David B Jaffe

Summary

Affiliation: Massachusetts Institute of Technology
Country: USA

Publications

  1. 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
  2. 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
  3. pmc Quality scores and SNP detection in sequencing-by-synthesis systems
    William Brockman
    Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02141, USA
    Genome Res 18:763-70. 2008
  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. 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 Genome-scale DNA methylation maps of pluripotent and differentiated cells
    Alexander Meissner
    Whitehead Institute for Biomedical Research, 9 Cambridge Center, Cambridge, Massachusetts 02142, USA
    Nature 454:766-70. 2008
  7. 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
  8. 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
  9. pmc Solution hybrid selection with ultra-long oligonucleotides for massively parallel targeted sequencing
    Andreas Gnirke
    Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, Massachusetts 02142, USA
    Nat Biotechnol 27:182-9. 2009
  10. pmc Analyzing and minimizing PCR amplification bias in Illumina sequencing libraries
    Daniel Aird
    Genome Sequencing and Analysis Program, Broad Institute of MIT and Harvard, 320 Charles Street, Cambridge, MA 02141, USA
    Genome Biol 12:R18. 2011

Detail Information

Publications35

  1. 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)...
  2. 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...
  3. pmc Quality scores and SNP detection in sequencing-by-synthesis systems
    William Brockman
    Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02141, USA
    Genome Res 18:763-70. 2008
    ..We demonstrate good specificity in single reads, and excellent specificity (no false positives in 215 kb of genome) in high-coverage data...
  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. 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 Genome-scale DNA methylation maps of pluripotent and differentiated cells
    Alexander Meissner
    Whitehead Institute for Biomedical Research, 9 Cambridge Center, Cambridge, Massachusetts 02142, USA
    Nature 454:766-70. 2008
    ..More generally, the results establish reduced representation bisulphite sequencing as a powerful technology for epigenetic profiling of cell populations relevant to developmental biology, cancer and regenerative medicine...
  7. 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...
  8. 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...
  9. pmc Solution hybrid selection with ultra-long oligonucleotides for massively parallel targeted sequencing
    Andreas Gnirke
    Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, Massachusetts 02142, USA
    Nat Biotechnol 27:182-9. 2009
    ..One lane of Illumina sequence was sufficient to call high-confidence genotypes for 89% of the targeted exon space...
  10. pmc Analyzing and minimizing PCR amplification bias in Illumina sequencing libraries
    Daniel Aird
    Genome Sequencing and Analysis Program, Broad Institute of MIT and Harvard, 320 Charles Street, Cambridge, MA 02141, USA
    Genome Biol 12:R18. 2011
    ..Our improved protocol significantly reduces amplification bias and minimizes the previously severe effects of PCR instrument and temperature ramp rate...
  11. 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...
  12. pmc ALLPATHS: de novo assembly of whole-genome shotgun microreads
    Jonathan Butler
    Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02141, USA
    Genome Res 18:810-20. 2008
    ..We describe a general method for genome assembly that can be applied to all types of DNA sequence data, not only short read data, but also conventional sequence reads...
  13. 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...
  14. 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...
  15. 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...
  16. pmc Paired-end sequencing of Fosmid libraries by Illumina
    Louise J S Williams
    Broad Institute of MIT and Harvard, Cambridge, MA 02141, USA
    Genome Res 22:2241-9. 2012
    ..Our Fosill-powered assembly of the mouse genome has an N50 scaffold length of 17.0 Mb, rivaling the connectivity (16.9 Mb) of the Sanger-sequencing based draft assembly...
  17. pmc A scalable, fully automated process for construction of sequence-ready barcoded libraries for 454
    Niall J Lennon
    Genome Sequencing Platform, Broad Institute of MIT and Harvard, 320 Charles St, Cambridge, MA 02141, USA
    Genome Biol 11:R15. 2010
    ..Using this methodology, one technician can create 96 sequence-ready 454 libraries in 2 days, a dramatic improvement over the standard method...
  18. pmc Integrative analysis of the melanoma transcriptome
    Michael F Berger
    The Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
    Genome Res 20:413-27. 2010
    ..Taken together, these results may indicate new avenues for target discovery in melanoma, while also providing a template for large-scale transcriptome studies across many tumor types...
  19. 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)...
  20. pmc High-resolution mapping of copy-number alterations with massively parallel sequencing
    Derek Y Chiang
    Broad Institute, Massachusetts Institute of Technology, 7 Cambridge Center, Cambridge, MA 02142, USA
    Nat Methods 6:99-103. 2009
    ....
  21. pmc Sensitive, specific polymorphism discovery in bacteria using massively parallel sequencing
    Chad Nusbaum
    Broad Institute of Massachusetts Institute of Technology and Harvard University, 320 Charles Street, Cambridge, MA 02141, USA
    Nat Methods 6:67-9. 2009
    ..VAAL also pinpointed a single mutation between Vibrio cholerae genomes, identifying an antibiotic's site of action by identifying sequence differences between drug-sensitive strains and drug-resistant derivatives...
  22. 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...
  23. pmc Genome-wide maps of chromatin state in pluripotent and lineage-committed cells
    Tarjei S Mikkelsen
    Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, USA
    Nature 448:553-60. 2007
    ..This study provides a framework for the application of comprehensive chromatin profiling towards characterization of diverse mammalian cell populations...
  24. pmc Assembly of polymorphic genomes: algorithms and application to Ciona savignyi
    Jade P Vinson
    Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02141 2023, USA
    Genome Res 15:1127-35. 2005
    ..Our method represented loci in a single copy more reliably and achieved greater contiguity than a conventional whole-genome assembly method...
  25. 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...
  26. 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
    ....
  27. 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
    ....
  28. ncbi request reprint Facilitating genome navigation: survey sequencing and dense radiation-hybrid gene mapping
    Christophe Hitte
    CNRS, UMR 6061, Genetique et Developpement, Faculte de Medecine, Rennes, France
    Nat Rev Genet 6:643-8. 2005
    ....
  29. 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...
  30. 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...
  31. 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...
  32. 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...
  33. ncbi request reprint Evolution of genes and genomes on the Drosophila phylogeny
    Andrew G Clark
    Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853, USA
    Nature 450:203-18. 2007
    ..These may prove to underlie differences in the ecology and behaviour of these diverse species...
  34. ncbi request reprint Insights from the genome of the biotrophic fungal plant pathogen Ustilago maydis
    Jörg Kämper
    Department of Organismic Interactions, Max Planck Institute for Terrestrial Microbiology, Karl von Frisch Strasse, D 35043 Marburg, Germany
    Nature 444:97-101. 2006
    ..Genomic analysis is, similarly, likely to open up new avenues for the discovery of virulence determinants in other pathogens...
  35. ncbi request reprint A genome-wide map of diversity in Plasmodium falciparum
    Sarah K Volkman
    Department of Immunology and Infectious Diseases, Harvard School of Public Health, Boston, Massachusetts 02115, USA
    Nat Genet 39:113-9. 2007
    ..We provide an initial map of genetic diversity in P. falciparum and demonstrate its potential utility in identifying genes subject to recent natural selection and in understanding the population genetics of this parasite...