A comparison of gene expression and DNA methylation patterns across tissues and species

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

(2018) Jenny Chen et al.   GENOME RESEARCH

Genetic effects on gene expression across human tissues

(2017) François Aguet et al.   NATURE

The human protein atlas: A spatial map of the human proteome

(2017) Peter J. Thul et al.   PROTEIN SCIENCE

Brain gene expression signature on primate genomic sequence evolution

(2017) Shahar Barbash et al.   Scientific Reports

Variance adaptive shrinkage (vash): flexible empirical Bayes estimation of variances

(2016) Mengyin Lu et al.   BIOINFORMATICS

False discovery rates: a new deal

(2016) Matthew Stephens   BIOSTATISTICS

The Human Protein Atlas – an important resource for basic and clinical research

(2016) Cecilia Lindskog   Expert Review of Proteomics

Enhancer Evolution across 20 Mammalian Species

(2015) Diego Villar et al.   CELL

Transcription factor binding dynamics during human ES cell differentiation

(2015) Alexander M. Tsankov et al.   NATURE

The interplay between DNA methylation and sequence divergence in recent human evolution

(2015) Irene Hernando-Herraez et al.   NUCLEIC ACIDS RESEARCH

limma powers differential expression analyses for RNA-sequencing and microarray studies

(2015) Matthew E. Ritchie et al.   NUCLEIC ACIDS RESEARCH

Complementing tissue characterization by integrating transcriptome profiling from the Human Protein Atlas and from the FANTOM5 consortium

(2015) Nancy Yiu-Lin Yu et al.   NUCLEIC ACIDS RESEARCH

Tissue-based map of the human proteome

(2015) M. Uhlen et al.   SCIENCE

Sharing and Specificity of Co-expression Networks across 35 Human Tissues

(2015) Emma Pierson et al.   PLoS Computational Biology

DNA Methylation: Insights into Human Evolution

(2015) Irene Hernando-Herraez et al.   PLoS Genetics

A panel of induced pluripotent stem cells from chimpanzees: a resource for comparative functional genomics

(2015) Irene Gallego Romero et al.   eLife

An atlas of active enhancers across human cell types and tissues

(2014) Robin Andersson et al.   NATURE

Conservation of trans-acting circuitry during mammalian regulatory evolution

(2014) Andrew B. Stergachis et al.   NATURE

Comparison of the transcriptional landscapes between human and mouse tissues

(2014) Shin Lin et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Methylation QTLs Are Associated with Coordinated Changes in Transcription Factor Binding, Histone Modifications, and Gene Expression Levels

(2014) Nicholas E. Banovich et al.   PLoS Genetics

voom: precision weights unlock linear model analysis tools for RNA-seq read counts

(2014) Charity W Law et al.   GENOME BIOLOGY

Large-scale hypomethylated blocks associated with Epstein-Barr virus-induced B-cell immortalization

(2013) K. D. Hansen et al.   GENOME RESEARCH

The UCSC Genome Browser database: 2014 update

(2013) Donna Karolchik et al.   NUCLEIC ACIDS RESEARCH

Many human accelerated regions are developmental enhancers

(2013) J. A. Capra et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Primate Transcript and Protein Expression Levels Evolve Under Compensatory Selection Pressures

(2013) Z. Khan et al.   SCIENCE

Dynamics of DNA Methylation in Recent Human and Great Ape Evolution

(2013) Irene Hernando-Herraez et al.   PLoS Genetics

TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions

(2013) Daehwan Kim et al.   GENOME BIOLOGY

Latent Regulatory Potential of Human-Specific Repetitive Elements

(2012) Michelle C. Ward et al.   MOLECULAR CELL

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

Comparative studies of gene expression and the evolution of gene regulation

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

A Selection Index for Gene Expression Evolution and Its Application to the Divergence between Humans and Chimpanzees

(2012) Maria Warnefors et al.   PLoS One

Social environment is associated with gene regulatory variation in the rhesus macaque immune system

(2012) J. Tung et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Evolutionary Dynamics of Gene and Isoform Regulation in Mammalian Tissues

(2012) J. Merkin et al.   SCIENCE

The Evolutionary Landscape of Alternative Splicing in Vertebrate Species

(2012) N. L. Barbosa-Morais et al.   SCIENCE

Extensive Evolutionary Changes in Regulatory Element Activity during Human Origins Are Associated with Altered Gene Expression and Positive Selection

(2012) Yoichiro Shibata et al.   PLoS Genetics

BSmooth: from whole genome bisulfite sequencing reads to differentially methylated regions

(2012) Kasper D Hansen et al.   GENOME BIOLOGY

Bismark: a flexible aligner and methylation caller for Bisulfite-Seq applications

(2011) Felix Krueger et al.   BIOINFORMATICS

Sperm Methylation Profiles Reveal Features of Epigenetic Inheritance and Evolution in Primates

(2011) Antoine Molaro et al.   CELL

Gene Expression Differences Among Primates Are Associated With Changes in a Histone Epigenetic Modification

(2011) C. E. Cain et al.   GENETICS

Phyloepigenomic comparison of great apes reveals a correlation between somatic and germline methylation states

(2011) D. I. K. Martin et al.   GENOME RESEARCH

DNA methylation profiles of human active and inactive X chromosomes

(2011) A. J. Sharp et al.   GENOME RESEARCH

The evolution of gene expression levels in mammalian organs

(2011) David Brawand et al.   NATURE

Increased methylation variation in epigenetic domains across cancer types

(2011) Kasper Daniel Hansen et al.   NATURE GENETICS

Needles in stacks of needles: finding disease-causal variants in a wealth of genomic data

(2011) Gregory M. Cooper et al.   NATURE REVIEWS GENETICS

REVIGO Summarizes and Visualizes Long Lists of Gene Ontology Terms

(2011) Fran Supek et al.   PLoS One

A Genome-Wide Study of DNA Methylation Patterns and Gene Expression Levels in Multiple Human and Chimpanzee Tissues

(2011) Athma A. Pai et al.   PLoS Genetics

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Both Noncoding and Protein-Coding RNAs Contribute to Gene Expression Evolution in the Primate Brain

(2010) Courtney C. Babbitt et al.   Genome Biology and Evolution

Sex-specific and lineage-specific alternative splicing in primates

(2009) R. Blekhman et al.   GENOME RESEARCH

Human DNA methylomes at base resolution show widespread epigenomic differences

(2009) Ryan Lister et al.   NATURE

Differences in human and chimpanzee gene expression patterns define an evolving network of transcription factors in brain

(2009) Katja Nowick et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A comprehensive functional analysis of tissue specificity of human gene expression

(2008) Zoltan Dezso et al.   BMC BIOLOGY

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

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

Gene Regulation in Primates Evolves under Tissue-Specific Selection Pressures

(2008) Ran Blekhman et al.   PLoS Genetics