Postdocs
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Ana Paula Zotta Mota
UCA JEDI fellow: January the 15th 2022– ongoing
Main topic: Pan-genomics of plant-parasitic nematodes, gene birth and loss, SNP and short indels.
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Georgios D Koutsovoulos
GDK Homepage|
ANR PRC ‘ADMIRE’ fellow: 04/05/2021 — 31/12/2021
UCA JEDI fellow: May the 4th 2019 — 03/05/2021
AgreensKills+ fellow: 01 Nov. 2016 — 03 May 2019
Main topic: Evolutionary trajectory of the root-knot nematodes, emergence and evolution of plant parasitism
Comparative genomics, phylogenetics and bioinformatics
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Romain Blanc-Mathieu
ANR JCJC ‘ASEXEVOL’ fellow: 01/01/2015 — 30/04/2015
University of Nice – Sophia Antipolis fellow: 01/01/2014 — 31/12/2014
Origin and consequences of the duplicated genome structures of tropical root-knot nematodes.
Now research scientist at the Cell & Plant Physiology Laboratory (CEA, Link), Grenoble, France.
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Celine Vens
Homepage
FWO fellow: 01/10/2009 — 31/07/2010
Bioinformatics, Machine Learning, Artificial Intelligence. Prediction of motifs in effectors, prediction of effector proteins using AI.
Now Associate Professor at the Faculty of Medicine at KULAK, a KU Leuven campus in Kortrijk, Belgium.
Engineers
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Djampa K Kozlowski
Center of Modeling, Simulation and Interactions (MSI) funding: Operational Research Engineer
AI approaches and integration of multi-omics data applied to plant health (link).
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Amandine Campan-Fournier
ANR NEMATARGETS Fellow
Identification of genes and proteins conserved in plant-parasitic nematodes but absent from non-parasitic species.
PhD Students
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Carole Belliardo (2019-2022)
Co-funded by Plant Health and Environment Dept of INRAE and Mycophyto
“Mining soil metagenomes to improve our knowledge on the origin of horizontal gene transfers in plant-parasitic nematodes.”
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Djampa K. Kozlowski (2017-2020)
Funded by the French Ministry for higher education, research and innovation
“Contribution of transposable elements to the genome plasticity and adaptation of root-knot nematodes.”
Defended November 13 2020
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Fabricio Arraes
“Genome assembly and annotation of the genome of the cotton boll weevil Anthonomus grandis”
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Ana Zotta Mota
“Identification of evolutionarily conserved plant genes responsive to nematode infection”
Master Students
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Lee Mariault (2022)
Master II, Life Sciences, “Biology Informatics Mathematics”, University Côte d’Azur (6 months)
“Contribution of structural variations to the genome plasticity of root-knot nematodes”.
Co-supervisors: Claire Lemaître (Inria, Rennes) and Marc Bailly-Bechet (GAME)
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Paola Porracciolo (2022)
Master I, Life Sciences, “Biology Informatics Mathematics”, University Côte d’Azur (5 months)
“Finding nematode effector motifs using AI and other approaches”
Co-supervisors: Djampa Kozlowski (MSI-GAME) and Silvia Bottini (MSI-MDlab)
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Mélanie Masson(2021)
Master II, Life Sciences, “Biology Informatics Mathematics”, University Côte d’Azur (6 months)
“Study of de novo gene birth events in the genomes of root-knot nematodes”
Co-supervisor: Dominique Collinet (GAME)
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Alyssia Mari(2021)
Master II, Life Sciences, “Biology Informatics Mathematics”, University Côte d’Azur (6 months)
“Neo-functionalization and protein subcellular relocalization after whole genome duplications in root-knot nematodes”
Co-supervisor: Dominique Collinet (GAME)
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ALEXIA KUNTZ (2020)
Master II bioinformatics, Univerisity of Bordeaux (6 months)
“Gene loss and pseudogenisation after whole genome duplications in root-knot nematodes”
