Lifestyle modifications: coordinating the tRNA epitranscriptome with codon bias to adapt translation during stress responses View Full Text


Ontology type: schema:ScholarlyArticle      Open Access: True


Article Info

DATE

2018-12

AUTHORS

Cheryl Chan, Phuong Pham, Peter C. Dedon, Thomas J. Begley

ABSTRACT

Cells adapt to stress by altering gene expression at multiple levels. Here, we propose a new mechanism regulating stress-dependent gene expression at the level of translation, with coordinated interplay between the tRNA epitranscriptome and biased codon usage in families of stress-response genes. In this model, auxiliary genetic information contained in synonymous codon usage enables regulation of codon-biased and functionally related transcripts by dynamic changes in the tRNA epitranscriptome. This model partly explains the association between synchronous stress-dependent epitranscriptomic marks and significant multi-codon usage skewing in families of translationally regulated transcripts. The model also predicts translational adaptation during viral infections. More... »

PAGES

228

References to SciGraph publications

  • 2016-08. Nucleoside modifications in the regulation of gene expression: focus on tRNA in CELLULAR AND MOLECULAR LIFE SCIENCES
  • 2014-05. The dynamic epitranscriptome: N6-methyladenosine and gene expression control in NATURE REVIEWS MOLECULAR CELL BIOLOGY
  • 2018-12. Elongator and codon bias regulate protein levels in mammalian peripheral neurons in NATURE COMMUNICATIONS
  • 2017-12. Epitranscriptomic influences on development and disease in GENOME BIOLOGY
  • 2013-03. Corrigendum: Global quantification of mammalian gene expression control in NATURE
  • 2010-04. On the Possible Role of tRNA Base Modifications in the Evolution of Codon Usage: Queuosine and Drosophila in JOURNAL OF MOLECULAR EVOLUTION
  • 1999-05. Selenocysteine-containing proteins in mammals in JOURNAL OF BIOMEDICAL SCIENCE
  • 2018-06. Codon-specific translation reprogramming promotes resistance to targeted therapy in NATURE
  • 2016-05. Synchronized mitochondrial and cytosolic translation programs in NATURE
  • 2012-01. Reprogramming of tRNA modifications controls the oxidative stress response by codon-biased translation of proteins in NATURE COMMUNICATIONS
  • 2011-05. Global quantification of mammalian gene expression control in NATURE
  • 2008-02. Mechanisms of post-transcriptional regulation by microRNAs: are the answers in sight? in NATURE REVIEWS GENETICS
  • 2003-10. Global analysis of protein expression in yeast in NATURE
  • 2016-11-11. tRNA-mediated codon-biased translation in mycobacterial hypoxic persistence in NATURE COMMUNICATIONS
  • 2014-04. Quantitative analysis of ribonucleoside modifications in tRNA by HPLC-coupled mass spectrometry in NATURE PROTOCOLS
  • 2008-06. DNA methylation landscapes: provocative insights from epigenomics in NATURE REVIEWS GENETICS
  • 2003-07. Selection Conflicts, Gene Expression, and Codon Usage Trends in Yeast in JOURNAL OF MOLECULAR EVOLUTION
  • 2016-04. RNA: Expanding the mRNA epitranscriptome in NATURE REVIEWS MOLECULAR CELL BIOLOGY
  • Identifiers

    URI

    http://scigraph.springernature.com/pub.10.1186/s13059-018-1611-1

    DOI

    http://dx.doi.org/10.1186/s13059-018-1611-1

    DIMENSIONS

    https://app.dimensions.ai/details/publication/pub.1110911707

    PUBMED

    https://www.ncbi.nlm.nih.gov/pubmed/30587213


    Indexing Status Check whether this publication has been indexed by Scopus and Web Of Science using the SN Indexing Status Tool
    Incoming Citations Browse incoming citations for this publication using opencitations.net

    JSON-LD is the canonical representation for SciGraph data.

    TIP: You can open this SciGraph record using an external JSON-LD service: JSON-LD Playground Google SDTT

