Gaining comprehensive biological insight into the transcriptome by performing a broad-spectrum RNA-seq analysis (Q38692147)

5 September 2017

Gaining comprehensive biological insight into the transcriptome by performing a broad-spectrum RNA-seq analysis (English)

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5 September 2017

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Robert Sebra

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5 September 2017

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Mark B Gerstein

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Eric Schadt

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5 September 2017

Sayed Mohammad Ebrahim Sahraeian

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5 September 2017

Marghoob Mohiyuddin

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5 September 2017

Hagen Tilgner

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5 September 2017

Pegah T Afshar

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5 September 2017

Kin Fai Au

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5 September 2017

Narges Bani Asadi

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5 September 2017

Wing Hung Wong

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5 September 2017

Michael P Snyder

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5 September 2017

Hugo Y K Lam

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5 September 2017

language of work or name

English

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publication date

5 July 2017

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5 September 2017

Nature Communications

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5 September 2017

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59

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Creative Commons Attribution 4.0 International

5 September 2017

start time

5 July 2017

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April 2022 Public Data File from Crossref

copyright status

copyrighted

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describes a project that uses

limma

1 reference

22 June 2022

https://europepmc.org/article/PMC/5498581

based on heuristic

inferred from PubMed Central ID database lookup

cites work

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Salmon provides fast and bias-aware quantification of transcript expression

6 September 2017

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Extensive sequencing of seven human genomes to characterize benchmark reference materials

6 September 2017

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Near-optimal probabilistic RNA-seq quantification

6 September 2017

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A survey of best practices for RNA-seq data analysis

6 September 2017

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6 September 2017

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Comprehensive evaluation of fusion transcript detection algorithms and a meta-caller to combine top performing methods in paired-end RNA-seq data.

6 September 2017

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6 September 2017

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6 September 2017

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Widespread Polycistronic Transcripts in Fungi Revealed by Single-Molecule mRNA Sequencing

6 September 2017

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Characterization of fusion genes and the significantly expressed fusion isoforms in breast cancer by hybrid sequencing.

6 September 2017

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6 September 2017

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6 September 2017

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HISAT: a fast spliced aligner with low memory requirements

6 September 2017

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Ballgown bridges the gap between transcriptome assembly and expression analysis

6 September 2017

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6 September 2017

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StringTie enables improved reconstruction of a transcriptome from RNA-seq reads

6 September 2017

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limma powers differential expression analyses for RNA-sequencing and microarray studies

6 September 2017

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VarSim: a high-fidelity simulation and validation framework for high-throughput genome sequencing with cancer applications.

6 September 2017

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

6 September 2017

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6 September 2017

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A comprehensive assessment of RNA-seq accuracy, reproducibility and information content by the Sequencing Quality Control Consortium

6 September 2017

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proovread: large-scale high-accuracy PacBio correction through iterative short read consensus

6 September 2017

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Defining a personal, allele-specific, and single-molecule long-read transcriptome

6 September 2017

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

6 September 2017

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Trimmomatic: a flexible trimmer for Illumina sequence data

6 September 2017

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SOAPdenovo-Trans: de novo transcriptome assembly with short RNA-Seq reads.

6 September 2017

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Characterization of the human ESC transcriptome by hybrid sequencing

6 September 2017

1 reference

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featureCounts: an efficient general purpose program for assigning sequence reads to genomic features

6 September 2017

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Fusion genes in solid tumors: an emerging target for cancer diagnosis and treatment

6 September 2017

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Assessment of transcript reconstruction methods for RNA-seq

6 September 2017

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Systematic evaluation of spliced alignment programs for RNA-seq data

6 September 2017

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A single-molecule long-read survey of the human transcriptome

6 September 2017

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

6 September 2017

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Human housekeeping genes, revisited

6 September 2017

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6 September 2017

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Accurate identification and analysis of human mRNA isoforms using deep long read sequencing

6 September 2017

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SOAPfuse: an algorithm for identifying fusion transcripts from paired-end RNA-Seq data

6 September 2017

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5498581

Identifying RNA editing sites using RNA sequencing data alone

6 September 2017

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Differential analysis of gene regulation at transcript resolution with RNA-seq

6 September 2017

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STAR: ultrafast universal RNA-seq aligner

6 September 2017

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5498581

Improving PacBio long read accuracy by short read alignment

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5498581

GENCODE: the reference human genome annotation for The ENCODE Project

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5498581

Hybrid error correction and de novo assembly of single-molecule sequencing reads

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5498581

Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5498581

Oases: robust de novo RNA-seq assembly across the dynamic range of expression levels

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5498581

Efficient de novo assembly of large genomes using compressed data structures

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5498581

TopHat-Fusion: an algorithm for discovery of novel fusion transcripts

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5498581

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

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5498581

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

6 September 2017

1 reference

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A framework for variation discovery and genotyping using next-generation DNA sequencing data

6 September 2017

1 reference

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De novo assembly and analysis of RNA-seq data.

6 September 2017

1 reference

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

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5498581

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

6 September 2017

1 reference

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The Sequence Alignment/Map format and SAMtools

6 September 2017

1 reference

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ToppGene Suite for gene list enrichment analysis and candidate gene prioritization

6 September 2017

1 reference

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The HLA genomic loci map: expression, interaction, diversity and disease

6 September 2017

1 reference

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Identification of T1D susceptibility genes within the MHC region by combining protein interaction networks and SNP genotyping data

6 September 2017

1 reference

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Velvet: algorithms for de novo short read assembly using de Bruijn graphs

6 September 2017

1 reference

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GMAP: a genomic mapping and alignment program for mRNA and EST sequences

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5498581

RNA editing enzyme APOBEC1 and some of its homologs can act as DNA mutators

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5498581

dbSNP: the NCBI database of genetic variation

6 September 2017

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dbEST--database for "expressed sequence tags"

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5498581

Accurate identification of A-to-I RNA editing in human by transcriptome sequencing

6 September 2017

1 reference

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RapMap: a rapid, sensitive and accurate tool for mapping RNA-seq reads to transcriptomes

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5498581

A benchmark for RNA-seq quantification pipelines

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5498581

Comprehensive transcriptome analysis using synthetic long-read sequencing reveals molecular co-association of distant splicing events

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5498581

Gene expression in human embryonic stem cell lines: unique molecular signature

14 September 2017

1 reference

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Grape RNA-Seq analysis pipeline environment.

14 September 2017

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Streaming fragment assignment for real-time analysis of sequencing experiments

23 June 2018

1 reference

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LoRDEC: accurate and efficient long read error correction.

23 June 2018

1 reference

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MTML-msBayes: approximate Bayesian comparative phylogeographic inference from multiple taxa and multiple loci with rate heterogeneity

31 August 2018

1 reference

Crossref

https://api.crossref.org/works/10.1038%2FS41467-017-00050-4

10.1038/S41467-017-00050-4

21 January 2018

Identifiers

DOI

1 reference

Dimensions Publication ID

5 September 2017

0 references

0 references

1 reference

5 September 2017

PubMed publication ID

28680106

1 reference