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

Density peaks of paralog pairs in human and mouse genomes

(2013) Alexander E. Vinogradov   GENE

Accelerated Evolution after Gene Duplication: A Time-Dependent Process Affecting Just One Copy

(2013) Cinta Pegueroles et al.   MOLECULAR BIOLOGY AND EVOLUTION

Functional and evolutionary implications of gene orthology

(2013) Toni Gabaldón et al.   NATURE REVIEWS GENETICS

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

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

Computational methods for Gene Orthology inference

(2011) D. M. Kristensen et al.   BRIEFINGS IN BIOINFORMATICS

Organ and Cell Type–Specific Complementary Expression Patterns and Regulatory Neofunctionalization between Duplicated Genes in Arabidopsis thaliana

(2011) Shao-Lun Liu et al.   Genome Biology and Evolution

The evolution of gene expression levels in mammalian organs

(2011) David Brawand et al.   NATURE

The Ecoresponsive Genome of Daphnia pulex

(2011) J. K. Colbourne et al.   SCIENCE

Testing the Ortholog Conjecture with Comparative Functional Genomic Data from Mammals

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

RNA sequencing shows no dosage compensation of the active X-chromosome

(2010) Yuanyan Xiong et al.   NATURE GENETICS

The evolution of gene duplications: classifying and distinguishing between models

(2010) Hideki Innan et al.   NATURE REVIEWS GENETICS

Maintenance of duplicate genes and their functional redundancy by reduced expression

(2010) Wenfeng Qian et al.   TRENDS IN GENETICS

A Problem With the Correlation Coefficient as a Measure of Gene Expression Divergence

(2009) Vini Pereira et al.   GENETICS

Posttranslational regulation impacts the fate of duplicated genes

(2009) G. D. Amoutzias et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

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

Phylogenetic and Functional Assessment of Orthologs Inference Projects and Methods

(2009) Adrian M. Altenhoff et al.   PLoS Computational Biology

Mapping and quantifying mammalian transcriptomes by RNA-Seq

(2008) Ali Mortazavi et al.   NATURE METHODS

Turning a hobby into a job: How duplicated genes find new functions

(2008) Gavin C. Conant et al.   NATURE REVIEWS GENETICS

RNA-Seq: a revolutionary tool for transcriptomics

(2008) Zhong Wang et al.   NATURE REVIEWS GENETICS