Selective Constraints on Coding Sequences of Nervous System Genes Are a Major Determinant of Duplicate Gene Retention in Vertebrates

Dosage sensitivity is a major determinant of human copy number variant pathogenicity

(2017) Alan M. Rice et al.   Nature Communications

Insights into the dN/dS ratio heterogeneity between brain specific genes and widely expressed genes in species of different complexity

(2016) Kakali Biswas et al.   GENOMICS

Near-optimal probabilistic RNA-seq quantification

(2016) Nicolas L Bray et al.   NATURE BIOTECHNOLOGY

The spotted gar genome illuminates vertebrate evolution and facilitates human-teleost comparisons

(2016) Ingo Braasch et al.   NATURE GENETICS

Evolution by gene loss

(2016) Ricard Albalat et al.   NATURE REVIEWS GENETICS

Coregulation of tandem duplicate genes slows evolution of subfunctionalization in mammals

(2016) X. Lan et al.   SCIENCE

Compensatory Drift and the Evolutionary Dynamics of Dosage-Sensitive Duplicate Genes

(2015) A. Thompson et al.   GENETICS

The sea lamprey meiotic map improves resolution of ancient vertebrate genome duplications

(2015) Jeramiah J. Smith et al.   GENOME RESEARCH

Maintenance and Loss of Duplicated Genes by Dosage Subfunctionalization

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

Determinants of the rate of protein sequence evolution

(2015) Jianzhi Zhang et al.   NATURE REVIEWS GENETICS

Brain evolution by brain pathway duplication

(2015) M. Chakraborty et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

The human transcriptome across tissues and individuals

(2015) M. Mele et al.   SCIENCE

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

(2015) et al.   SCIENCE

Identification of Ohnolog Genes Originating from Whole Genome Duplication in Early Vertebrates, Based on Synteny Comparison across Multiple Genomes

(2015) Param Priya Singh et al.   PLoS Computational Biology

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

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

Genomic evidence for adaptation by gene duplication

(2014) Wenfeng Qian et al.   GENOME RESEARCH

Transcriptomics of developing embryos and organs: A raising tool for evo-devo

(2014) Sophie Pantalacci et al.   JOURNAL OF EXPERIMENTAL ZOOLOGY PART B-MOLECULAR AND DEVELOPMENTAL EVOLUTION

UniProt: a hub for protein information

(2014)   NUCLEIC ACIDS RESEARCH

On the retention of gene duplicates prone to dominant deleterious mutations

(2014) Giulia Malaguti et al.   THEORETICAL POPULATION BIOLOGY

Mean of the Typical Decoding Rates: A New Translation Efficiency Index Based on the Analysis of Ribosome Profiling Data

(2014) Alexandra Dana et al.   G3-Genes Genomes Genetics

Identification of 2R-ohnologue gene families displaying the same mutation-load skew in multiple cancers

(2014) M. Tinti et al.   Open Biology

A Synergism between Adaptive Effects and Evolvability Drives Whole Genome Duplication to Fixation

(2014) Thomas D. Cuypers et al.   PLoS Computational Biology

Human Dominant Disease Genes Are Enriched in Paralogs Originating from Whole Genome Duplication

(2014) Param Priya Singh et al.   PLoS Computational Biology

Unification of multi-species vertebrate anatomy ontologies for comparative biology in Uberon

(2014) Melissa A Haendel et al.   Journal of Biomedical Semantics

Predicting whole genome protein interaction networks from primary sequence data in model and non-model organisms using ENTS

(2013) Eli Rodgers-Melnick et al.   BMC GENOMICS

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

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

The zebrafish reference genome sequence and its relationship to the human genome

(2013) Kerstin Howe et al.   NATURE

The genome of the platyfish, Xiphophorus maculatus, provides insights into evolutionary adaptation and several complex traits

(2013) Manfred Schartl et al.   NATURE GENETICS

The mouse Gene Expression Database (GXD): 2014 update

(2013) Constance M. Smith et al.   NUCLEIC ACIDS RESEARCH

Ohnologs are overrepresented in pathogenic copy number mutations

(2013) A. McLysaght et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Human Monogenic Disease Genes Have Frequently Functionally Redundant Paralogs

(2013) Wei-Hua Chen et al.   PLoS Computational Biology

The Roles of Whole-Genome and Small-Scale Duplications in the Functional Specialization of Saccharomyces cerevisiae Genes

(2013) Mario A. Fares et al.   PLoS Genetics

EMAP/EMAPA ontology of mouse developmental anatomy: 2013 update

(2013) Terry F Hayamizu et al.   Journal of Biomedical Semantics

Evolution of Vertebrate Tissues Driven by Differential Modes of Gene Duplication

(2012) M. Satake et al.   DNA RESEARCH

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

Gene balance hypothesis: Connecting issues of dosage sensitivity across biological disciplines

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

Gene duplication as a mechanism of genomic adaptation to a changing environment

(2012) F. A. Kondrashov   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

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

On the Expansion of “Dangerous” Gene Repertoires by Whole-Genome Duplications in Early Vertebrates

