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

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

Protein misinteraction avoidance causes highly expressed proteins to evolve slowly

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

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

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

When orthologs diverge between human and mouse

(2011) W. H. Gharib et al.   BRIEFINGS IN BIOINFORMATICS

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

A panorama of mammalian gene expression evolution

(2011) J. Zhang   Molecular Systems Biology

The evolution of gene expression levels in mammalian organs

(2011) David Brawand et al.   NATURE

The Gene Ontology: enhancements for 2011

(2011)   NUCLEIC ACIDS RESEARCH

Measuring the evolutionary rate of protein-protein interaction

(2011) W. Qian et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Testing the Ortholog Conjecture with Comparative Functional Genomic Data from Mammals

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

Analysis of a genome-wide set of gene deletions in the fission yeast Schizosaccharomyces pombe

(2010) Dong-Uk Kim et al.   NATURE BIOTECHNOLOGY

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

(2010) Yuanyan Xiong et al.   NATURE GENETICS

Ensembl 2011

(2010) P. Flicek et al.   NUCLEIC ACIDS RESEARCH

Systematic discovery of nonobvious human disease models through orthologous phenotypes

(2010) K. L. McGary et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Maintenance of duplicate genes and their functional redundancy by reduced expression

(2010) Wenfeng Qian et al.   TRENDS IN GENETICS

The use of gene ontology evidence codes in preventing classifier assessment bias

(2009) Mark F. Rogers et al.   BIOINFORMATICS

Estimating accuracy of RNA-Seq and microarrays with proteomics

(2009) Xing Fu et al.   BMC GENOMICS

Nrarp Coordinates Endothelial Notch and Wnt Signaling to Control Vessel Density in Angiogenesis

(2009) Li-Kun Phng et al.   DEVELOPMENTAL CELL

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

(2009) Vini Pereira et al.   GENETICS

Protein Subcellular Relocalization in the Evolution of Yeast Singleton and Duplicate Genes

(2009) Wenfeng Qian et al.   Genome Biology and Evolution

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

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

Semantic Similarity in Biomedical Ontologies

(2009) Catia Pesquita et al.   PLoS Computational Biology

Rad6B Is a Positive Regulator of  -Catenin Stabilization

(2008) M. P.V. Shekhar et al.   CANCER RESEARCH

Mistranslation-Induced Protein Misfolding as a Dominant Constraint on Coding-Sequence Evolution

(2008) D. Allan Drummond et al.   CELL

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

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

Mapping and quantifying mammalian transcriptomes by RNA-Seq

(2008) Ali Mortazavi et al.   NATURE METHODS

RNA-Seq: a revolutionary tool for transcriptomics

(2008) Zhong Wang et al.   NATURE REVIEWS GENETICS

The GOA database in 2009--an integrated Gene Ontology Annotation resource

(2008) D. Barrell et al.   NUCLEIC ACIDS RESEARCH

Null mutations in human and mouse orthologs frequently result in different phenotypes

(2008) B.-Y. Liao et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA