StringTie enables improved reconstruction of a transcriptome from RNA-seq reads (Q34463372)

2 August 2017

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

1 reference

2 August 2017

0 references

0 references

1 reference

6

1 reference

2 August 2017

Mihaela Pertea

1

0 references

author name string

Geo M Pertea

2

1 reference

2 August 2017

Corina M Antonescu

3

1 reference

2 August 2017

Tsung-Cheng Chang

4

1 reference

2 August 2017

Joshua T Mendell

5

1 reference

2 August 2017

18 February 2015

1 reference

2 August 2017

1 reference

2 August 2017

33

1 reference

2 August 2017

290-295

1 reference

2 August 2017

3

1 reference

https://scigraph.springernature.com/pub.10.1038/nbt.3122

2 August 2017

0 references

cites work

Blind spots of quantitative RNA-seq: the limits for assessing abundance, differential expression, and isoform switching

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4643835

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4643835

The UCSC Genome Browser database: 2014 update

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4643835

Assessment of transcript reconstruction methods for 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=4643835

The MaSuRCA genome assembler

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4643835

MITIE: Simultaneous RNA-Seq-based transcript identification and quantification in multiple samples

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4643835

A novel min-cost flow method for estimating transcript expression 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=4643835

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

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4643835

iReckon: simultaneous isoform discovery and abundance estimation 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=4643835

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=4643835

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=4643835

An integrated encyclopedia of DNA elements in 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=4643835

Optimizing de novo transcriptome assembly from short-read RNA-Seq data: a comparative study

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4643835

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

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4643835

Sparse linear modeling of next-generation mRNA sequencing (RNA-Seq) data for isoform discovery and abundance estimation

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4643835

IsoLasso: a LASSO regression approach to RNA-Seq based transcriptome assembly

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4643835

Integrative annotation of human large intergenic noncoding RNAs reveals global properties and specific subclasses

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4643835

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=4643835

Computational methods for transcriptome annotation and quantification using 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=4643835

Full-length transcriptome assembly from RNA-Seq data 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=4643835

Inference of isoforms from short sequence 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=4643835

Recent advances in RNA sequence analysis

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4643835

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=4643835

Ab initio reconstruction of cell type-specific transcriptomes in mouse reveals the conserved multi-exonic structure of lincRNAs

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4643835

Biases in Illumina transcriptome sequencing caused by random hexamer priming

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4643835

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=4643835

Evolution and functions of long noncoding RNAs

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4643835

Alternative isoform regulation in human tissue transcriptomes

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4643835

NCBI Reference Sequences: current status, policy and new initiatives

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4643835

Alternative splicing: new insights from global analyses

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4643835

A new approach to the maximum-flow problem

6 July 2018

1 reference

Crossref

https://api.crossref.org/works/10.1038%2FNBT.3122

inferred from DOI database lookup

7 January 2021

based on heuristic

Identifiers

DOI

10.1038/NBT.3122

1 reference

Dimensions Publication ID

2 August 2017

0 references

1 reference

2 August 2017

1 reference