Research Topics
Genomes and Genes | Mitchell GuttmanSummaryAffiliation: Massachusetts Institute of Technology Country: USA Publications
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Publications
Assessing the significance of conserved genomic aberrations using high resolution genomic microarraysMitchell Guttman
Penn Center for Bioinformatics, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
PLoS Genet 3:e143. 2007..The algorithm has been fully implemented and tested and is freely available as a Java application at http://www.cbil.upenn.edu/MSA...- 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... - 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... 
Modular regulatory principles of large non-coding RNAsMitchell Guttman
Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, Massachusetts 02142, USA
Nature 482:339-46. 2012..Here we synthesize these studies to provide an emerging model whereby large ncRNAs might achieve regulatory specificity through modularity, assembling diverse combinations of proteins and possibly RNA and DNA interactions...- 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... - 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... - 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... - 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.... - 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... - Large intergenic non-coding RNA-RoR modulates reprogramming of human induced pluripotent stem cellsSabine Loewer
Stem Cell Transplantation Program, Division of Pediatric Hematology and Oncology, Manton Center for Orphan Disease Research, Children s Hospital Boston and Dana Farber Cancer Institute, Boston, Massachusetts, USA
Nat Genet 42:1113-7. 2010.... - Many human large intergenic noncoding RNAs associate with chromatin-modifying complexes and affect gene expressionAhmad M Khalil
The Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, MA 02142, USA
Proc Natl Acad Sci U S A 106:11667-72. 2009..We propose a model in which some lincRNAs guide chromatin-modifying complexes to specific genomic loci to regulate gene expression... - 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... - Digital transcriptome profiling from attomole-level RNA samplesFatih Ozsolak
Helicos BioSciences Corporation, Cambridge, MA 02139, USA
Genome Res 20:519-25. 2010.... - 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...