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Florent LASSALLE Florent LASSALLE Post-Doctoral Research Associate Personal e-mail: [email protected] Personal phone (FR): +33 6 79 60 11 72 Professional e-mail: [email protected] Personal phone (UK): +44 7 58 662 2048 RESEARCH EXPERIENCES 2016 - today Research Associate, MRC Center for Outbreak Analysis and Modelling, Imperial College London Topics: development of phylogenetic framework for the modelling of horizontal gene transfer and gene linkage evolution in bacterial genomes. Application to understanding of selective mechanisms driving AMR gene spread within and between bacterial pathogens. Methods: theoretical modelling of pangenome evolution and implementation in simulator; ABC infe- rence; development of phylogenetic models integrating population heterogeneity of genome gene content and linkage. 2014 - 2015 Research Associate, UCL Genetics Institute, University College London http://www.ucl.ac.uk/computational-biology-group Topics: Evolution and recombination of human cytomegalovirus; comparative metagenomics of oral microbiota; development of phylogenetic reconciliation methods. Methods: evaluation of genome-wide phylogenetic conflict; recombination detection; positive selection scans; metagenomic data mining; taxonomic assignation; phylodiversity analysis; functional annotation of genes and gene trees. 2009 - 2013 PhD, Microbial Ecology Dept. / Biometry and Evolutionary Biology Dept., University of Lyon Supervisors: Dr. Vincent Daubin and Dr. Xavier Nesme Topics: Evaluating the role of ecological adaptation in bacterial cladogenesis by the exploration of genomic diversity in A. tumefaciens species complex; Evolution of genomic GC-content in bacterial genomes and the role of homologous recombination Methods: ancestral genome reconstruction; gene tree/species tree reconciliation; modelisation of neighbour gene co-evolution; modelisation of genome composition evolution. 2009 Intern, Department of Structural and Molecular Biology, University College London Topic: Rhizobium sp. NT-26: a genome-enabled analysis of trophic versatility 2008 Intern, Laboratory of Molecular Genetics, Genomics, Microbiology, University of Strasbourg Topic: Exploration of genome of the arsenite-oxidizerRhizobium sp. NT-26 2008 Intern, Microbial Ecology Dept., University of Lyon Topic: Role of bacterial species-specific genes in adaptation to ecological niches TEACHING EXPERIENCES 2009-2012 Practical courses in statistics and bioinformatics to 2nd-year students at University Claude Bernard Lyon 1 2011-2012 Settling apractical course about annotation of prokaryotic genomesto 3rd-year students at ENS Lyon 2009-2013 Supervising 3 interns, one undergraduate and two graduate STUDIES 2009 - 2013 PhD in Biology, University Claude Bernard Lyon 1, University of Lyon, Lyon, France 2007 - 2009 MSc in Biology « Biosciences », Ecole Normale Supérieure de Lyon, Lyon, France 2006-2007 Bsc in Biology «Molecular and Cellular Biology», Ecole Normale Supérieure de Lyon, Lyon, France 2006 Admitted on competitive exam (Normalien),Ecole Normale Supérieure de Lyon, Lyon, France 2004 - 2006 Preparatory class for competitive exams (BCPST), Descartes high school, Tours, France 2004 Baccalauréat (high school diploma in sciences), Leonard de Vinci high school, Amboise, France ACADEMIC RECOGNITION International Conferences Symposium Annual Meeting of the Society for Molecular Biology and Evolution (SMBE) 2015, Vienna, Austria: chair Symposium on the Evolution and Ecology of Microbial Communities. Invited talks Rencontres Doctorales 2015, annual meeting of Doctoral School E2M2, University of Lyon (talk and jury of the PhD student competiton) Contributed Annual Meeting of the SMBE 2015, Vienna, Austria talks 13th Symposium on Bacterial Genetics and Ecology (BAGECO) 2015, Milan, Italy Annual Meeting of the SMBE 2013, Chicago, USA Otto Warburg International Summerschool and Research Symposium 2011, Berlin, Germany Journée des Microbiologistes de l’INRA 2010, Poitiers, France Peer review Reviewer for PLOS Genetics, PLOS Computational Biology, Science Reports, Bioinformatics, Mole- cular Ecology and Molecular Biology and Evolution. COMPETITIVE RESEARCH FUNDING 2006-2010 «Normalien» scholarship, Ecole Normale Supérieure de Lyon 2010-2013 Doctoral scholarship, Ecole Normale Supérieure de Lyon PERSONAL DEVELOPMENTS Phylogenomic database Agrogenom http://phylariane.univ-lyon1.fr/db/agrogenom/3 Integration of syntenic, functional and phylogenetic information, including reconstructed