An annotation agnostic algorithm for detecting nascent RNA transcripts in GRO-seq (Q40037734)

26829802

16 September 2017

title

An annotation agnostic algorithm for detecting nascent RNA transcripts in GRO-seq (English)

1 reference

16 September 2017

3

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https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26829802%20AND%20SRC:MED&resulttype=core&format=json

11 June 2020

Robin D. Dowell

series ordinal

4

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https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26829802%20AND%20SRC:MED&resulttype=core&format=json

11 June 2020

author name string

Joseph G Azofeifa

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1

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https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26829802%20AND%20SRC:MED&resulttype=core&format=json

11 June 2020

Mary A Allen

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2

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https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26829802%20AND%20SRC:MED&resulttype=core&format=json

11 June 2020

publication date

26 January 2016

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26829802

IEEE/ACM Transactions on Computational Biology and Bioinformatics

16 September 2017

published in

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https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26829802%20AND%20SRC:MED&resulttype=core&format=json

11 June 2020

volume

14

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11 June 2020

issue

5

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11 June 2020

page(s)

1070-1081

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groHMM: a computational tool for identifying unannotated and cell type-specific transcription units from global run-on sequencing data

11 June 2020

cites work

1 reference

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Identification of active transcriptional regulatory elements from GRO-seq data

14 September 2018

1 reference

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Comparative overview of RNA polymerase II and III transcription cycles, with focus on RNA polymerase III termination and reinitiation

14 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5667649

Determination of in vivo RNA kinetics using RATE-seq

14 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5667649

Global analysis of p53-regulated transcription identifies its direct targets and unexpected regulatory mechanisms.

14 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5667649

Transcriptional enhancers: from properties to genome-wide predictions

14 September 2018

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Active enhancer positions can be accurately predicted from chromatin marks and collective sequence motif data

14 September 2018

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Vespucci: a system for building annotated databases of nascent transcripts

14 September 2018

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RefSeq: an update on mammalian reference sequences

14 September 2018

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A high-resolution map of the three-dimensional chromatin interactome in human cells

14 September 2018

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Comprehensive evaluation of differential gene expression analysis methods for RNA-seq data

14 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5667649

The little elongation complex functions at initiation and elongation phases of snRNA gene transcription

14 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5667649

Functional roles of enhancer RNAs for oestrogen-dependent transcriptional activation

14 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5667649

SR proteins collaborate with 7SK and promoter-associated nascent RNA to release paused polymerase

14 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5667649

Enhancer transcripts mark active estrogen receptor binding sites

14 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5667649

eRNAs are required for p53-dependent enhancer activity and gene transcription

14 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5667649

How to stop: the mysterious links among RNA polymerase II occupancy 3' of genes, mRNA 3' processing and termination

14 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5667649

The long-range interaction landscape of gene promoters

14 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5667649

An integrated encyclopedia of DNA elements in the human genome

14 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5667649

Cell type-specific binding patterns reveal that TCF7L2 can be tethered to the genome by association with GATA3.

14 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5667649

Insights into p53 transcriptional function via genome-wide chromatin occupancy and gene expression analysis

14 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5667649

The NIH Roadmap Epigenomics Program data resource

14 September 2018

1 reference

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Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration

14 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5667649

Differential DNase I hypersensitivity reveals factor-dependent chromatin dynamics

14 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5667649

Discovery of active enhancers through bidirectional expression of short transcripts

14 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5667649

Genome-wide profiling of DNA methylation in human cancer cells

14 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5667649

PROMoter uPstream Transcripts share characteristics with mRNAs and are produced upstream of all three major types of mammalian promoters

14 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5667649

Reprogramming transcription by distinct classes of enhancers functionally defined by eRNA

14 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5667649

A rapid, extensive, and transient transcriptional response to estrogen signaling in breast cancer cells

14 September 2018

1 reference

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Regulating RNA polymerase pausing and transcription elongation in embryonic stem cells

14 September 2018

1 reference

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Role of p53 serine 46 in p53 target gene regulation

14 September 2018

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X chromosome dosage compensation via enhanced transcriptional elongation in Drosophila

14 September 2018

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Integrative model of genomic factors for determining binding site selection by estrogen receptor-α

14 September 2018

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Aligning short sequencing reads with Bowtie

14 September 2018

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Differential expression analysis for sequence count data

14 September 2018

1 reference

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Widespread transcription at neuronal activity-regulated enhancers

14 September 2018

1 reference

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An oestrogen-receptor-α-bound human chromatin interactome

14 September 2018

1 reference

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Defining mechanisms that regulate RNA polymerase II transcription in vivo

14 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5667649

Nascent RNA sequencing reveals widespread pausing and divergent initiation at human promoters

14 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5667649

Divergent transcription from active promoters

14 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5667649

Characterization of genome-wide p53-binding sites upon stress response.

14 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5667649

Robust speech recognition based on joint model and feature space optimization of hidden Markov models

14 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5667649

Genome-wide transcription and the implications for genomic organization

14 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5667649

Metagene projection for cross-platform, cross-species characterization of global transcriptional states

14 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5667649

A hybrid SEM algorithm for high-dimensional unsupervised learning using a finite generalized Dirichlet mixture.

14 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5667649

A global map of p53 transcription-factor binding sites in the human genome

14 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5667649

Logistic regression and artificial neural network classification models: a methodology review

14 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5667649

Fitting mixture models to grouped and truncated data via the EM algorithm

14 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5667649

10.1109/TCBB.2016.2520919

14 September 2018

Identifiers

DOI

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https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26829802%20AND%20SRC:MED&resulttype=core&format=json

11 June 2020

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https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26829802%20AND%20SRC:MED&resulttype=core&format=json

11 June 2020

26829802

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