(2012) Param Priya Singh et al.   Cell Reports

Uberon, an integrative multi-species anatomy ontology

(2012) Christopher J Mungall et al.   GENOME BIOLOGY

2R and remodeling of vertebrate signal transduction engine

(2011) Lukasz Huminiecki et al.   BMC BIOLOGY

Contrasting patterns of evolution following whole genome versus tandem duplication events in Populus

(2011) E. Rodgers-Melnick et al.   GENOME RESEARCH

Evolution of vertebrate central nervous system is accompanied by novel expression changes of duplicate genes

(2011) Yuan Chen et al.   Journal of Genetics and Genomics

On the Origins of Mendelian Disease Genes in Man: The Impact of Gene Duplication

(2011) J. E. Dickerson et al.   MOLECULAR BIOLOGY AND EVOLUTION

The evolution of gene expression levels in mammalian organs

(2011) David Brawand et al.   NATURE

Two-Phase Resolution of Polyploidy in theArabidopsisMetabolic Network Gives Rise to Relative and Absolute Dosage Constraints

(2011) Michaël Bekaert et al.   PLANT CELL

Quantitative Expression Profile of Distinct Functional Regions in the Adult Mouse Brain

(2011) Takeya Kasukawa et al.   PLoS One

A High-Resolution Anatomical Atlas of the Transcriptome in the Mouse Embryo

(2011) Graciana Diez-Roux et al.   PLOS BIOLOGY

Cellular Heterogeneity: Do Differences Make a Difference?

(2010) Steven J. Altschuler et al.   CELL

Impact of translational error-induced and error-free misfolding on the rate of protein evolution

(2010) Jian-Rong Yang et al.   Molecular Systems Biology

The evolution of gene duplications: classifying and distinguishing between models

(2010) Hideki Innan et al.   NATURE REVIEWS GENETICS

Dosage Sensitivity Shapes the Evolution of Copy-Number Varied Regions

(2010) Benjamin Schuster-Böckler et al.   PLoS One

Ohnologs in the human genome are dosage balanced and frequently associated with disease

(2010) T. Makino et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Translationally optimal codons associate with aggregation-prone sites in proteins

(2010) Yaelim Lee et al.   PROTEOMICS

The Relationship among Gene Expression, the Evolution of Gene Dosage, and the Rate of Protein Evolution

(2010) Jean-François Gout et al.   PLoS Genetics

BioMart – biological queries made easy

(2009) Damian Smedley et al.   BMC GENOMICS

Intrinsic Protein Disorder and Interaction Promiscuity Are Widely Associated with Dosage Sensitivity

(2009) Tanya Vavouri et al.   CELL

Genomics and the evolutionary origins of nervous system complexity

(2009) Todd H Oakley et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

Evolution of gene function and regulatory control after whole-genome duplication: Comparative analyses in vertebrates

(2009) K. S. Kassahn et al.   GENOME RESEARCH

Heterogeneous Patterns of Gene-Expression Diversification in Mammalian Gene Duplicates

(2009) D. Farre et al.   MOLECULAR BIOLOGY AND EVOLUTION

Differential Retention of Metabolic Genes Following Whole-Genome Duplication

(2009) J.-F. Gout et al.   MOLECULAR BIOLOGY AND EVOLUTION

Translationally Optimal Codons Associate with Structurally Sensitive Sites in Proteins

(2009) T. Zhou et al.   MOLECULAR BIOLOGY AND EVOLUTION

The evolutionary consequences of erroneous protein synthesis

(2009) D. Allan Drummond et al.   NATURE REVIEWS GENETICS

The evolutionary significance of ancient genome duplications

(2009) Yves Van de Peer et al.   NATURE REVIEWS GENETICS

Chordate roots of the vertebrate nervous system: expanding the molecular toolkit

(2009) Linda Z. Holland   NATURE REVIEWS NEUROSCIENCE

Gene duplication and evolutionary novelty in plants

(2009) Lex E. Flagel et al.   NEW PHYTOLOGIST

The complex relationship of gene duplication and essentiality

(2009) Takashi Makino et al.   TRENDS IN GENETICS

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

(2008) D. Allan Drummond et al.   CELL

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

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

Constraints imposed by non-functional protein–protein interactions on gene expression and proteome size

(2008) Jingshan Zhang et al.   Molecular Systems Biology

The amphioxus genome and the evolution of the chordate karyotype

(2008) Nicholas H. Putnam et al.   NATURE

Use and misuse of the gene ontology annotations

(2008) Seung Yon Rhee et al.   NATURE REVIEWS GENETICS

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

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

Ensembl 2009

(2008) T. J. P. Hubbard et al.   NUCLEIC ACIDS RESEARCH

Cellular reactions to gene dosage imbalance: genomic, transcriptomic and proteomic effects

(2008) Reiner A. Veitia et al.   TRENDS IN GENETICS

Developmental Constraints on Vertebrate Genome Evolution

(2008) Julien Roux et al.   PLoS Genetics