CV
Philippe CUBRY
Post-Doctoral Researcher
Population genetics / Evolution / Molecular (genetic) biology
Born : 11/11/1980 in Nîmes, FRANCE. 1 child born september 2012. Permanent postal adress : 42, route de Boissières, 30420 Calvisson (FRANCE)- Scientific project management, supervision, teaching
- Communication, articles and projects writing
Professional Experience
November 2015 – current : Post-Doctoral fellow at IRD-DIADE, Montpellier, France
- Spatial modelisation and population genetics of african crops domestication, part of the Africrop ANR project
March 2014 – October 2015 : Post-Doctoral fellow at INRA-URFM (Ecologie of Mediterranean Forests), Avignon, France
- Investigate the effect of fragmented local environment on adaptive selection, trees as a case-study
June 2012 – June 2013 : Post-doctoral Research Associate at National Botanic Gardens of Ireland, Dublin, Ireland
- Assess genetic diversity and phylogeography of Irish Forest trees species
July 2009 – December 2010 : Post-doctoral position for Michelin at CIRAD Montpellier, UMR DAP
- Development and testing of molecular markers for candidate genes implicated in the field resistance of Hevea brasiliensis to Microcyclus ulei.
- Genetic mapping / Marker development (use of bioinformatics tools) / PCR / High Resolution Melting Analysis / Microsatellites / SNPs
2005 : 6 months period of work experience for the obtention of DEA. CIRAD, Montpellier, France, UMR DAP. “Diversity and preliminary study of linkage disequilibrium in some populations of Coffea canephora coffee trees”
- Microsatellite genotyping / diversity analysis / population genetics
- Genetic resources management
2004 : 3 months period of work experience for the obtention of Maîtrise. CIRAD, Montpellier, France. “Microsatellites genotyping of 48 banana trees accessions from the Musa genus”
- Part of an international program, Challenge Program “Generation”
- DNA extraction and purification / PCR / microsatellite genotyping
- Adaptation and development of a genotyping protocol
Education And Training
2005 –2008 : PhD (French Doctorat) in population genetics, selection, evolution / Université Montpellier 2 – CIRAD (Centre for International Cooperation in Development), UMR DAP. “Genetic diversity structure and linkage disequilibrium analysis of the species Coffea canephora Pierre”.
2004 – 2005 : MSct (French DEA) in Phytogenetic Resources and Biologic Interactions / Université Montpellier 2, Montpellier, France
- Population genetics / plant breeding / biostatistics / host-parasite interactions / quantitative genetics / evolution
2003 – 2004 : 1st year of MSc (French Maîtrise) in Populations and Ecosystems Biology / Université Montpellier 2, Montpellier, France
- Plant and animal biology and physiology / Population genetics / biostatistics / evolution / ecology / conservation biology
Teaching Experience
Université Montpellier 2 and Supagro Montpellier, Montpellier, France
2009-2011 : Lectures in genetic mapping and association, 2nd year of Master of biology
2008-2009 : Lectures 7h, tutorials 1h30 in plant reproduction and association geneticsAudience: 1st and 2d years Master of Biology
2007-2008 : Lectures 3h, tutorials 37h in plant reproduction and formal geneticsAudience: 1st year Licence of Biology, 1st year Master of Biology
2006-2007 : Lectures 3h and 54h tutorials in plant reproduction, formal genetics, conservation biologyAudience : 1st and 2d year Licence of Biology, 1st and 2d year Master of biology
Personal Skills and Competences
Languages
Mother tongue : French English : Correct – Self assesment European Level : independant to proficient user in the different skills (Understanding, Speaking, Writing both spoken and written)
Computer skills