    [
      {
        "@context": "https://springernature.github.io/scigraph/jsonld/sgcontext.json", 
        "about": [
          {
            "id": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/0604", 
            "inDefinedTermSet": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/", 
            "name": "Genetics", 
            "type": "DefinedTerm"
          }, 
          {
            "id": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/06", 
            "inDefinedTermSet": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/", 
            "name": "Biological Sciences", 
            "type": "DefinedTerm"
          }, 
          {
            "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
            "name": "Adaptation, Physiological", 
            "type": "DefinedTerm"
          }, 
          {
            "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
            "name": "Epigenesis, Genetic", 
            "type": "DefinedTerm"
          }, 
          {
            "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
            "name": "Models, Biological", 
            "type": "DefinedTerm"
          }, 
          {
            "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
            "name": "Mycobacterium bovis", 
            "type": "DefinedTerm"
          }, 
          {
            "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
            "name": "Protein Biosynthesis", 
            "type": "DefinedTerm"
          }, 
          {
            "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
            "name": "RNA, Transfer", 
            "type": "DefinedTerm"
          }, 
          {
            "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
            "name": "Stress, Physiological", 
            "type": "DefinedTerm"
          }, 
          {
            "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
            "name": "Transcriptome", 
            "type": "DefinedTerm"
          }, 
          {
            "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
            "name": "Virus Diseases", 
            "type": "DefinedTerm"
          }
        ], 
        "author": [
          {
            "affiliation": {
              "alternateName": "Singapore-MIT Alliance for Research and Technology", 
              "id": "https://www.grid.ac/institutes/grid.429485.6", 
              "name": [
                "Singapore-MIT Alliance for Research and Technology, 138602, 1 CREATE Way, Singapore"
              ], 
              "type": "Organization"
            }, 
            "familyName": "Chan", 
            "givenName": "Cheryl", 
            "type": "Person"
          }, 
          {
            "affiliation": {
              "alternateName": "Massachusetts Institute of Technology", 
              "id": "https://www.grid.ac/institutes/grid.116068.8", 
              "name": [
                "Department of Biological Engineering, Massachusetts Institute of Technology, 02139, Cambridge, MA, USA"
              ], 
              "type": "Organization"
            }, 
            "familyName": "Pham", 
            "givenName": "Phuong", 
            "id": "sg:person.014712576357.77", 
            "sameAs": [
              "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.014712576357.77"
            ], 
            "type": "Person"
          }, 
          {
            "affiliation": {
              "alternateName": "Massachusetts Institute of Technology", 
              "id": "https://www.grid.ac/institutes/grid.116068.8", 
              "name": [
                "Singapore-MIT Alliance for Research and Technology, 138602, 1 CREATE Way, Singapore", 
                "Department of Biological Engineering, Massachusetts Institute of Technology, 02139, Cambridge, MA, USA"
              ], 
              "type": "Organization"
            }, 
            "familyName": "Dedon", 
            "givenName": "Peter C.", 
            "id": "sg:person.0772755577.30", 
            "sameAs": [
              "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0772755577.30"
            ], 
            "type": "Person"
          }, 
          {
            "affiliation": {
              "alternateName": "University at Albany, State University of New York", 
              "id": "https://www.grid.ac/institutes/grid.265850.c", 
              "name": [
                "The RNA Institute, College of Arts and Science, University at Albany, SUNY, 12222, Albany, NY, USA"
              ], 
              "type": "Organization"
            }, 
            "familyName": "Begley", 
            "givenName": "Thomas J.", 
            "id": "sg:person.0622457264.38", 
            "sameAs": [
              "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0622457264.38"
            ], 
            "type": "Person"
          }
        ], 
        "citation": [
          {
            "id": "https://doi.org/10.1093/nar/gkv322", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1000551344"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1016/j.molcel.2007.09.021", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1001443835"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1016/j.bmc.2013.01.056", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1001881893"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1128/mcb.00170-15", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1002433740"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1016/j.bpj.2012.06.025", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1003370839"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.2217/fmb.12.14", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1003966577"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/nature11848", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1005045690", 
              "https://doi.org/10.1038/nature11848"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1038/msb.2009.71", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1006249640"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1038/msb.2009.71", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1006249640"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1016/j.ymeth.2016.03.016", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1007562552"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1016/j.ymeth.2016.03.016", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1007562552"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1016/j.ymeth.2016.03.016", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1007562552"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1016/j.ymeth.2016.03.016", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1007562552"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1016/j.ymeth.2016.03.016", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1007562552"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1261/rna.033266.112", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1007813738"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1371/journal.pgen.1003647", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1009991108"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1093/nar/15.3.1281", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1010536976"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1098/rsob.160287", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1012544693"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1261/rna.044115.113", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1012781945"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/nrm.2016.35", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1013053737", 
              "https://doi.org/10.1038/nrm.2016.35"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1007/bf02255899", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1013253567", 
              "https://doi.org/10.1007/bf02255899"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1007/bf02255899", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1013253567", 
              "https://doi.org/10.1007/bf02255899"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1016/j.ymeth.2016.05.010", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1013604021"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1016/j.ymeth.2016.05.010", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1013604021"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1016/j.ymeth.2016.05.010", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1013604021"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1016/j.ymeth.2016.05.010", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1013604021"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1016/j.ymeth.2016.05.010", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1013604021"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.4161/cc.21919", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1014298715"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1128/mcb.22.5.1402-1411.2002", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1015855877"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1093/bioinformatics/btu192", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1016003966"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1371/journal.ppat.1002642", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1016024113"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/nature02046", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1016490499", 
              "https://doi.org/10.1038/nature02046"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/nature02046", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1016490499", 
              "https://doi.org/10.1038/nature02046"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1093/nar/gkv971", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1016565847"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/nprot.2014.047", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1016600712", 
              "https://doi.org/10.1038/nprot.2014.047"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1016/s0076-6879(07)25009-8", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1017108161"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/ncomms13302", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1018608148", 
              "https://doi.org/10.1038/ncomms13302"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1093/nar/gks1007", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1020268741"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/nrm3785", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1021026337", 
              "https://doi.org/10.1038/nrm3785"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1016/bs.mie.2015.03.004", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1025235991"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1093/nar/gkw608", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1026274721"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1371/journal.pbio.1002150", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1026329726"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1016/j.cell.2015.05.022", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1026989211"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1093/nar/28.1.292", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1027297769"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1016/j.ymeth.2016.03.019", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1028111560"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1016/j.ymeth.2016.03.019", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1028111560"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1007/s00239-010-9329-z", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1028720748", 
              "https://doi.org/10.1007/s00239-010-9329-z"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1007/s00239-010-9329-z", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1028720748", 
