Research Topics
Genomes and Genes | David B JaffeSummaryAffiliation: Massachusetts Institute of Technology Country: USA Publications
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Publications
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)...
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...- Quality scores and SNP detection in sequencing-by-synthesis systemsWilliam 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... - Finished bacterial genomes from shotgun sequence dataFilipe 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... - Genome-scale DNA methylation maps of pluripotent and differentiated cellsAlexander 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... - 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... - Solution hybrid selection with ultra-long oligonucleotides for massively parallel targeted sequencingAndreas 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... - High-quality draft assemblies of mammalian genomes from massively parallel sequence dataSante 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... - Analyzing and minimizing PCR amplification bias in Illumina sequencing librariesDaniel 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... - 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... - ARACHNE: a whole-genome shotgun assemblerSerafim 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... - ALLPATHS: de novo assembly of whole-genome shotgun microreadsJonathan 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... - 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... - 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... - Assisted assembly: how to improve a de novo genome assembly by using related speciesSante 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... - Paired-end sequencing of Fosmid libraries by IlluminaLouise 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... - A scalable, fully automated process for construction of sequence-ready barcoded libraries for 454Niall 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... - Integrative analysis of the melanoma transcriptomeMichael 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... - ALLPATHS 2: small genomes assembled accurately and with high continuity from short paired readsIain 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)... - High-resolution mapping of copy-number alterations with massively parallel sequencingDerek Y Chiang
Broad Institute, Massachusetts Institute of Technology, 7 Cambridge Center, Cambridge, MA 02142, USA
Nat Methods 6:99-103. 2009.... - Sensitive, specific polymorphism discovery in bacteria using massively parallel sequencingChad 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... - Genome-wide maps of chromatin state in pluripotent and lineage-committed cellsTarjei 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... - Assembly of polymorphic genomes: algorithms and application to Ciona savignyiJade 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... - 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... 
Mutations causing medullary cystic kidney disease type 1 lie in a large VNTR in MUC1 missed by massively parallel sequencingAndrew 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...- 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.... - An initial strategy for the systematic identification of functional elements in the human genome by low-redundancy comparative sequencingElliott 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.... - Facilitating genome navigation: survey sequencing and dense radiation-hybrid gene mappingChristophe Hitte
CNRS, UMR 6061, , , Rennes, France
Nat Rev Genet 6:643-8. 2005.... - 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... - 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... - Analyses of deep mammalian sequence alignments and constraint predictions for 1% of the human genomeElliott 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... - 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... - Evolution of genes and genomes on the Drosophila phylogenyAndrew 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... - Insights from the genome of the biotrophic fungal plant pathogen Ustilago maydisJörg 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... - A genome-wide map of diversity in Plasmodium falciparumSarah 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...