Evolution by gene loss, Nature Reviews Genetics, vol.17, issue.7, pp.379-391, 2016. ,
Resolving the Ortholog Conjecture: Orthologs Tend to Be Weakly, but Significantly, More Similar in Function than Paralogs, PLoS Comput Biol, vol.8, issue.5, p.1002514, 2012. ,
, , vol.2, p.13
Gene ontology: tool for the unification of biology. The Gene Ontology Consortium, Nat Genet, vol.25, issue.1, pp.25-34, 2000. ,
, Mouse large-scale phenotyping initiatives: overview of the European Mouse Disease Clinic (EUMODIC) and of the Wellcome Trust Sanger Institute Mouse Genetics Project, vol.23, pp.600-610, 2012.
From evolutionary genetics to human immunology: how selection shapes host defence genes, Nature Reviews Genetics, vol.11, issue.1, pp.17-30, 2010. ,
Optimization of gene expression by natural selection, Proceedings of the National Academy of Sciences, vol.106, issue.4, pp.1133-1138, 2009. ,
Reconciling gene trees with species trees, 2020. ,
URL : https://hal.archives-ouvertes.fr/hal-02535529
, The spotted gar genome illuminates vertebrate evolution and facilitates human-teleost comparisons, vol.48, pp.427-437, 2016.
URL : https://hal.archives-ouvertes.fr/hal-01595410
The evolution of gene expression levels in mammalian organs, Nature, vol.478, issue.7369, pp.343-348, 2011. ,
Gene Loss and Evolutionary Rates Following Whole-Genome Duplication in Teleost Fishes, Molecular Biology and Evolution, vol.23, issue.9, pp.1808-1816, 2006. ,
URL : https://hal.archives-ouvertes.fr/hal-00093159
The Ortholog Conjecture Is Untestable by the Current Gene Ontology but Is Supported by RNA Sequencing Data, PLoS Comput Biol, vol.8, issue.11, p.1002784, 2012. ,
A cautionary note on the use of Ornstein Uhlenbeck models in macroevolutionary studies, Biological Journal of the Linnean Society, vol.118, issue.1, pp.64-77, 2016. ,
Adaptation and Conservation throughout the Drosophila melanogaster Life-Cycle, Genome Biology and Evolution, vol.11, issue.5, pp.1463-1482, 2019. ,
Evidence for Polygenic Adaptation to Pathogens in the Human Genome, Molecular Biology and Evolution, 2013. ,
REFERENCES Detection of Pathways Affected by Positive Selection in Primate Lineages Ancestral to Humans, Molecular Biology and Evolution, vol.34, issue.6, pp.1391-1402, 2017. ,
Gene Regulatory Networks and the Evolution of Animal Body Plans, Science, vol.311, issue.5762, pp.796-800, 2006. ,
Preferential Duplication of Conserved Proteins in Eukaryotic Genomes, PLoS Biology, vol.2, issue.3, p.55, 2004. ,
The life and death of gene families, BioEssays, vol.31, issue.1, pp.29-39, 2009. ,
The Gene Ontology Handbook, Methods in Molecular Biology, vol.1446, 2016. ,
Is junk DNA bunk? A critique of ENCODE, Proceedings of the National Academy of Sciences, 2013. ,
We simply cannot go on being so vague about 'function', Genome Biology, vol.19, issue.1, p.223, 2018. ,
Distinguishing between "function" and "effect" in genome biology, Genome Biology and Evolution, 2014. ,
The evolutionary consequences of erroneous protein synthesis, Nat Rev Genet, vol.10, issue.10, pp.715-724, 2009. ,
Mistranslation-Induced Protein Misfolding as a Dominant Constraint on Coding-Sequence Evolution, Cell, vol.134, issue.2, pp.341-352, 2008. ,
Phylogenetic Analysis of Gene Expression, Integrative and Comparative Biology, 2013. ,
Pairwise comparisons across species are problematic when analyzing functional genomic data, Proceedings of the National Academy of Sciences, vol.115, issue.3, pp.409-417, 2018. ,
Determinants of Substitution Rates in Mammalian Genes: Expression Pattern Affects Selection Intensity but Not Mutation Rate, Mol Biol Evol, vol.17, issue.1, pp.68-70, 2000. ,
URL : https://hal.archives-ouvertes.fr/hal-00427068
The ENCODE project: Missteps overshadowing a success, Current biology : CB, vol.23, issue.7, pp.259-261, 2013. ,
Phylogenomics: Improving Functional Predictions for Uncharacterized Genes by Evolutionary Analysis, Genome Research, vol.8, issue.3, pp.163-167, 1998. ,
Viruses are a dominant driver of protein adaptation in mammals. eLife, vol.5, p.12469, 2016. ,