              "https://doi.org/10.1007/s00239-010-9329-z"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1016/j.celrep.2012.04.001", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1031173409"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1038/sj.embor.7400341", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1031305210"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1261/rna.5040605", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1032187951"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1146/annurev-biophys-060414-034333", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1032774313"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1146/annurev-biophys-060414-034333", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1032774313"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1073/pnas.1300781110", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1033653653"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/nature10098", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1033777014", 
              "https://doi.org/10.1038/nature10098"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1016/j.molcel.2005.10.036", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1033919234"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1038/msb.2011.14", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1034705210"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1038/msb.2011.14", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1034705210"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1021/acs.chemrestox.5b00004", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1035531526"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1016/j.cell.2012.01.050", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1035537532"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/nrg2341", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1036150552", 
              "https://doi.org/10.1038/nrg2341"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1093/nar/gkv1272", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1036641041"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1007/s00239-003-2459-9", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1037470011", 
              "https://doi.org/10.1007/s00239-003-2459-9"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1101/gad.12.23.3650", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1038408324"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1084/jem.20160397", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1041075733"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1371/journal.pgen.1005706", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1041288200"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/ncomms1938", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1042966138", 
              "https://doi.org/10.1038/ncomms1938"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1007/s00018-016-2217-y", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1043253011", 
              "https://doi.org/10.1007/s00018-016-2217-y"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1007/s00018-016-2217-y", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1043253011", 
              "https://doi.org/10.1007/s00018-016-2217-y"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1091/mbc.e14-06-1145", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1044616758"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1093/nar/gkq1028", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1045255575"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1016/j.molcel.2015.05.035", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1046387693"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1016/j.coviro.2016.05.007", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1046727892"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/nrg2290", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1048988578", 
              "https://doi.org/10.1038/nrg2290"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1016/j.molcel.2016.05.004", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1049016147"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1016/j.cell.2013.06.043", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1049067502"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/nature18015", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1050029090", 
              "https://doi.org/10.1038/nature18015"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1371/journal.pone.0131335", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1051757736"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1093/nar/gki242", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1052037751"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1016/j.cell.2016.05.046", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1052052425"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1371/journal.pgen.1001247", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1052179678"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1371/journal.pbio.1002015", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1052499879"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1371/journal.pgen.1005668", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1052819451"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1371/journal.pgen.1002603", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1053297773"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1021/bi050343f", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1055200282"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1021/bi050343f", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1055200282"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1074/mcp.m115.054718", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1058216013"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1080/15476286.2016.1267096", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1058403181"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1080/15476286.2016.1267098", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1058403183"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1126/science.1083516", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1062448022"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.4161/cc.22689", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1072297008"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.4161/rna.20531", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1072310017"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://app.dimensions.ai/details/publication/pub.1082384714", 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1186/s13059-017-1336-6", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1092310893", 
              "https://doi.org/10.1186/s13059-017-1336-6"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1016/j.tcb.2017.10.001", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1092502917"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.3390/ijms18112387", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1092619147"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1093/nar/gky029", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1100409456"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1016/j.bbagrm.2018.01.015", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1100723550"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/s41467-018-03221-z", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1101201638", 
              "https://doi.org/10.1038/s41467-018-03221-z"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/s41467-018-03221-z", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1101201638", 
              "https://doi.org/10.1038/s41467-018-03221-z"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/s41586-018-0243-7", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1104915647", 
              "https://doi.org/10.1038/s41586-018-0243-7"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/s41586-018-0243-7", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1104915647", 
              "https://doi.org/10.1038/s41586-018-0243-7"
            ], 
            "type": "CreativeWork"
          }
        ], 
        "datePublished": "2018-12", 
        "datePublishedReg": "2018-12-01", 
        "description": "Cells adapt to stress by altering gene expression at multiple levels. Here, we propose a new mechanism regulating stress-dependent gene expression at the level of translation, with coordinated interplay between the tRNA epitranscriptome and biased codon usage in families of stress-response genes. In this model, auxiliary genetic information contained in synonymous codon usage enables regulation of codon-biased and functionally related transcripts by dynamic changes in the tRNA epitranscriptome. This model partly explains the association between synchronous stress-dependent epitranscriptomic marks and significant multi-codon usage skewing in families of translationally regulated transcripts. The model also predicts translational adaptation during viral infections.", 
        "genre": "research_article", 
        "id": "sg:pub.10.1186/s13059-018-1611-1", 
        "inLanguage": [
          "en"
        ], 
        "isAccessibleForFree": true, 
        "isFundedItemOf": [
          {
            "id": "sg:grant.2435432", 
            "type": "MonetaryGrant"
          }, 
          {
            "id": "sg:grant.6377419", 
            "type": "MonetaryGrant"
          }, 
          {
            "id": "sg:grant.3801704", 
            "type": "MonetaryGrant"
          }, 
          {
            "id": "sg:grant.2439086", 
            "type": "MonetaryGrant"
          }
        ], 
        "isPartOf": [
          {
            "id": "sg:journal.1023439", 
            "issn": [
              "1474-760X", 
              "1465-6906"
            ], 
            "name": "Genome Biology", 
            "type": "Periodical"
          }, 
          {
            "issueNumber": "1", 
            "type": "PublicationIssue"
          }, 
          {
            "type": "PublicationVolume", 
            "volumeNumber": "19"
          }
        ], 
        "name": "Lifestyle modifications: coordinating the tRNA epitranscriptome with codon bias to adapt translation during stress responses", 
        "pagination": "228", 
        "productId": [
          {
            "name": "readcube_id", 
            "type": "PropertyValue", 
            "value": [
              "4dc5a87f22a924c52e11b5c4e303317bd979bcac5b6c51efcdc7c5027afed2bb"
            ]
          }, 
          {
            "name": "pubmed_id", 
            "type": "PropertyValue", 
            "value": [
              "30587213"
            ]
          }, 
          {
            "name": "nlm_unique_id", 
            "type": "PropertyValue", 
            "value": [
              "100960660"
            ]
          }, 
          {
            "name": "doi", 
            "type": "PropertyValue", 
            "value": [
              "10.1186/s13059-018-1611-1"
            ]
          }, 
          {
            "name": "dimensions_id", 
            "type": "PropertyValue", 
            "value": [
              "pub.1110911707"
            ]
          }
        ], 
        "sameAs": [
          "https://doi.org/10.1186/s13059-018-1611-1", 
          "https://app.dimensions.ai/details/publication/pub.1110911707"
        ], 
        "sdDataset": "articles", 
        "sdDatePublished": "2019-04-11T11:10", 
        "sdLicense": "https://scigraph.springernature.com/explorer/license/", 
        "sdPublisher": {
          "name": "Springer Nature - SN SciGraph project", 
          "type": "Organization"
        }, 
        "sdSource": "s3://com-uberresearch-data-dimensions-target-20181106-alternative/cleanup/v134/2549eaecd7973599484d7c17b260dba0a4ecb94b/merge/v9/a6c9fde33151104705d4d7ff012ea9563521a3ce/jats-lookup/v90/0000000353_0000000353/records_45348_00000002.jsonl", 
        "type": "ScholarlyArticle", 
        "url": "https://link.springer.com/10.1186%2Fs13059-018-1611-1"
      }
    ]
     

