Genomes and Genes
Affiliation: Massachusetts Institute of Technology
- Genome reannotation of the lizard Anolis carolinensis based on 14 adult and embryonic deep transcriptomesWalter L Eckalbar
School of Life Sciences, Arizona State University, PO Box 874501, Tempe, AZ, 85287 4501, USA
BMC Genomics 14:49. 2013..A second generation annotation based on tissue-specific transcriptomes would provide a valuable resource for molecular studies...
- 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...
- 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 dog and rat olfactory receptor repertoiresPascale Quignon
UMR 6061, Génétique et Développement CNRS Université de Rennes 1, 35043 Rennes Cedex, France
Genome Biol 6:R83. 2005..Previous analyses have shown that the olfactory receptors (ORs) that specifically bind odorant molecules are encoded by the largest gene family sequenced in mammals so far...
- Analysis of a set of Australian northern brown bandicoot expressed sequence tags with comparison to the genome sequence of the South American grey short tailed opossumMichelle L Baker
Center for Evolutionary and Theoretical Immunology, Department of Biology, University of New Mexico, Albuquerque, NM 87131, USA
BMC Genomics 8:50. 2007....
- Comparative physical maps derived from BAC end sequences of tilapia (Oreochromis niloticus)Lucile Soler
CIRAD PERSYST, Aquaculture Research Unit, TA B 20 A, Campus International de Baillarguet, 34398 Montpellier Cedex 5, France
BMC Genomics 11:636. 2010..Here we analyze BAC end-sequences to develop comparative physical maps, and estimate the number of genome rearrangements, between tilapia and other model fish species...
- High resolution mapping and positional cloning of ENU-induced mutations in the Rw region of mouse chromosome 5Yung Hao Ching
Department of Biomedical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, New York 14853, USA
BMC Genet 11:106. 2010..Previously, a large scale ENU mutagenesis screen was conducted to query the functional content of a ~50 Mb region of the mouse genome on proximal Chr 5. The majority of phenotypic mutants recovered were embryonic lethals...
- 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...
- Systematic discovery of regulatory motifs in human promoters and 3' UTRs by comparison of several mammalsXiaohui Xie
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: SatsumaManfred 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)...
- Efficient mapping of mendelian traits in dogs through genome-wide associationElinor 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....
- The genome of the green anole lizard and a comparative analysis with birds and mammalsJessica Alföldi
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 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)...
- Systematic discovery of regulatory motifs in conserved regions of the human genome, including thousands of CTCF insulator sitesXiaohui Xie
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...
- The mosaic structure of variation in the laboratory mouse genomeClaire M Wade
Whitehead Institute for Biomedical Research and Whitehead MIT Center for Genome Research, 9 Cambridge Center, Cambridge, Massachusetts 02139, USA
Nature 420:574-8. 2002..These observations have important implications for the design and interpretation of positional cloning experiments...
- Distinguishing protein-coding and noncoding genes in the human genomeMichele Clamp
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...
- Genomic maps and comparative analysis of histone modifications in human and mouseBradley 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...
- 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...
- 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...
- The Naked Mole Rat Genome Resource: facilitating analyses of cancer and longevity-related adaptationsMichael Keane
Integrative Genomics of Ageing Group, Institute of Integrative Biology, University of Liverpool, Liverpool, UK, Broad Institute of MIT and Harvard, Cambridge, MA, USA, Department of Biology, University of Rochester, NY, USA, Vertebrate and Health Genomics, The Genome Analysis Center, Norwich, UK, Department of Medical Biochemistry and Microbiology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden and Department of Genetics, Harvard Medical School, Boston, MA, USA
Bioinformatics 30:3558-60. 2014..Although its genome was previously sequenced, here we report a new assembly sequenced by us with substantially higher N50 values for scaffolds and contigs...
- Comparative genomics as a tool to understand evolution and diseaseJessica Alföldi
Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
Genome Res 23:1063-8. 2013..Furthermore, we anticipate discoveries related to evolutionary mechanisms, adaptation, and disease to quickly accelerate in the coming years. ..
- Full-length transcriptome assembly from RNA-Seq data without a reference genomeManfred 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...
- Heart development in fibronectin-null mice is governed by a genetic modifier on chromosome fourSophie Astrof
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...