Orthology: Definitions, prediction, and impact on species phylogeny inference, 2020. ,
Preservation of Duplicate Genes by Complementary, Degenerative Mutations, Genetics, vol.151, issue.4, pp.1531-1545, 1999. ,
Junk or functional DNA? ENCODE and the function controversy, Biology & Philosophy, pp.1-25, 2014. ,
ECO, the Evidence & Conclusion Ontology: community standard for evidence information, Nucleic Acids Research. REFERENCES, vol.4, p.15, 2018. ,
A reanalysis of mouse ENCODE comparative gene expression data, vol.4, p.121, 1000. ,
The Relationship among Gene Expression, the Evolution of Gene Dosage, and the Rate of Protein Evolution, PLoS Genet, vol.6, issue.5, p.1000944, 2010. ,
URL : https://hal.archives-ouvertes.fr/hal-00539474
Molecular and genome evolution, 2016. ,
An evolutionary classification of genomic function, Genome Biology and Evolution, 2015. ,
On the immortality of television sets: "function" in the human genome according to the evolution-free gospel of ENCODE, Genome Biology and Evolution, 2013. ,
Tissue-driven hypothesis of genomic evolution and sequenceexpression correlations, Proceedings of the National Academy of Sciences, vol.104, issue.8, pp.2779-2784, 2007. ,
Why Do Hubs Tend to Be Essential in Protein Networks?, PLoS Genetics, vol.2, issue.6, p.88, 2006. ,
Evolutionary rate analyses of orthologs and paralogs from 12 Drosophila genomes, Genome Res, p.6249707, 2007. ,
The Chemical Genomic Portrait of Yeast: Uncovering a Phenotype for All Genes, Science, vol.320, issue.5874, pp.362-365, 2008. ,
Intrinsic inference difficulties for trait evolution with Ornstein-Uhlenbeck models, Methods in Ecology and Evolution, vol.5, issue.11, pp.1133-1146, 2014. ,
Hox clusters as models for vertebrate genome evolution, Trends in Genetics, vol.21, issue.8, pp.421-424, 2005. ,
Hox genes and evolution, vol.5, p.859, 1000. ,
Improving Hox Protein Classification across the Major Model Organisms, PLOS ONE, vol.5, issue.5, p.10820, 2010. ,
Do essential genes evolve slowly?, Current Biology, vol.9, issue.14, pp.747-750, 1999. ,
Positive Darwinian selection and the birth of an olfactory receptor clade in teleosts, Proceedings of the National Academy of Sciences, vol.106, issue.11, pp.4313-4318, 2009. ,
, Nature, vol.431, issue.7011, pp.946-957, 2004.
Protein moonlighting: what is it, and why is it important? Philosophical, Transactions of the Royal Society B: Biological Sciences, vol.373, 1738. ,
, Genome Biology, vol.17, issue.1, p.184, 2016.
Systematic humanization of yeast genes reveals conserved functions and genetic modularity, Science, vol.348, issue.6237, pp.921-925, 2015. ,
RNA-based gene duplication: mechanistic and evolutionary insights, Nature Reviews Genetics, vol.10, issue.1, pp.19-31, 2009. ,
Patterns of Positive Selection in Six Mammalian Genomes, PLoS Genetics, vol.4, issue.8, p.1000144, 2008. ,
Tissue-Specific Evolution of Protein Coding Genes in Human and Mouse, PLOS ONE, vol.10, issue.6, p.131673, 2015. ,
Tissue-Specificity of Gene Expression Diverges Slowly between Orthologs, and Rapidly between Paralogs, PLOS Computational Biology, vol.12, issue.12, p.1005274, 2016. ,
A benchmark of gene expression tissue-specificity metrics, Briefings in Bioinformatics, vol.18, issue.2, pp.205-214, 2017. ,
Evolution of protein-coding genes in Drosophila, Trends in Genetics, 2008. ,
The Role of Lineage-Specific Gene Family Expansion in the Evolution of Eukaryotes, Genome Research, vol.12, issue.7, pp.1048-1059, 2002. ,
Evolutionary Conservation of Expression Profiles Between Human and Mouse Orthologous Genes, Mol Biol Evol, vol.23, issue.3, pp.530-540, 2006. ,
Mouse duplicate genes are as essential as singletons, Trends in Genetics, vol.23, issue.8, pp.378-381, 2007. ,
Null mutations in human and mouse orthologs frequently result in different phenotypes, Proceedings of the National Academy of Sciences, p.800387105, 2008. ,
The Atlantic salmon genome provides insights into rediploidization, Nature, vol.533, issue.7602, pp.200-205, 2016. ,
