A comprehensive comparison of RNA-Seq-based transcriptome analysis from reads to differential gene expression and cross-comparison with microarrays: a case study in Saccharomyces cerevisiae
Published 2012 View Full Article
- Home
- Publications
- Publication Search
- Publication Details
Title
A comprehensive comparison of RNA-Seq-based transcriptome analysis from reads to differential gene expression and cross-comparison with microarrays: a case study in Saccharomyces cerevisiae
Authors
Keywords
-
Journal
NUCLEIC ACIDS RESEARCH
Volume 40, Issue 20, Pages 10084-10097
Publisher
Oxford University Press (OUP)
Online
2012-09-11
DOI
10.1093/nar/gks804
References
Ask authors/readers for more resources
Related references
Note: Only part of the references are listed.- Oases: robust de novo RNA-seq assembly across the dynamic range of expression levels
- (2012) Marcel H. Schulz et al. BIOINFORMATICS
- De novo sequencing, assembly and analysis of the genome of the laboratory strain Saccharomyces cerevisiae CEN.PK113-7D, a model for modern industrial biotechnology
- (2012) Jurgen F Nijkamp et al. Microbial Cell Factories
- Comparative analysis of RNA-Seq alignment algorithms and the RNA-Seq unified mapper (RUM)
- (2011) Gregory R. Grant et al. BIOINFORMATICS
- Optimizing de novo transcriptome assembly from short-read RNA-Seq data: a comparative study
- (2011) Qiong-Yi Zhao et al. BMC BIOINFORMATICS
- Microarrays, deep sequencing and the true measure of the transcriptome
- (2011) John H Malone et al. BMC BIOLOGY
- Whole genome sequencing of Saccharomyces cerevisiae: from genotype to phenotype for improved metabolic engineering applications
- (2011) José Otero et al. BMC GENOMICS
- Using RNA-seq to determine the transcriptional landscape and the hypoxic response of the pathogenic yeast Candida parapsilosis
- (2011) Alessandro Guida et al. BMC GENOMICS
- Differential expression in RNA-seq: A matter of depth
- (2011) S. Tarazona et al. GENOME RESEARCH
- A powerful and flexible statistical framework for testing hypotheses of allele-specific gene expression from RNA-seq data
- (2011) D. A. Skelly et al. GENOME RESEARCH
- XUTs are a class of Xrn1-sensitive antisense regulatory non-coding RNA in yeast
- (2011) E. L. van Dijk et al. NATURE
- Full-length transcriptome assembly from RNA-Seq data without a reference genome
- (2011) Manfred G Grabherr et al. NATURE BIOTECHNOLOGY
- Computational methods for transcriptome annotation and quantification using RNA-seq
- (2011) Manuel Garber et al. NATURE METHODS
- Genotype and SNP calling from next-generation sequencing data
- (2011) Rasmus Nielsen et al. NATURE REVIEWS GENETICS
- Compatibility with Killer Explains the Rise of RNAi-Deficient Fungi
- (2011) I. A. Drinnenberg et al. SCIENCE
- BEDTools: a flexible suite of utilities for comparing genomic features
- (2010) Aaron R. Quinlan et al. BIOINFORMATICS
- Fast and SNP-tolerant detection of complex variants and splicing in short reads
- (2010) T. D. Wu et al. BIOINFORMATICS
- SolexaQA: At-a-glance quality assessment of Illumina second-generation sequencing data
- (2010) Murray P Cox et al. BMC BIOINFORMATICS
- Evaluation of statistical methods for normalization and differential expression in mRNA-Seq experiments
- (2010) James H Bullard et al. BMC BIOINFORMATICS
- baySeq: Empirical Bayesian methods for identifying differential expression in sequence count data
- (2010) Thomas J Hardcastle et al. BMC BIOINFORMATICS
- A comparison of massively parallel nucleotide sequencing with oligonucleotide microarrays for global transcription profiling
- (2010) James R Bradford et al. BMC GENOMICS
- Stampy: A statistical algorithm for sensitive and fast mapping of Illumina sequence reads
- (2010) G. Lunter et al. GENOME RESEARCH
- The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data
