Comparative genomics as a tool to understand evolution and disease, Genome Res, vol.23, pp.1063-1068, 2013. ,
Standardized benchmarking in the quest for orthologs, Nature Methods, vol.13, pp.425-430, 2016. ,
URL : https://hal.archives-ouvertes.fr/hal-01636892
Resolving the ortholog conjecture: orthologs tend to be weakly, but significantly, more similar in function than paralogs, PLoS Comput. Biol, vol.8, p.1002514, 2012. ,
The rainbow trout genome provides novel insights into evolution after whole-genome duplication in vertebrates, Nat Commun, vol.5, pp.1-10, 2014. ,
URL : https://hal.archives-ouvertes.fr/hal-01193812
The gain and loss of genes during 600 million years of vertebrate evolution, Genome Biology, vol.7, p.43, 2006. ,
A comparison of normalization methods for high density oligonucleotide array data based on variance and bias, Bioinformatics, vol.19, pp.185-193, 2003. ,
The spotted gar genome illuminates vertebrate evolution and facilitates human-teleost comparisons, Nature Genetics, vol.48, pp.427-437, 2016. ,
URL : https://hal.archives-ouvertes.fr/hal-01594468
Near-optimal probabilistic RNA-seq quantification, Nature Biotechnology, vol.34, pp.525-527, 2016. ,
The Yeast Gene Order Browser: Combining curated homology and syntenic context reveals gene fate in polyploid species, Genome Res, vol.15, pp.1456-1461, 2005. ,
Automated identification of conserved synteny after whole-genome duplication, Genome Res, vol.19, pp.1497-1505, 2009. ,
Duplication, Rearrangement and Reconciliation: A Follow-Up 13 Years Later, Computational Biology, pp.47-62, 2013. ,
URL : https://hal.archives-ouvertes.fr/hal-00847155
The ortholog conjecture is untestable by the current gene ontology but is supported by RNA sequencing data, PLoS Comput. Biol, vol.8, p.1002784, 2012. ,
Convergent gene loss following gene and genome duplications creates single-copy families in flowering plants, Proc. Natl. Acad. Sci. U.S.A, vol.110, pp.2898-2903, 2013. ,
Redundancy and rewiring of genetic networks following genome-wide duplication events, Current Opinion in Plant Biology, vol.15, pp.168-176, 2012. ,
A hybrid micro-macroevolutionary approach to gene tree reconstruction, J. Comput. Biol, vol.13, pp.320-335, 2006. ,
Cone Types and Cone Arrangements in Teleost Retinae1, Acta Zoologica, vol.44, pp.179-243, 1963. ,
Preservation of duplicate genes by complementary, degenerative mutations, Genetics, vol.151, pp.1531-1545, 1999. ,
Community structure in social and biological networks, PNAS, vol.99, pp.7821-7826, 2002. ,
The Relationship among Gene Expression, the Evolution of Gene Dosage, and the Rate of Protein Evolution, PLoS Genet, vol.6, p.1000944, 2010. ,
URL : https://hal.archives-ouvertes.fr/hal-00539474
New Algorithms and Methods to Estimate Maximum-Likelihood Phylogenies: Assessing the Performance of PhyML 3.0, Syst Biol, vol.59, pp.307-321, 2010. ,
URL : https://hal.archives-ouvertes.fr/lirmm-00511784
The evolution of duplicate gene expression in mammalian organs, Genome Res, 2017. ,
Distinguishing Among Evolutionary Models for the Maintenance of Gene Duplicates, J Hered, vol.100, pp.605-617, 2009. ,
, Ensembl comparative genomics resources. Database (Oxford), 2016.
Metabolic Adaptation after Whole Genome Duplication, Mol Biol Evol, vol.26, pp.2441-2453, 2009. ,
Divergence of spatial gene expression profiles following species-specific gene duplications in human and mouse, Genome Res, vol.14, pp.1870-1879, 2004. ,
Rapid genome reshaping by multiple-gene loss after whole-genome duplication in teleost fish suggested by mathematical modeling, Proc Natl Acad Sci U S A, vol.112, pp.14918-14923, 2015. ,
Ancestral whole-genome duplication in the marine chelicerate horseshoe crabs, Heredity, vol.116, pp.190-199, 2016. ,
An Efficient Heuristic Procedure for Partitioning Graphs, Bell System Technical Journal, vol.49, pp.291-307, 1970. ,
Orthologs, paralogs, and evolutionary genomics, Annu. Rev. Genet, vol.39, pp.309-338, 2005. ,
Snakemake-a scalable bioinformatics workflow engine, Bioinformatics, vol.28, pp.2520-2522, 2012. ,
Polytomy refinement for the correction of dubious duplications in gene trees, Bioinformatics, vol.30, pp.519-526, 2014. ,
Gene tree correction guided by orthology, BMC Bioinformatics, vol.14, p.5, 2013. ,
URL : https://hal.archives-ouvertes.fr/hal-00873235
Gene Duplicability of Core Genes Is Highly Consistent across All Angiosperms, The Plant Cell, vol.28, pp.326-344, 2016. ,
WebGestalt 2019: gene set analysis toolkit with revamped UIs and APIs, Nucleic Acids Res, vol.47, pp.199-205, 2019. ,
Taurine, glutamate and GABA modulate the outgrowth from goldfish retinal explants and its concentrations are affected by the crush of the optic nerve, Amino Acids, vol.15, pp.195-209, 1998. ,
