John L Rinn

Summary

Affiliation: Harvard University
Country: USA

Publications

  1. pmc Genomics in 2011: challenges and opportunities
    David J Adams
    Wellcome Trust Sanger Institute
    Genome Biol 12:137. 2011
  2. pmc Identification of proteins binding coding and non-coding human RNAs using protein microarrays
    Zurab Siprashvili
    The Program in Epithelial Biology, Stanford University School of Medicine, 269 Campus Drive, Room 2145, Stanford, CA 94305, USA
    BMC Genomics 13:633. 2012
  3. pmc Genome regulation by long noncoding RNAs
    John L Rinn
    Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, Massachusetts 02138, USA
    Annu Rev Biochem 81:145-66. 2012
  4. pmc Improving RNA-Seq expression estimates by correcting for fragment bias
    Adam Roberts
    Department of Computer Science, 387 Soda Hall, UC Berkeley, Berkeley, CA 94720, USA
    Genome Biol 12:R22. 2011
  5. pmc Long noncoding RNAs regulate adipogenesis
    Lei Sun
    Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
    Proc Natl Acad Sci U S A 110:3387-92. 2013
  6. pmc Topological organization of multichromosomal regions by the long intergenic noncoding RNA Firre
    Ezgi Hacisuleyman
    1 Department of Molecular and Cellular Biology, Harvard University, Cambridge, Massachusetts, USA 2 Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, Massachusetts, USA 3 Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts, USA 4
    Nat Struct Mol Biol 21:198-206. 2014
  7. pmc Ribosome profiling reveals resemblance between long non-coding RNAs and 5' leaders of coding RNAs
    Guo Liang Chew
    Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA
    Development 140:2828-34. 2013
  8. pmc Differential analysis of gene regulation at transcript resolution with RNA-seq
    Cole Trapnell
    Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, Massachusetts, USA
    Nat Biotechnol 31:46-53. 2013
  9. pmc Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks
    Cole Trapnell
    Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
    Nat Protoc 7:562-78. 2012
  10. pmc Peptidomic discovery of short open reading frame-encoded peptides in human cells
    Sarah A Slavoff
    Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts, USA
    Nat Chem Biol 9:59-64. 2013