Adaptive Evolution of Animal Proteins over Development: Support for the Darwin Selection Opportunity Hypothesis of Evo-Devo, Molecular Biology and Evolution, vol.35, issue.12, pp.2862-2872, 2018. ,
The Evolutionary Fate and Consequences of Duplicate Genes, Science, vol.290, issue.5494, pp.1151-1155, 2000. ,
The complex relationship of gene duplication and essentiality, Trends in Genetics, vol.25, issue.4, pp.152-155, 2009. ,
Positionally biased gene loss after whole genome duplication: evidence from human, yeast, and plant, Genome Research, vol.22, issue.12, pp.2427-2435, 2012. ,
Fifty-five years of enzyme classification: advances and difficulties, The FEBS Journal, vol.281, issue.2, pp.583-592, 2014. ,
Systematic discovery of nonobvious human disease models through orthologous phenotypes, Proceedings of the National Academy of Sciences, vol.107, issue.14, pp.6544-6549, 2010. ,
The genomic architecture and molecular evolution of ant odorant receptors, Genome Research, pp.237123-118, 2018. ,
Structure, function, and evolution of transient and obligate protein-protein interactions, vol.102, pp.10930-10935, 2005. ,
Integrating phenotype ontologies across multiple species, Genome Biology, vol.11, issue.1, p.2, 2010. ,
The Monarch Initiative: an integrative data and analytic platform connecting phenotypes to genotypes across species, Nucleic Acids Research, vol.45, issue.D1, pp.712-722, 2017. ,
Reconstruction of the vertebrate ancestral genome reveals dynamic genome reorganization in early vertebrates, 2007. ,
, Genome Res, p.6316407
Phylogenomics and genome annotation, Phylogenetics in the Genomic Era, 2020. ,
URL : https://hal.archives-ouvertes.fr/hal-02535669
Testing the Ortholog Conjecture with Comparative Functional Genomic Data from Mammals, PLoS Comput Biol, vol.7, issue.6, p.1002073, 2011. ,
Extreme expansion of the olfactory receptor gene repertoire in African elephants and evolutionary dynamics of orthologous gene groups in 13 placental mammals, Genome Research, pp.169532-113, 2014. ,
Metabolite-Enzyme Coevolution: From Single Enzymes to Metabolic Pathways and Networks, Annual Review of Biochemistry, vol.87, issue.1, pp.187-216, 2018. ,
URL : https://hal.archives-ouvertes.fr/hal-02020715
Quantifying Adaptive Evolution in the Drosophila Immune System, PLOS Genetics, vol.5, issue.10, p.1000698, 2009. ,
Global synthetic-lethality analysis and yeast functional profiling, Trends in Genetics, vol.22, issue.1, pp.56-63, 2006. ,
Adaptive evolution of bacterial metabolic networks by horizontal gene transfer, Nat Genet, vol.37, issue.12, pp.1372-1375, 2005. ,
An integrated view of protein evolution, Nat Rev Genet, vol.7, issue.5, pp.337-348, 2006. ,
ENCODE Project Writes Eulogy for Junk DNA, Science, vol.337, issue.6099, pp.1159-1161, 2012. ,
A Problem With the Correlation Coefficient as a Measure of Gene Expression Divergence, Genetics, vol.183, issue.4, pp.1597-1600, 2009. ,
Inferring the timescale of phylogenetic trees from fossil data, Phylogenetics in the Genomic Era, 2020. ,
URL : https://hal.archives-ouvertes.fr/hal-02536361
Comparative modular analysis of gene expression in vertebrate organs, BMC Genomics, vol.13, issue.1, p.124, 2012. ,
The Hourglass and the Early Conservation Models?ÄîCo-Existing Patterns of Developmental Constraints in Vertebrates, PLoS Genet, vol.9, issue.4, p.1003476, 2013. ,
Correcting for the bias due to expression specificity improves the estimation of constrained evolution of expression between mouse and human, Bioinformatics, vol.28, issue.14, pp.1865-1872, 2012. ,
The functional repertoires of metazoan genomes, Nat Rev Genet, vol.9, issue.9, pp.689-698, 2008. ,
The evolutionary dynamics of the Saccharomyces cerevisiae protein interaction network after duplication, Proceedings of the National Academy of Sciences, p.707293105, 2008. ,
Mutant phenotypes for thousands of bacterial genes of unknown function, Nature, vol.557, issue.7706, pp.503-509, 2018. ,
, , vol.2, p.19
