Post-Doc

I am currently working at the Computer Science Laboratory of Paris Sud University with Flora Jay.

We are developing deep learning methods for bacterial population genetics.

Publications
  • Cury J., Haller B.C., Achaz G., Jay F., (2020) Simulation of bacterial populations with SLiM [Read preprint]
  • Sanchez T., Cury J., Charpiat G., Jay F. (2020) Deep learning for population size history inference: Design, comparison and combination with approximate Bayesian computation [Read]
  • Nivina A., Grieb M.S., Loot C., Bikard B., Cury J., Shehata L., Bernardes J., Mazel D., (2020) Structure-specific DNA recombination sites: Design, validation, and machine learning–based refinement [Read]
  • Cury J., Abby S.S., Doppelt-Azeroual O., Néron B., Rocha E.P.C, (2020) Identifying Conjugative Plasmids and Integrative Conjugative Elements with CONJscan (Book chapter) [Read]
  • D’Humières C., Touchon M., Dion S., Cury J., Ghozlane A., Garcia-Garcera M., Bouchier C., Ma L, Denamur E., Rocha E.P.C., (2019) A simple, reproducible and cost-effective procedure to analyse gut phageome: from phage isolation to bioinformatic approach [Read]
  • Cury J., Oliveira P.H., de la Cruz F, Rocha E.P.C., (2018) Host range and genetic plasticity explain the coexistence of integrative and extrachromosomal mobile genetic elements [Read] SMBE 2019 best graduate student paper award
  • Oliveira P.H., Touchon M., Cury J., Rocha E.P.C., (2017) The chromosomal organization of horizontal gene transfer in Bacteria [Read]
  • Cury J., Touchon M., and Rocha E.P.C., (2017) Integrative and conjugative elements and their hosts: composition, distribution, and organization [Read]
  • Perrin A. et al. (8th author), (2017) Evolutionary dynamics and genomic features of the Elizabethkingia anophelis 2015 to 2016 Wisconsin outbreak strain [Read]
  • Loot C., Nivina A., Cury J., Escudero J.A., Ducos-Galand M., Bikard D., Rocha E.P.C. and Mazel D., (2017) Differences in Integron Cassette Excision Dynamics Shape a Trade-Off between Evolvability and Genetic Capacitance [Read]
  • Cury J., Jové T., Touchon M., Néron B. and Rocha E.P.C., (2016) Identification and analysis of integrons and cassette arrays in bacterial genomes [Read]
  • Abby S.S., Cury J., Guglielmini J., Néron B., Touchon M. and Rocha E.P.C., (2016) Identification of protein secretion systems in bacterial genomes. [Read]
  • Touchon M., Cury J., et al., (2014) The Genomic Diversification of the Whole Acinetobacter Genus: Origins, Mechanisms, and Consequences. [Read]

Thesis: Evolutionary genomics of conjugative elements and integrons (2013-2017) [Read]

Communications
  • 2019 - European Society for Evolutionary Biology (ESEB) - Turku, Finland - Oral Communication
  • 2019 - New Approaches and Concepts in Microbiology - EMBL, Heidelberg, Germany - Poster
  • 2019 - Mathematical and Computational Evolutionary Biology - Porquerolles, France - Oral communication
  • 2018 - Joint Congress on Evolutionary Biology - Montpellier, France - Poster
  • 2018 - Data Science Summer School - Palaiseau, France - Poster
  • 2017 - Seminar at LRI (invited) - Oral Communication
  • 2017 - Departmental Days of Genomes and Genetics department of the Pasteur Institute - Oral Communication
  • 2017 - Alphy - Lyon - Oral Communication
  • 2016 - Bacterial Genome Evolution Workshop - Bertinoro, Italy - Oral communication
  • 2016 - International Society for Plasmid Biology (ISPB) - Cambridge, UK - Poster
  • 2016 - JOBIM - Lyon, France - Oral communication
  • 2015 - Society of Molecular Biology and Evolution (SMBE) - Vienna, Austria - Oral communication
  • 2014 - International Society for Plasmid Biology (ISPB) - Cairns, Australia - Oral communication
Software and tools

2018 -

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Post doc @ LRI

Deep learning for bacterial population genetics 

With Flora Jay

PhD in Interdisciplinary Biology

Evolutionary Genomics of
Conjugative Elements and Integrons

Microbial Evolutionary Genomics lab
Pasteur Institute, Paris
Supervisor: Eduardo Rocha

2013 - 2017

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2012 - 2013

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Interdisciplinary Approaches in Life Science (AIV)
Centre de Recherche Interdisciplinaire (CRI) – Paris Descartes

Biology (Genomics and Genetics)

2010 - 2013

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