Computational methods for transcriptome annotation and quantification using RNA-seq
Published 2011 View Full Article
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Title
Computational methods for transcriptome annotation and quantification using RNA-seq
Authors
Keywords
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Journal
NATURE METHODS
Volume 8, Issue 6, Pages 469-477
Publisher
Springer Nature
Online
2011-05-28
DOI
10.1038/nmeth.1613
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Note: Only part of the references are listed.- GASSST: global alignment short sequence search tool
- (2010) Guillaume Rizk et al. BIOINFORMATICS
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- (2010) T. D. Wu et al. BIOINFORMATICS
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- (2010) B. T. Wilhelm et al. BLOOD
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- (2010) A. Mortazavi et al. GENOME RESEARCH
- Integrative analysis of the melanoma transcriptome
- (2010) M. F. Berger et al. GENOME RESEARCH
- Optimization of de novo transcriptome assembly from next-generation sequencing data
- (2010) Y. Surget-Groba et al. GENOME RESEARCH
- Formation, regulation and evolution of Caenorhabditis elegans 3′UTRs
- (2010) Calvin H. Jan et al. NATURE
- Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation
- (2010) Cole Trapnell et al. NATURE BIOTECHNOLOGY
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- (2010) Mitchell Guttman et al. NATURE BIOTECHNOLOGY
- Linking promoters to functional transcripts in small samples with nanoCAGE and CAGEscan
- (2010) Charles Plessy et al. NATURE METHODS
- De novo assembly and analysis of RNA-seq data
- (2010) Gordon Robertson et al. NATURE METHODS
- Alternative expression analysis by RNA sequencing
- (2010) Malachi Griffith et al. NATURE METHODS
- Comprehensive comparative analysis of strand-specific RNA sequencing methods
- (2010) Joshua Z Levin et al. NATURE METHODS
- Analysis and design of RNA sequencing experiments for identifying isoform regulation
- (2010) Yarden Katz et al. NATURE METHODS
- Detection of splice junctions from paired-end RNA-seq data by SpliceMap
- (2010) K. F. Au et al. NUCLEIC ACIDS RESEARCH
- Accurate quantification of transcriptome from RNA-Seq data by effective length normalization
- (2010) Soohyun Lee et al. NUCLEIC ACIDS RESEARCH
- MapSplice: Accurate mapping of RNA-seq reads for splice junction discovery
- (2010) Kai Wang et al. NUCLEIC ACIDS RESEARCH
- The Landscape of C. elegans 3'UTRs
- (2010) M. Mangone et al. SCIENCE
- Cloud-scale RNA-sequencing differential expression analysis with Myrna
- (2010) Ben Langmead et al. GENOME BIOLOGY
- A scaling normalization method for differential expression analysis of RNA-seq data
- (2010) Mark D Robinson et al. GENOME BIOLOGY
- Differential expression analysis for sequence count data
- (2010) Simon Anders et al. GENOME BIOLOGY
- ISOFORM ABUNDANCE INFERENCE PROVIDES A MORE ACCURATE ESTIMATION OF GENE EXPRESSION LEVELS IN RNA-SEQ
- (2010) XI WANG et al. Journal of Bioinformatics and Computational Biology
- Statistical inferences for isoform expression in RNA-Seq
- (2009) Hui Jiang et al. BIOINFORMATICS
- RNA-Seq gene expression estimation with read mapping uncertainty
- (2009) Bo Li et al. BIOINFORMATICS
- Effect of read-mapping biases on detecting allele-specific expression from RNA-sequencing data
- (2009) Jacob F. Degner et al. BIOINFORMATICS
- RNA-MATE: a recursive mapping strategy for high-throughput RNA-sequencing data
- (2009) Nicole Cloonan et al. BIOINFORMATICS
- De novo transcriptome assembly with ABySS
- (2009) I. Birol et al. BIOINFORMATICS
- DEGseq: an R package for identifying differentially expressed genes from RNA-seq data
- (2009) Likun Wang et al. BIOINFORMATICS
- TopHat: discovering splice junctions with RNA-Seq
- (2009) Cole Trapnell et al. BIOINFORMATICS
- SOAP2: an improved ultrafast tool for short read alignment
- (2009) R. Li et al. BIOINFORMATICS
- Fast and accurate short read alignment with Burrows-Wheeler transform
- (2009) H. Li et al. BIOINFORMATICS
- edgeR: a Bioconductor package for differential expression analysis of digital gene expression data
- (2009) M. D. Robinson et al. BIOINFORMATICS
- Transcript length bias in RNA-seq data confounds systems biology
- (2009) Alicia Oshlack et al. Biology Direct
- Next is now: new technologies for sequencing of genomes, transcriptomes, and beyond
- (2009) Ryan Lister et al. CURRENT OPINION IN PLANT BIOLOGY
- Current-generation high-throughput sequencing: deepening insights into mammalian transcriptomes
- (2009) B. J. Blencowe et al. GENES & DEVELOPMENT
- Sex-specific and lineage-specific alternative splicing in primates
- (2009) R. Blekhman et al. GENOME RESEARCH
- Transcriptome sequencing to detect gene fusions in cancer
- (2009) Christopher A. Maher et al. NATURE
- Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals
- (2009) Mitchell Guttman et al. NATURE
- Computation for ChIP-seq and RNA-seq studies
- (2009) Shirley Pepke et al. NATURE METHODS
- BFAST: An Alignment Tool for Large Scale Genome Resequencing
- (2009) Nils Homer et al. PLoS One
- Ab initio construction of a eukaryotic transcriptome by massively parallel mRNA sequencing
- (2009) M. Yassour et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- SHRiMP: Accurate Mapping of Short Color-space Reads
- (2009) Stephen M. Rumble et al. PLoS Computational Biology
- Ultrafast and memory-efficient alignment of short DNA sequences to the human genome
- (2009) Ben Langmead et al. GENOME BIOLOGY
- Optimal spliced alignments of short sequence reads
- (2008) F. De Bona et al. BIOINFORMATICS
- SeqMap: mapping massive amount of oligonucleotides to the genome
- (2008) H. Jiang et al. BIOINFORMATICS
- SOAP: short oligonucleotide alignment program
- (2008) R. Li et al. BIOINFORMATICS
- Using quality scores and longer reads improves accuracy of Solexa read mapping
- (2008) Andrew D Smith et al. BMC BIOINFORMATICS
- Highly Integrated Single-Base Resolution Maps of the Epigenome in Arabidopsis
- (2008) Ryan Lister et al. CELL
- RNA-seq: An assessment of technical reproducibility and comparison with gene expression arrays
- (2008) J. C. Marioni et al. GENOME RESEARCH
- Mapping short DNA sequencing reads and calling variants using mapping quality scores
- (2008) H. Li et al. GENOME RESEARCH
- Velvet: Algorithms for de novo short read assembly using de Bruijn graphs
- (2008) D. R. Zerbino et al. GENOME RESEARCH
- Alternative isoform regulation in human tissue transcriptomes
- (2008) Eric T. Wang et al. NATURE
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- Annotating genomes with massive-scale RNA sequencing
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