(Q40199664)

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26679539%20AND%20SRC:MED&resulttype=core&format=json

2 March 2020

title

Transcriptome-wide RNA processing kinetics revealed using extremely short 4tU labeling (English)

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26679539%20AND%20SRC:MED&resulttype=core&format=json

2 March 2020

0 references

4

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26679539%20AND%20SRC:MED&resulttype=core&format=json

2 March 2020

Sander Granneman

7

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26679539%20AND%20SRC:MED&resulttype=core&format=json

2 March 2020

David Barrass

1

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26679539%20AND%20SRC:MED&resulttype=core&format=json

2 March 2020

Jane E A Reid

2

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26679539%20AND%20SRC:MED&resulttype=core&format=json

2 March 2020

Yuanhua Huang

3

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26679539%20AND%20SRC:MED&resulttype=core&format=json

2 March 2020

6

Jean D Beggs

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26679539%20AND%20SRC:MED&resulttype=core&format=json

2 March 2020

author name string

Guido Sanguinetti

5

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26679539%20AND%20SRC:MED&resulttype=core&format=json

2 March 2020

publication date

17 December 2015

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26679539%20AND%20SRC:MED&resulttype=core&format=json

2 March 2020

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26679539%20AND%20SRC:MED&resulttype=core&format=json

2 March 2020

volume

16

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26679539%20AND%20SRC:MED&resulttype=core&format=json

2 March 2020

issue

1

1 reference

28 June 2019

page(s)

282

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26679539%20AND%20SRC:MED&resulttype=core&format=json

Creative Commons Attribution 4.0 International

2 March 2020

copyright license

start time

1 December 2015

1 reference

April 2022 Public Data File from Crossref

copyright status

copyrighted

0 references

describes a project that uses

DESeq2

object named as

DESeq2

DESeq

1 reference

CZ Software Mentions: A large dataset of software mentions in the biomedical literature

DESeq2

0 references

cites work

The long non-coding RNA world in yeasts

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4699367

Nucleotide sequence composition adjacent to intronic splice sites improves splicing efficiency via its effect on pre-mRNA local folding in fungi

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4699367

Non-coding transcription by RNA polymerase II in yeast: Hasard or nécessité?

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4699367

Quantification of co-transcriptional splicing from RNA-Seq data

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4699367

Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4699367

Determination of in vivo RNA kinetics using RATE-seq

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4699367

FLEXBAR-Flexible Barcode and Adapter Processing for Next-Generation Sequencing Platforms

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4699367

SnapShot-Seq: a method for extracting genome-wide, in vivo mRNA dynamics from a single total RNA sample

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4699367

PAR-CLIP data indicate that Nrd1-Nab3-dependent transcription termination regulates expression of hundreds of protein coding genes in yeast

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4699367

Dealing with pervasive transcription.

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4699367

Transcriptome surveillance by selective termination of noncoding RNA synthesis.

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4699367

4-thiouridine inhibits rRNA synthesis and causes a nucleolar stress response

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4699367

Lariat sequencing in a unicellular yeast identifies regulated alternative splicing of exons that are evolutionarily conserved with humans

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4699367

STAR: ultrafast universal RNA-seq aligner

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4699367

Extensive degradation of RNA precursors by the exosome in wild-type cells

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4699367

Deep sequencing of subcellular RNA fractions shows splicing to be predominantly co-transcriptional in the human genome but inefficient for lncRNAs

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4699367

Cryptic transcription and early termination in the control of gene expression

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4699367

Ultrashort and progressive 4sU-tagging reveals key characteristics of RNA processing at nucleotide resolution

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4699367

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4699367

Spliceosome Structure and Function

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4699367

Dynamic transcriptome analysis measures rates of mRNA synthesis and decay in yeast

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4699367

Analysis and design of RNA sequencing experiments for identifying isoform regulation

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4699367

RiboSys, a high-resolution, quantitative approach to measure the in vivo kinetics of pre-mRNA splicing and 3'-end processing in Saccharomyces cerevisiae.

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4699367

The differential interaction of snRNPs with pre-mRNA reveals splicing kinetics in living cells

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4699367

Rates of in situ transcription and splicing in large human genes

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4699367

Bidirectional promoters generate pervasive transcription in yeast

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4699367

Correlation between the secondary structure of pre-mRNA introns and the efficiency of splicing in Saccharomyces cerevisiae.

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4699367

Distinct pathways for snoRNA and mRNA termination

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4699367

WebLogo: A Sequence Logo Generator

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4699367

Direct sorting of the yeast uracil permease to the endosomal system is controlled by uracil binding and Rsp5p-dependent ubiquitylation.

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4699367

RNA-binding protein Nrd1 directs poly(A)-independent 3'-end formation of RNA polymerase II transcripts

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4699367

Identification of a regulated pathway for nuclear pre-mRNA turnover.

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4699367

Genome-wide bioinformatic and molecular analysis of introns in Saccharomyces cerevisiae

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4699367

Seven novel methylation guide small nucleolar RNAs are processed from a common polycistronic transcript by Rat1p and RNase III in yeast.

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4699367

The putative nucleic acid helicase Sen1p is required for formation and stability of termini and for maximal rates of synthesis and levels of accumulation of small nucleolar RNAs in Saccharomyces cerevisiae

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4699367

The ORF YBL042 of Saccharomyces cerevisiae encodes a uridine permease

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4699367

Snapshots of pre-rRNA structural flexibility reveal eukaryotic 40S assembly dynamics at nucleotide resolution

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4699367

LaSSO, a strategy for genome-wide mapping of intronic lariats and branch points using RNA-seq

17 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4699367

High-resolution gene expression profiling for simultaneous kinetic parameter analysis of RNA synthesis and decay

17 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4699367

Deciphering 3'ss selection in the yeast genome reveals an RNA thermosensor that mediates alternative splicing

17 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4699367

XUTs are a class of Xrn1-sensitive antisense regulatory non-coding RNA in yeast.

20 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4699367

Biosynthetic labeling of RNA with uracil phosphoribosyltransferase allows cell-specific microarray analysis of mRNA synthesis and decay

20 August 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/26679539

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Splice site choice and splicing efficiency are positively influenced by pre-mRNA intramolecular base pairing in yeast

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/26679539

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1186/S13059-015-0848-1

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26679539%20AND%20SRC:MED&resulttype=core&format=json

Dimensions Publication ID

2 March 2020

0 references

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26679539%20AND%20SRC:MED&resulttype=core&format=json

2 March 2020

PubMed publication ID

26679539

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26679539%20AND%20SRC:MED&resulttype=core&format=json