Le mot de Jay

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Curriculum vitae

Agricultural engineer specialized in plant breeding, PhD in systems biology

I am currently working on the MĂ©diMoinsQuart project,
the first monthly subscription box that allow you to cook middle-age recipes 🙂

Reach me on ResearchGate / LinkedIn / Viadeo

 

Professionnal experience

Jul. 2015 – Oct. 2018 : PhD student, Biogemma/Montpellier University. PhD thesis realized between the UMR Diade, Cereal Root Systems (CERES) lab (IRD Montpellier), and the biotech company Biogemma. Subject : Adaptation of cereal crops to water deprivation : looking for master root development genes through a systems biology approach.

Feb.-Apr. 2015 : Part time microbiology technician, CNRS. Participating in an experimental ecology project based on the Pseudomonas fluorescens model. Institute of Evolutionary Sciences of Montpellier, Evolution and Community Ecology lab.

Feb.-Aug. 2014 : Assistant breeder, Vilmorin. Cauliflower species, California, USA. Operational management of the breeding activities in recurrent populations. Design, setup and follow-up of the crossing cages, experimental and commercial trials, and experimental plots for improvement of the breeding process.

Oct.-Nov. 2013 : Research assistant, Think tank « seed treatment », Montpellier SupAgro. Prospective work about the issues regarding the prohibition of neonicotinoid molecules on seed treatment in Europe.

 

Education

  • 2018 : PhD in systems biology, Montpellier University, France. Thesis title : « Adaptation of cereal crops to water deprivation : looking for master root development genes through a systems biology approach ».
  • 2013 : Agricultural engineer (M.Sc), specialized in plant breeding, Montpellier SupAgro, France. Thesis title : « Setup of a controlled conditions laboratory test to evaluate the resistance of new banana varieties from Guadeloupe to black sigatoka ».
  • Feb.-Jul. 2012 : USTH, Hanoi, Vietnam. Master exchange program, plant biotechnology.
  • 2010-2013 : VetAgro Sup Clermont-Ferrand, France. Training in agricultural engineering.
  • 2007-2010 : B.Sc in Biology, Nice Sophia Antipolis University, France. Basic training in biology, focused on plant molecular biology and genetics.

 

Training periods

  • Mar.-Sep. 2013 : Research intern, Cirad, Guadeloupe (French West Indies). Fine-tuning of a controlled conditions laboratory test, in order to evaluate resistance to the Sigatoka diseases of new banana varieties in Guadeloupe, French Carribean. UMR AGAP, APMV lab.
  • Feb. 2012 :  Kickstart internship, Cirad, Montpellier. Development of a statistical analysis pipeline for the treatment of phenotyping data from Magnaporthe oryzae agressivity traits. UMR BGPI, BECphy lab.
  • Mar.-Jul. 2012 : Research intern, LMI Rice (IRD), Hanoi, Vietnam. Cloning in binary vectors of rice gene promoters for Gus-based expression pattern studies.

 

Research interests/keywords

  • Agriculture and agronomy
  • Gene regulatory networks
  • Systems biology
  • Developmental biology
  • Plant breeding
  • Roots
  • Cereals
  • Drought

 

Skills

  • Molecular biology : DNA and RNA extraction and quality assessment (NanoDrop One, Agilent 2100 Bioanalyzer & 4200 Tapestation), PCR, RT-qPCR (Agilent MX3005p), molecular cloning
  • Histology : tissue fixation and embedding (agarose, paraffin), sample preparation (vibratome and microtome), laser capture microdissection (Leica LMD 7000)
  • Microscopy : clear field & fluorescent (Zeiss Axio Imager Z2m), confocal (Zeiss LSM 880)
  • Image analysis : ImageJ. Fiji, Noesis Visilog, Bitplane Imaris (3D microscopy)
  • Expression analysis : Transcriptome Analysis Console (Affymetrix), Tuxedo suite (RNAseq)
  • Programming & data analysis : R, Python, Unix distributed computing (PBS)
  • Network science : network inference from time-series (TDCor) and perturbation (WGCNA), network manipulation (Cytoscape, Gephi), static and boolean-based dynamic analysis (identification of atraction basins and switches, robustness assessment)
  • Data management : MySQL, Microsoft Excel
  • Communication and editing : Microsoft Office, LaTeX, Mendeley, Adobe Photoshop
  • Professional certifications : 6.00.1x: Introduction to Computer Science and Programming Using Python (MITx), Certiphyto CSPP (licence OF-0000-31265), Pesticide Hazardous Communication Plus + Respirator training & Fit check + Tractor Safety Training (Licence 007213, CSTC), Perfect Pint Craftsman (Guinness)
  • Languages : French (mother tongue), English (full proficiency, TOEIC 975), Italian (to be reactivated), Spanish (beginner), Vietnamese (survival skills)

 

Publications

You’ll find my work referenced in ResearchGate / Google Scholar

Peer-reviewed articles

LAVARENNE J., GUYOMARC’H S., SALLAUD C., GANTET P., LUCAS M., 2018, The spring of systems biology-driven breeding. Trends in Plant Science, 23: 706-720, doi: 10.1016/j.tplants.2018.04.005

