Computational methods for transcriptome annotation and quantification using RNA-seq (Q34660508)

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scientific article published on May 27, 2011

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English	Computational methods for transcriptome annotation and quantification using RNA-seq	scientific article published on May 27, 2011

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scholarly article

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Europe PubMed Central

PubMed publication ID

21623353

retrieved

3 August 2017

review article

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Europe PubMed Central

title

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

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Europe PubMed Central

PubMed publication ID

21623353

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3 August 2017

main subject

transcriptome

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RNA sequencing

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inferred from title

RNA-Seq

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author

Cole Trapnell

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Cole Trapnell

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Europe PubMed Central

PubMed publication ID

21623353

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3 August 2017

Manuel Garber

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Manuel Garber

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Europe PubMed Central

PubMed publication ID

21623353

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3 August 2017

Mitchell Guttman

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3

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Mitchell Guttman

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Europe PubMed Central

PubMed publication ID

21623353

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3 August 2017

Manfred Grabherr

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2

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Manfred G. Grabherr

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Europe PubMed Central

PubMed publication ID

21623353

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

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3 December 2024

language of work or name

English

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publication date

27 May 2011

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PubMed publication ID

21623353

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3 August 2017

full work available at URL

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

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Portable Document Format

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Crossref

DOI

10.1038/NMETH.1613

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https://api.crossref.org/works/10.1038/NMETH.1613

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3 December 2024

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

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Crossref

DOI

10.1038/NMETH.1613

reference URL

https://api.crossref.org/works/10.1038/NMETH.1613

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3 December 2024

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

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Portable Document Format

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Crossref

DOI

10.1038/NMETH.1613

reference URL

https://api.crossref.org/works/10.1038/NMETH.1613

retrieved

3 December 2024

published in

Nature Methods

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Europe PubMed Central

PubMed publication ID

21623353

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3 August 2017

volume

8

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Europe PubMed Central

PubMed publication ID

21623353

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3 August 2017

issue

6

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Europe PubMed Central

PubMed publication ID

21623353

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3 August 2017

page(s)

469-477

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PubMed publication ID

21623353

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3 August 2017

describes a project that uses

RNA-Seq

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cites work

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

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

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PubMed

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https://pubmed.ncbi.nlm.nih.gov/21623353

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Analysis and management of microarray gene expression data.

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PubMed

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RNA-Seq: a revolutionary tool for transcriptomics

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PubMed

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https://pubmed.ncbi.nlm.nih.gov/21623353

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12 December 2020

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Sex-specific and lineage-specific alternative splicing in primates

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

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PubMed

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12 December 2020

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SOAP2: an improved ultrafast tool for short read alignment

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12 December 2020

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

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Scaffolding a Caenorhabditis nematode genome with RNA-seq

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De novo assembly and analysis of RNA-seq data.

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

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BLAT—The BLAST-Like Alignment Tool

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https://pubmed.ncbi.nlm.nih.gov/21623353

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Transcriptome sequencing to detect gene fusions in cancer

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12 December 2020

based on heuristic

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

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Optimal spliced alignments of short sequence reads

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Stem cell transcriptome profiling via massive-scale mRNA sequencing

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Quantitative monitoring of gene expression patterns with a complementary DNA microarray

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12 December 2020

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

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https://pubmed.ncbi.nlm.nih.gov/21623353

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12 December 2020

based on heuristic

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

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https://pubmed.ncbi.nlm.nih.gov/21623353

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12 December 2020

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Annotating genomes with massive-scale RNA sequencing

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12 December 2020

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

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https://pubmed.ncbi.nlm.nih.gov/21623353

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12 December 2020

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

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PubMed

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https://pubmed.ncbi.nlm.nih.gov/21623353

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12 December 2020

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An encyclopedia of mouse genes

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12 December 2020

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Mapping and quantifying mammalian transcriptomes by RNA-Seq

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PubMed

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https://pubmed.ncbi.nlm.nih.gov/21623353

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12 December 2020

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

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12 December 2020

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

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12 December 2020

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Differential expression analysis for sequence count data