- (2010) A. McKenna et al. GENOME RESEARCH
- The MicroArray Quality Control (MAQC)-II study of common practices for the development and validation of microarray-based predictive models
- (2010) NATURE BIOTECHNOLOGY
- Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation
- (2010) Cole Trapnell et al. NATURE BIOTECHNOLOGY
- De novo assembly and analysis of RNA-seq data
- (2010) Gordon Robertson et al. NATURE METHODS
- Comprehensive comparative analysis of strand-specific RNA sequencing methods
- (2010) Joshua Z Levin et al. NATURE METHODS
- Defining transcribed regions using RNA-seq
- (2010) Brian T Wilhelm et al. Nature Protocols
- RNA sequencing: advances, challenges and opportunities
- (2010) Fatih Ozsolak et al. NATURE REVIEWS GENETICS
- Comprehensive Survey of SNPs in the Affymetrix Exon Array Using the 1000 Genomes Dataset
- (2010) Eric R. Gamazon et al. PLoS One
- Integrated multilaboratory systems biology reveals differences in protein metabolism between two reference yeast strains
- (2010) André B. Canelas et al. Nature Communications
- Differential expression analysis for sequence count data
- (2010) Simon Anders et al. GENOME BIOLOGY
- Effect of read-mapping biases on detecting allele-specific expression from RNA-sequencing data
- (2009) Jacob F. Degner et al. BIOINFORMATICS
- TopHat: discovering splice junctions with RNA-Seq
- (2009) Cole Trapnell et al. BIOINFORMATICS
- The Sequence Alignment/Map format and SAMtools
- (2009) H. 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
- 3' tag digital gene expression profiling of human brain and universal reference RNA using Illumina Genome Analyzer
- (2009) Yan W Asmann et al. BMC GENOMICS
- Estimating accuracy of RNA-Seq and microarrays with proteomics
- (2009) Xing Fu et al. BMC GENOMICS
- A SNP discovery method to assess variant allele probability from next-generation resequencing data
- (2009) Y. Shen et al. GENOME RESEARCH
- RNA-Seq—quantitative measurement of expression through massively parallel RNA-sequencing
- (2009) Brian T. Wilhelm et al. METHODS
- Evaluation of Microarray Preprocessing Algorithms Based on Concordance with RT-PCR in Clinical Samples
- (2009) Balazs Gyorffy et al. PLoS One
- Architecture of transcriptional regulatory circuits is knitted over the topology of bio-molecular interaction networks
- (2008) Ana Oliveira et al. BMC Systems Biology
- RNA-seq: An assessment of technical reproducibility and comparison with gene expression arrays
- (2008) J. C. Marioni et al. GENOME RESEARCH
- Stem cell transcriptome profiling via massive-scale mRNA sequencing
- (2008) Nicole Cloonan et al. NATURE METHODS
- Mapping and quantifying mammalian transcriptomes by RNA-Seq
- (2008) Ali Mortazavi et al. NATURE METHODS
- RNA-Seq: a revolutionary tool for transcriptomics
- (2008) Zhong Wang et al. NATURE REVIEWS GENETICS
- Deep sequencing-based expression analysis shows major advances in robustness, resolution and inter-lab portability over five microarray platforms
- (2008) Peter A. C. 't Hoen et al. NUCLEIC ACIDS RESEARCH
- Genomic Convergence Analysis of Schizophrenia: mRNA Sequencing Reveals Altered Synaptic Vesicular Transport in Post-Mortem Cerebellum
- (2008) Joann Mudge et al. PLoS One
- The Transcriptional Landscape of the Yeast Genome Defined by RNA Sequencing
- (2008) U. Nagalakshmi et al. SCIENCE
- A Global View of Gene Activity and Alternative Splicing by Deep Sequencing of the Human Transcriptome
- (2008) M. Sultan et al. SCIENCE
Find the ideal target journal for your manuscript
Explore over 38,000 international journals covering a vast array of academic fields.
SearchAdd your recorded webinar
Do you already have a recorded webinar? Grow your audience and get more views by easily listing your recording on Peeref.
Upload Now