Curriculum vitae

Agricultural engineer specialized in plant breeding, PhD in systems biology

Enthusiastic about science, agriculture, and technology, with a dose of geekyness on top. I benefited from a curriculum in agronomy and plant breeding, and a starting career at the crossroads between fundamental and applied research. I like to solve problems, and enjoy working both in the wetlab and on my computer in front of large amounts of data. I define myself as a systems biologist, and i’m particularly fond of graph/network-based approaches, and believe they are tools that will allow us – along with machine learning – to better comprehend this world of complexity.

During my PhD thesis, i participated in the deciphering of the gene regulatory network governing crown root development in rice, by inferring it from transcriptomic time-series. Though there is much left to be done on the subject, i am interested by a broad range of topics, and i am open to discuss about any relevant topic.

At the end of my PhD fellowship, i worked on publishing the results of my research while setting up and leading a startup related to food history named MédiMoinsQuart, an online shop (a real one, not a dropshipping thingy) for which i partnered up with a renowned researcher in medieval studies to design, assemble and sell kits to learn how to cook XIII~XIVth Century recipes.

I am now R&D lead for Sowit, a french-moroccan agtech startup.

Reach me on ResearchGate / LinkedIn / Viadeo

Professionnal experience

Jan. 2020 – now : R&D lead, SOWIT.
SOWIT combine la télédétection (drone et satellite), l’agronomie et l’intelligence artificielle pour fournir aux agriculteurs africains des informations leur permettant d’intensifier durablement leurs productions. SOWIT participe notamment à l’optimisation des opérations critiques de culture telles que la fertilisation, l’irrigation ou la récolte via des outils d’aide à la décision adaptés aux conditions de culture.

Oct. 2018 – December 2019 : Founder and CEO, MédiMoinsQuart. Making kits with ingredients and video tutorials to learn how to cook French medieval recipes.
Business planning & accounting, crowdfunding campaign organization, content production (articles, booklets, video editing, podcast production), logistics operations (sourcing and orders, stock management, orders prepping and shipping), community management (Jarvee, Hootsuite), digital marketing (Mailchimp, Facebook ads, Hubspot), webdev (self-hosted WordPress/Prestashop + Chargebee/Stripe/Paypal payment APIs).

Jul. 2015 – Oct. 2018 : Joint PhD fellowship, Biogemma/Montpellier University. PhD thesis realized between the UMR Diade, Cereal Root Systems (CERES) lab (IRD Montpellier), and the biotech company Biogemma. Thesis title : « Adaptation of cereal crops to water deprivation : looking for master root development genes through a systems biology approach« .
I used an inducible genetic system to generate a time-series transcriptomic dataset (270k datapoints x 16 timepoints) from which i inferred a gene regulatory network model of crown root development in rice. Previously unknown regulatory interactions between known players were validated using transient protoplast transactivation assays, and published (doi:10.1111/tpj.14487). I performed the formal analysis of the obtained network and integration with third party datasets to provide a shortlist of putative master regulatory genes to be validated for functional validation in CRISPR-Cas mutants. I think such network models and their rewiring can be of utmost interest for plant breeding (10.1016/j.tplants.2018.04.005). I generated a new in situ transcriptomic dataset of embryonic crown roots using laser capture microdissection.

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. Transferring and optimizing a evolutionary experimental protocol requiring FACS.

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

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 Caribbean. 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
  • Data science
  • Developmental biology
  • Boolean modelling
  • 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 & machine learning : R, Python, shell, Unix distributed computing (PBS), cloud computing (AWS, Google Cloud Platform), PyTorch+fast.ai
  • Network science : network inference from time-series (TDCor, TD-ARACNE) and perturbation (WGCNA), network manipulation (Cytoscape, Gephi), static and boolean-based dynamic analysis (identification of attraction basins and switches, robustness assessment via NetDS, Atlantis, Pythonis alpha)
  • Geomatics : QGIS
  • Webdev: CodeIgniter
  • Data management : MySQL, Microsoft Access, Microsoft Excel
  • Communication and editing : Microsoft Office, Libre Office, GDocs, LaTeX, Mendeley, Adobe Photoshop, InkScape
  • 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), German (i can order a beer and a sausage)