    Download the RDF metadata as:  json-ld nt turtle xml License info

    HOW TO GET THIS DATA PROGRAMMATICALLY:

    JSON-LD is a popular format for linked data which is fully compatible with JSON.

    curl -H 'Accept: application/ld+json' 'https://scigraph.springernature.com/pub.10.1186/s13059-018-1611-1'

    N-Triples is a line-based linked data format ideal for batch operations.

    curl -H 'Accept: application/n-triples' 'https://scigraph.springernature.com/pub.10.1186/s13059-018-1611-1'

    Turtle is a human-readable linked data format.

    curl -H 'Accept: text/turtle' 'https://scigraph.springernature.com/pub.10.1186/s13059-018-1611-1'

    RDF/XML is a standard XML format for linked data.

    curl -H 'Accept: application/rdf+xml' 'https://scigraph.springernature.com/pub.10.1186/s13059-018-1611-1'


     

    This table displays all metadata directly associated to this object as RDF triples.

    406 TRIPLES      21 PREDICATES      121 URIs      30 LITERALS      18 BLANK NODES

    Subject Predicate Object
    1 sg:pub.10.1186/s13059-018-1611-1 schema:about N05401664666040cf9fa1df1ca9d1a4a0
    2 N2e175ffc97134f7fa079138c250a6bc2
    3 N2f4237b87b6e4c57b25d42f78ef08090
    4 N68be996582ae426684fac44d6f4ccf91
    5 Na0040f1a7696454bba102ad5e6a94b13
    6 Nac2c735a6db9420389339c59f2741a5f
    7 Ne07fe191b2a2413b8f6ff2b27d5a28bf
    8 Ne7f1bcf525af4a728805cd91d13404c8
    9 Nf3df21bcf0fa49ce81494ce6d3e5defb
    10 anzsrc-for:06
    11 anzsrc-for:0604
    12 schema:author Ncc403311e5204afebbdedca44c285b17
    13 schema:citation sg:pub.10.1007/bf02255899
    14 sg:pub.10.1007/s00018-016-2217-y
    15 sg:pub.10.1007/s00239-003-2459-9
    16 sg:pub.10.1007/s00239-010-9329-z
    17 sg:pub.10.1038/nature02046
    18 sg:pub.10.1038/nature10098
    19 sg:pub.10.1038/nature11848
    20 sg:pub.10.1038/nature18015
    21 sg:pub.10.1038/ncomms13302
    22 sg:pub.10.1038/ncomms1938
    23 sg:pub.10.1038/nprot.2014.047
    24 sg:pub.10.1038/nrg2290
    25 sg:pub.10.1038/nrg2341
    26 sg:pub.10.1038/nrm.2016.35
    27 sg:pub.10.1038/nrm3785
    28 sg:pub.10.1038/s41467-018-03221-z
    29 sg:pub.10.1038/s41586-018-0243-7
    30 sg:pub.10.1186/s13059-017-1336-6
    31 https://app.dimensions.ai/details/publication/pub.1082384714
    32 https://doi.org/10.1016/bs.mie.2015.03.004
    33 https://doi.org/10.1016/j.bbagrm.2018.01.015
    34 https://doi.org/10.1016/j.bmc.2013.01.056
    35 https://doi.org/10.1016/j.bpj.2012.06.025
    36 https://doi.org/10.1016/j.cell.2012.01.050
    37 https://doi.org/10.1016/j.cell.2013.06.043
    38 https://doi.org/10.1016/j.cell.2015.05.022
    39 https://doi.org/10.1016/j.cell.2016.05.046
    40 https://doi.org/10.1016/j.celrep.2012.04.001
    41 https://doi.org/10.1016/j.coviro.2016.05.007
    42 https://doi.org/10.1016/j.molcel.2005.10.036
    43 https://doi.org/10.1016/j.molcel.2007.09.021
    44 https://doi.org/10.1016/j.molcel.2015.05.035
    45 https://doi.org/10.1016/j.molcel.2016.05.004
    46 https://doi.org/10.1016/j.tcb.2017.10.001
    47 https://doi.org/10.1016/j.ymeth.2016.03.016
    48 https://doi.org/10.1016/j.ymeth.2016.03.019
    49 https://doi.org/10.1016/j.ymeth.2016.05.010
    50 https://doi.org/10.1016/s0076-6879(07)25009-8
    51 https://doi.org/10.1021/acs.chemrestox.5b00004
    52 https://doi.org/10.1021/bi050343f
    53 https://doi.org/10.1038/msb.2009.71
    54 https://doi.org/10.1038/msb.2011.14
    55 https://doi.org/10.1038/sj.embor.7400341
    56 https://doi.org/10.1073/pnas.1300781110
    57 https://doi.org/10.1074/mcp.m115.054718
    58 https://doi.org/10.1080/15476286.2016.1267096
    59 https://doi.org/10.1080/15476286.2016.1267098
    60 https://doi.org/10.1084/jem.20160397
    61 https://doi.org/10.1091/mbc.e14-06-1145
    62 https://doi.org/10.1093/bioinformatics/btu192
    63 https://doi.org/10.1093/nar/15.3.1281
    64 https://doi.org/10.1093/nar/28.1.292
    65 https://doi.org/10.1093/nar/gki242
    66 https://doi.org/10.1093/nar/gkq1028
    67 https://doi.org/10.1093/nar/gks1007
    68 https://doi.org/10.1093/nar/gkv1272
    69 https://doi.org/10.1093/nar/gkv322
    70 https://doi.org/10.1093/nar/gkv971
    71 https://doi.org/10.1093/nar/gkw608
    72 https://doi.org/10.1093/nar/gky029
    73 https://doi.org/10.1098/rsob.160287
    74 https://doi.org/10.1101/gad.12.23.3650
    75 https://doi.org/10.1126/science.1083516
    76 https://doi.org/10.1128/mcb.00170-15
    77 https://doi.org/10.1128/mcb.22.5.1402-1411.2002
    78 https://doi.org/10.1146/annurev-biophys-060414-034333
    79 https://doi.org/10.1261/rna.033266.112
    80 https://doi.org/10.1261/rna.044115.113
    81 https://doi.org/10.1261/rna.5040605
    82 https://doi.org/10.1371/journal.pbio.1002015
    83 https://doi.org/10.1371/journal.pbio.1002150
    84 https://doi.org/10.1371/journal.pgen.1001247
    85 https://doi.org/10.1371/journal.pgen.1002603
    86 https://doi.org/10.1371/journal.pgen.1003647
    87 https://doi.org/10.1371/journal.pgen.1005668
    88 https://doi.org/10.1371/journal.pgen.1005706
    89 https://doi.org/10.1371/journal.pone.0131335
    90 https://doi.org/10.1371/journal.ppat.1002642
    91 https://doi.org/10.2217/fmb.12.14
    92 https://doi.org/10.3390/ijms18112387
    93 https://doi.org/10.4161/cc.21919
    94 https://doi.org/10.4161/cc.22689
    95 https://doi.org/10.4161/rna.20531
    96 schema:datePublished 2018-12
    97 schema:datePublishedReg 2018-12-01
