Tissue-Specificity of Gene Expression Diverges Slowly between Orthologs, and Rapidly between Paralogs

Coregulation of tandem duplicate genes slows evolution of subfunctionalization in mammals

(2016) X. Lan et al.   SCIENCE

Rapid divergence and diversification of mammalian duplicate gene functions

(2015) Raquel Assis et al.   BMC EVOLUTIONARY BIOLOGY

Most Highly Expressed Protein-Coding Genes Have a Single Dominant Isoform

(2015) Iakes Ezkurdia et al.   JOURNAL OF PROTEOME RESEARCH

Maintenance and Loss of Duplicated Genes by Dosage Subfunctionalization

(2015) Jean-Francois Gout et al.   MOLECULAR BIOLOGY AND EVOLUTION

The Split-Apply-Combine Strategy for Data Analysis

(2015) Hadley Wickham   Journal of Statistical Software

Tissue-Specific Evolution of Protein Coding Genes in Human and Mouse

(2015) Nadezda Kryuchkova-Mostacci et al.   PLoS One

Gene Family Level Comparative Analysis of Gene Expression in Mammals Validates the Ortholog Conjecture

(2014) Igor B. Rogozin et al.   Genome Biology and Evolution

Comparison of D. melanogaster and C. elegans developmental stages, tissues, and cells by modENCODE RNA-seq data

(2014) J. J. Li et al.   GENOME RESEARCH

Genome-wide identification of transcript start and end sites by transcript isoform sequencing

(2014) Vicent Pelechano et al.   Nature Protocols

Evolutionary dynamics of coding and non-coding transcriptomes

(2014) Anamaria Necsulea et al.   NATURE REVIEWS GENETICS

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

Functional and evolutionary implications of gene orthology

(2013) Toni Gabaldón et al.   NATURE REVIEWS GENETICS

Current status and new features of the Consensus Coding Sequence database

(2013) Catherine M. Farrell et al.   NUCLEIC ACIDS RESEARCH

Correcting for the bias due to expression specificity improves the estimation of constrained evolution of expression between mouse and human

(2012) Barbara Piasecka et al.   BIOINFORMATICS

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

(2012) Cole Trapnell et al.   Nature Protocols

Ensembl 2013

(2012) Paul Flicek et al.   NUCLEIC ACIDS RESEARCH

Evolutionary Dynamics of Gene and Isoform Regulation in Mammalian Tissues

(2012) J. Merkin et al.   SCIENCE

Mechanisms and Evolutionary Patterns of Mammalian and Avian Dosage Compensation

(2012) Philippe Julien et al.   PLOS BIOLOGY

On the Use of Gene Ontology Annotations to Assess Functional Similarity among Orthologs and Paralogs: A Short Report

(2012) Paul D. Thomas et al.   PLoS Computational Biology

The Ortholog Conjecture Is Untestable by the Current Gene Ontology but Is Supported by RNA Sequencing Data

(2012) Xiaoshu Chen et al.   PLoS Computational Biology

Resolving the Ortholog Conjecture: Orthologs Tend to Be Weakly, but Significantly, More Similar in Function than Paralogs

(2012) Adrian M. Altenhoff et al.   PLoS Computational Biology

Evidence for short-time divergence and long-time conservation of tissue-specific expression after gene duplication

(2011) J. Huerta-Cepas et al.   BRIEFINGS IN BIOINFORMATICS

The evolution of gene expression levels in mammalian organs

(2011) David Brawand et al.   NATURE

Mouse genomic variation and its effect on phenotypes and gene regulation

(2011) Thomas M. Keane et al.   NATURE

A User's Guide to the Encyclopedia of DNA Elements (ENCODE)

(2011)   PLOS BIOLOGY

Testing the Ortholog Conjecture with Comparative Functional Genomic Data from Mammals

(2011) Nathan L. Nehrt et al.   PLoS Computational Biology

Large-Scale Analysis of Orthologs and Paralogs under Covarion-Like and Constant-but-Different Models of Amino Acid Evolution

(2010) R. A. Studer et al.   MOLECULAR BIOLOGY AND EVOLUTION

How confident can we be that orthologs are similar, but paralogs differ?

(2009) Romain A. Studer et al.   TRENDS IN GENETICS

Pervasive positive selection on duplicated and nonduplicated vertebrate protein coding genes

(2008) R. A. Studer et al.   GENOME RESEARCH

EnsemblCompara GeneTrees: Complete, duplication-aware phylogenetic trees in vertebrates

(2008) A. J. Vilella et al.   GENOME RESEARCH