Thomas R Gingeras
Affiliation: Cold Spring Harbor Laboratory
- Implications of chimaeric non-co-linear transcriptsThomas 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...
- Evidence for transcript networks composed of chimeric RNAs in human cellsSarah 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...
- High resolution transcriptome maps for wild-type and nonsense-mediated decay-defective Caenorhabditis elegansArun 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...
- Landscape of transcription in human cellsSarah 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...
- The GENCODE v7 catalog of human long noncoding RNAs: analysis of their gene structure, evolution, and expressionThomas 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...
- Prominent use of distal 5' transcription start sites and discovery of a large number of additional exons in ENCODE regionsFrance 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....
- STAR: ultrafast universal RNA-seq alignerAlexander 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...
- Deep sequencing of subcellular RNA fractions shows splicing to be predominantly co-transcriptional in the human genome but inefficient for lncRNAsHagen 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...
- De novo DNA demethylation and noncoding transcription define active intergenic regulatory elementsFelix Schlesinger
Watson School of Biological Sciences, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
Genome Res 23:1601-14. 2013....
- Large-scale transcriptional activity in chromosomes 21 and 22Philipp 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...
- EGASP: the human ENCODE Genome Annotation Assessment ProjectRoderic 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...
- RAMPAGE: Promoter Activity Profiling by Paired-End Sequencing of 5'-Complete cDNAsPhilippe 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. ..