PHUNG T.P.N., MAI D.C., HOANG T.G., TRUONG T.M.H., LAVARENNE J., GONIN M., NGUYEN L.K., HA P.T., DO N.V., GANTET P. COURTOIS B., 2016, Genome-wide association mapping for root traits in a panel of rice accessions from Vietnam. BMC Plant Biology, 16, 64, doi: 10.1186/s12870-016-0747-y

HOANG T.G., MAI D.C., NGUYEN T. H., LAVARENNE J. GONIN M., NGUYEN T.H. DO N.V., GANTET P., 2015, HoĂ n thi?n quy trĂŹnh chuy?n gen cho gi?ng lĂșa taichung 65 thĂŽng qua vi khu?n Agrobacterium tumefaciens (Optimization of Transformation Protocol for Japonica Rice cv.Taichung 65 through Agrobacterium tumefaciens), T?p chĂ­ Khoa h?c vĂ  PhĂĄt tri?n, t?p 13, s? 5:764-773 (J. Sci. & Devel. 2015 , Vol. 13, No. 5 : 764-773)

 

Oral communication in meetings

Adaptation des céréales au déficit hydrique : recherche de gÚnes maßtres du développement racinaire par une approche de biologie des systÚmes, Journées NetBio 2018 (réseau méthodologique MIA « Inférence de réseaux »), Montpellier, France, 13 December 2018

LAVARENNE J., GONIN M., GUYOMARC’H S., ROUSTER J., CHAMPION A., , LAPLAZE L., SALLAUD C., GANTET P., LUCAS M.,  Crown root development in rice, a systems biology approach, Net4FS Third dissemination event, Montpellier, France, 17 October 2017

PHUNG T. P. N., MAI D. C., LAVARENNE J., TRUONG T.M.H., TA K. N., LE T.L., TRAN T.T.H., JOUANNIC S., LA T.N., LE H.H., HA T.T., DO N.V. , COURTOIS B., GANTET P. First steps in the evaluation of the genetic and root development diversity in a collection of rice varieties from Vietnam. Workshop on Biotechnology Research and Development in Plant Production and Protection, Vietnam Academy of Agronomical Science, Hanoi, Vietnam, 15 September, 2012.

 

Vulgarization articles

LAVARENNE J., LUCAS M., GANTET P. 2018 De Facebook au dĂ©veloppement des plantes : quand les rĂ©seaux s’en mĂȘlent. The Conversation, 7 fĂ©vrier 2018, 23:48 CET

 

Posters

LAVARENNE J., GONIN M., ROUSTER J., GUYOMARC’H S., CHAMPION A., , LAPLAZE L., SALLAUD C., GANTET P., LUCAS M., Looking for master regulatory genes of rice root development through a systems biology approach, 1st international Plant Systems Biology meeting, ConfĂ©rences Jacques Monod, CNRS, Roscoff, France September 10-14, 2018

GONIN M. , LAVARENNE J. , COUDERT Y. , BOURRIE I., LAPLAZE L., GANTET P., CHAMPION A. The rice CRL1 LBD transcription factor binds DNA with a relaxed specificity. 12th congress of the International Plant Molecular Biology, Montpellier, France, 5-10 august 2018

LAVARENNE J., GONIN M., GUYOMARC’H S., ROUSTER J., CHAMPION A., , LAPLAZE L., SALLAUD C., GANTET P., LUCAS M. Adaptation of cereals to water deficit : looking for root development master regulatory genes through a systems biology approach Visite de l’AcadĂ©mie d’Agriculture de France « Des avancĂ©es sur les recherches en biologie et gĂ©nĂ©tique au service de la riziculture » Montpellier, France, June 6 2018

GONIN M., LAVARENNE J., COUDERT Y., BOURRIE I., LAPLAZE L., GANTET P., CHAMPION A. The rice CRL1 LBD transcription factor binds DNA with a relaxed specificity. Visite de l’AcadĂ©mie d’Agriculture de France « Des avancĂ©es sur les recherches en biologie et gĂ©nĂ©tique au service de la riziculture » Montpellier, France, June 6 2018

HOANG T.G., TO T.M.H., GONIN M., LAVARENNE J., MAI D.C., PARIZOT B., BEECKMAN T., LEBRUN M., CHAMPION A., LAPLAZE L, GANTET P., Research of CRL1-regulated genes that complement crl1 mutant for the formation of crown roots, 14th International Rice Functional Genomics Symposium, Montpellier, France, 26-29 September 2016

LAVARENNE J. ROUSTER J., GUYOMARC’H S., CHAMPION A., MOUKOUANGA D., LAPLAZE L., SALLAUD C., GANTET P., LUCAS M. Adaptation of cereals to water deficit: looking for master regulatory genes of root development though a systems biology approach Summer School 2016, From gene expression to genomic network, Labex Science des Plantes de Saclay, France, 17 – 22 juillet 2016.

 

Participation to meetings and workshops

 

Miscellaneous

Interests

Prizes and awards

  • JĂ©rĂ©my Lavarenne

    Ingénieur agronome et docteur en biologie des systÚmes, je suis à mes heures perdues un internaute averti, ainsi qu'un biologeek définitivement atteint.
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