RNA-Seq alignment to individualized genomes improves transcript abundance estimates in multiparent populations. (Q34243017)

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25236449%20AND%20SRC:MED&resulttype=core&format=json

16 February 2020

title

RNA-Seq alignment to individualized genomes improves transcript abundance estimates in multiparent populations (English)

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25236449%20AND%20SRC:MED&resulttype=core&format=json

16 February 2020

1 reference

1 reference

1

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25236449%20AND%20SRC:MED&resulttype=core&format=json

16 February 2020

Narayanan Raghupathy

2

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25236449%20AND%20SRC:MED&resulttype=core&format=json

16 February 2020

Kwangbom Choi

3

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25236449%20AND%20SRC:MED&resulttype=core&format=json

16 February 2020

Joel H. Graber

11

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25236449%20AND%20SRC:MED&resulttype=core&format=json

16 February 2020

13

Gary A Churchill

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25236449%20AND%20SRC:MED&resulttype=core&format=json

16 February 2020

12

Elissa J Chesler

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25236449%20AND%20SRC:MED&resulttype=core&format=json

16 February 2020

5

Daniel M Gatti

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25236449%20AND%20SRC:MED&resulttype=core&format=json

16 February 2020

7

Karen L Svenson

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25236449%20AND%20SRC:MED&resulttype=core&format=json

16 February 2020

author name string

Allen K Simons

4

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25236449%20AND%20SRC:MED&resulttype=core&format=json

16 February 2020

Douglas A Hinerfeld

6

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25236449%20AND%20SRC:MED&resulttype=core&format=json

16 February 2020

Mark P Keller

8

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25236449%20AND%20SRC:MED&resulttype=core&format=json

16 February 2020

Alan D Attie

9

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25236449%20AND%20SRC:MED&resulttype=core&format=json

16 February 2020

Matthew A Hibbs

10

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25236449%20AND%20SRC:MED&resulttype=core&format=json

16 February 2020

language of work or name

English

0 references

publication date

1 September 2014

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25236449%20AND%20SRC:MED&resulttype=core&format=json

16 February 2020

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25236449%20AND%20SRC:MED&resulttype=core&format=json

16 February 2020

volume

198

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25236449%20AND%20SRC:MED&resulttype=core&format=json

16 February 2020

issue

1

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25236449%20AND%20SRC:MED&resulttype=core&format=json

16 February 2020

page(s)

59-73

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25236449%20AND%20SRC:MED&resulttype=core&format=json

Quantitative trait locus mapping methods for diversity outbred mice

16 February 2020

cites work

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4174954

Sailfish enables alignment-free isoform quantification from RNA-seq reads using lightweight algorithms

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4174954

A review of post-GWAS prioritization approaches

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4174954

Characterizing the genetic basis of transcriptome diversity through RNA-sequencing of 922 individuals

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4174954

Transcriptome and genome sequencing uncovers functional variation in humans

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4174954

Sources of bias in measures of allele-specific expression derived from RNA-sequence data aligned to a single reference genome

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4174954

Integrative eQTL-based analyses reveal the biology of breast cancer risk loci

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4174954

Alternative strategies for development of a reference transcriptome for quantification of allele specific expression in organisms having sparse genomic resources

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4174954

Streaming fragment assignment for real-time analysis of sequencing experiments

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4174954

Pseudogenes: newly discovered players in human cancer

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4174954

Modelling and simulating generic RNA-Seq experiments with the flux simulator

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4174954

ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4174954

The Diversity Outbred mouse population.

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4174954

A new strategy to reduce allelic bias in RNA-Seq readmapping

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4174954

Haplotype probabilities in advanced intercross populations

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4174954

Accelerating the inbreeding of multi-parental recombinant inbred lines generated by sibling matings

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4174954

High-resolution genetic mapping using the Mouse Diversity outbred population

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4174954

Allelic imbalance in Drosophila hybrid heads: exons, isoforms, and evolution

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4174954

DNase I sensitivity QTLs are a major determinant of human expression variation

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4174954

Effects of sequence variation on differential allelic transcription factor occupancy and gene expression

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4174954

Fast computation and applications of genome mappability

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4174954

Mapping personal functional data to personal genomes.

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4174954

Mouse genomic variation and its effect on phenotypes and gene regulation

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4174954

A powerful and flexible statistical framework for testing hypotheses of allele-specific gene expression from RNA-seq data

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4174954

Functional evidence of post-transcriptional regulation by pseudogenes.

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4174954

RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4174954

AlleleSeq: analysis of allele-specific expression and binding in a network framework

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4174954

QTLRel: an R package for genome-wide association studies in which relatedness is a concern

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4174954

Estimation of alternative splicing isoform frequencies from RNA-Seq data

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4174954

Genetic analysis of complex traits in the emerging Collaborative Cross

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4174954

Haplotype and isoform specific expression estimation using multi-mapping RNA-seq reads.

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4174954

From noncoding variant to phenotype via SORT1 at the 1p13 cholesterol locus

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4174954

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

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4174954

Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4174954

Regulatory divergence in Drosophila revealed by mRNA-seq.

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4174954

Understanding mechanisms underlying human gene expression variation with RNA sequencing

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4174954

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

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4174954

RNA-Seq gene expression estimation with read mapping uncertainty

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4174954

Effect of read-mapping biases on detecting allele-specific expression from RNA-sequencing data

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4174954

Fast and accurate short read alignment with Burrows-Wheeler transform

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4174954

TopHat: discovering splice junctions with RNA-Seq

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4174954

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4174954

RNA-Seq: a revolutionary tool for transcriptomics

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4174954

Mapping and quantifying mammalian transcriptomes by RNA-Seq

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4174954

The transcriptional landscape of the yeast genome defined by RNA sequencing

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4174954

Highly integrated single-base resolution maps of the epigenome in Arabidopsis

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4174954

Variations in DNA elucidate molecular networks that cause disease

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4174954

Genetics of gene expression and its effect on disease

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4174954

SNPs matter: impact on detection of differential expression.

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4174954

Genetics of global gene expression

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4174954

Complex trait analysis of gene expression uncovers polygenic and pleiotropic networks that modulate nervous system function

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4174954

Regulatory polymorphisms underlying complex disease traits

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4174954

Efficient computation of significance levels for multiple associations in large studies of correlated data, including genomewide association studies

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4174954

Initial sequencing and comparative analysis of the mouse genome

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4174954

The ambiguous boundary between genes and pseudogenes: the dead rise up, or do they?

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4174954

10.1534/GENETICS.114.165886

28 October 2018

Identifiers

DOI

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25236449%20AND%20SRC:MED&resulttype=core&format=json

16 February 2020

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25236449%20AND%20SRC:MED&resulttype=core&format=json

16 February 2020

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25236449%20AND%20SRC:MED&resulttype=core&format=json