Proficient user of Microsoft Office Suite (word, excel, powerpoint) and basic user of databases (access), intermediate user of Image Processing Software (Photoshop) and Adobe CS4 suite, basis on Web Site Design (Dreamweaver). Good knowledge and use of population genetics analysis softwares (Arlequin, Genetix, PowerMarker,…) and statistical program (R); Basis on Sequence Analysis softwares (CodonCode Aligner, DNAsp). Python programing language (acquired through MOOC)
MOOC and life-long learning courses taken (certificates availables)
Through Coursera : Computational Molecular Evolution (Technical University of Denmark – earned 94.7%) – Learn to Program: The fundamentals (University of Toronto – earned 99.6%, This course provides an introduction to computer programming using Python. Topics include elementary data types (numeric types, strings, lists, tuples, dictionaries and files), control flow (if, for, while), functions, modules, objects, methods, fields and mutability)
Python programming through codecademy (whole course achieved)
Bioinformatics learning using Python and the Rosalind platform, current level 24
Community involvment
2000 – 2012 : secretary then vice-president of Centre Artistique Oratorio, association which is interested in teaching scenic and graphic art (singing, theatre, dance, music, painting) http://www.centreoratorio.fr
Social skills
Team spirit, good communication skills gained through my experience as vice-president of an association; good capabilities to interact with a pluridisciplinal team
Organisational skills
Sense of organisation, abilities on project management (acquired through my PhD and my leisure activities), experience on communication
Technical skills
Good knowledge of population genetics and evolutionary processes; primer development; microsatellites markers development; PCR; migration on automated sequencer, High Resolution Melting Analysis, data processing and analysis
Others
Skiing / cycling / singing in a chorus
Communications
Articles
Cubry P., Muratorio S., Scotti I., Lefevre F. Polygenic adaptation in a hierarchical population structure. In prep
Cubry P., Lefevre F. Generalized framework for the study of adaptive differentiation in hierarchically structured populations. Submitted to Genetics
Cubry P., Gallagher E., O’Connor E., Kelleher C.T. 2015. Phylogeography and population genetics of black alder (Alnus glutinosa (L.) Gaertn.) in Ireland: putting it in a European context. Tree Genetics and Genomes (11)5
Leroy T., De Bellis F., Legnate H., Musoli P., Kalonji A., Loor Solòrzano RG., Cubry P. Developing core collections to optimize the management and the exploitation of diversity of the coffee Coffea canephora. Genetica 2014 http://dx.doi.org/10.1007/s10709-014-9766-5
Cubry P., Pujade-Renaud V., Garcia D., Espeout S., Le Guen V., Granet F. and Seguin M. Development and characterization of a new set of 164 polymorphic EST-SSR markers for rubber tree (Hevea spp.). Plant Breeding 2014 http://dx.doi.org/10.1111/pbr.12158
Cubry P., De Bellis F., Avia K., Bouchet S., Pot D., Dufour M., Legnate H. and Leroy T. 2013. An initial assessment of linkage disequilibrium (LD) in coffee trees: LD patterns in groups of Coffea canephora Pierre using microsatellite analysis. BMC Genomics 2013, 14:10 http://dx.doi.org/10.1186/1471-2164-14-10
Cubry P., De Bellis F., Musoli P., Pot D., Leroy T. Diversity and population structure of Coffea canephora (Rubiaceae) assessed by microsatellites. Genetic Resources and crop evolution, 2013 http://dx.doi.org/10.1007/s10722-012-9851-5
Cubry P., Musoli P., Legnate H., Pot D., de Bellis F., Poncet V., Anthony F., Dufour M., Leroy T. 2008. Diversity in coffee assessed with SSR markers: Structure of the genus Coffea and perspectives for breeding. Genome 51(1) 50-63 http://dx.doi.org/10.1139/G07-096
