Manuel Garber

Summary

Affiliation: Massachusetts Institute of Technology
Country: USA

Publications

  1. pmc Closing gaps in the human genome using sequencing by synthesis
    Manuel Garber
    Genome Sequencing and Analysis Program, Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, MA 02142, USA
    Genome Biol 10:R60. 2009
  2. ncbi request reprint Analysis of the DNA sequence and duplication history of human chromosome 15
    Michael C Zody
    Broad Institute of MIT and Harvard, 320 Charles Street, Cambridge, Massachusetts 02141, USA
    Nature 440:671-5. 2006
  3. pmc Metabolic labeling of RNA uncovers principles of RNA production and degradation dynamics in mammalian cells
    Michal Rabani
    Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
    Nat Biotechnol 29:436-42. 2011
  4. pmc A high-resolution map of human evolutionary constraint using 29 mammals
    Kerstin Lindblad-Toh
    Broad Institute of Harvard and Massachusetts Institute of Technology, 7 Cambridge Center, Cambridge, Massachusetts 02142, USA
    Nature 478:476-82. 2011
  5. ncbi request reprint 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
  6. pmc A large intergenic noncoding RNA induced by p53 mediates global gene repression in the p53 response
    Maite Huarte
    The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
    Cell 142:409-19. 2010
  7. pmc DNA sequence of human chromosome 17 and analysis of rearrangement in the human lineage
    Michael C Zody
    Broad Institute of MIT and Harvard, 7 Cambridge Center, Massachusetts 02142, USA
    Nature 440:1045-9. 2006
  8. pmc A high-throughput chromatin immunoprecipitation approach reveals principles of dynamic gene regulation in mammals
    Manuel Garber
    Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
    Mol Cell 47:810-22. 2012
  9. doi request reprint A composite of multiple signals distinguishes causal variants in regions of positive selection
    Sharon R Grossman
    Center for Systems Biology, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
    Science 327:883-6. 2010
  10. pmc Systematic identification of long noncoding RNAs expressed during zebrafish embryogenesis
    Andrea Pauli
    Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA
    Genome Res 22:577-91. 2012

Detail Information

Publications22

  1. pmc Closing gaps in the human genome using sequencing by synthesis
    Manuel 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...
  2. ncbi request reprint Analysis of the DNA sequence and duplication history of human chromosome 15
    Michael 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...
  3. pmc Metabolic labeling of RNA uncovers principles of RNA production and degradation dynamics in mammalian cells
    Michal 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...
  4. pmc A high-resolution map of human evolutionary constraint using 29 mammals
    Kerstin 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...
  5. ncbi request reprint 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...
  6. pmc A large intergenic noncoding RNA induced by p53 mediates global gene repression in the p53 response
    Maite 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...
  7. pmc DNA sequence of human chromosome 17 and analysis of rearrangement in the human lineage
    Michael 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...
  8. pmc A high-throughput chromatin immunoprecipitation approach reveals principles of dynamic gene regulation in mammals
    Manuel Garber
    Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
    Mol Cell 47:810-22. 2012
    ....
  9. doi request reprint A composite of multiple signals distinguishes causal variants in regions of positive selection
    Sharon 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...
  10. pmc Systematic identification of long noncoding RNAs expressed during zebrafish embryogenesis
    Andrea 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...
  11. pmc lincRNAs act in the circuitry controlling pluripotency and differentiation
    Mitchell 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...
  12. ncbi request reprint DNA sequence and analysis of human chromosome 8
    Chad 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...
  13. pmc Ab initio reconstruction of cell type-specific transcriptomes in mouse reveals the conserved multi-exonic structure of lincRNAs
    Mitchell 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...
  14. pmc Quality scores and SNP detection in sequencing-by-synthesis systems
    William 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...
  15. doi request reprint Computational methods for transcriptome annotation and quantification using RNA-seq
    Manuel 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...
  16. ncbi request reprint Genome sequence, comparative analysis and haplotype structure of the domestic dog
    Kerstin 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...
  17. pmc Unbiased reconstruction of a mammalian transcriptional network mediating pathogen responses
    Ido 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...
  18. pmc Identifying novel constrained elements by exploiting biased substitution patterns
    Manuel 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...
  19. ncbi request reprint DNA sequence and analysis of human chromosome 18
    Chad 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...
  20. pmc Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals
    Mitchell 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...
  21. pmc Systematic discovery of TLR signaling components delineates viral-sensing circuits
    Nicolas 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...
  22. doi request reprint Semiconductor-based DNA sequencing of histone modification states
    Christine S Cheng
    Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
    Nat Commun 4:2672. 2013
    ..We leverage this method for epigenetic profiling of tumour tissues. ..