The amphioxus genome and the evolution of the chordate karyotype, Nature, vol.453, issue.7198, pp.1064-1071, 2008. ,
Dosage-sensitive genes in evolution and disease, BMC Biology, vol.15, issue.1, p.78, 2017. ,
Improved exome prioritization of disease genes through cross-species phenotype comparison, Genome Research, vol.24, issue.2, pp.340-348, 2014. ,
The expression comparison tool in bgee, Phylogenetics in the Genomic Era, 2020. ,
URL : https://hal.archives-ouvertes.fr/hal-02535720
The quest for the universals of protein evolution, Trends in Genetics, vol.22, issue.8, pp.412-416, 2006. ,
An Analysis of Determinants of Amino Acids Substitution Rates in Bacterial Proteins, Mol Biol Evol, vol.21, issue.1, pp.108-116, 2004. ,
Gene family level comparative analysis of gene expression in mammals validates the ortholog conjecture, Genome Biology and Evolution, 2014. ,
Selective Constraints on Coding Sequences of Nervous System Genes Are a Major Determinant of Duplicate Gene Retention in Vertebrates, Molecular Biology and Evolution, vol.34, issue.11, pp.2773-2791, 2017. ,
Developmental Constraints on Vertebrate Genome Evolution, PLoS Genetics, vol.4, issue.12, p.1000311, 2008. ,
What to compare and how: Comparative transcriptomics for Evo-Devo, J Exp Zool B Mol Dev Evol, 2015. ,
Fitness Assays Reveal Incomplete Functional Redundancy of the HoxA1 and HoxB1 Paralogs of Mice, Genetics, vol.201, issue.2, pp.727-736, 2015. ,
Mapping Selection within Drosophila melanogaster Embryo's Anatomy, Molecular Biology and Evolution, vol.35, issue.1, pp.66-79, 2018. ,
Subfunctionalization versus neofunctionalization after whole-genome duplication, Nature Genetics, vol.50, issue.7, pp.908-909, 2018. ,
Biases in the Experimental Annotations of Protein Function and Their Effect on our Understanding of Protein Function Space, PLoS Comput Biol, vol.9, issue.5, p.1003063, 2013. ,
The sources of phylogenetic conflicts, Phylogenetics in the Genomic Era, 2020. ,
URL : https://hal.archives-ouvertes.fr/hal-02535482
To what extent current limits of phylogenomics can be overcome, 2020. ,
URL : https://hal.archives-ouvertes.fr/hal-02535366
On the Expansion of "Dangerous" Gene Repertoires by Whole-Genome Duplications in Early Vertebrates, Cell Reports, vol.2, issue.5, pp.1387-1398, 2012. ,
Human Dominant Disease Genes Are Enriched in Paralogs Originating from Whole Genome Duplication, PLoS Comput Biol, vol.10, issue.7, p.1003754, 2014. ,
Darkness in the Human Gene and Protein Function Space: Widely Modest or Absent Illumination by the Life Science Literature and the Trend for Fewer Protein Function Discoveries Since, PROTEOMICS, vol.18, p.1800093, 2000. ,
Integrated evolutionary and structural analysis reveals xenobiotics and pathogens as the major drivers of mammalian adaptation. bioRxiv, p.762690, 2019. ,
The Evolution of Gene Expression Underlying Vision Loss in Cave Animals, Molecular Biology and Evolution, vol.35, issue.8, pp.2005-2014, 2018. ,
Pervasive positive selection on duplicated and nonduplicated vertebrate protein coding genes, Genome Res, vol.18, issue.9, pp.1393-1402, 2008. ,
URL : https://hal.archives-ouvertes.fr/hal-00428199
How confident can we be that orthologs are similar, but paralogs differ?, Trends in Genetics, vol.25, pp.210-216, 2009. ,
, An integrated encyclopedia of DNA elements in the human genome, The ENCODE Project Consortium, vol.489, pp.57-74, 2012.
The Gene Ontology and the Meaning of Biological Function, Methods in Molecular Biology, pp.15-24, 2017. ,
On the Use of Gene Ontology Annotations to Assess Functional Similarity among Orthologs and Paralogs: A Short Report, PLoS Comput Biol, vol.8, issue.2, p.1002386, 2012. ,
Natural history and evolutionary principles of gene duplication in fungi, Nature, vol.449, issue.7158, pp.54-61, 2007. ,
Evolution of the Correlation between Expression Divergence and Protein Divergence in Mammals, Genome Biology and Evolution, vol.5, issue.7, pp.1324-1335, 2013. ,
Yesterday's polyploids and the mystery of diploidization, Nat Rev Genet, vol.2, issue.5, pp.333-341, 2001. ,