Genomes and Genes
Affiliation: Massachusetts Institute of Technology
- 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...
- 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)...
- 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...
- 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...
- 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...
- 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...
- Genetic evidence for complex speciation of humans and chimpanzeesNick 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...
- 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...
- De novo assembly of highly diverse viral populationsXiao Yang
The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
BMC Genomics 13:475. 2012....
- The difficulty of avoiding false positives in genome scans for natural selectionSwapan 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...
- The genome sequence of the filamentous fungus Neurospora crassaJames 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...
- 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...
- 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...
- The Fusarium graminearum genome reveals a link between localized polymorphism and pathogen specializationChristina 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...
- 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)...
- 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...
- 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...
- A direct characterization of human mutation based on microsatellitesJames 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...