- Mutation discovery in mice by whole exome sequencing
The Jackson Laboratory, 600 Main St, Bar Harbor, ME 04609, USA
Genome Biol 12:R86. 2011
..We found strong candidate mutations for the majority of mutant exomes sequenced, including new models of orofacial clefting, urogenital dysmorphology, kyphosis and autoimmune hepatitis...
- Comparison of buccal and blood-derived canine DNA, either native or whole genome amplified, for array-based genome-wide association studies
Department of Animal Science, University of California, Davis, CA 95616, USA
BMC Res Notes 4:226. 2011
- A high-resolution map of human evolutionary constraint using 29 mammals
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...
- Genome sequence, comparative analysis and haplotype structure of the domestic dog
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 genome of the green anole lizard and a comparative analysis with birds and mammals
Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
Nature 477:587-91. 2011
..Comparative gene analysis shows that amniote egg proteins have evolved significantly more rapidly than other proteins. An anole phylogeny resolves basal branches to illuminate the history of their repeated adaptive radiations...
- 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)...
- Systematic discovery of regulatory motifs in human promoters and 3' UTRs by comparison of several mammals
Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02141, USA
Nature 434:338-45. 2005
..The overall results provide a systematic view of gene regulation in the human, which will be refined as additional mammalian genomes become available...
- Genome-wide synteny through highly sensitive sequence alignment: Satsuma
Manfred G Grabherr
Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, MA 02142, USA
Bioinformatics 26:1145-51. 2010
..From an engineering perspective, the problem here is to provide maximum sensitivity (to find all there is to find), specificity (to only find real homology) and speed (to accommodate the billions of base pairs of vertebrate genomes)...
- Genomic maps and comparative analysis of histone modifications in human and mouse
Bradley E Bernstein
Howard Hughes Medical Institute, Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, MA 02138, USA
Cell 120:169-81. 2005
..This suggests that the DNA elements that direct the methylation represent only a small fraction of the region or lie at some distance from the site...
- Systematic discovery of regulatory motifs in conserved regions of the human genome, including thousands of CTCF insulator sites
Broad Institute of MIT and Harvard, Massachusetts Institute of Technology and Harvard Medical School, Cambridge, MA 02142, USA
Proc Natl Acad Sci U S A 104:7145-50. 2007
..These sites may thus partition the human genome into domains of expression...
- 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...
- Human immunodeficiency virus type 1 V1-to-V5 envelope variants from the chronic phase of infection use CCR5 and fuse more efficiently than those from early after infection
Department of Medicine, Brigham and Women s Hospital, Harvard Medical School, Cambridge, Massachusetts 02139, USA
J Virol 83:9694-708. 2009
..Thus, envelope modifications over time within a host potentially enhance replication capacity...
- Full-length transcriptome assembly from RNA-Seq data without a reference genome
Manfred G Grabherr
Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts, USA
Nat Biotechnol 29:644-52. 2011
..Our approach provides a unified solution for transcriptome reconstruction in any sample, especially in the absence of a reference genome...
- Distinguishing protein-coding and noncoding genes in the human genome
Broad Institute of Massachusetts Institute of Technology and Harvard, 7 Cambridge Center, Cambridge, MA 02142, USA
Proc Natl Acad Sci U S A 104:19428-33. 2007
..It also provides a principled methodology for evaluating future proposed additions to the human gene catalog. Finally, the results indicate that there has been relatively little true innovation in mammalian protein-coding genes...
- Leader of the pack: gene mapping in dogs and other model organisms
Elinor K Karlsson
Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge Center, 02142, USA
Nat Rev Genet 9:713-25. 2008
..Here, we review the different trait-mapping strategies, some key biological findings emerging from recent studies and the implications for human health. We also discuss the development of similar resources for other vertebrate organisms...
- Efficient mapping of mendelian traits in dogs through genome-wide association
Elinor 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
- Heart development in fibronectin-null mice is governed by a genetic modifier on chromosome four
Howard Hughes Medical Institute, Center for Cancer Research, Department of Biology, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
Mech Dev 124:551-8. 2007
..Identification of the modifier would significantly enhance our understanding of the molecular underpinning of heart development and disease...
- Assisted assembly: how to improve a de novo genome assembly by using related species
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...
- Human immunodeficiency virus type 1 V1-V2 envelope loop sequences expand and add glycosylation sites over the course of infection, and these modifications affect antibody neutralization sensitivity
Department of Medicine, Brigham and Women's Hospital, Cambridge, Massachusetts 02139, USA
J Virol 80:9586-98. 2006
..These studies suggest that changes within the V1-V2 envelope domains over the course of an infection influence sensitivity to autologous neutralizing antibodies and may also impact host receptor/coreceptor interactions...