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

EBSeq: an empirical Bayes hierarchical model for inference in RNA-seq experiments

(2013) Ning Leng et al.   BIOINFORMATICS

Evolutionary Ecological Genomics

(2013) Luisa Orsini et al.   MOLECULAR ECOLOGY

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

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

Causal reasoning on biological networks: interpreting transcriptional changes

(2012) Leonid Chindelevitch et al.   BIOINFORMATICS

Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration

(2012) H. Thorvaldsdottir et al.   BRIEFINGS IN BIOINFORMATICS

Progress in Ion Torrent semiconductor chip based sequencing

(2012) Barry Merriman et al.   ELECTROPHORESIS

Detecting differential usage of exons from RNA-seq data

(2012) S. Anders et al.   GENOME RESEARCH

The proteomics of feather development in pied flycatchers (Ficedula hypoleuca) with different plumage coloration

(2012) Paula K. Leskinen et al.   MOLECULAR ECOLOGY

Exploring local immunological adaptation of two stickleback ecotypes by experimental infection and transcriptome-wide digital gene expression analysis

(2012) Tobias L. Lenz et al.   MOLECULAR ECOLOGY

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

The simple fool's guide to population genomics via RNA-Seq: an introduction to high-throughput sequencing data analysis

(2012) Pierre De Wit et al.   Molecular Ecology Resources

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks

(2012) Cole Trapnell et al.   Nature Protocols

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

(2012) Intawat Nookaew et al.   NUCLEIC ACIDS RESEARCH

NGS QC Toolkit: A Toolkit for Quality Control of Next Generation Sequencing Data

(2012) Ravi K. Patel et al.   PLoS One

Population-scale sequencing reveals genetic differentiation due to local adaptation in Atlantic herring

(2012) S. Lamichhaney et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

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

(2011) Jochen BW Wolf et al.   BMC GENOMICS

Bioinformatics tools and databases for analysis of next-generation sequence data

(2011) H. C. Lee et al.   Briefings in Functional Genomics

Next-generation sequencing technologies for gene expression profiling in plants

(2011) M. Jain   Briefings in Functional Genomics

Multiplexed shotgun genotyping for rapid and efficient genetic mapping

(2011) P. Andolfatto et al.   GENOME RESEARCH

Synthetic spike-in standards for RNA-seq experiments

(2011) L. Jiang et al.   GENOME RESEARCH

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

Evaluation of next-generation sequencing software in mapping and assembly

(2011) Suying Bao et al.   JOURNAL OF HUMAN GENETICS

The evolution of gene expression levels in mammalian organs

(2011) David Brawand et al.   NATURE

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

(2011) Manfred G Grabherr et al.   NATURE BIOTECHNOLOGY

A framework for variation discovery and genotyping using next-generation DNA sequencing data

(2011) Mark A DePristo et al.   NATURE GENETICS

Computational methods for transcriptome annotation and quantification using RNA-seq

(2011) Manuel Garber et al.   NATURE METHODS

Next-generation transcriptome assembly

(2011) Jeffrey A. Martin et al.   NATURE REVIEWS GENETICS

Genotype and SNP calling from next-generation sequencing data

(2011) Rasmus Nielsen et al.   NATURE REVIEWS GENETICS

A Robust, Simple Genotyping-by-Sequencing (GBS) Approach for High Diversity Species

(2011) Robert J. Elshire et al.   PLoS One

From RNA-seq reads to differential expression results

(2011) Alicia Oshlack et al.   GENOME BIOLOGY

Haplotype and isoform specific expression estimation using multi-mapping RNA-seq reads

(2011) Ernest Turro et al.   GENOME BIOLOGY

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   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

Statistical Design and Analysis of RNA Sequencing Data

(2010) P. L. Auer et al.   GENETICS

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

Ascertainment Biases in SNP Chips Affect Measures of Population Divergence

(2010) A. Albrechtsen et al.   MOLECULAR BIOLOGY AND EVOLUTION

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

Next Generation Molecular Ecology

(2010) DIETHARD TAUTZ 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

Sequence signatures and mRNA concentration can explain two-thirds of protein abundance variation in a human cell line

(2010) Christine Vogel et al.   Molecular Systems Biology

Cloud computing and the DNA data race

(2010) Michael C Schatz et al.   NATURE BIOTECHNOLOGY

In situ detection and genotyping of individual mRNA molecules

(2010) Chatarina Larsson 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

RNA sequencing: advances, challenges and opportunities

(2010) Fatih Ozsolak et al.   NATURE REVIEWS GENETICS

Prediction of alternative isoforms from exon expression levels in RNA-Seq experiments

(2010) Hugues Richard et al.   NUCLEIC ACIDS RESEARCH

The STRING database in 2011: functional interaction networks of proteins, globally integrated and scored

(2010) D. Szklarczyk et al.   NUCLEIC ACIDS RESEARCH

Adaptation genomics: the next generation

(2010) Jessica Stapley et al.   TRENDS IN ECOLOGY & EVOLUTION

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

(2010) Mark D Robinson et al.   GENOME BIOLOGY

Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences

(2010) Jeremy Goecks et al.   GENOME BIOLOGY

Differential expression analysis for sequence count data

(2010) Simon Anders et al.   GENOME BIOLOGY

Bioinformatics for Next Generation Sequencing Data

(2010) Alberto Magi et al.   Genes

MapView: visualization of short reads alignment on a desktop computer

(2009) H. Bao et al.   BIOINFORMATICS

Tablet--next generation sequence assembly visualization

(2009) I. Milne 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

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

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

Divergence in gene regulation at young life history stages of whitefish (Coregonus sp.) and the emergence of genomic isolation

(2009) Arne W Nolte et al.   BMC EVOLUTIONARY BIOLOGY

How to map billions of short reads onto genomes

(2009) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

Computation for ChIP-seq and RNA-seq studies

(2009) Shirley Pepke et al.   NATURE METHODS

Sequencing technologies — the next generation

(2009) Michael L. Metzker   NATURE REVIEWS GENETICS

A Yeast Hybrid Provides Insight into the Evolution of Gene Expression Regulation

(2009) I. Tirosh et al.   SCIENCE

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

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

Rapid transcriptome characterization for a nonmodel organism using 454 pyrosequencing

(2008) J. CRISTOBAL VERA et al.   MOLECULAR ECOLOGY

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

Rapid SNP Discovery and Genetic Mapping Using Sequenced RAD Markers

(2008) Nathan A. Baird et al.   PLoS One

Real-Time DNA Sequencing from Single Polymerase Molecules

(2008) J. Eid et al.   SCIENCE

Pleiotropy in the melanocortin system, coloration and behavioural syndromes

(2008) A DUCREST et al.   TRENDS IN ECOLOGY & EVOLUTION

The impact of next-generation sequencing technology on genetics

(2008) Elaine R. Mardis   TRENDS IN GENETICS

TECHNICAL ADVANCES: A microarray for large-scale genomic and transcriptional analyses of the zebra finch (Taeniopygia guttata) and other passerines

(2007) SARA NAURIN et al.   Molecular Ecology Resources