bioinformatics; development; evolution; genomics; database; selection
(2014), IQRray, a new method for Affymetrix microarray quality control, and the homologous organ conservation score, a new benchmark method for quality control metrics, in Bioinformatics
, 30(10), 1392-1399.
(2014), Patterns of Positive Selection in Seven Ant Genomes, in Molecular Biology and Evolution
, 31(7), 1661-1685.
(2014), Selectome update: quality control and computational improvements to a database of positive selection, in Nucleic Acids Research
, 42(D1), D917-D921.
(2014), Unification of multi-species vertebrate anatomy ontologies for comparative biology in Uberon, in Journal of Biomedical Semantics
, 5, 21.
(2013), The branch-site test of positive selection is surprisingly robust but lacks power under synonymous substitution saturation and variation in GC, in Molecular Biology and Evolution
, 30, 1675-1686.
(2013), The Hourglass and the Early Conservation Models—Co-Existing Patterns of Developmental Constraints in Vertebrates, in PLOS Genetics
, 9, e1003476.
(2013), Uncovering hidden duplicated content in public transcriptomics data, in Database
, 2013, bat010.
(2012), Comparative analysis of human and mouse expression data illuminates tissue-specific evolutionary patterns of miRNAs., in Nucleic acids research
, 40(13), 5890-900.
(2012), How much does the amphioxus genome represent the ancestor of chordates?, in Briefings in functional genomics
, 11(2), 89-95.
(2012), Resolving the ortholog conjecture: orthologs tend to be weakly, but significantly, more similar in function than paralogs., in PLoS computational biology
, 8(5), 1002514-1002514.
(2012), vHOG, a multispecies vertebrate ontology of homologous organs groups., in Bioinformatics (Oxford, England)
, 28(7), 1017-20.
A few years ago, we seemed on the verge of determining "universals of protein evolution", i.e. features of proteins which would explain most of the variance in their evolutionary rates and patterns, across the tree of life. Some level of optimism was justified by consistent results from yeast and bacteria. But more recently, the rules have been shown not to apply in a straightforward manner in animals. Results from flies, human, mouse and zebrafish, have shown that many relations between features of protein evolution and function are influenced either by gene expression patterns, or by the developmental role of genes. In other words, the anatomy and development of the animals in which genes are active influences their molecular evolution in a fundamental way.In this project, I propose to study this influence systematically, taking advantage of new bioinformatic resources developed in my lab, and when necessary extending them. This project is organized in two subprojects, which are strongly integrated. The first will focus on data analysis in mouse and zebrafish, organisms in which my lab already has experience, and for which the bioinformatic framework is well established. This will also allow us to take into account the role of whole genome duplications. The second subproject will integrate fly into our bioinformatic resources, and allow a systematic comparison of the evolutionary patterns between model vertebrates, and an arthropod.This project aims to shed light on fundamental features of molecular evolution in animals. In addition, we hope to contribute both to linking genome evolution and evolutionary developmental biology (Evo-Devo), and to new bioinformatic resources which will be of wide use to the community.