request reprint Common deletion polymorphisms in the human genome
    Steven A McCarroll
    Department of Molecular Biology, Massachusetts General Hospital, 55 Fruit Street, Boston, Massachusetts 02114, USA
    Nat Genet 38:86-92. 2006
    ....
  26. pmc Why do human diversity levels vary at a megabase scale?
    Ines Hellmann
    Max Planck Institute for Evolutionary Anthropology, D 04103 Leipzig, Germany
    Genome Res 15:1222-31. 2005
    ..Because there are indications that recombination rates may have changed rapidly during human evolution, we favor the latter explanation...
  27. ncbi request reprint Genome duplication in the teleost fish Tetraodon nigroviridis reveals the early vertebrate proto-karyotype
    Olivier Jaillon
    UMR 8030 Genoscope, CNRS and Université d Evry, 2 rue Gaston Cremieux, 91057 Evry Cedex, France
    Nature 431:946-57. 2004
    ....
  28. 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
    ....
  29. 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...