Gene Expression Networks Across Multiple Tissues Are Associated with Rates of Molecular Evolution in Wild House Mice

Ten hub genes associated with progression and prognosis of pancreatic carcinoma identified by co-expression analysis

(2018) Zhou Zhou et al.   International Journal of Biological Sciences

Gene regulation underlies environmental adaptation in house mice

(2018) Katya L Mack et al.   GENOME RESEARCH

The Relationship between Selection, Network Connectivity, and Regulatory Variation within a Population of Capsella grandiflora

(2017) Emily B. Josephs et al.   Genome Biology and Evolution

Genetic effects on gene expression across human tissues

(2017) François Aguet et al.   NATURE

Ensembl 2018

(2017) Daniel R Zerbino et al.   NUCLEIC ACIDS RESEARCH

Connectivity in gene coexpression networks negatively correlates with rates of molecular evolution in flowering plants

(2017) Rishi R. Masalia et al.   PLoS One

Co-expression network analysis identified six hub genes in association with metastasis risk and prognosis in hepatocellular carcinoma

(2017) Pengfei Chen et al.   Oncotarget

Understanding Tissue-Specific Gene Regulation

(2017) Abhijeet Rajendra Sonawane et al.   Cell Reports

Gene co-expression network connectivity is an important determinant of selective constraint

(2017) Niklas Mähler et al.   PLoS Genetics

Comparative analysis of weighted gene co-expression networks in human and mouse

(2017) Marius Eidsaa et al.   PLoS One

PANTHER version 11: expanded annotation data from Gene Ontology and Reactome pathways, and data analysis tool enhancements

(2016) Huaiyu Mi et al.   NUCLEIC ACIDS RESEARCH

The STRING database in 2017: quality-controlled protein–protein association networks, made broadly accessible

(2016) Damian Szklarczyk et al.   NUCLEIC ACIDS RESEARCH

Genomic resources for wild populations of the house mouse, Mus musculus and its close relative Mus spretus

(2016) Bettina Harr et al.   Scientific Data

Identification of Tissue-Specific Protein-Coding and Noncoding Transcripts across 14 Human Tissues Using RNA-seq

(2016) Jinhang Zhu et al.   Scientific Reports

The role of regulatory variation in complex traits and disease

(2015) Frank W. Albert et al.   NATURE REVIEWS GENETICS

The Genotype-Tissue Expression (GTEx) pilot analysis: Multitissue gene regulation in humans

(2015) et al.   SCIENCE

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

(2015) Emma Pierson et al.   PLoS Computational Biology

Insights into mammalian biology from the wild house mouse Mus musculus

(2015) Megan Phifer-Rixey et al.   eLife

HTSeq--a Python framework to work with high-throughput sequencing data

(2014) S. Anders et al.   BIOINFORMATICS

Analysis of the Human Tissue-specific Expression by Genome-wide Integration of Transcriptomics and Antibody-based Proteomics

(2013) Linn Fagerberg et al.   MOLECULAR & CELLULAR PROTEOMICS

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

(2013) Daehwan Kim et al.   GENOME BIOLOGY

A high-performance computing toolset for relatedness and principal component analysis of SNP data

(2012) X. Zheng et al.   BIOINFORMATICS

Using probabilistic estimation of expression residuals (PEER) to obtain increased power and interpretability of gene expression analyses

(2012) Oliver Stegle et al.   Nature Protocols

Evolutionary conservation of codon optimality reveals hidden signatures of cotranslational folding

(2012) Sebastian Pechmann et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Gene regulatory networks and the role of robustness and stochasticity in the control of gene expression

(2011) L. T. MacNeil et al.   GENOME RESEARCH

Classic Selective Sweeps Were Rare in Recent Human Evolution

(2011) R. D. Hernandez et al.   SCIENCE

The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data

(2010) A. McKenna et al.   GENOME RESEARCH

Key considerations for measuring allelic expression on a genomic scale using high-throughput sequencing

(2010) PIERRE FONTANILLAS et al.   MOLECULAR ECOLOGY

A Bayesian Framework to Account for Complex Non-Genetic Factors in Gene Expression Levels Greatly Increases Power in eQTL Studies

(2010) Oliver Stegle et al.   PLoS Computational Biology

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

WGCNA: an R package for weighted correlation network analysis

(2008) Peter Langfelder et al.   BMC BIOINFORMATICS

THE LOCI OF EVOLUTION: HOW PREDICTABLE IS GENETIC EVOLUTION?

(2008) David L. Stern et al.   EVOLUTION