Title |
Engineer
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Mail |
This e-mail address is being protected from spam bots, you need JavaScript enabled to view it
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Address |
Symbiose
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INRIA/Irisa - Campus de Beaulieu
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35042 RENNES Cedex - France
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Tel |
+33 2 99 84 71 18
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Fax |
+33 2 99 84 71 71
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Current position |
INRA Bioinformaticist |
Current Scientific Interest
Setup a bioinformatics platform dedicated to insect pest genomics using open-source software. Its main goals are to supply the needs on automatically or manually annotation, genome browsing or genome comparative analyses as well as to write sophisticated procedures such as ontology driven annotation pipelines and help and teach users and curators by organizing workshop and seminars
Support to various genomics research activities (genome
annotation, physical and genetic maps, miRNA identification,
comparative genomics and evolution)
Work experience
Since 2007 : bioinformaticist and software ingeneer at INRA's
BiO3P laboratory (Rennes, France) in the genomics group leaded by
Denis Tagu, but detached in the GenOuest group of the INRIA's
Symbiose project leaded by J. Nicolas.
From 2000 to 2007 : bioinformaticist and software ingeneer at
INRA's URGI laboratory (Versailles, France, leaded by Hadi Quesneville) in charge of the
development and maintenance of annotation pipelines, physical mapping
data management, web services, software maintenance and installation,
projects support...
From 1998 to 2000 : bioinformaticist at Aventis Pharma (Evry and
Vitry sur Seine, France)
Teaching
since 2002 : Perl, perl-object and bioperl for biologist at Evry
university, INSERM, CNRS, INRIA
from 2003 to 2006 : curation and assembly of genomic sequences with the
Phred-Phrap-Consed Package at Evry university
Publications
Jaquiéry J, Stoeckel S, Nouhaud P, Mieuzet L, Mahéo F, Legeai F, Bernard N, Bonvoisin A, Vitalis R, Simon JC. Genome scans reveal candidate regions involved
in the adaptation to host plant in the pea aphid complex. Mol Ecol. 2012 Nov;21(21):5251-64.
Le Trionnaire G, Jaubert-Possamai S, Bonhomme J, Gauthier JP, Guernec G, Le Cam A, Legeai F, Monfort J, Tagu D. Transcriptomic profiling of the reproductive
mode switch in the pea aphid in response to natural autumnal photoperiod. J Insect Physiol. 2012 Dec;58(12):1517-24.
Jacquin-Joly E, Legeai F, Montagné N, Monsempes C, François MC, Poulain J,Gavory F, Walker WB 3rd, Hansson BS, Larsson MC. Candidate chemosensory genes in
female antennae of the noctuid moth Spodoptera littoralis. Int J Biol Sci.2012;8(7):1036-50.
Leroy P, Guilhot N, Sakai H, Bernard A, Choulet F, Theil S, Reboux S, Amano N, Flutre T, Pelegrin C, Ohyanagi H, Seidel M, Giacomoni F, Reichstadt M, Alaux M,
Gicquello E, Legeai F, Cerutti L, Numa H, Tanaka T, Mayer K, Itoh T, Quesneville H, Feuillet C. TriAnnot: A Versatile and High Performance Pipeline for the
Automated Annotation of Plant Genomes. Front Plant Sci. 2012;3:5. .
Ollivier M, Gabaldón T, Poulain J, Gavory F, Leterme N, Gauthier JP, Legeai F,Tagu D, Simon JC, Rispe C. Comparison of gene repertoires and patterns of
evolutionary rates in eight aphid species that differ by reproductive mode. Genome Biol Evol. 2012;4(2):155-67.
Dubois A, Remay A, Raymond O, Balzergue S, Chauvet A, Maene M, Pécrix Y, Yang SH, Jeauffre J, Thouroude T, Boltz V, Martin-Magniette ML, Janczarski S, Legeai F, Renou JP, Vergne P, Le Bris M, Foucher F, Bendahmane M. Genomic approach to
study floral development genes in Rosa sp. PLoS One. 2011;6(12
Jaquiéry J, Stoeckel S, Rispe C, Mieuzet L, Legeai F, Simon JC. Accelerated evolution of sex chromosomes in aphids, an x0 system. Mol Biol Evol. 2012
Feb;29(2):837-47.
Vialette-Guiraud AC, Alaux M, Legeai F, Finet C, Chambrier P, Brown SC, Chauvet A, Magdalena C, Rudall PJ, Scutt CP. Cabomba as a model for studies of early angiosperm evolution. Ann Bot. 2011 Sep;108(4):589-98.
Legeai F, Malpel S, Montagné N, Monsempes C, Cousserans F, Merlin C, François MC, Maïbèche-Coisné M, Gavory F, Poulain J, Jacquin-Joly E. An Expressed Sequence
Tag collection from the male antennae of the Noctuid moth Spodoptera littoralis:
a resource for olfactory and pheromone detection research. BMC Genomics. 2011 Jan
29;12:86.