    98 schema:description Cells adapt to stress by altering gene expression at multiple levels. Here, we propose a new mechanism regulating stress-dependent gene expression at the level of translation, with coordinated interplay between the tRNA epitranscriptome and biased codon usage in families of stress-response genes. In this model, auxiliary genetic information contained in synonymous codon usage enables regulation of codon-biased and functionally related transcripts by dynamic changes in the tRNA epitranscriptome. This model partly explains the association between synchronous stress-dependent epitranscriptomic marks and significant multi-codon usage skewing in families of translationally regulated transcripts. The model also predicts translational adaptation during viral infections.
    99 schema:genre research_article
    100 schema:inLanguage en
    101 schema:isAccessibleForFree true
    102 schema:isPartOf N1083729b31214c699730688109dfa407
    103 Neeecae41756a44fd858f6b01414ba726
    104 sg:journal.1023439
    105 schema:name Lifestyle modifications: coordinating the tRNA epitranscriptome with codon bias to adapt translation during stress responses
    106 schema:pagination 228
    107 schema:productId N20cd299b4c3e4f9fbed4803c0252a16d
    108 Na3f33babc1684356bdd7d049da9068ee
    109 Ne78d8a86009c418abbbe8e9176c88f04
    110 Nf0a2d0cef49b40f688728849493e1da2
    111 Nffbeb79b34894272bebaf302e81d5f08
    112 schema:sameAs https://app.dimensions.ai/details/publication/pub.1110911707
    113 https://doi.org/10.1186/s13059-018-1611-1
    114 schema:sdDatePublished 2019-04-11T11:10
    115 schema:sdLicense https://scigraph.springernature.com/explorer/license/
    116 schema:sdPublisher N57d2b6309f2547618ef61051058b3546
    117 schema:url https://link.springer.com/10.1186%2Fs13059-018-1611-1
    118 sgo:license sg:explorer/license/
    119 sgo:sdDataset articles
    120 rdf:type schema:ScholarlyArticle
    121 N0044d4cba6de4087bac508c9f2924350 rdf:first sg:person.0772755577.30
    122 rdf:rest N96531d8739054570bda512b502961d51
    123 N05401664666040cf9fa1df1ca9d1a4a0 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    124 schema:name Adaptation, Physiological
    125 rdf:type schema:DefinedTerm
    126 N1083729b31214c699730688109dfa407 schema:volumeNumber 19
    127 rdf:type schema:PublicationVolume
    128 N20cd299b4c3e4f9fbed4803c0252a16d schema:name nlm_unique_id
    129 schema:value 100960660
    130 rdf:type schema:PropertyValue
    131 N2e175ffc97134f7fa079138c250a6bc2 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    132 schema:name Protein Biosynthesis
    133 rdf:type schema:DefinedTerm
    134 N2f4237b87b6e4c57b25d42f78ef08090 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    135 schema:name Transcriptome
    136 rdf:type schema:DefinedTerm
    137 N57d2b6309f2547618ef61051058b3546 schema:name Springer Nature - SN SciGraph project
    138 rdf:type schema:Organization
    139 N68be996582ae426684fac44d6f4ccf91 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    140 schema:name Stress, Physiological
    141 rdf:type schema:DefinedTerm
    142 N6f795b81b0d04d86beb473cfe42a4f28 rdf:first sg:person.014712576357.77
    143 rdf:rest N0044d4cba6de4087bac508c9f2924350
    144 N96531d8739054570bda512b502961d51 rdf:first sg:person.0622457264.38
    145 rdf:rest rdf:nil
    146 Na0040f1a7696454bba102ad5e6a94b13 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    147 schema:name RNA, Transfer
    148 rdf:type schema:DefinedTerm
    149 Na3f33babc1684356bdd7d049da9068ee schema:name dimensions_id
    150 schema:value pub.1110911707
    151 rdf:type schema:PropertyValue
    152 Nac2c735a6db9420389339c59f2741a5f schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    153 schema:name Virus Diseases
    154 rdf:type schema:DefinedTerm
    155 Nbf836b77e0714d82b1c9be2dfb656045 schema:affiliation https://www.grid.ac/institutes/grid.429485.6
    156 schema:familyName Chan
    157 schema:givenName Cheryl
    158 rdf:type schema:Person
    159 Ncc403311e5204afebbdedca44c285b17 rdf:first Nbf836b77e0714d82b1c9be2dfb656045
    160 rdf:rest N6f795b81b0d04d86beb473cfe42a4f28
    161 Ne07fe191b2a2413b8f6ff2b27d5a28bf schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    162 schema:name Mycobacterium bovis
    163 rdf:type schema:DefinedTerm
    164 Ne78d8a86009c418abbbe8e9176c88f04 schema:name readcube_id
    165 schema:value 4dc5a87f22a924c52e11b5c4e303317bd979bcac5b6c51efcdc7c5027afed2bb
    166 rdf:type schema:PropertyValue
    167 Ne7f1bcf525af4a728805cd91d13404c8 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    168 schema:name Models, Biological
    169 rdf:type schema:DefinedTerm
    170 Neeecae41756a44fd858f6b01414ba726 schema:issueNumber 1
    171 rdf:type schema:PublicationIssue
    172 Nf0a2d0cef49b40f688728849493e1da2 schema:name pubmed_id
    173 schema:value 30587213
    174 rdf:type schema:PropertyValue
    175 Nf3df21bcf0fa49ce81494ce6d3e5defb schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    176 schema:name Epigenesis, Genetic
    177 rdf:type schema:DefinedTerm
    178 Nffbeb79b34894272bebaf302e81d5f08 schema:name doi
    179 schema:value 10.1186/s13059-018-1611-1
    180 rdf:type schema:PropertyValue
    181 anzsrc-for:06 schema:inDefinedTermSet anzsrc-for:
    182 schema:name Biological Sciences
    183 rdf:type schema:DefinedTerm
    184 anzsrc-for:0604 schema:inDefinedTermSet anzsrc-for:
    185 schema:name Genetics