Communications

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

Peer-reviewed articles

LAVARENNE J., GONIN M., CHAMPION A., JAVELLE M., ADAM H., ROUSTER J., CONEJERO G., LARTAUD M., VERDEILJ.-L., LAPLAZE L., SALLAUD C., LUCAS M.,  GANTET P., 2020, Transcriptome profiling of laser-captured crown root primordia reveals new pathways activated during early stages of crown root formation in rice. PLoS ONE, 15(11), doi: 10.1371/journal.pone.0238736

TO H.T.M., NGUYEN H.T., DANG N.T.M., NGUYEN N.H., BUI T.X., LAVARENNE J., PHUNG N.T.P., GANTET P., LEBRUN M., BELLAFIORE S., CHAMPION A., 2019, Unraveling the genetic elements involved in shoot and root growth regulation by jasmonate in rice using a genome-wide association study. Rice, 12:69, doi: 10.1186/s12284-019-0327-5

LAVARENNE J., GONIN M., GUYOMARC’H S., ROUSTER J., CHAMPION A., SALLAUD C., LAPLAZE L., GANTET P., LUCAS M., 2019, Inference of the gene regulatory network acting downstream of CROWN ROOTLESS1 in rice reveals a regulatory cascade linking genes involved in auxin signaling, crown root initiation and root meristem specification and maintenance. The Plant Journal, 100:5 : 954-968, doi: 10.1111/tpj.14487

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, Hoàn thiên quy trình chuyên gen cho giong lúa taichung 65 thông qua vi khuân Agrobacterium tumefaciens (Optimization of Transformation Protocol for Japonica Rice cv.Taichung 65 through Agrobacterium tumefaciens), Tap chí Khoa hoc và Phát trien, tap 13, so 5:764-773 (J. Sci. & Devel. 2015 , Vol. 13, No. 5 : 764-773)

So far, I also contributed to 29 papers in human genetics by sharing my genotyping data with 23andme research partner institutions

Oral communication in meetings

Adaptation des céréales au déficit hydrique : recherche de gènes maîtres du développement racinaire par une approche de biologie des systèmes, 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.

Posters

KORINKOVÁ N., NGUYEN D.T., GONIN M., LAVARENNE J., GANTET P., BERGOUGNOUX V., Understanding crown-root initiation in barley (Hordeum vulgare L.), ISRR-10 Exposing the Hidden Half, Root research at the forefront of science international symposium, 8-12 July 2018, Israel.

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, Conférences 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’Académie d’Agriculture de France « Des avancées sur les recherches en biologie et génétique 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’Académie d’Agriculture de France « Des avancées sur les recherches en biologie et génétique 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.

Vulgarization and teaching

Member of the FranceAgriTwittos nonprofit for positive ag communication

« L’intelligence artificielle et les robots au service de l’agriculture » :
– Intervention (45 min) donnéhttps://sites.google.com/view/franceagritwittos/accueile dans le cadre d’une « session agro » au sein d’itk Clapiers, le 12 décembre 2019
– Intervention (3h) auprès d’élèves-ingénieurs agronomes de dernière année, VetAgroSup campus agronomique de Clermont-Ferrand, le 9 décembre 2019.
– Conférence de vulgarisation (45 min) donnée dans le cadre d’une journée spéciale « intelligence artificielle » proposée par l’Atelier numérique Google Montpellier, le 4 octobre 2019.

LAVARENNE J., LUCAS M., GANTET P. 2018 De Facebook au développement des plantes : quand les réseaux s’en mêlent. The Conversation, 7 février 2018, 23:48 CET

Participation to meetings and workshops

Miscellaneous

Membership to scientific societies

Interests

Prizes and awards

Driving licences

  • Car (B), Motorbike (A), Paraglider (IPPI ParaPro P2), Drone (training of pilots of civil unmanned aircraft, DGAC)