A quantitative framework for characterizing the evolutionary history of mammalian gene expression

Improving genetic diagnosis in Mendelian disease with transcriptome sequencing

(2017) Beryl B. Cummings et al.   Science Translational Medicine

Adaptive Evolution of Gene Expression in Drosophila

(2017) Armita Nourmohammad et al.   Cell Reports

Ensembl 2017

(2016) Bronwen L. Aken et al.   NUCLEIC ACIDS RESEARCH

Mouse Genome Database (MGD)-2017: community knowledge resource for the laboratory mouse

(2016) Judith A. Blake et al.   NUCLEIC ACIDS RESEARCH

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology

(2015) Sue Richards et al.   GENETICS IN MEDICINE

Identification of cis-suppression of human disease mutations by comparative genomics

(2015) Daniel M. Jordan et al.   NATURE

ClinGen — The Clinical Genome Resource

(2015) Heidi L. Rehm et al.   NEW ENGLAND JOURNAL OF MEDICINE

Phylogenetic ANOVA: The Expression Variance and Evolution Model for Quantitative Trait Evolution

(2015) Rori V. Rohlfs et al.   SYSTEMATIC BIOLOGY

Measurement errors should always be incorporated in phylogenetic comparative analysis

(2015) Daniele Silvestro et al.   Methods in Ecology and Evolution

Decoupling of evolutionary changes in transcription factor binding and gene expression in mammals

(2014) Emily S. Wong et al.   GENOME RESEARCH

Measuring error rates in genomic perturbation screens: gold standards for human functional genomics

(2014) T. Hart et al.   Molecular Systems Biology

A comparative encyclopedia of DNA elements in the mouse genome

(2014) Feng Yue et al.   NATURE

Origins and functional evolution of Y chromosomes across mammals

(2014) Diego Cortez et al.   NATURE

Integrated physiology and systems biology of PPARα

(2014) Sander Kersten   Molecular Metabolism

Comparative genomics as a tool to understand evolution and disease

(2013) J. Alfoldi et al.   GENOME RESEARCH

Modeling Gene Expression Evolution with an Extended Ornstein–Uhlenbeck Process Accounting for Within-Species Variation

(2013) Rori V. Rohlfs et al.   MOLECULAR BIOLOGY AND EVOLUTION

The Genotype-Tissue Expression (GTEx) project

(2013) John Lonsdale et al.   NATURE GENETICS

From Mouse to Human: Evolutionary Genomics Analysis of Human Orthologs of Essential Genes

(2013) Benjamin Georgi et al.   PLoS Genetics

RNA-SeQC: RNA-seq metrics for quality control and process optimization

(2012) David S. DeLuca et al.   BIOINFORMATICS

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

The non-human primate reference transcriptome resource (NHPRTR) for comparative functional genomics

(2012) Lenore Pipes et al.   NUCLEIC ACIDS RESEARCH

Evolutionary Dynamics of Gene and Isoform Regulation in Mammalian Tissues

(2012) J. Merkin et al.   SCIENCE

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

(2011) Bo Li et al.   BMC BIOINFORMATICS

Signatures of positive selection in Toll-like receptor (TLR) genes in mammals

(2011) Helena Areal et al.   BMC EVOLUTIONARY BIOLOGY

Comparative RNA sequencing reveals substantial genetic variation in endangered primates

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

A high-resolution map of human evolutionary constraint using 29 mammals

(2011) Kerstin Lindblad-Toh et al.   NATURE

The evolution of gene expression levels in mammalian organs

(2011) David Brawand et al.   NATURE

Exome sequencing in sporadic autism spectrum disorders identifies severe de novo mutations

(2011) Brian J O'Roak et al.   NATURE GENETICS

SFARI Gene: an evolving database for the autism research community

(2010) S. Banerjee-Basu et al.   Disease Models & Mechanisms

Genome-wide analysis of alternative splicing evolution amongMussubspecies

(2010) BETTINA HARR et al.   MOLECULAR ECOLOGY

Gene expression divergence recapitulates the developmental hourglass model

(2010) Alex T. Kalinka et al.   NATURE

Comprehensive comparative analysis of strand-specific RNA sequencing methods

(2010) Joshua Z Levin et al.   NATURE METHODS

Evidence for widespread adaptive evolution of gene expression in budding yeast

(2010) H. B. Fraser et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

(2010) Mark D Robinson et al.   GENOME BIOLOGY

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

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

GOrilla: a tool for discovery and visualization of enriched GO terms in ranked gene lists

(2009) Eran Eden et al.   BMC BIOINFORMATICS

Optimization of gene expression by natural selection

(2009) T. Bedford et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Genetic diagnosis by whole exome capture and massively parallel DNA sequencing

(2009) Murim Choi et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Gene Regulation in Primates Evolves under Tissue-Specific Selection Pressures

(2008) Ran Blekhman et al.   PLoS Genetics

Patterns of Positive Selection in Six Mammalian Genomes

(2008) Carolin Kosiol et al.   PLoS Genetics