Allelome.PRO, a pipeline to define allele-specific genomic features from high-throughput sequencing data. (Q30982170)

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26202974%20AND%20SRC:MED&resulttype=core&format=json

20 February 2020

title

Allelome.PRO, a pipeline to define allele-specific genomic features from high-throughput sequencing data (English)

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26202974%20AND%20SRC:MED&resulttype=core&format=json

high-throughput sequencing

20 February 2020

main subject

RNA sequencing

0 references

1 reference

3

1 reference

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20 February 2020

Quanah J Hudson

8

1 reference

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20 February 2020

author name string

Daniel Andergassen

1

1 reference

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20 February 2020

Christoph P Dotter

2

1 reference

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20 February 2020

Philipp M Guenzl

4

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26202974%20AND%20SRC:MED&resulttype=core&format=json

20 February 2020

Philipp C Bammer

5

1 reference

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20 February 2020

Denise P Barlow

6

1 reference

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20 February 2020

Florian M Pauler

7

1 reference

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20 February 2020

language of work or name

English

0 references

publication date

21 July 2015

1 reference

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20 February 2020

published in

Nucleic Acids Research

1 reference

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20 February 2020

volume

43

1 reference

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20 February 2020

issue

21

1 reference

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20 February 2020

page(s)

e146

1 reference

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Creative Commons Attribution 4.0 International

20 February 2020

copyright license

start time

11 November 2016

1 reference

April 2022 Public Data File from Crossref

copyright status

copyrighted

0 references

cites work

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Allelic expression analysis of the osteoarthritis susceptibility locus that maps to chromosome 3p21 reveals cis-acting eQTLs at GNL3 and SPCS1

21 June 2018

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21 June 2018

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Post-natal imprinting: evidence from marsupials

21 June 2018

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Single-cell RNA-seq reveals dynamic, random monoallelic gene expression in mammalian cells

21 June 2018

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Characterization of the imprinting signature of mouse embryo fibroblasts by RNA deep sequencing

21 June 2018

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Singular expression of olfactory receptor genes

21 June 2018

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Genetic architecture of skewed X inactivation in the laboratory mouse

21 June 2018

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Analysis of allele-specific expression in mouse liver by RNA-Seq: a comparison with Cis-eQTL identified using genetic linkage

21 June 2018

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Whole transcriptome RNA-Seq allelic expression in human brain

21 June 2018

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21 June 2018

Clustered protocadherins

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Genome-wide generation and systematic phenotyping of knockout mice reveals new roles for many genes

21 June 2018

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Gene regulation by the act of long non-coding RNA transcription

21 June 2018

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TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions

21 June 2018

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Different flavors of X-chromosome inactivation in mammals

21 June 2018

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Imprinted silencing is extended over broad chromosomal domains in mouse extra-embryonic lineages

21 June 2018

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STAR: ultrafast universal RNA-seq aligner

21 June 2018

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Large-scale profiling and identification of potential regulatory mechanisms for allelic gene expression in colorectal cancer cells

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4666383

A survey of tissue-specific genomic imprinting in mammals

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4666383

A simple strand-specific RNA-Seq library preparation protocol combining the Illumina TruSeq RNA and the dUTP methods

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4666383

Critical evaluation of imprinted gene expression by RNA-Seq: a new perspective

21 June 2018

1 reference

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Identification of allele-specific alternative mRNA processing via transcriptome sequencing

21 June 2018

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Autosomal monoallelic expression in the mouse

21 June 2018

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Base-resolution analyses of sequence and parent-of-origin dependent DNA methylation in the mouse genome

21 June 2018

1 reference

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Next-generation DNA sequencing-based assay for measuring allelic expression imbalance (AEI) of candidate neuropsychiatric disorder genes in human brain

21 June 2018

1 reference

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Mouse genomic variation and its effect on phenotypes and gene regulation

21 June 2018

1 reference

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A survey for novel imprinted genes in the mouse placenta by mRNA-seq

21 June 2018

1 reference

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Extra-embryonic-specific imprinted expression is restricted to defined lineages in the post-implantation embryo.

21 June 2018

1 reference

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The study of eQTL variations by RNA-seq: from SNPs to phenotypes

21 June 2018

1 reference

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Identification and resolution of artifacts in the interpretation of imprinted gene expression

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4666383

The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4666383

High-resolution analysis of parent-of-origin allelic expression in the mouse brain

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4666383

Global survey of escape from X inactivation by RNA-sequencing in mouse

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4666383

Fast and SNP-tolerant detection of complex variants and splicing in short reads

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4666383

BEDTools: a flexible suite of utilities for comparing genomic features

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4666383

Transcriptome analysis by strand-specific sequencing of complementary DNA.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4666383

The Sequence Alignment/Map format and SAMtools

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4666383

The function of non-coding RNAs in genomic imprinting

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4666383

Transcriptome-wide identification of novel imprinted genes in neonatal mouse brain

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4666383

Global survey of genomic imprinting by transcriptome sequencing

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4666383

Transcript- and tissue-specific imprinting of a tumour suppressor gene

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4666383

Revealing the architecture of gene regulation: the promise of eQTL studies

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4666383

Differential allelic expression in the human genome: a robust approach to identify genetic and epigenetic cis-acting mechanisms regulating gene expression

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4666383

Control of imprinting at the Gnas cluster.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4666383

Widespread monoallelic expression on human autosomes

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4666383

Active and repressive chromatin are interspersed without spreading in an imprinted gene cluster in the mammalian genome.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4666383

Genome-wide maps of chromatin state in pluripotent and lineage-committed cells

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4666383

A screen for retrotransposed imprinted genes reveals an association between X chromosome homology and maternal germ-line methylation

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4666383

Genetic control of X chromosome inactivation in mice: definition of the Xce candidate interval

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4666383

A census of mammalian imprinting.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4666383

A novel variant of Inpp5f is imprinted in brain, and its expression is correlated with differential methylation of an internal CpG island

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4666383

The lingering enigma of the allelic exclusion mechanism

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4666383

Identification of novel imprinted genes in a genome-wide screen for maternal methylation.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4666383

The human genome browser at UCSC

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4666383

The imprinted gene and parent-of-origin effect database

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4666383

Migration of mesonephric cells into the mammalian gonad depends on Sry.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4666383

Identification of imprinted loci by transcriptome sequencing.

21 June 2018

1 reference

Crossref

https://api.crossref.org/works/10.1093%2FNAR%2FGKV727

Paternal deletion of Meg1/Grb10 DMR causes maternalization of the Meg1/Grb10 cluster in mouse proximal Chromosome 11 leading to severe pre- and postnatal growth retardation.

21 January 2018

1 reference

Crossref

https://api.crossref.org/works/10.1093%2FNAR%2FGKV727

Re-investigation and RNA sequencing-based identification of genes with placenta-specific imprinted expression

21 January 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/26202974

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1093/NAR/GKV727

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26202974%20AND%20SRC:MED&resulttype=core&format=json

20 February 2020

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26202974%20AND%20SRC:MED&resulttype=core&format=json

20 February 2020

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26202974%20AND%20SRC:MED&resulttype=core&format=json