(Q31097750)

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Challenges and strategies in transcriptome assembly and differential gene expression quantification. A comprehensive in silico assessment of RNA-seq experiments

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scholarly article

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Europe PubMed Central

PubMed publication ID

28 June 2017

Challenges and strategies in transcriptome assembly and differential gene expression quantification. A comprehensive in silico assessment of RNA-seq experiments (English)

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Europe PubMed Central

PubMed publication ID

28 June 2017

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Axel Künstner

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Nagarjun Vijay

1

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Europe PubMed Central

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28 June 2017

Jelmer W Poelstra

2

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Europe PubMed Central

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28 June 2017

Jochen B W Wolf

4

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Europe PubMed Central

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28 June 2017

publication date

24 September 2012

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Europe PubMed Central

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28 June 2017

Molecular Ecology

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Europe PubMed Central

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28 June 2017

22

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Europe PubMed Central

PubMed publication ID

28 June 2017

3

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Europe PubMed Central

PubMed publication ID

28 June 2017

620-634

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Europe PubMed Central

PubMed publication ID

28 June 2017

Validation of internal reference genes for quantitative real-time PCR in a non-model organism, the yellow-necked mouse, Apodemus flavicollis

1 reference

https://api.crossref.org/works/10.1111%2FMEC.12014

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Derivation of species-specific hybridization-like knowledge out of cross-species hybridization results

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DNA assembly with gaps (Dawg): simulating sequence evolution.

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Assessing performance of orthology detection strategies applied to eukaryotic genomes

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Modernizing reference genome assemblies

1 reference

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Evidence for compensatory upregulation of expressed X-linked genes in mammals, Caenorhabditis elegans and Drosophila melanogaster

1 reference

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Applications of next generation sequencing in molecular ecology of non-model organisms

1 reference

https://api.crossref.org/works/10.1111%2FMEC.12014

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Comparison between Normalised and Unnormalised 454-Sequencing Libraries for Small-Scale RNA-Seq Studies.

1 reference

https://api.crossref.org/works/10.1111%2FMEC.12014

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Rapid evolution and selection inferred from the transcriptomes of sympatric crater lake cichlid fishes

1 reference

https://api.crossref.org/works/10.1111%2FMEC.12014

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Estimating accuracy of RNA-Seq and microarrays with proteomics

1 reference

https://api.crossref.org/works/10.1111%2FMEC.12014

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Genome 10K: a proposal to obtain whole-genome sequence for 10,000 vertebrate species

1 reference

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A genetic basis for the phenotypic differentiation between siscowet and lean lake trout (Salvelinus namaycush).

1 reference

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A bioinformatics approach for determining sample identity from different lanes of high-throughput sequencing data

1 reference

https://api.crossref.org/works/10.1111%2FMEC.12014

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Genome-wide synteny through highly sensitive sequence alignment: Satsuma

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Full-length transcriptome assembly from RNA-Seq data without a reference genome

1 reference

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baySeq: empirical Bayesian methods for identifying differential expression in sequence count data

1 reference

https://api.crossref.org/works/10.1111%2FMEC.12014

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Computational methods for Gene Orthology inference

1 reference

https://api.crossref.org/works/10.1111%2FMEC.12014

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Comparative genomics based on massive parallel transcriptome sequencing reveals patterns of substitution and selection across 10 bird species

1 reference

https://api.crossref.org/works/10.1111%2FMEC.12014

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Versatile and open software for comparing large genomes

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https://api.crossref.org/works/10.1111%2FMEC.12014

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A comparison of statistical methods for detecting differentially expressed genes from RNA-seq data

1 reference

https://api.crossref.org/works/10.1111%2FMEC.12014

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

1 reference

https://api.crossref.org/works/10.1111%2FMEC.12014

21 January 2018

The Sequence Alignment/Map format and SAMtools

1 reference

https://api.crossref.org/works/10.1111%2FMEC.12014

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Stampy: a statistical algorithm for sensitive and fast mapping of Illumina sequence reads

1 reference

https://api.crossref.org/works/10.1111%2FMEC.12014

21 January 2018

RNA-seq: an assessment of technical reproducibility and comparison with gene expression arrays

1 reference

https://api.crossref.org/works/10.1111%2FMEC.12014

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28-way vertebrate alignment and conservation track in the UCSC Genome Browser

1 reference

https://api.crossref.org/works/10.1111%2FMEC.12014

21 January 2018

The sex-biased brain: sexual dimorphism in gene expression in two species of songbirds

1 reference

https://api.crossref.org/works/10.1111%2FMEC.12014

21 January 2018

RNA sequencing: advances, challenges and opportunities

1 reference

https://api.crossref.org/works/10.1111%2FMEC.12014

21 January 2018

Mapping accuracy of short reads from massively parallel sequencing and the implications for quantitative expression profiling

1 reference

https://api.crossref.org/works/10.1111%2FMEC.12014

21 January 2018

Sequencing technologies and genome sequencing

1 reference

https://api.crossref.org/works/10.1111%2FMEC.12014

21 January 2018

Comparative RNA sequencing reveals substantial genetic variation in endangered primates

1 reference

https://api.crossref.org/works/10.1111%2FMEC.12014

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BEDTools: a flexible suite of utilities for comparing genomic features

1 reference

https://api.crossref.org/works/10.1111%2FMEC.12014

21 January 2018

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data

1 reference

https://api.crossref.org/works/10.1111%2FMEC.12014

21 January 2018

GAGE: A critical evaluation of genome assemblies and assembly algorithms

1 reference

https://api.crossref.org/works/10.1111%2FMEC.12014

21 January 2018

ROCR: visualizing classifier performance in R

1 reference

https://api.crossref.org/works/10.1111%2FMEC.12014

21 January 2018

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

1 reference

https://api.crossref.org/works/10.1111%2FMEC.12014

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Alternative isoform regulation in human tissue transcriptomes

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https://api.crossref.org/works/10.1111%2FMEC.12014

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Evaluation of the coverage and depth of transcriptome by RNA-Seq in chickens

1 reference

https://api.crossref.org/works/10.1111%2FMEC.12014

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The genome of a songbird

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General lack of global dosage compensation in ZZ/ZW systems? Broadening the perspective with RNA-seq

1 reference

https://api.crossref.org/works/10.1111%2FMEC.12014

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Nucleotide divergence vs. gene expression differentiation: comparative transcriptome sequencing in natural isolates from the carrion crow and its hybrid zone with the hooded crow

1 reference

https://api.crossref.org/works/10.1111%2FMEC.12014

21 January 2018

Identifiers

10.1111/MEC.12014

1 reference

Europe PubMed Central

PubMed publication ID

28 June 2017

PubMed publication ID

1 reference

Europe PubMed Central

PubMed publication ID

28 June 2017

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