Sante Gnerre

Summary

Affiliation: Massachusetts Institute of Technology
Country: USA

Publications

  1. pmc Assisted assembly: how to improve a de novo genome assembly by using related species
    Sante Gnerre
    Broad Institute of Harvard and MIT, Cambridge Center, Cambridge, Massachusetts 02142, USA
    Genome Biol 10:R88. 2009
  2. 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
  3. 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
  4. pmc High-quality draft assemblies of mammalian genomes from massively parallel sequence data
    Sante Gnerre
    Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
    Proc Natl Acad Sci U S A 108:1513-8. 2011
  5. pmc Finished bacterial genomes from shotgun sequence data
    Filipe J Ribeiro
    Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
    Genome Res 22:2270-7. 2012
  6. 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
  7. ncbi request reprint Genetic evidence for complex speciation of humans and chimpanzees
    Nick Patterson
    Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, Massachusetts 02142, USA
    Nature 441:1103-8. 2006
  8. 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
  9. 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
  10. pmc The difficulty of avoiding false positives in genome scans for natural selection
    Swapan Mallick
    Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
    Genome Res 19:922-33. 2009

Detail Information

Publications18

  1. pmc Assisted assembly: how to improve a de novo genome assembly by using related species
    Sante Gnerre
    Broad Institute of Harvard and MIT, Cambridge Center, Cambridge, Massachusetts 02142, USA
    Genome Biol 10:R88. 2009
    ..We show that the information provided by aligning the whole-genome shotgun reads of the target against a reference genome can be used to substantially improve the quality of the resulting assembly...
  2. 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)...
  3. 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...
  4. pmc High-quality draft assemblies of mammalian genomes from massively parallel sequence data
    Sante Gnerre
    Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
    Proc Natl Acad Sci U S A 108:1513-8. 2011
    ..The ALLPATHS-LG program is available at http://www.broadinstitute.org/science/programs/genome-biology/crd...
  5. pmc Finished bacterial genomes from shotgun sequence data
    Filipe J Ribeiro
    Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
    Genome Res 22:2270-7. 2012
    ..Cost and time requirements are thus dramatically reduced...
  6. 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...
  7. ncbi request reprint Genetic evidence for complex speciation of humans and chimpanzees
    Nick Patterson
    Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, Massachusetts 02142, USA
    Nature 441:1103-8. 2006
    ..These unexpected features would be explained if the human and chimpanzee lineages initially diverged, then later exchanged genes before separating permanently...
  8. 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...
  9. 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
    ....
  10. pmc The difficulty of avoiding false positives in genome scans for natural selection
    Swapan Mallick
    Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
    Genome Res 19:922-33. 2009
    ..Inaccuracies in the genome sequence at even a tiny fraction of genes can produce false-positive signals, which make it difficult to identify loci that have genuinely been targets of selection...
  11. ncbi request reprint The genome sequence of the filamentous fungus Neurospora crassa
    James E Galagan
    Whitehead Institute Center for Genome Research, 320 Charles Street, Cambridge, Massachusetts 02141, USA
    Nature 422:859-68. 2003
    ..Genome analysis suggests that RIP has had a profound impact on genome evolution, greatly slowing the creation of new genes through genomic duplication and resulting in a genome with an unusually low proportion of closely related genes...
  12. doi 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...
  13. 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...
  14. ncbi request reprint The Fusarium graminearum genome reveals a link between localized polymorphism and pathogen specialization
    Christina A Cuomo
    Broad Institute of the Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA
    Science 317:1400-2. 2007
    ..These regions of genome innovation may result from selection due to interactions of F. graminearum with its plant hosts...
  15. pmc ALLPATHS 2: small genomes assembled accurately and with high continuity from short paired reads
    Iain MacCallum
    Broad Institute of MIT and Harvard, Charles Street, Cambridge, MA 02141, USA
    Genome Biol 10:R103. 2009
    ..Velvet and EULER-SR were less accurate. For example, for Escherichia coli, the fraction of 10-kb stretches that were perfect was 99.8% (ALLPATHS2), 68.7% (Velvet), and 42.1% (EULER-SR)...
  16. 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...
  17. pmc ARACHNE: a whole-genome shotgun assembler
    Serafim Batzoglou
    Laboratory for Computer Science, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
    Genome Res 12:177-89. 2002
    ..The assembly was rapid: the Drosophila assembly required only 21 hours on a single 667 MHz processor and used 8.4 Gb of memory...
  18. pmc A direct characterization of human mutation based on microsatellites
    James X Sun
    Division of Health Sciences and Technology, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
    Nat Genet 44:1161-5. 2012
    ..We infer that the sequence mutation rate is 1.4-2.3×10(-8) mutations per base pair per generation (90% credible interval) and that human-chimpanzee speciation occurred 3.7-6.6 million years ago...