People

Postdocs

  • Ana Paula Zotta Mota

Scholar

UCA JEDI fellow: January the 15th 2022– ongoing

Main topic: Pan-genomics of plant-parasitic nematodes, gene birth and loss, SNP and short indels.

  • Georgios D Koutsovoulos

GDK Homepage|Scholar

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

  • 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.

  • 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

  • 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).

  • Amandine Campan-Fournier

ANR NEMATARGETS Fellow

Identification of genes and proteins conserved in plant-parasitic nematodes but absent from non-parasitic species.

PhD Students

  • 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.”

  • 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

  • Fabricio Arraes

“Genome assembly and annotation of the genome of the cotton boll weevil Anthonomus grandis”

  • Ana Zotta Mota

“Identification of evolutionarily conserved plant genes responsive to nematode infection”

Master Students

  • 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)

  • 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)

  • 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)

  • 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)

  • ALEXIA KUNTZ (2020)

Master II bioinformatics, Univerisity of Bordeaux (6 months)

“Gene loss and pseudogenisation after whole genome duplications in root-knot nematodes”

  • 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”

  • 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)

  • 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

  • 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.

  • 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.

  • 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.

  • 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”

  • 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”

  • 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

  • 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

  • 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

  • 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“