Thomas R Gingeras

Summary

Affiliation: Cold Spring Harbor Laboratory
Country: USA

Publications

  1. pmc Implications of chimaeric non-co-linear transcripts
    Thomas R Gingeras
    Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, New York 11724, USA
    Nature 461:206-11. 2009
  2. pmc Evidence for transcript networks composed of chimeric RNAs in human cells
    Sarah Djebali
    Bioinformatics and Genomics, Centre for Genomic Regulation and Universitat Pompeu Fabra, Barcelona, Catalonia, Spain
    PLoS ONE 7:e28213. 2012
  3. pmc High resolution transcriptome maps for wild-type and nonsense-mediated decay-defective Caenorhabditis elegans
    Arun K Ramani
    Donnelly CCBR, College Street, University of Toronto, Toronto, M5S 3E1, Canada
    Genome Biol 10:R101. 2009
  4. pmc Landscape of transcription in human cells
    Sarah Djebali
    Centre for Genomic Regulation and UPF, Doctor Aiguader 88, Barcelona 08003, Catalonia, Spain
    Nature 489:101-8. 2012
  5. pmc The GENCODE v7 catalog of human long noncoding RNAs: analysis of their gene structure, evolution, and expression
    Thomas Derrien
    Bioinformatics and Genomics, Centre for Genomic Regulation and UPF, 08003 Barcelona, Catalonia, Spain
    Genome Res 22:1775-89. 2012
  6. pmc Prominent use of distal 5' transcription start sites and discovery of a large number of additional exons in ENCODE regions
    France Denoeud
    Grup de Recerca en Informàtica Biomèdica, Institut Municipal d Investigació Mèdica Universitat Pompeu Fabra, 08003 Barcelona, Catalonia, Spain
    Genome Res 17:746-59. 2007
  7. pmc STAR: ultrafast universal RNA-seq aligner
    Alexander Dobin
    Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
    Bioinformatics 29:15-21. 2013
  8. pmc Deep sequencing of subcellular RNA fractions shows splicing to be predominantly co-transcriptional in the human genome but inefficient for lncRNAs
    Hagen Tilgner
    Centre for Genomic Regulation and UPF, E 08003, Barcelona, Catalonia, Spain
    Genome Res 22:1616-25. 2012
  9. pmc De novo DNA demethylation and noncoding transcription define active intergenic regulatory elements
    Felix Schlesinger
    Watson School of Biological Sciences, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
    Genome Res 23:1601-14. 2013
  10. ncbi request reprint Large-scale transcriptional activity in chromosomes 21 and 22
    Philipp Kapranov
    Affymetrix, Santa Clara, CA 95051, USA, National Cancer Institute, Bethesda, MD 20892, USA
    Science 296:916-9. 2002

Collaborators

Detail Information

Publications12

  1. pmc Implications of chimaeric non-co-linear transcripts
    Thomas R Gingeras
    Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, New York 11724, USA
    Nature 461:206-11. 2009
    ..The existence of such chimaeric RNAs has far-reaching implications for the potential information content of genomes and the way it is arranged...
  2. pmc Evidence for transcript networks composed of chimeric RNAs in human cells
    Sarah Djebali
    Bioinformatics and Genomics, Centre for Genomic Regulation and Universitat Pompeu Fabra, Barcelona, Catalonia, Spain
    PLoS ONE 7:e28213. 2012
    ..The non-random nature of the connection of the genes involved suggest that chimeric transcripts should not be studied in isolation, but together, as an RNA network...
  3. pmc High resolution transcriptome maps for wild-type and nonsense-mediated decay-defective Caenorhabditis elegans
    Arun K Ramani
    Donnelly CCBR, College Street, University of Toronto, Toronto, M5S 3E1, Canada
    Genome Biol 10:R101. 2009
    ..We utilized this framework to identify transcriptome changes in animals lacking the nonsense-mediated decay (NMD) pathway...
  4. pmc Landscape of transcription in human cells
    Sarah Djebali
    Centre for Genomic Regulation and UPF, Doctor Aiguader 88, Barcelona 08003, Catalonia, Spain
    Nature 489:101-8. 2012
    ..These observations, taken together, prompt a redefinition of the concept of a gene...
  5. pmc The GENCODE v7 catalog of human long noncoding RNAs: analysis of their gene structure, evolution, and expression
    Thomas Derrien
    Bioinformatics and Genomics, Centre for Genomic Regulation and UPF, 08003 Barcelona, Catalonia, Spain
    Genome Res 22:1775-89. 2012
    ..Expression correlation analysis indicates that lncRNAs show particularly striking positive correlation with the expression of antisense coding genes. This GENCODE annotation represents a valuable resource for future studies of lncRNAs...
  6. pmc Prominent use of distal 5' transcription start sites and discovery of a large number of additional exons in ENCODE regions
    France Denoeud
    Grup de Recerca en Informàtica Biomèdica, Institut Municipal d Investigació Mèdica Universitat Pompeu Fabra, 08003 Barcelona, Catalonia, Spain
    Genome Res 17:746-59. 2007
    ....
  7. pmc STAR: ultrafast universal RNA-seq aligner
    Alexander Dobin
    Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
    Bioinformatics 29:15-21. 2013
    ..Currently available RNA-seq aligners suffer from high mapping error rates, low mapping speed, read length limitation and mapping biases...
  8. pmc Deep sequencing of subcellular RNA fractions shows splicing to be predominantly co-transcriptional in the human genome but inefficient for lncRNAs
    Hagen Tilgner
    Centre for Genomic Regulation and UPF, E 08003, Barcelona, Catalonia, Spain
    Genome Res 22:1616-25. 2012
    ..For alternative exons and long noncoding RNAs, splicing tends to occur later, and the latter might remain unspliced in some cases...
  9. pmc De novo DNA demethylation and noncoding transcription define active intergenic regulatory elements
    Felix Schlesinger
    Watson School of Biological Sciences, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
    Genome Res 23:1601-14. 2013
    ....
  10. ncbi request reprint Large-scale transcriptional activity in chromosomes 21 and 22
    Philipp Kapranov
    Affymetrix, Santa Clara, CA 95051, USA, National Cancer Institute, Bethesda, MD 20892, USA
    Science 296:916-9. 2002
    ..When compared with the sequence annotations available for these chromosomes, it is noted that as much as an order of magnitude more of the genomic sequence is transcribed than accounted for by the predicted and characterized exons...
  11. pmc EGASP: the human ENCODE Genome Annotation Assessment Project
    Roderic Guigo
    Centre de Regulacio Genomica, Institut Municipal d Investigació Mèdica Universitat Pompeu Fabra, E08003 Barcelona, Catalonia, Spain
    Genome Biol 7:S2.1-31. 2006
    ..These annotations were not available to the prediction groups prior to the submission deadline, so that their predictions were blind and an external advisory committee could perform a fair assessment...
  12. ncbi request reprint RAMPAGE: Promoter Activity Profiling by Paired-End Sequencing of 5'-Complete cDNAs
    Philippe Batut
    Watson School of Biological Sciences, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York
    Curr Protoc Mol Biol 104:25B.11.1-25B.11.16. 2013
    ..This method has been applied successfully to human and Drosophila samples, and in principle should be applicable to any eukaryotic system. Curr. Protoc. Mol. Biol. 104:25B.11.1-25B.11.16. © 2013 by John Wiley & Sons, Inc. ..