    186 rdf:type schema:DefinedTerm
    187 sg:grant.2435432 http://pending.schema.org/fundedItem sg:pub.10.1186/s13059-018-1611-1
    188 rdf:type schema:MonetaryGrant
    189 sg:grant.2439086 http://pending.schema.org/fundedItem sg:pub.10.1186/s13059-018-1611-1
    190 rdf:type schema:MonetaryGrant
    191 sg:grant.3801704 http://pending.schema.org/fundedItem sg:pub.10.1186/s13059-018-1611-1
    192 rdf:type schema:MonetaryGrant
    193 sg:grant.6377419 http://pending.schema.org/fundedItem sg:pub.10.1186/s13059-018-1611-1
    194 rdf:type schema:MonetaryGrant
    195 sg:journal.1023439 schema:issn 1465-6906
    196 1474-760X
    197 schema:name Genome Biology
    198 rdf:type schema:Periodical
    199 sg:person.014712576357.77 schema:affiliation https://www.grid.ac/institutes/grid.116068.8
    200 schema:familyName Pham
    201 schema:givenName Phuong
    202 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.014712576357.77
    203 rdf:type schema:Person
    204 sg:person.0622457264.38 schema:affiliation https://www.grid.ac/institutes/grid.265850.c
    205 schema:familyName Begley
    206 schema:givenName Thomas J.
    207 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0622457264.38
    208 rdf:type schema:Person
    209 sg:person.0772755577.30 schema:affiliation https://www.grid.ac/institutes/grid.116068.8
    210 schema:familyName Dedon
    211 schema:givenName Peter C.
    212 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0772755577.30
    213 rdf:type schema:Person
    214 sg:pub.10.1007/bf02255899 schema:sameAs https://app.dimensions.ai/details/publication/pub.1013253567
    215 https://doi.org/10.1007/bf02255899
    216 rdf:type schema:CreativeWork
    217 sg:pub.10.1007/s00018-016-2217-y schema:sameAs https://app.dimensions.ai/details/publication/pub.1043253011
    218 https://doi.org/10.1007/s00018-016-2217-y
    219 rdf:type schema:CreativeWork
    220 sg:pub.10.1007/s00239-003-2459-9 schema:sameAs https://app.dimensions.ai/details/publication/pub.1037470011
    221 https://doi.org/10.1007/s00239-003-2459-9
    222 rdf:type schema:CreativeWork
    223 sg:pub.10.1007/s00239-010-9329-z schema:sameAs https://app.dimensions.ai/details/publication/pub.1028720748
    224 https://doi.org/10.1007/s00239-010-9329-z
    225 rdf:type schema:CreativeWork
    226 sg:pub.10.1038/nature02046 schema:sameAs https://app.dimensions.ai/details/publication/pub.1016490499
    227 https://doi.org/10.1038/nature02046
    228 rdf:type schema:CreativeWork
    229 sg:pub.10.1038/nature10098 schema:sameAs https://app.dimensions.ai/details/publication/pub.1033777014
    230 https://doi.org/10.1038/nature10098
    231 rdf:type schema:CreativeWork
    232 sg:pub.10.1038/nature11848 schema:sameAs https://app.dimensions.ai/details/publication/pub.1005045690
    233 https://doi.org/10.1038/nature11848
    234 rdf:type schema:CreativeWork
    235 sg:pub.10.1038/nature18015 schema:sameAs https://app.dimensions.ai/details/publication/pub.1050029090
    236 https://doi.org/10.1038/nature18015
    237 rdf:type schema:CreativeWork
    238 sg:pub.10.1038/ncomms13302 schema:sameAs https://app.dimensions.ai/details/publication/pub.1018608148
    239 https://doi.org/10.1038/ncomms13302
    240 rdf:type schema:CreativeWork
    241 sg:pub.10.1038/ncomms1938 schema:sameAs https://app.dimensions.ai/details/publication/pub.1042966138
    242 https://doi.org/10.1038/ncomms1938
    243 rdf:type schema:CreativeWork
    244 sg:pub.10.1038/nprot.2014.047 schema:sameAs https://app.dimensions.ai/details/publication/pub.1016600712
    245 https://doi.org/10.1038/nprot.2014.047
    246 rdf:type schema:CreativeWork
    247 sg:pub.10.1038/nrg2290 schema:sameAs https://app.dimensions.ai/details/publication/pub.1048988578
    248 https://doi.org/10.1038/nrg2290
    249 rdf:type schema:CreativeWork
    250 sg:pub.10.1038/nrg2341 schema:sameAs https://app.dimensions.ai/details/publication/pub.1036150552
    251 https://doi.org/10.1038/nrg2341
    252 rdf:type schema:CreativeWork
    253 sg:pub.10.1038/nrm.2016.35 schema:sameAs https://app.dimensions.ai/details/publication/pub.1013053737
    254 https://doi.org/10.1038/nrm.2016.35
    255 rdf:type schema:CreativeWork
    256 sg:pub.10.1038/nrm3785 schema:sameAs https://app.dimensions.ai/details/publication/pub.1021026337
    257 https://doi.org/10.1038/nrm3785
    258 rdf:type schema:CreativeWork
    259 sg:pub.10.1038/s41467-018-03221-z schema:sameAs https://app.dimensions.ai/details/publication/pub.1101201638
    260 https://doi.org/10.1038/s41467-018-03221-z
    261 rdf:type schema:CreativeWork
    262 sg:pub.10.1038/s41586-018-0243-7 schema:sameAs https://app.dimensions.ai/details/publication/pub.1104915647
    263 https://doi.org/10.1038/s41586-018-0243-7
    264 rdf:type schema:CreativeWork
    265 sg:pub.10.1186/s13059-017-1336-6 schema:sameAs https://app.dimensions.ai/details/publication/pub.1092310893
    266 https://doi.org/10.1186/s13059-017-1336-6
    267 rdf:type schema:CreativeWork
    268 https://app.dimensions.ai/details/publication/pub.1082384714 schema:CreativeWork
    269 https://doi.org/10.1016/bs.mie.2015.03.004 schema:sameAs https://app.dimensions.ai/details/publication/pub.1025235991
    270 rdf:type schema:CreativeWork
    271 https://doi.org/10.1016/j.bbagrm.2018.01.015 schema:sameAs https://app.dimensions.ai/details/publication/pub.1100723550
    272 rdf:type schema:CreativeWork