transfere- vents and ancestral genomes) for a dataset of 49 genomes of Rhizobiales. Implemented in PostgreSQL; browsable through a dynamic web interface. Python programming modules tree2 https://github.com/flass/tree2 manipulation of phylogenies and their topology; gene tree/species tree reconciliation and ancestral genome reconstruction; forward pangenome simulation with duplication, transfer and loss. Python and R programming modules genomescan https://github.com/flass/genomescan exploration of recombination and linkage landscapes in genomic datasets SKILLS Design and administration of SQL databases Programming in R, shell, Python Use of computer cluster / HPC facilities (PBS and SGE systems) Masterred use of bioinformatic tools, including: Metagenomics: MG-RAST, Kraken, MOCAT, pplacer, Phylosift Phylogeny: PhyML, RAxML, HyPhy, ClonalFrame/Origin, MrBayes Gene/Species Tree Reconciliation: Prunier, Count, ALE Data manipulation: PostgreSQL/MySQL, ACNUC, BioMart, R Genome annotation: Artemis, MaGe, RATT, GenMark, Sequin Graphic design: InkScape and SVG production with Python SCIENTIFIC PUBLICATIONS (H-index: 5) Research Lassalle F, Planel R, Daubin V, Nesme X et al. (2016). Ancestral genome reconstruction reveals the history of ecological diversification in Agrobacterium. (sumbitted) Lassalle F, Spagnoletti M, Fumagalli M, Balloux F et al. (2016). Deep sequencing of oral microbiomes from hunter-gatherers and traditional agriculturalists reveals shifts in commensal taxon balance and pathogen load linked to subsistance strategy. (submitted) Lassalle F, Depledge DP, Reeves M, Milne RSB, Balloux F, Breuer J et al. (2016). Islands of linkage in an ocean of pervasive recombination reveals two-speed evolution of human cytomegaloviru.Virus Evol. 2(1):vew17 Vieira FG, Lassalle F, Korneliussen TS, Fumagalli M (2015). Improving the accuracy of genetic distances estimation from Next-Generation Sequencing data. Biol. J. Linn. Soc. Lond. 117(1):139-149. Lassalle F, Périan S, Bataillon T, Nesme X, Duret L, Daubin V (2015). GC-content evolution in bacterial genomes: the biased gene conversion hypothesis expands. PLOS Genetics 11(2): e1004941. Ramírez-Bahena MH, Vial L, Lassalle F, Daubin V, Nesme X, Muller D et al. (2014). Single acquisition of protelomerase gave rise to speciation of a large and diverse clade within the Agrobacterium/Rhi- zobium supercluster characterized by the presence of a linear chromid. Mol. Phyl. Evol. 73:202-207. Andres J, Lassalle F, Médigues C, Vallenet D, Santini JM, Bertin P et al. (2013) Life in an arsenic-contai- ning gold mine: genome and physiology of the autotrophic arsenite-oxidizing bacterium Rhizobium sp. NT-26. Genome Biol. Evol. 5(5):934-53. Bigot T, Lassalle F, Daubin V, Perrière G (2013). TPMS: a set of utilities for querying collections of gene trees. BMC Bioinformatics 14:109. Lassalle F, Campillo T, Daubin V, Muller D, Nesme X et al. (2011). Genomic Species Are Ecological Species as Revealed by Comparative Genomics in Agrobacterium tumefaciens. Genome Biol. Evol. 3:762-781. Reviews Lassalle F, Muller D, Nesme X (2015). Ecological speciation in bacteria: Reverse ecology approaches reveal the adaptive part of bacterial cladogenesis. Res. Microbiol. 166(10):729-741. Ravenhall M, Škunca N, Lassalle F, Dessimoz C (2014). Inferring horizontal gene transfer. Accepted in PLOS Comp. Biol. 11(5): e1004095. Book Lassalle F, Daubin V. (2012). Evolution of Prokaryotic Pangenomes. in: Horizontal gene transfer in chapters Microorganisms p23-32, editor: M. P. Francino, Horizon Scientific Press (Norwich, UK), ISBN:978-1-908230-10-2. REFEREES Xavier Didelot, Lecturer Imperial College, Dept. of Infectious Disease Epidemiology MRC Centre for Outbreak Analysis and Modelling, Imperial College London [email protected] / +44 (0) 20 7594 3622 Francois Balloux, Pr UCL, “Computational Biology” group, UCL Genetics Institute, University College London [email protected] / Tel: +44 (0) 20 3108 1601 Judith Breuer, Pr UCL, “Centre for Molecular Virology“ group, Div of Infection & Immunity, University College London [email protected] / Tel: +44 (0) 020 3108 2130 Vincent DAUBIN, DR CNRS, “Bioinformatics and evolutionary genomics” group, Laboratoire de Biometrie et Biologie Evolutive, University of Lyon [email protected] / Tel: +33 (0)4 26 23 44 74 Xavier NESME, IR/HDR INRA, “Speciation of phytopathogeneous bacteria” group, Laboratoire d’Ecologie Microbienne, University of Lyon [email protected] / Tel: +33 (0)4 72 44 82 89.
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