Research Topics
Genomes and Genes
| Michael C ZodySummaryAffiliation: Massachusetts Institute of Technology Country: USA Publications
| Collaborators
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Detail Information
Publications
DNA sequence of human chromosome 17 and analysis of rearrangement in the human lineageMichael 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...
Genome of the marsupial Monodelphis domestica reveals innovation in non-coding sequencesTarjei 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...- Analysis of the DNA sequence and duplication history of human chromosome 15Michael 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... - DNA sequence and analysis of human chromosome 18Chad 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... - Highly sensitive and specific detection of rare variants in mixed viral populations from massively parallel sequence dataAlexander 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... - DNA sequence and analysis of human chromosome 8Chad 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... - Genome sequence, comparative analysis and haplotype structure of the domestic dogKerstin 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... - A high-resolution map of human evolutionary constraint using 29 mammalsKerstin 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... - Identifying novel constrained elements by exploiting biased substitution patternsManuel 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... - Efficient mapping of mendelian traits in dogs through genome-wide associationElinor 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.... - Closing gaps in the human genome using sequencing by synthesisManuel 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... 
Genome sequence and analysis of the Irish potato famine pathogen Phytophthora infestansBrian 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...- Evolutionary toggling of the MAPT 17q21.31 inversion regionMichael 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... - Whole-genome sequence assembly for mammalian genomes: Arachne 2David 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)... - Complete viral RNA genome sequencing of ultra-low copy samples by sequence-independent amplificationChristine M Malboeuf
Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
Nucleic Acids Res 41:e13. 2013.... - Whole genome deep sequencing of HIV-1 reveals the impact of early minor variants upon immune recognition during acute infectionMatthew R Henn
Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
PLoS Pathog 8:e1002529. 2012.... - Identification of mixups among DNA sequencing platesNikola Stojanovic
Whitehead Institute, Center for Genome Research, 320 Charles Street, Cambridge MA 02141, USA
Bioinformatics 18:1418-26. 2002..While these methods have been designed for use in a high-throughput DNA sequencing environment processing thousands of clones, they can be applied in any situation where distinct sequencing projects are performed at redundant coverage... - The mosaic structure of variation in the laboratory mouse genomeClaire 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... - Initial sequencing and comparative analysis of the mouse genomeRobert 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.... - Genome duplication in the teleost fish Tetraodon nigroviridis reveals the early vertebrate proto-karyotypeOlivier Jaillon
UMR 8030 Genoscope, , , 91057 Evry Cedex, France
Nature 431:946-57. 2004.... - 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... - Common deletion polymorphisms in the human genomeSteven A McCarroll
Department of Molecular Biology, Massachusetts General Hospital, 55 Fruit Street, Boston, Massachusetts 02114, USA
Nat Genet 38:86-92. 2006.... - Human chromosome 11 DNA sequence and analysis including novel gene identificationTodd 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... - Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot projectEwan Birney
Nature 447:799-816. 2007..Together, these studies are defining a path for pursuit of a more comprehensive characterization of human genome function...