Samuel BlanquartResearch scientist, Inria. Dyliss team, Irisa / Inria Rennes-Bretagne Atlantique, Email: samuel.blanquart@inria.fr |
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Research topics
Phylogenetic
Phylogenetic modelling (PhD thesis 2007), phylogenetic inferences and ancestral sequence reconstruction (e.g. see Blanquart et al. 2021). Phylogenetic and functional analysis of a complex multi-paralog and multidomaine gene familly, the ADAM TS/TSL (PhD student: Olivier Dennler).
Metagenomics
Reconstruction of phylogenetic markers from WGS metagenomic data (PhD student, Pierre Pericard).
Transcriptomics
Modelling of the gene orthologous splicing structures and prediction of orthologous isoforms (PhD student: Nicolas Guillaudeux 2018-2021. Postdoctoral fellow: Antoine Aymeric-Lorquin, 2018). Evolution of the TRPM8 isoforms in Amniota (Blanquart et al 2019).
System biology
Estimating ecosystem metabolisms from the 16S RNA sequenced in environmental samples (PhD student Arnaud Belcour).
PhD students
Arnaud Belcour
Title : Design of synthetic minimal microbial communities.
Start in 2019. Funding Inria.
Olivier Dennler
Title : Functional prediction of ADAM proteins.
Start in 2019. Rennes University.
Nicolas Guillaudeux
Title : To compare gene structures for prediction of alternative coding transcripts in human, mouse and dog.
Defended in 2021, December the 16th. Funding Rennes University.
Pierre Péricard
Title : Algorithms for conserved markers sequences reconstruction in metagenomics data.
Defended in 2017, October the 27th. Funding Lille University.
Positions
Since 2018. Junior researcher at Inria Rennes – Bretagne Atlantique, DYLISS team (Rennes, France).
2010 to 2018. Junior researcher at Inria Lille – Nord Europe, BONSAI team (Lille France).
2010. Posdoctoral fellow at ISEM, Molecular evolution team (Montpellier, France).
2009. Postdoctoral fellow at EBI, Goldman group (Cambridge, UK).
2007 to 2009. Postdoctoral fellow at LIRMM, MAB team (Montepellier, France).
2004 to 2007. PhD student at LIRMM, MAB team (Montpellier, France).
Softwares
Esmecata (Belcour et al, in preparation). The software retrieves from the UniProt database the core and pan proteomes associated to a taxonomic rank provided as input. Retrieved proteins are suitable for metabolic network reconstruction.
Aucome (Belcour et al, in preparation). The software takes as input genomes with sparse annotations and it completes them applying comparative genomics principles. Outputs are suitable for metabolic networks reconstruction.
MATAM (Pericard et al 2017). Taking short reads from metagenomics environmental samples as input, the software provides targeted genes assembly, typicaly of 16S / 18S ribosomal RNA genes. The produced gene scaffolds are highly accurate and suitable for precise taxonomic assignation. The software outputs the scaffolds and their RDP classification. Github
CG-Alcode (Blanquart et al 2016). The software infers comparative genomics analysis of the gene structures involved in alternative splicing and alternative transcription. The software outputs predicted isoform orthologs.
ProCARs (Perrin et al 2015). The software reconstruct ancestral gene orders with a progressive homology-based method.