Montagnon C., Cubry P., Leroy T. 2012. Amélioration génétique du caféier Coffea canephora Pierre : connaissances acquises, stratégies et perspectives. Cahiers Agriculture 21(2-3) 143-153 http://dx.doi.org/10.1684/agr.2012.0556
Musoli P., Cubry P., Aluka P., Billot C., Dufour M., De Bellis F., Pot D., Kyetere D., Ochugo J., Bieysse D., Charrier A., Leroy T. Genetic differentiation of wild and cultivated populations: diversity of Coffea canephora in Uganda . Genome 52: 634-646 http://dx.doi.org/10.1139/G09-037
Chair A., Duroy P.O., Cubry P., Sinsin B., Pham J.L. Impact of past climatic and recent anthropogenic factors on wild yam genetic diversity. Molecular Ecology 20(8) 1612-1623 http://dx.doi.org/10.1111/j.1365-294X.2011.05041.x
Leroy T., De Bellis F., Legnate H., Kananura E., Gonzales G., Pereira L., Andrade A., Charmetant P., Montagnon C., Cubry P., Marraccini P., Pot D., de Kochko A. Improving the quality of African robustas: QTLs for yield- and quality-related traits in Coffea canephora. Tree Genetics & Genomes (28 February 2011), pp. 1-18. http://dx.doi.org/10.1007/s11295-011-0374-6
Hippolyte I., Jenny C., Gardes L., Bakry F., Rivallan R., Pomies V., Cubry P., Tomekpe K., Risterucci A.M., Roux N., Rouard M., Arnaud E., Kolesnikova-Allen M., Perrier X. Foundation characteristics of edible Musa triploids revealed from allelic distribution of SSR markers. Annals of Botany (2012) 109 (5): 937-951. http://dx.doi.org/10.1093/aob/mcs010
Conferences proceedings (orals communications)
Cubry P., Oddou-Muratorio S., Scotti I., Lefevre F. Consequences of multiple-scale variation in selection on microgeographic adaptation. ESEB2015 (congress of the European Society for Evolutionary Biology), August 10-15, 2015, Lausanne, Switzerland.
Cubry P., Kelleher CT. Assessing provenance of Irish tree species in a European context – a part of the FORGEN project. IPSAM (Irish Plant Scientists Association Meeting) 2013 – NUI Galway, Galway, Ireland.
Cubry P., Pot D., De Bellis F., Legnathe H., Musoli P., Leroy T. 2008. Genetic Structure of Coffea canephora Pierre Species Assessed By Microsatellites Markers (Proceedings of the Plant & Animal Genomes XVI Conference , January 12-16, 2008 , San Diego, CA)
Leroy T., Cubry P., Durand N., Dufour M., De Bellis F., Jourdan I., Vieira L.G.E., Musoli P., Aluka P., Legnaté H., Marraccini P., Pot D. 2007. Coffea spp. and Coffea canephora diversity evaluated with microsatellites and SNPs. Lessons from comparative analysis .In: Proceedings of the 21st International Conference on Coffee Science. Paris, France: ASIC. Colloque Scientifique International sur le Café. 21, 2006/09/11-15, Montpellier, France.
Cubry P., Musoli P., Legnaté H., Aluka P., Dufour M., Pot D., De Bellis F., Leroy T. 2007. Genetic diversity within Coffea canephoragermplasm maintained in RCI using SSR markers, results and future prospects. In: Proceedings of the 21st International Conference on Coffee Science. Paris, France: ASIC. Colloque Scientifique International sur le Café. 21, 2006/09/11-15, Montpellier, France.
Conferences proceedings (posters)
Cubry P., O’Connor Helen, Gallagher Evelyn, Kelleher C.T.. 2013. Black Alder in Ireland: putting it in a European context. EGG(Ecological Genetics Group)2013, Queen’s University, Belfast, United Kingdom. https://www.researchgate.net/publication/236472577_Black_Alder_in_Ireland_putting_it_in_a_European_context
Cubry P., Pot D., De Bellis F., Musoli P., Aluka P., Legnaté H., Dufour M., Leroy T. 2007. Genetic diversity in Coffeagenus using microsatellites loci .In: Proceedings of the 21st International Conference on Coffee Science. Paris, France: ASIC. Colloque Scientifique International sur le Café. 21, 2006/09/11-15, Montpellier, France.
Contact
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