The power and promise of RNA-seq in ecology and evolution

Designing alternative splicing RNA-seq studies. Beyond generic guidelines

(2015) Camille Stephan-Otto Attolini et al.   BIOINFORMATICS

Experimental validation of methods for differential gene expression analysis and sample pooling in RNA-seq

(2015) Anto P. Rajkumar et al.   BMC GENOMICS

The use of exome capture RNA-seq for highly degraded RNA with application to clinical cancer sequencing

(2015) Marcin Cieslik et al.   GENOME RESEARCH

The Technology and Biology of Single-Cell RNA Sequencing

(2015) Aleksandra A. Kolodziejczyk et al.   MOLECULAR CELL

Ten years of transcriptomics in wild populations: what have we learned about their ecology and evolution?

(2015) Mariano Alvarez et al.   MOLECULAR ECOLOGY

Simultaneous generation of many RNA-seq libraries in a single reaction

(2015) Alexander A Shishkin et al.   NATURE METHODS

Molecular processes of transgenerational acclimation to a warming ocean

(2015) Heather D. Veilleux et al.   Nature Climate Change

The Genome 10K Project: A Way Forward

(2015) Klaus-Peter Koepfli et al.   Annual Review of Animal Biosciences

Large-scale transcriptome sequencing reveals novel expression patterns for key sex-related genes in a sex-changing fish

(2015) Hui Liu et al.   Biology of Sex Differences

subSeq: Determining Appropriate Sequencing Depth Through Efficient Read Subsampling

(2014) David G. Robinson et al.   BIOINFORMATICS

PROPER: comprehensive power evaluation for differential expression using RNA-seq

(2014) Hao Wu et al.   BIOINFORMATICS

Transcriptome analyses and differential gene expression in a non-model fish species with alternative mating tactics

(2014) Celia Schunter et al.   BMC GENOMICS

Regulatory gene networks that shape the development of adaptive phenotypic plasticity in a cichlid fish

(2014) Ralf F. Schneider et al.   MOLECULAR ECOLOGY

Sequencing depth and coverage: key considerations in genomic analyses

(2014) David Sims et al.   NATURE REVIEWS GENETICS

Phenotypic and genomic plasticity of alternative male reproductive tactics in sailfin mollies

(2014) B. A. Fraser et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Power analysis and sample size estimation for RNA-Seq differential expression

(2014) Travers Ching et al.   RNA

RNA-seq differential expression studies: more sequence or more replication?

(2013) Yuwen Liu et al.   BIOINFORMATICS

Scotty: a web tool for designing RNA-Seq experiments to measure differential gene expression

(2013) Michele A. Busby et al.   BIOINFORMATICS

Sample size calculation based on exact test for assessing differential expression analysis in RNA-seq data

(2013) Chung-I Li et al.   BMC BIOINFORMATICS

A comparison of methods for differential expression analysis of RNA-seq data

(2013) Charlotte Soneson et al.   BMC BIOINFORMATICS

A comparison across non-model animals suggests an optimal sequencing depth for de novo transcriptome assembly

(2013) Warren R Francis et al.   BMC GENOMICS

Optimizing de novo assembly of short-read RNA-seq data for phylogenomics

(2013) Ya Yang et al.   BMC GENOMICS

RNA-seq analysis reveals extensive transcriptional plasticity to temperature stress in a freshwater fish species

(2013) Steve Smith et al.   BMC GENOMICS

Calculating Sample Size Estimates for RNA Sequencing Data

(2013) Steven N. Hart et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

Annotated genes and nonannotated genomes: cross-species use of Gene Ontology in ecology and evolution research

(2013) C. R. Primmer et al.   MOLECULAR ECOLOGY

Shaping development through mechanical strain: the transcriptional basis of diet-induced phenotypic plasticity in a cichlid fish

(2013) Helen M. Gunter et al.   MOLECULAR ECOLOGY

Principles of transcriptome analysis and gene expression quantification: an RNA-seq tutorial

(2013) Jochen B. W. Wolf   Molecular Ecology Resources

Preservation of RNA and DNA from mammal samples under field conditions

(2013) Miguel Camacho-Sanchez et al.   Molecular Ecology Resources

Comparative analysis of RNA sequencing methods for degraded or low-input samples

(2013) Xian Adiconis et al.   NATURE METHODS

De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis

(2013) Brian J Haas et al.   Nature Protocols

A new shrinkage estimator for dispersion improves differential expression detection in RNA-seq data

(2012) H. Wu et al.   BIOSTATISTICS

How deep is deep enough for RNA-Seq profiling of bacterial transcriptomes?

(2012) Brian J Haas et al.   BMC GENOMICS

5S rRNA and Accompanying Proteins in Gonads: Powerful Markers to Identify Sex and Reproductive Endocrine Disruption in Fish

(2012) Oihane Diaz de Cerio et al.   ENVIRONMENTAL SCIENCE & TECHNOLOGY

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

(2012) Nagarjun Vijay et al.   MOLECULAR ECOLOGY

Proteomics in evolutionary ecology: linking the genotype with the phenotype

(2012) ANGEL P. DIZ et al.   MOLECULAR ECOLOGY

Comparative studies of gene expression and the evolution of gene regulation

(2012) Irene Gallego Romero et al.   NATURE REVIEWS GENETICS

Exome RNA sequencing reveals rare and novel alternative transcripts

(2012) Jonatan Halvardson et al.   NUCLEIC ACIDS RESEARCH

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

(2011) Ying Wang et al.   BMC BIOINFORMATICS

Expression divergence measured by transcriptome sequencing of four yeast species

(2011) Michele A Busby et al.   BMC GENOMICS

RNA-seq: technical variability and sampling

(2011) Lauren M McIntyre et al.   BMC GENOMICS

Differential expression in RNA-seq: A matter of depth

(2011) S. Tarazona et al.   GENOME RESEARCH

Sequencing technology does not eliminate biological variability

(2011) Kasper D Hansen et al.   NATURE BIOTECHNOLOGY

Rapid evolution of disease resistance is accompanied by functional changes in gene expression in a wild bird

(2011) C. Bonneaud et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

(2010) James H Bullard et al.   BMC BIOINFORMATICS

Statistical Design and Analysis of RNA Sequencing Data

(2010) P. L. Auer et al.   GENETICS

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

(2010) R Ekblom et al.   HEREDITY

RNA sequencing: advances, challenges and opportunities

(2010) Fatih Ozsolak et al.   NATURE REVIEWS GENETICS

Differential expression analysis for sequence count data

(2010) Simon Anders et al.   GENOME BIOLOGY

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

(2009) M. D. Robinson et al.   BIOINFORMATICS

Genomic reaction norms: using integrative biology to understand molecular mechanisms of phenotypic plasticity

(2009) NADIA AUBIN-HORTH et al.   MOLECULAR ECOLOGY

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

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

RNA-Seq: a revolutionary tool for transcriptomics

(2008) Zhong Wang et al.   NATURE REVIEWS GENETICS

Social determination of sex in reef fishes

(2008) John Godwin   SEMINARS IN CELL & DEVELOPMENTAL BIOLOGY