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PubMed

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https://pubmed.ncbi.nlm.nih.gov/21623353

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12 December 2020

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TopHat: discovering splice junctions with RNA-Seq

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PubMed

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https://pubmed.ncbi.nlm.nih.gov/21623353

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12 December 2020

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

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PubMed

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https://pubmed.ncbi.nlm.nih.gov/21623353

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12 December 2020

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

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PubMed

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https://pubmed.ncbi.nlm.nih.gov/21623353

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12 December 2020

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Statistical inferences for isoform expression in RNA-Seq

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PubMed

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https://pubmed.ncbi.nlm.nih.gov/21623353

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12 December 2020

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Large-scale transcriptional activity in chromosomes 21 and 22

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PubMed

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https://pubmed.ncbi.nlm.nih.gov/21623353

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12 December 2020

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Alternative expression analysis by RNA sequencing

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PubMed

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https://pubmed.ncbi.nlm.nih.gov/21623353

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12 December 2020

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

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12 December 2020

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

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

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12 December 2020

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The transcriptional landscape of the yeast genome defined by RNA sequencing

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Computation for ChIP-seq and RNA-seq studies

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

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Improving the Arabidopsis genome annotation using maximal transcript alignment assemblies

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Formation, regulation and evolution of Caenorhabditis elegans 3'UTRs

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

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Cloud-scale RNA-sequencing differential expression analysis with Myrna

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

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PubMed

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BFAST: an alignment tool for large scale genome resequencing

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PubMed

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RNA-Seq gene expression estimation with read mapping uncertainty

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PubMed

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GASSST: global alignment short sequence search tool

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PubMed

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

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

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

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Integrative analysis of the melanoma transcriptome

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Comprehensive comparative analysis of strand-specific RNA sequencing methods

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

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SHRiMP: accurate mapping of short color-space reads

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SeqMap: mapping massive amount of oligonucleotides to the genome

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

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

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Transcript length bias in RNA-seq data confounds systems biology

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1-Tuple DNA sequencing: computer analysis

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

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

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https://pubmed.ncbi.nlm.nih.gov/21623353

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12 December 2020

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

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https://pubmed.ncbi.nlm.nih.gov/21623353

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12 December 2020

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Alternative isoform regulation in human tissue transcriptomes

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12 December 2020

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

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12 December 2020

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

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

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Moderated statistical tests for assessing differences in tag abundance

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12 December 2020

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

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

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12 December 2020

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De novo transcriptome assembly with ABySS.

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Fast and accurate short read alignment with Burrows-Wheeler transform

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SOAP: short oligonucleotide alignment program

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PubMed

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https://pubmed.ncbi.nlm.nih.gov/21623353

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12 December 2020

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Significance analysis of microarrays applied to the ionizing radiation response

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

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PubMed

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https://pubmed.ncbi.nlm.nih.gov/21623353

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The landscape of C. elegans 3'UTRs

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12 December 2020

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

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12 December 2020

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

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Complementary DNA sequencing: expressed sequence tags and human genome project

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https://pubmed.ncbi.nlm.nih.gov/21623353

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12 December 2020

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Analysis and design of RNA sequencing experiments for identifying isoform regulation

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Crossref

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7 January 2021

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An experimental study of a compressed index

series ordinal

43

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Crossref

DOI

10.1038/NMETH.1613

reference URL

https://api.crossref.org/works/10.1038/NMETH.1613

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3 December 2024

Sciences

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56

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46

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NG De Bruijn

publication date

1946

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Crossref

DOI

10.1038/NMETH.1613

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https://api.crossref.org/works/10.1038/NMETH.1613

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3 December 2024

Identifiers

DOI

10.1038/NMETH.1613

1 reference

stated in

Europe PubMed Central

PubMed publication ID

21623353

retrieved

3 August 2017

Dimensions Publication ID

1009798986

0 references

PubMed publication ID

21623353

1 reference

stated in

Europe PubMed Central

PubMed publication ID

21623353

retrieved

3 August 2017

ResearchGate publication ID

51175498

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