genome annotation, transcriptome annotation, transcriptome assembly, phylogenetics, phylogenomics, comparative genomics, evolutionary sequence analysis
I studied Bioinformatics at the Science University of Montpellier (France), and obtained a Phd in Bioinformatics, Structural biochemistry and Genomics at the Marseille University (France). During my Phd I focused on the analysis and the detection of unitary pseudogenes in eukaryotes. For this purpose, I developed expert system modules that generate and analyze heterogeneous data (e.g phylogenetic trees, protein predictions, sequence ancestral reconstructions, sequence comparisons, parsimony reconstruction of events, etc.). This approach allowing detecting loss and pseudogenization events occurred during evolution and also detecting intact genes not yet annotated. Pseudogenization process at genomic level can be observed for recent pseudogenes. I was equally involved in the creation and analysis of phylome of the chordata proteome.
Then I was PostDoc during one year at the International Center for Higher Education In Agricultural Sciences. My work focused on the detection of positive selection at large scale among angiosperm genomes thanks to an original method. Instead to traditional method used (codeml) we used MapNH that provides a prior estimation of parameters, which allows to considerably improving the computational time. The aim is to study the impact of recurrent gene duplication on adaptation of plant genomes. I also worked on the highlight of the species tree of Triticeae. To address this issue I used super matrix and super tree methods.
I joined NBIS in 2014 as expert in genome annotation. I perform functional and structural annotation of any type of organisms (e.g. plants, animals, fungi, bacteria). I carry out also different types of tasks (e.g. transcriptome assembly, abinitio training, manual curation, lift-over, data submission, synteny analysis, COG analysis), and develop tools and scripts for handling the related data.
Tiukova, I. A., Jiang, H., Dainat, J., Hoeppner, M. P., Lantz, H., Piskur, J., Sandgren, M., Nielsen, J., and Gu, Z. (2019) Assembly and Analysis of the Genome Sequence of the Yeast Brettanomyces naardenensis CBS 7540. Microorganisms
Wik, E., Olin, H., Haughey, C., Klasson, L., and Dainat, J. (2019) GUESSmyLT: Software to guess the RNA-Seq library type of paired and single end read files. Journal of Open Source Software
Tiukova, I. A., Pettersson, M. E., Hoeppner, M. P., Olsen, R. A., Käller, M., Nielsen, J., Dainat, J., Lantz, H., Söderberg, J., and Passoth, V. (2019) Chromosomal genome assembly of the ethanol production strain CBS 11270 indicates a highly dynamic genome structure in the yeast species Brettanomyces bruxellensis. PLoS ONE
Glémin, S., Scornavacca, C., Dainat, J., Burgarella, C., Viader, V., Ardisson, M., Sarah, G., Santoni, S., David, J., and Ranwez, V. (2019) Pervasive hybridizations in the history of wheat relatives. Science Advances
Norling, M., Jareborg, N., and Dainat, J. (2018) EMBLmyGFF3: A converter facilitating genome annotation submission to European Nucleotide Archive. BMC Research Notes
Nielsen, J. C., Grijseels, S., Prigent, S., Ji, B., Dainat, J., Nielsen, K. F., Frisvad, J. C., Workman, M., and Nielsen, J. (2017) Global analysis of biosynthetic gene clusters reveals vast potential of secondary metabolite production in Penicillium species. Nature Microbiology
Moreno, A. D., Tellgren-roth, C., Soler, L., Dainat, J., Olsson, L., and Geijer, C. (2017) Complete genome sequences of the xylose-fermenting Candida intermedia strains CBS 141442 and PYCC 4715. Genome Announcements
Cornman, R. S., Dainat, J., Miranda, J. R. D., Doublet, V., Emery, O., Evans, J. D., Farinelli, L., Schmid-hempel, P., Schmid-hempel, R., Song, J., and Schwarz, R. S. (2016) The Bee Microbiome: Impact on Bee Health and Model for Evolution and Ecology of Host-Microbe Interactions. mBio
Barrio, A. M. et al.
(2016) The genetic basis for ecological adaptation of the Atlantic herring revealed by genome sequencing. eLife
Fischer, I., Dainat, J., Ranwez, V., Glémin, S., Dufayard, J. F., and Chantret, N. (2014) Impact of recurrent gene duplication on adaptation of plant genomes. BMC Plant Biology
Zamani, N., Sundström, G., Meadows, J. R. S., Höppner, M. P., Dainat, J., Lantz, H., Haas, B. J., and Grabherr, M. G. (2014) A universal genomic coordinate translator for comparative genomics. BMC Bioinformatics
Dainat, J. and Pontarotti, P. (2014) Methods to Study the Occurrence and the Evolution of Pseudogenes Through a Phylogenetic Approach. In, Poliseno,L. (ed), Pseudogenes: Functions and Protocols, Methods in Molecular Biology, Vol. 1167
. Humana Press, pp. 87–99.
Dainat, J., Paganini, J., Pontarotti, P., and Gouret, P. (2012) GLADX: An automated approach to analyze the lineage-specific loss and pseudogenization of genes. PLoS ONE
Levasseur, A., Paganini, J., Dainat, J., Thompson, J. D., Poch, O., Pontarotti, P., and Gouret, P. (2012) The chordate proteome history database. Evolutionary bioinformatics online
Gouret, P., Paganini, J., Dainat, J., Louati, D., Darbo, E., Levasseur, P. P., Anthony, Pontarotti, P., and Levasseur, A. (2011) Integration of evolutionary biology concepts for functional annotation and automation of complex research in evolution: The multi-agent software system DAGOBAH. In, Pontarotti,P. (ed), Evolutionary Biology – Concepts, Biodiversity, Macroevolution and Genome Evolution
. Springer Berlin Heidelberg, Berlin, Heidelberg, pp. 71–87.