Research Topics
Genomes and Genes
| Manuel GarberSummaryAffiliation: Massachusetts Institute of Technology Country: USA Publications
| Collaborators
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Detail Information
Publications
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...
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...- Metabolic labeling of RNA uncovers principles of RNA production and degradation dynamics in mammalian cellsMichal Rabani
Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
Nat Biotechnol 29:436-42. 2011..Certain transcripts, including those encoding cytokines and transcription factors, mature faster. Our study provides a quantitative approach to study the integrative process of RNA regulation... - 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... - A large intergenic noncoding RNA induced by p53 mediates global gene repression in the p53 responseMaite Huarte
The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
Cell 142:409-19. 2010..We propose a model whereby transcription factors activate lincRNAs that serve as key repressors by physically associating with repressive complexes and modulate their localization to sets of previously active genes... - 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... 
A composite of multiple signals distinguishes causal variants in regions of positive selectionSharon R Grossman
Center for Systems Biology, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
Science 327:883-6. 2010..CMS can not just identify individual loci but implicates precise variants selected by evolution...- Systematic identification of long noncoding RNAs expressed during zebrafish embryogenesisAndrea Pauli
Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA
Genome Res 22:577-91. 2012..Our study provides the first systematic identification of lncRNAs in a vertebrate embryo and forms the foundation for future genetic, genomic, and evolutionary studies... - lincRNAs act in the circuitry controlling pluripotency and differentiationMitchell Guttman
Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, Massachusetts 02142, USA
Nature 477:295-300. 2011..Together, the results demonstrate that lincRNAs have key roles in the circuitry controlling ES cell state... - 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... - 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... - Ab initio reconstruction of cell type-specific transcriptomes in mouse reveals the conserved multi-exonic structure of lincRNAsMitchell Guttman
Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
Nat Biotechnol 28:503-10. 2010..Our results open the way to direct experimental manipulation of thousands of noncoding RNAs and demonstrate the power of ab initio reconstruction to render a comprehensive picture of mammalian transcriptomes... - Computational methods for transcriptome annotation and quantification using RNA-seqManuel Garber
Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts, USA
Nat Methods 8:469-77. 2011..Finally, we highlight the interdependence between these categories and discuss the benefits for different biological applications... - 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... - A high-throughput chromatin immunoprecipitation approach reveals principles of dynamic gene regulation in mammalsManuel Garber
Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
Mol Cell 47:810-22. 2012.... - Unbiased reconstruction of a mammalian transcriptional network mediating pathogen responsesIdo Amit
Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, MA 02142, USA
Science 326:257-63. 2009..This study establishes a broadly applicable, comprehensive, and unbiased approach to reveal the wiring and functions of a regulatory network controlling a major transcriptional response in primary mammalian cells... - Identifying novel constrained elements by exploiting biased substitution patternsManuel Garber
Department of Biology, Broad Institute of MIT and Harvard, 7 Cambridge Center, MIT, Cambridge, MA 02142, USA
Bioinformatics 25:i54-62. 2009..Many methods have been developed to identify conserved sequences across species; however, existing methods only model conservation as a decrease in the rate of mutation and have ignored selection acting on the pattern of mutations... - Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammalsMitchell Guttman
Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, Massachusetts 02142, USA
Nature 458:223-7. 2009..Together, these results define a unique collection of functional lincRNAs that are highly conserved and implicated in diverse biological processes... - 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... - Systematic discovery of TLR signaling components delineates viral-sensing circuitsNicolas Chevrier
Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, MA 02142, USA
Cell 147:853-67. 2011..Our study illustrates the power of combining systematic measurements and perturbations to elucidate complex signaling circuits and discover potential therapeutic targets... - 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...