    273 https://doi.org/10.1016/j.bmc.2013.01.056 schema:sameAs https://app.dimensions.ai/details/publication/pub.1001881893
    274 rdf:type schema:CreativeWork
    275 https://doi.org/10.1016/j.bpj.2012.06.025 schema:sameAs https://app.dimensions.ai/details/publication/pub.1003370839
    276 rdf:type schema:CreativeWork
    277 https://doi.org/10.1016/j.cell.2012.01.050 schema:sameAs https://app.dimensions.ai/details/publication/pub.1035537532
    278 rdf:type schema:CreativeWork
    279 https://doi.org/10.1016/j.cell.2013.06.043 schema:sameAs https://app.dimensions.ai/details/publication/pub.1049067502
    280 rdf:type schema:CreativeWork
    281 https://doi.org/10.1016/j.cell.2015.05.022 schema:sameAs https://app.dimensions.ai/details/publication/pub.1026989211
    282 rdf:type schema:CreativeWork
    283 https://doi.org/10.1016/j.cell.2016.05.046 schema:sameAs https://app.dimensions.ai/details/publication/pub.1052052425
    284 rdf:type schema:CreativeWork
    285 https://doi.org/10.1016/j.celrep.2012.04.001 schema:sameAs https://app.dimensions.ai/details/publication/pub.1031173409
    286 rdf:type schema:CreativeWork
    287 https://doi.org/10.1016/j.coviro.2016.05.007 schema:sameAs https://app.dimensions.ai/details/publication/pub.1046727892
    288 rdf:type schema:CreativeWork
    289 https://doi.org/10.1016/j.molcel.2005.10.036 schema:sameAs https://app.dimensions.ai/details/publication/pub.1033919234
    290 rdf:type schema:CreativeWork
    291 https://doi.org/10.1016/j.molcel.2007.09.021 schema:sameAs https://app.dimensions.ai/details/publication/pub.1001443835
    292 rdf:type schema:CreativeWork
    293 https://doi.org/10.1016/j.molcel.2015.05.035 schema:sameAs https://app.dimensions.ai/details/publication/pub.1046387693
    294 rdf:type schema:CreativeWork
    295 https://doi.org/10.1016/j.molcel.2016.05.004 schema:sameAs https://app.dimensions.ai/details/publication/pub.1049016147
    296 rdf:type schema:CreativeWork
    297 https://doi.org/10.1016/j.tcb.2017.10.001 schema:sameAs https://app.dimensions.ai/details/publication/pub.1092502917
    298 rdf:type schema:CreativeWork
    299 https://doi.org/10.1016/j.ymeth.2016.03.016 schema:sameAs https://app.dimensions.ai/details/publication/pub.1007562552
    300 rdf:type schema:CreativeWork
    301 https://doi.org/10.1016/j.ymeth.2016.03.019 schema:sameAs https://app.dimensions.ai/details/publication/pub.1028111560
    302 rdf:type schema:CreativeWork
    303 https://doi.org/10.1016/j.ymeth.2016.05.010 schema:sameAs https://app.dimensions.ai/details/publication/pub.1013604021
    304 rdf:type schema:CreativeWork
    305 https://doi.org/10.1016/s0076-6879(07)25009-8 schema:sameAs https://app.dimensions.ai/details/publication/pub.1017108161
    306 rdf:type schema:CreativeWork
    307 https://doi.org/10.1021/acs.chemrestox.5b00004 schema:sameAs https://app.dimensions.ai/details/publication/pub.1035531526
    308 rdf:type schema:CreativeWork
    309 https://doi.org/10.1021/bi050343f schema:sameAs https://app.dimensions.ai/details/publication/pub.1055200282
    310 rdf:type schema:CreativeWork
    311 https://doi.org/10.1038/msb.2009.71 schema:sameAs https://app.dimensions.ai/details/publication/pub.1006249640
    312 rdf:type schema:CreativeWork
    313 https://doi.org/10.1038/msb.2011.14 schema:sameAs https://app.dimensions.ai/details/publication/pub.1034705210
    314 rdf:type schema:CreativeWork
    315 https://doi.org/10.1038/sj.embor.7400341 schema:sameAs https://app.dimensions.ai/details/publication/pub.1031305210
    316 rdf:type schema:CreativeWork
    317 https://doi.org/10.1073/pnas.1300781110 schema:sameAs https://app.dimensions.ai/details/publication/pub.1033653653
    318 rdf:type schema:CreativeWork
    319 https://doi.org/10.1074/mcp.m115.054718 schema:sameAs https://app.dimensions.ai/details/publication/pub.1058216013
    320 rdf:type schema:CreativeWork
    321 https://doi.org/10.1080/15476286.2016.1267096 schema:sameAs https://app.dimensions.ai/details/publication/pub.1058403181
    322 rdf:type schema:CreativeWork
    323 https://doi.org/10.1080/15476286.2016.1267098 schema:sameAs https://app.dimensions.ai/details/publication/pub.1058403183
    324 rdf:type schema:CreativeWork
    325 https://doi.org/10.1084/jem.20160397 schema:sameAs https://app.dimensions.ai/details/publication/pub.1041075733
    326 rdf:type schema:CreativeWork
    327 https://doi.org/10.1091/mbc.e14-06-1145 schema:sameAs https://app.dimensions.ai/details/publication/pub.1044616758
    328 rdf:type schema:CreativeWork
    329 https://doi.org/10.1093/bioinformatics/btu192 schema:sameAs https://app.dimensions.ai/details/publication/pub.1016003966
    330 rdf:type schema:CreativeWork
    331 https://doi.org/10.1093/nar/15.3.1281 schema:sameAs https://app.dimensions.ai/details/publication/pub.1010536976
    332 rdf:type schema:CreativeWork
    333 https://doi.org/10.1093/nar/28.1.292 schema:sameAs https://app.dimensions.ai/details/publication/pub.1027297769
    334 rdf:type schema:CreativeWork
    335 https://doi.org/10.1093/nar/gki242 schema:sameAs https://app.dimensions.ai/details/publication/pub.1052037751
    336 rdf:type schema:CreativeWork
    337 https://doi.org/10.1093/nar/gkq1028 schema:sameAs https://app.dimensions.ai/details/publication/pub.1045255575
    338 rdf:type schema:CreativeWork
    339 https://doi.org/10.1093/nar/gks1007 schema:sameAs https://app.dimensions.ai/details/publication/pub.1020268741
    340 rdf:type schema:CreativeWork
