(Q34660508)

3 August 2017

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title

Computational methods for transcriptome annotation and quantification using RNA-seq (English)

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3 August 2017

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Cole Trapnell

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3 August 2017

Manuel Garber

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3 August 2017

Mitchell Guttman

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3 August 2017

Manfred G. Grabherr

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https://www.ebi.ac.uk/europepmc/webservices/rest/search?resulttype=core&format=json&query=SRC%3AMED%20AND%20EXT_ID%3A21623353

3 December 2024

language of work or name

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27 May 2011

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full work available at URL

3 August 2017

http://www.nature.com/articles/nmeth.1613.pdf

file format

Portable Document Format

1 reference

http://www.nature.com/articles/nmeth.1613

3 December 2024

1 reference

http://www.nature.com/articles/nmeth.1613.pdf

3 December 2024

file format

Portable Document Format

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3 December 2024

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3 August 2017

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3 August 2017

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3 August 2017

page(s)

469-477

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describes a project that uses

3 August 2017

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A global view of gene activity and alternative splicing by deep sequencing of the human transcriptome

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12 December 2020

Next is now: new technologies for sequencing of genomes, transcriptomes, and beyond

1 reference

12 December 2020

Analysis and management of microarray gene expression data.

1 reference

12 December 2020

RNA-Seq: a revolutionary tool for transcriptomics

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12 December 2020

Sex-specific and lineage-specific alternative splicing in primates

1 reference

12 December 2020

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

1 reference

12 December 2020

SOAP2: an improved ultrafast tool for short read alignment

1 reference

12 December 2020

Genome of the marsupial Monodelphis domestica reveals innovation in non-coding sequences

1 reference

12 December 2020

Scaffolding a Caenorhabditis nematode genome with RNA-seq

1 reference

12 December 2020

De novo assembly and analysis of RNA-seq data.

1 reference

12 December 2020

Mapping short DNA sequencing reads and calling variants using mapping quality scores

1 reference

12 December 2020

BLAT—The BLAST-Like Alignment Tool

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12 December 2020

Transcriptome sequencing to detect gene fusions in cancer

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12 December 2020

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

1 reference

12 December 2020

Optimal spliced alignments of short sequence reads

1 reference

12 December 2020

Stem cell transcriptome profiling via massive-scale mRNA sequencing

1 reference

12 December 2020

Quantitative monitoring of gene expression patterns with a complementary DNA microarray

1 reference

12 December 2020

Expression of 24,426 human alternative splicing events and predicted cis regulation in 48 tissues and cell lines

1 reference

12 December 2020

Detection of splice junctions from paired-end RNA-seq data by SpliceMap.

1 reference

12 December 2020

Annotating genomes with massive-scale RNA sequencing

1 reference

12 December 2020

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

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12 December 2020

Isoform abundance inference provides a more accurate estimation of gene expression levels in RNA-seq

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12 December 2020

An encyclopedia of mouse genes

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12 December 2020

Mapping and quantifying mammalian transcriptomes by RNA-Seq

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12 December 2020

Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals

1 reference

12 December 2020

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

1 reference

12 December 2020

Differential expression analysis for sequence count data

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12 December 2020

TopHat: discovering splice junctions with RNA-Seq

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12 December 2020

Identification of human chromosome 22 transcribed sequences with ORF expressed sequence tags

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12 December 2020

Ab initio construction of a eukaryotic transcriptome by massively parallel mRNA sequencing

1 reference

12 December 2020

Statistical inferences for isoform expression in RNA-Seq

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12 December 2020

Large-scale transcriptional activity in chromosomes 21 and 22

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12 December 2020

Alternative expression analysis by RNA sequencing

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12 December 2020

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

1 reference

12 December 2020

RNA-seq analysis of 2 closely related leukemia clones that differ in their self-renewal capacity.

