Challenges and strategies in transcriptome assembly and differential gene expression quantification. A comprehensivein silicoassessment of RNA-seq experiments

A comparison of statistical methods for detecting differentially expressed genes from RNA-seq data

(2012) Vanessa M. Kvam et al.   AMERICAN JOURNAL OF BOTANY

Comparison between Normalised and Unnormalised 454-Sequencing Libraries for Small-Scale RNA-Seq Studies

(2012) Robert Ekblom et al.   COMPARATIVE AND FUNCTIONAL GENOMICS

Evaluation of the coverage and depth of transcriptome by RNA-Seq in chickens

(2011) Ying Wang et al.   BMC BIOINFORMATICS

RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome

(2011) Bo Li et al.   BMC BIOINFORMATICS

The sex-biased brain: sexual dimorphism in gene expression in two species of songbirds

(2011) Sara Naurin et al.   BMC GENOMICS

General lack of global dosage compensation in ZZ/ZW systems? Broadening the perspective with RNA-seq

(2011) Jochen BW Wolf et al.   BMC GENOMICS

Computational methods for Gene Orthology inference

(2011) D. M. Kristensen et al.   BRIEFINGS IN BIOINFORMATICS

Comparative RNA sequencing reveals substantial genetic variation in endangered primates

(2011) G. H. Perry et al.   GENOME RESEARCH

GAGE: A critical evaluation of genome assemblies and assembly algorithms

(2011) S. L. Salzberg et al.   GENOME RESEARCH

Sequencing technologies and genome sequencing

(2011) Chandra Shekhar Pareek et al.   JOURNAL OF APPLIED GENETICS

Full-length transcriptome assembly from RNA-Seq data without a reference genome

(2011) Manfred G Grabherr et al.   NATURE BIOTECHNOLOGY

Evidence for compensatory upregulation of expressed X-linked genes in mammals, Caenorhabditis elegans and Drosophila melanogaster

(2011) Xinxian Deng et al.   NATURE GENETICS

A Bioinformatics Approach for Determining Sample Identity from Different Lanes of High-Throughput Sequencing Data

(2011) Rachel L. Goldfeder et al.   PLoS One

Modernizing Reference Genome Assemblies

(2011) Deanna M. Church et al.   PLOS BIOLOGY

Genome-wide synteny through highly sensitive sequence alignment: Satsuma

(2010) M. G. Grabherr et al.   BIOINFORMATICS

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

baySeq: Empirical Bayesian methods for identifying differential expression in sequence count data

(2010) Thomas J Hardcastle et al.   BMC BIOINFORMATICS

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

(2010) G. Lunter et al.   GENOME RESEARCH

Applications of next generation sequencing in molecular ecology of non-model organisms

(2010) R Ekblom et al.   HEREDITY

Genome-wide analysis of alternative splicing evolution amongMussubspecies

(2010) BETTINA HARR et al.   MOLECULAR ECOLOGY

Comparative genomics based on massive parallel transcriptome sequencing reveals patterns of substitution and selection across 10 bird species

(2010) AXEL KÜNSTNER et al.   MOLECULAR ECOLOGY

A genetic basis for the phenotypic differentiation between siscowet and lean lake trout (Salvelinus namaycush)

(2010) FREDERICK GOETZ et al.   MOLECULAR ECOLOGY

Nucleotide divergence vs. gene expression differentiation: comparative transcriptome sequencing in natural isolates from the carrion crow and its hybrid zone with the hooded crow

(2010) JOCHEN B. W. WOLF et al.   MOLECULAR ECOLOGY

Rapid evolution and selection inferred from the transcriptomes of sympatric crater lake cichlid fishes

(2010) K. R. ELMER et al.   MOLECULAR ECOLOGY

The genome of a songbird

(2010) Wesley C. Warren 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

RNA sequencing: advances, challenges and opportunities

(2010) Fatih Ozsolak et al.   NATURE REVIEWS GENETICS

The Sequence Alignment/Map format and SAMtools

(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

Estimating accuracy of RNA-Seq and microarrays with proteomics

(2009) Xing Fu et al.   BMC GENOMICS

Genome 10K: A Proposal to Obtain Whole-Genome Sequence for 10 000 Vertebrate Species

(2009)   JOURNAL OF HEREDITY

Mapping Accuracy of Short Reads from Massively Parallel Sequencing and the Implications for Quantitative Expression Profiling

(2009) Nicola Palmieri et al.   PLoS One

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

(2008) J. C. Marioni et al.   GENOME RESEARCH

Alternative isoform regulation in human tissue transcriptomes

(2008) Eric T. Wang et al.   NATURE