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Adrien Deceneux (2019)
Master II, Life Sciences, University of Nice – Sophia Antipolis (6 months)
Co-supervisor: Marc Bailly-Bechet (GAME)
“Mining soil metagenomes to identify horizontal gene transfers in root-knot nematodes”
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Marine Poullet (2018)
Master II, Life Sciences, “Biology Informatics Mathematics”, University of Nice – Sophia Antipolis (6 months)
Co-supervisor: Georgios D Koutsovoulos
“Exploring the genome structure of the root-knot nematode Meloidogyne enterolobii”
Now PhD student in the lab of Dr. Ludovic Orlando (Toulouse, France)
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Julie Dazeniere (2018)
Master II, Life Sciences, “Biology Informatics Mathematics”, University of Nice – Sophia Antipolis (6 months)
Co-supervisor: Marc Bailly-Bechet
“Spatial organization and expression of parasitism genes in the nematode pest Meloidogyne incognita”
Now PhD student in the lab of Dr. Bousios, University of Sussex, UK
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Carole Belliardo (2017)
Master II, Life Sciences, “Biology Informatics Mathematics”, University of Nice – Sophia Antipolis (6 months)
Co-supervisor: Marc Bailly-Bechet
“Horizontal gene transfers of viral origin in the genomes of root-knot nematodes”
Now PhD student in our lab.
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David Pratella (2016)
Master I, Life Sciences, “Biology Informatics Mathematics”, University of Nice – Sophia Antipolis (5 months)
Co-supervisor: Martine Da Rocha
“Detecting functional impact of the duplicated genome structure of the root-knot nematode Meloidogyne incognita at the homeologous gene copy expression level”
Now engineer in the lab of Dr. Silvia Bottini.
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Djampa K Kozlowski (2015)
Master I, Life Sciences, “Biology Informatics Mathematics”, University of Nice – Sophia Antipolis (5 months)
“Deciphering the phylogenetic relationship of the major root-knot nematode species using concatenated mitochondrial markers”
Now PhD student in our lab.
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Morgane Demeocq (2014)
Master I, Life Sciences, “Biology Informatics Mathematics”, University of Nice – Sophia Antipolis (5 months)
Co-supervisors: Etienne Danchin, Laetitia Zurletto, Martine Da Rocha
“Annotation of transposable elements in root-knot nematode genomes”
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Nicolas Nottet (2013)
Master II, Life Sciences, “Biology Informatics Mathematics”, University of Nice – Sophia Antipolis (6 months)
Co-supervisor: Laetita Zurletto
“Analysis of gene expression patterns during the developmenta life cycle of the root-knot nematode Meloidogyne incognita”
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Lauriane Massardier (2012)
Master I, Life Sciences, “Biology Informatics Mathematics”, University of Nice – Sophia Antipolis (5 months)
Co-supervisor: Laetita Zurletto
“Identification of functional divergence at the expression level between gene copies resulting from whole genome duplication in the root-knot nematode Meloidoyne incognita”
Now postdoc at I3S laboratory
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Vivien Deshaies (2011)
Master I, Bioinformatics, modeling and statistics, University of Rouen (4 months)
Co-supervisor: Laetita Zurletto
“Reconstruction of the mitochondrial genomes of the root-knot nematodes M. incognita and M. hapla and phylognetic analysis”
Now bioinformatics engineer in Institut Curie
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Martine Da Rocha (2010)
Master II, Bioinformatics, modeling and statistics, University of Rouen (12 months)
“Development of a web server ‘NEMESIS (Nematode Electronic Sequence Information and Services )’, to mine, compare and retrieve sequences in root-knot nematode genomes and transcriptomes”
Now bioinformatics engineer at INRA in the bioinformatics and genomics platform of Agrobiotech Institute
Other Students
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Mathilde Boyer
DUT Génie Biologique option bioinfirmatique (4 months)
“Detections and analysis of horizontal gene transfers of non-metazoan origin in the genome of the white fly Bemisia tabaci“