1 reference

12 December 2020

Targeting a complex transcriptome: the construction of the mouse full-length cDNA encyclopedia

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12 December 2020

The transcriptional landscape of the yeast genome defined by RNA sequencing

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12 December 2020

Computation for ChIP-seq and RNA-seq studies

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12 December 2020

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

1 reference

12 December 2020

Improving the Arabidopsis genome annotation using maximal transcript alignment assemblies

1 reference

12 December 2020

Formation, regulation and evolution of Caenorhabditis elegans 3'UTRs

1 reference

12 December 2020

A scaling normalization method for differential expression analysis of RNA-seq data

1 reference

12 December 2020

Cloud-scale RNA-sequencing differential expression analysis with Myrna

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12 December 2020

MapSplice: accurate mapping of RNA-seq reads for splice junction discovery.

1 reference

12 December 2020

BFAST: an alignment tool for large scale genome resequencing

1 reference

12 December 2020

RNA-Seq gene expression estimation with read mapping uncertainty

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12 December 2020

GASSST: global alignment short sequence search tool

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12 December 2020

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

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12 December 2020

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

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12 December 2020

Accurate quantification of transcriptome from RNA-Seq data by effective length normalization

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12 December 2020

Integrative analysis of the melanoma transcriptome

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12 December 2020

Comprehensive comparative analysis of strand-specific RNA sequencing methods

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12 December 2020

Optimization of de novo transcriptome assembly from next-generation sequencing data

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12 December 2020

SHRiMP: accurate mapping of short color-space reads

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12 December 2020

SeqMap: mapping massive amount of oligonucleotides to the genome

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12 December 2020

DEGseq: an R package for identifying differentially expressed genes from RNA-seq data

1 reference

12 December 2020

Using quality scores and longer reads improves accuracy of Solexa read mapping

1 reference

12 December 2020

Transcript length bias in RNA-seq data confounds systems biology

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12 December 2020

1-Tuple DNA sequencing: computer analysis

1 reference

12 December 2020

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

1 reference

12 December 2020

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

1 reference

12 December 2020

Linking promoters to functional transcripts in small samples with nanoCAGE and CAGEscan

1 reference

12 December 2020

Alternative isoform regulation in human tissue transcriptomes

1 reference

12 December 2020

Revealing global regulatory features of mammalian alternative splicing using a quantitative microarray platform

1 reference

12 December 2020

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

1 reference

12 December 2020

RNA-MATE: a recursive mapping strategy for high-throughput RNA-sequencing data

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12 December 2020

Moderated statistical tests for assessing differences in tag abundance

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12 December 2020

A practical false discovery rate approach to identifying patterns of differential expression in microarray data

1 reference

12 December 2020

Evaluation of statistical methods for normalization and differential expression in mRNA-Seq experiments

1 reference

12 December 2020

De novo transcriptome assembly with ABySS.

1 reference

12 December 2020

Fast and accurate short read alignment with Burrows-Wheeler transform

1 reference

12 December 2020

SOAP: short oligonucleotide alignment program

1 reference

12 December 2020

Significance analysis of microarrays applied to the ionizing radiation response

1 reference

12 December 2020

Using the Velvet de novo assembler for short-read sequencing technologies

1 reference

12 December 2020

The landscape of C. elegans 3'UTRs

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12 December 2020

Current-generation high-throughput sequencing: deepening insights into mammalian transcriptomes

1 reference

12 December 2020

Molecular classification of cancer: class discovery and class prediction by gene expression monitoring

1 reference

12 December 2020

Complementary DNA sequencing: expressed sequence tags and human genome project

1 reference

12 December 2020

Analysis and design of RNA sequencing experiments for identifying isoform regulation

1 reference

Crossref

https://api.crossref.org/works/10.1038%2FNMETH.1613

7 January 2021

inferred from DOI database lookup

An experimental study of a compressed index

1 reference

3 December 2024

NG De Bruijn

1946

1 reference

3 December 2024

Identifiers

DOI

10.1038/NMETH.1613

1 reference

Dimensions Publication ID

3 August 2017

1009798986

0 references

1 reference