User profiles for T. R. Gingeras
Thomas GingerasProfessor of Functional Genomics, Cold Spring Harbor Laboratory Verified email at cshl.edu Cited by 139865 |
[HTML][HTML] Long non-coding RNAs: definitions, functions, challenges and recommendations
Genes specifying long non-coding RNAs (lncRNAs) occupy a large fraction of the genomes
of complex organisms. The term ‘lncRNAs’ encompasses RNA polymerase I (Pol I), Pol II …
of complex organisms. The term ‘lncRNAs’ encompasses RNA polymerase I (Pol I), Pol II …
High density synthetic oligonucleotide arrays
Experimental genomics involves taking advantage of sequence information to investigate and
understand the workings of genes, cells and organisms. We have developed an approach …
understand the workings of genes, cells and organisms. We have developed an approach …
Mapping RNA‐seq reads with STAR
A Dobin, TR Gingeras - Current protocols in bioinformatics, 2015 - Wiley Online Library
Mapping of large sets of high‐throughput sequencing reads to a reference genome is one
of the foundational steps in RNA‐seq data analysis. The STAR software package performs …
of the foundational steps in RNA‐seq data analysis. The STAR software package performs …
STAR: ultrafast universal RNA-seq aligner
Motivation: Accurate alignment of high-throughput RNA-seq data is a challenging and yet
unsolved problem because of the non-contiguous transcript structure, relatively short read …
unsolved problem because of the non-contiguous transcript structure, relatively short read …
The transcriptional landscape of the mammalian genome
…, M Gariboldi, P Georgii-Hemming, TR Gingeras… - science, 2005 - science.org
This study describes comprehensive polling of transcription start and termination sites and
analysis of previously unidentified full-length complementary DNAs derived from the mouse …
analysis of previously unidentified full-length complementary DNAs derived from the mouse …
[HTML][HTML] Landscape of transcription in human cells
Eukaryotic cells make many types of primary and processed RNAs that are found either in
specific subcellular compartments or throughout the cells. A complete catalogue of these …
specific subcellular compartments or throughout the cells. A complete catalogue of these …
Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project
We report the generation and analysis of functional data from multiple, diverse experiments
performed on a targeted 1% of the human genome as part of the pilot phase of the ENCODE …
performed on a targeted 1% of the human genome as part of the pilot phase of the ENCODE …
The GENCODE v7 catalog of human long noncoding RNAs: analysis of their gene structure, evolution, and expression
…, CA Davis, R Shiekhattar, TR Gingeras… - Genome …, 2012 - genome.cshlp.org
The human genome contains many thousands of long noncoding RNAs (lncRNAs). While
several studies have demonstrated compelling biological and disease roles for individual …
several studies have demonstrated compelling biological and disease roles for individual …
CD127 expression inversely correlates with FoxP3 and suppressive function of human CD4+ T reg cells
Regulatory T (T reg) cells are critical regulators of immune tolerance. Most T reg cells are
defined based on expression of CD4, CD25, and the transcription factor, FoxP3. However, …
defined based on expression of CD4, CD25, and the transcription factor, FoxP3. However, …
RNA maps reveal new RNA classes and a possible function for pervasive transcription
…, V Sementchenko, H Tammana, TR Gingeras - Science, 2007 - science.org
Significant fractions of eukaryotic genomes give rise to RNA, much of which is unannotated
and has reduced protein-coding potential. The genomic origins and the associations of …
and has reduced protein-coding potential. The genomic origins and the associations of …