Teleost Fish-Specific Preferential Retention of Pigmentation Gene-Containing Families After Whole Genome Duplications in Vertebrates, Bethesda), vol.3, pp.1795-1806, 2018. ,
URL : https://hal.archives-ouvertes.fr/hal-01806995
PhylDiag: identifying complex synteny blocks that include tandem duplications using phylogenetic gene trees, BMC Bioinformatics, 2014. ,
Cone Arrangements in Teleost Retinae, Journal of Cell Science, vol.3, pp.189-201, 1957. ,
The Evolutionary Fate and Consequences of Duplicate Genes, Science, vol.290, pp.1151-1155, 2000. ,
Ohnologs in the human genome are dosage balanced and frequently associated with disease, Proc Natl Acad Sci U S A, vol.107, pp.9270-9274, 2010. ,
Evolution of the fish heart by sub/neofunctionalization of an elastin gene, Nat Commun, vol.7, pp.1-10, 2016. ,
Genomicus: a database and a browser to study gene synteny in modern and ancestral genomes, Bioinformatics, vol.26, pp.1119-1121, 2010. ,
Efficient Gene Tree Correction Guided by Genome Evolution, PLOS ONE, vol.11, p.159559, 2016. ,
URL : https://hal.archives-ouvertes.fr/hal-01162963
Polyploidy: Duplication of the Entire Genome, pp.98-106, 1970. ,
Immunocytochemical localization of taurine in the fish retina under light and dark adaptations, Amino Acids, vol.19, pp.593-604, 2000. ,
Evolution of gene expression after whole-genome duplication: New insights from the spotted gar genome, J. Exp. Zool. B Mol. Dev. Evol, vol.328, pp.709-721, 2017. ,
URL : https://hal.archives-ouvertes.fr/hal-01788671
Gene evolution and gene expression after whole genome duplication in fish: the PhyloFish database, BMC Genomics, vol.17, p.368, 2016. ,
URL : https://hal.archives-ouvertes.fr/hal-01487023
Accurate gene-tree reconstruction by learning gene-and species-specific substitution rates across multiple complete genomes, Genome Research, vol.17, pp.1932-1942, 2007. ,
A Bayesian approach for fast and accurate gene tree reconstruction, Mol. Biol. Evol, vol.28, pp.273-290, 2011. ,
Rare genomic changes as a tool for phylogenetics, Trends in Ecology & Evolution, vol.15, pp.454-459, 2000. ,
Revisiting ancestral polyploidy in plants, Sci Adv, vol.3, p.1603195, 2017. ,
Chromosome evolution at the origin of the ancestral vertebrate genome, Genome Biology, vol.19, p.166, 2018. ,
URL : https://hal.archives-ouvertes.fr/hal-02415626
Multiple rounds of speciation associated with reciprocal gene loss in polyploid yeasts, Nature, vol.440, p.341, 2006. ,
Joint amalgamation of most parsimonious reconciled gene trees, Bioinformatics, vol.31, pp.841-848, 2015. ,
URL : https://hal.archives-ouvertes.fr/hal-02154935
An Approximately Unbiased Test of Phylogenetic Tree Selection, Syst Biol, vol.51, pp.492-508, 2002. ,
CONSEL: for assessing the confidence of phylogenetic tree selection, Bioinformatics, vol.17, pp.1246-1247, 2001. ,
On the Expansion of "Dangerous" Gene Repertoires by Whole-Genome Duplications in Early Vertebrates, Cell Reports, vol.2, pp.1387-1398, 2012. ,
Identification of Ohnolog Genes Originating from Whole Genome Duplication in Early Vertebrates, Based on Synteny Comparison across Multiple Genomes, PLoS Comput. Biol, vol.11, p.1004394, 2015. ,
URL : https://hal.archives-ouvertes.fr/hal-01236668
OHNOLOGS v2: a comprehensive resource for the genes retained from whole genome duplication in vertebrates, Nucleic Acids Res, 2019. ,
URL : https://hal.archives-ouvertes.fr/hal-02398956
Genome sequence and genetic diversity of European ash trees, Nature, vol.541, pp.212-216, 2017. ,
Causes, consequences and solutions of phylogenetic incongruence, Brief Bioinform, vol.16, pp.536-548, 2015. ,
RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies, Bioinformatics, vol.30, pp.1312-1313, 2014. ,
Characterization and Evolution of the Spotted Gar Retina, J Exp Zool B Mol Dev Evol, vol.326, pp.403-421, 2016. ,
Efficient Exploration of the Space of Reconciled Gene Trees, Syst Biol, vol.62, pp.901-912, 2013. ,
The Inference of Gene Trees with Species Trees, Syst Biol, vol.64, pp.42-62, 2015. ,
2R or not 2R is not the question anymore, Nat Rev Genet, vol.11, pp.166-166, 2010. ,
The evolutionary significance of polyploidy, Nature Reviews Genetics, vol.18, pp.411-424, 2017. ,
The Grayling Genome Reveals Selection on Gene Expression Regulation after Whole-Genome Duplication, 2018. ,
, Genome Biol Evol, vol.10, pp.2785-2800
Cellular reactions to gene dosage imbalance: genomic, transcriptomic and proteomic effects, Trends in Genetics, vol.24, pp.390-397, 2008. ,
EnsemblCompara GeneTrees: Complete, duplication-aware phylogenetic trees in vertebrates, Genome Res, vol.19, pp.327-335, 2009. ,
Automatic genome-wide reconstruction of phylogenetic gene trees, Bioinformatics, vol.23, pp.549-558, 2007. ,
TreeFix: Statistically Informed Gene Tree Error Correction Using Species Trees, Syst Biol, vol.62, pp.110-120, 2013. ,