    341 https://doi.org/10.1093/nar/gkv1272 schema:sameAs https://app.dimensions.ai/details/publication/pub.1036641041
    342 rdf:type schema:CreativeWork
    343 https://doi.org/10.1093/nar/gkv322 schema:sameAs https://app.dimensions.ai/details/publication/pub.1000551344
    344 rdf:type schema:CreativeWork
    345 https://doi.org/10.1093/nar/gkv971 schema:sameAs https://app.dimensions.ai/details/publication/pub.1016565847
    346 rdf:type schema:CreativeWork
    347 https://doi.org/10.1093/nar/gkw608 schema:sameAs https://app.dimensions.ai/details/publication/pub.1026274721
    348 rdf:type schema:CreativeWork
    349 https://doi.org/10.1093/nar/gky029 schema:sameAs https://app.dimensions.ai/details/publication/pub.1100409456
    350 rdf:type schema:CreativeWork
    351 https://doi.org/10.1098/rsob.160287 schema:sameAs https://app.dimensions.ai/details/publication/pub.1012544693
    352 rdf:type schema:CreativeWork
    353 https://doi.org/10.1101/gad.12.23.3650 schema:sameAs https://app.dimensions.ai/details/publication/pub.1038408324
    354 rdf:type schema:CreativeWork
    355 https://doi.org/10.1126/science.1083516 schema:sameAs https://app.dimensions.ai/details/publication/pub.1062448022
    356 rdf:type schema:CreativeWork
    357 https://doi.org/10.1128/mcb.00170-15 schema:sameAs https://app.dimensions.ai/details/publication/pub.1002433740
    358 rdf:type schema:CreativeWork
    359 https://doi.org/10.1128/mcb.22.5.1402-1411.2002 schema:sameAs https://app.dimensions.ai/details/publication/pub.1015855877
    360 rdf:type schema:CreativeWork
    361 https://doi.org/10.1146/annurev-biophys-060414-034333 schema:sameAs https://app.dimensions.ai/details/publication/pub.1032774313
    362 rdf:type schema:CreativeWork
    363 https://doi.org/10.1261/rna.033266.112 schema:sameAs https://app.dimensions.ai/details/publication/pub.1007813738
    364 rdf:type schema:CreativeWork
    365 https://doi.org/10.1261/rna.044115.113 schema:sameAs https://app.dimensions.ai/details/publication/pub.1012781945
    366 rdf:type schema:CreativeWork
    367 https://doi.org/10.1261/rna.5040605 schema:sameAs https://app.dimensions.ai/details/publication/pub.1032187951
    368 rdf:type schema:CreativeWork
    369 https://doi.org/10.1371/journal.pbio.1002015 schema:sameAs https://app.dimensions.ai/details/publication/pub.1052499879
    370 rdf:type schema:CreativeWork
    371 https://doi.org/10.1371/journal.pbio.1002150 schema:sameAs https://app.dimensions.ai/details/publication/pub.1026329726
    372 rdf:type schema:CreativeWork
    373 https://doi.org/10.1371/journal.pgen.1001247 schema:sameAs https://app.dimensions.ai/details/publication/pub.1052179678
    374 rdf:type schema:CreativeWork
    375 https://doi.org/10.1371/journal.pgen.1002603 schema:sameAs https://app.dimensions.ai/details/publication/pub.1053297773
    376 rdf:type schema:CreativeWork
    377 https://doi.org/10.1371/journal.pgen.1003647 schema:sameAs https://app.dimensions.ai/details/publication/pub.1009991108
    378 rdf:type schema:CreativeWork
    379 https://doi.org/10.1371/journal.pgen.1005668 schema:sameAs https://app.dimensions.ai/details/publication/pub.1052819451
    380 rdf:type schema:CreativeWork
    381 https://doi.org/10.1371/journal.pgen.1005706 schema:sameAs https://app.dimensions.ai/details/publication/pub.1041288200
    382 rdf:type schema:CreativeWork
    383 https://doi.org/10.1371/journal.pone.0131335 schema:sameAs https://app.dimensions.ai/details/publication/pub.1051757736
    384 rdf:type schema:CreativeWork
    385 https://doi.org/10.1371/journal.ppat.1002642 schema:sameAs https://app.dimensions.ai/details/publication/pub.1016024113
    386 rdf:type schema:CreativeWork
    387 https://doi.org/10.2217/fmb.12.14 schema:sameAs https://app.dimensions.ai/details/publication/pub.1003966577
    388 rdf:type schema:CreativeWork
    389 https://doi.org/10.3390/ijms18112387 schema:sameAs https://app.dimensions.ai/details/publication/pub.1092619147
    390 rdf:type schema:CreativeWork
    391 https://doi.org/10.4161/cc.21919 schema:sameAs https://app.dimensions.ai/details/publication/pub.1014298715
    392 rdf:type schema:CreativeWork
    393 https://doi.org/10.4161/cc.22689 schema:sameAs https://app.dimensions.ai/details/publication/pub.1072297008
    394 rdf:type schema:CreativeWork
    395 https://doi.org/10.4161/rna.20531 schema:sameAs https://app.dimensions.ai/details/publication/pub.1072310017
    396 rdf:type schema:CreativeWork
    397 https://www.grid.ac/institutes/grid.116068.8 schema:alternateName Massachusetts Institute of Technology
    398 schema:name Department of Biological Engineering, Massachusetts Institute of Technology, 02139, Cambridge, MA, USA
    399 Singapore-MIT Alliance for Research and Technology, 138602, 1 CREATE Way, Singapore
    400 rdf:type schema:Organization
    401 https://www.grid.ac/institutes/grid.265850.c schema:alternateName University at Albany, State University of New York
    402 schema:name The RNA Institute, College of Arts and Science, University at Albany, SUNY, 12222, Albany, NY, USA
    403 rdf:type schema:Organization
    404 https://www.grid.ac/institutes/grid.429485.6 schema:alternateName Singapore-MIT Alliance for Research and Technology
    405 schema:name Singapore-MIT Alliance for Research and Technology, 138602, 1 CREATE Way, Singapore
    406 rdf:type schema:Organization
     




    Preview window. Press ESC to close (or click here)


    ...