Collaborators

Detail Information

Publications19

  1. pmc Genomics in 2011: challenges and opportunities
    David J Adams
    Wellcome Trust Sanger Institute
    Genome Biol 12:137. 2011
    ..What was their favorite paper of 2011? What are the challenges in their particular research area? Who has had the biggest influence on their careers? What advice would they give to young researchers embarking on a career in research?..
  2. pmc Identification of proteins binding coding and non-coding human RNAs using protein microarrays
    Zurab Siprashvili
    The Program in Epithelial Biology, Stanford University School of Medicine, 269 Campus Drive, Room 2145, Stanford, CA 94305, USA
    BMC Genomics 13:633. 2012
    ..To overcome these limitations, we have developed a rapid and large-scale approach to characterize binding of in vitro transcribed labeled RNA to ~9,400 human recombinant proteins spotted on protein microarrays...
  3. pmc Genome regulation by long noncoding RNAs
    John L Rinn
    Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, Massachusetts 02138, USA
    Annu Rev Biochem 81:145-66. 2012
    ..The importance of these modes of regulation is underscored by the newly recognized roles of long RNAs for proper gene control across all kingdoms of life...
  4. pmc Improving RNA-Seq expression estimates by correcting for fragment bias
    Adam Roberts
    Department of Computer Science, 387 Soda Hall, UC Berkeley, Berkeley, CA 94720, USA
    Genome Biol 12:R22. 2011
    ..We find improvements in expression estimates as measured by correlation with independently performed qRT-PCR and show that correction of bias leads to improved replicability of results across libraries and sequencing technologies...
  5. pmc Long noncoding RNAs regulate adipogenesis
    Lei Sun
    Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
    Proc Natl Acad Sci U S A 110:3387-92. 2013
    ..RNAi-mediated loss of function screens identified functional lncRNAs with varying impact on adipogenesis. Collectively, we have identified numerous lncRNAs that are functionally required for proper adipogenesis...
  6. pmc Topological organization of multichromosomal regions by the long intergenic noncoding RNA Firre
    Ezgi Hacisuleyman
    1 Department of Molecular and Cellular Biology, Harvard University, Cambridge, Massachusetts, USA 2 Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, Massachusetts, USA 3 Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts, USA 4
    Nat Struct Mol Biol 21:198-206. 2014
    ..Thus, our data suggest a model in which lncRNAs such as Firre can interface with and modulate nuclear architecture across chromosomes. ..
  7. pmc Ribosome profiling reveals resemblance between long non-coding RNAs and 5' leaders of coding RNAs
    Guo Liang Chew
    Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA
    Development 140:2828-34. 2013
    ..In addition, our computational pipeline and ribosome profiling data provide a powerful resource for the identification of translated open reading frames during zebrafish development...
  8. pmc Differential analysis of gene regulation at transcript resolution with RNA-seq
    Cole Trapnell
    Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, Massachusetts, USA
    Nat Biotechnol 31:46-53. 2013
    ..Cuffdiff 2 performs robust differential analysis in RNA-seq experiments at transcript resolution, revealing a layer of regulation not readily observable with other high-throughput technologies...
  9. pmc Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks
    Cole Trapnell
    Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
    Nat Protoc 7:562-78. 2012
    ..The protocol's execution time depends on the volume of transcriptome sequencing data and available computing resources but takes less than 1 d of computer time for typical experiments and ∼1 h of hands-on time...
  10. pmc Peptidomic discovery of short open reading frame-encoded peptides in human cells
    Sarah A Slavoff
    Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts, USA
    Nat Chem Biol 9:59-64. 2013
    ..In addition, coding sORFs are present in a small fraction (8 out of 1,866) of long intergenic noncoding RNAs. Together, these results provide strong evidence that the human proteome is more complex than previously appreciated...
  11. pmc Computational analysis of noncoding RNAs
    Stefan Washietl
    Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA, USA
    Wiley Interdiscip Rev RNA 3:759-78. 2012
    ....
  12. 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...
  13. ncbi request reprint Gene co-regulation by Fezf2 selects neurotransmitter identity and connectivity of corticospinal neurons
    Simona Lodato
    Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, Massachusetts, USA
    Nat Neurosci 17:1046-54. 2014
    ..Our data indicate that co-regulated expression of neuron subtype-specific and pan-neuronal gene batteries by a single transcription factor is one component of the regulatory logic responsible for the establishment of CSMN identity. ..
  14. ncbi request reprint The dynamics and regulators of cell fate decisions are revealed by pseudotemporal ordering of single cells
    Cole Trapnell
    1 Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, Massachusetts, USA 2 The Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA 3
    Nat Biotechnol 32:381-6. 2014
    ..Monocle can in principle be used to recover single-cell gene expression kinetics from a wide array of cellular processes, including differentiation, proliferation and oncogenic transformation. ..
  15. doi request reprint Poly-combing the genome for RNA
    Loyal A Goff
    Stem Cell and Regenerative Biology Department, Harvard University, Cambridge, Massachusetts, USA, and The Broad Institute, Cambridge, Massachusetts, USA
    Nat Struct Mol Biol 20:1344-6. 2013
    ..Two recent studies now provide critical new insights into an intriguing genome-wide role for RNA in PRC2 regulation...
  16. pmc A Keystone for ncRNA
    Ezgi Hacisuleyman
    Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA
    Genome Biol 13:315. 2012
    ..A report on the Keystone symposium 'Non-coding RNAs' held at Snowbird, Utah, USA, 31 March to 5 April 2012...
  17. pmc Integrative annotation of human large intergenic noncoding RNAs reveals global properties and specific subclasses
    Moran N Cabili
    Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts 02142, USA
    Genes Dev 25:1915-27. 2011
    ..Our integrated, comprehensive, yet conservative reference catalog of human lincRNAs reveals the global properties of lincRNAs and will facilitate experimental studies and further functional classification of these genes...
  18. doi request reprint Modular regulatory principles of large non-coding RNAs
    Mitchell 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...
  19. pmc RNA-protein interactions in human health and disease
    Ahmad M Khalil
    The Broad Institute of Harvard and MIT, Cambridge, MA, USA
    Semin Cell Dev Biol 22:359-65. 2011
    ..Finally, we propose that mis-regulation of ncRNAs interactions with their protein partners may contribute to human disease, and open up a novel approach to therapeutic interventions...