Volkoff AN, Jouan V, Urbach S, Samain S, Bergoin M, Wincker P, Demettre E, Cousserans F, Provost B, Coulibaly F, Legeai F, Béliveau C, Cusson M, Gyapay G,
Drezen JM. Analysis of virion structural components reveals vestiges of the ancestral ichnovirus genome. PLoS Pathog. 2010 May 27;6(5)
d’Alençon, E,
Sezutsu H, Legeai F, Permal, E, Bernard-Samain, S., Gimeneza, S.,
Gagneur, C., Cousserans, F., Shimomura, M., Brun-Barale, A., Flutre,
T., Couloux, A., East, P., Gordong, K., Mita, K., Quesneville, H.,
Fournier P., Feyereisen, R. Extensive synteny conservation of
holocentric chromosomes in Lepidoptera despite high rates of local
genome rearrangements, (2010) PNAS
Apr
27;107(17):7680-5.
Volkoff, A-N, Jouan, V., Urbach, S., Samain, S., Bergoin, M., Wincker, P., Demettre, E., Cousserans, F., Provost, B., Fasseli
Coulibaly, F., Legeai, F., Béliveau, C., Cusson, M., Gyapay, G., Drezen, J-M, (2010) Analysis of Virion Structural Components Reveals Vestiges of the Ancestral Ichnovirus Genome.PLoS Pathogens in press
International Aphid
Genomics Consortium. Genome sequence of the pea aphid Acyrthosiphon
pisum. PLoS Biol. 2010 Feb 23;8(2)
Legeai F, Shigenobu
S, Gauthier JP, Colbourne J, Rispe C, Collin O, Richards S, Wilson
ACC, Tagu D (2010) AphidBase: A centralized bioinformatic resource
for annotation of the pea aphid genome. Insect Molecular Biology
vol19,0,5-12
Ollivier M., Legeai
F., Rispe C. (2010) Comparative analysis of the Acyrthosiphon pisum
genome and expressed sequence tag-based gene sets from other aphid
species. Ins. Mol. Biol. Vol19,0,33-45
Legeai F., Rizk
G., Walsh T., Edwards O., Gordon K., Lavenier D.,
Leterme N., Méreau A., Nicolas J., Tagu D., Jaubert-Possamai S.
(2010) Bioinformatic prediction, deep sequencing of microRNAs and
expression analysis during phenotypic plasticity in the pea aphid,
Acyrthosiphon pisum. BMC Genomics
2010
May 5;11(1):281
Legeai F., Malpel
S., Montagné N., Monsempes C., Cousseran F., Merlin C., François
MC., Maïbèche-Coisné M., Gavory F., Poulain J., Jacquin-Joly E.
(2010) An Expressed Sequence Tag collection from the male antennae of
the Noctuid moth Spodoptera littoralis: a resource for olfactory and
pheromone detection research (Submitted to BMC Genomics)
Le
Trionnaire G, Francis F, Jaubert-Possamai S, Bonhomme J, De Pauw E,
Gauthier JP, Haubruge E, Legeai F, Prunier-Leterme N, Simon JC, Tanguy
S, Tagu D. (2009)
Transcriptomic and proteomic analyses of seasonal photoperiodism in the pea aphid BMC Genomics. 2009 Sep 29;10:456.
Foucher, F, Chevalier, M, Corre, C, Soufflet-Freslon V, Legeai, F, and Hibrand-Saint Oyant L. (2008) New resources for studying the rose flowering process. Genome 51(10):
827–837
Moroldo, M, Paillard, S, Marconi, R,
Legeai, F, Canaguier,
A, Cruaud, C, De Berardinis, V, Guichard, C, Brunaud, V, Le Clainche,
I, Scalabrin, S, Testolin, R, Di Gaspero, G, Morgante, M,
Adam-Blondon, AF (2008). A physical map of the heterozygous
grapevine 'Cabernet Sauvignon' allows mapping candidate genes for
disease resistance. BMC Plant Biol., 8:66.
Legeai, F, Paux, E, Guilhot, N, Adam-Blondon, AF, Alaux, M,
Salse, J, Sourdille, P, Leroy, P, Feuillet, C (2008). Physical
mapping in large genomes: accelerating anchoring of BAC contigs to
genetic maps through in silico analysis. Funct. Integr. Genomics,
8, 1:29-32.
Rispe, C, Kutsukake, M, Doublet, V, Hudaverdian, S, Legeai, F,
Simon, JC, Tagu, D, Fukatsu, T (2008). Large gene family
expansion and variable selective pressures for cathepsin B in aphids.
Mol. Biol. Evol., 25, 1:5-17.
Rispe, C, Legeai, F, Gauthier, JP, Tagu, D (2007).
Strong heterogeneity in nucleotidic composition and codon bias in the
pea aphid (Acyrthosiphon pisum) shown by EST-based coding genome
reconstruction. J. Mol. Evol., 65, 4:413-24.
Jaillon, O, Aury, JM, Noel, B, Policriti, A, Clepet, C,
Casagrande, A, Choisne, N, Aubourg, S, Vitulo, N, Jubin, C, Vezzi, A,
Legeai, F, Hugueney, P, Dasilva, C, Horner, D, Mica, E,
Jublot, D, Poulain, J, Bruyère, C, Billault, A, Segurens, B,
Gouyvenoux, M, Ugarte, E, Cattonaro, F, Anthouard, V, Vico, V, Del
Fabbro, C, Alaux, M, Di Gaspero, G, Dumas, V, Felice, N, Paillard, S,
Juman, I, Moroldo, M, Scalabrin, S, Canaguier, A, Le Clainche, I,
Malacrida, G, Durand, E, Pesole, G, Laucou, V, Chatelet, P,
Merdinoglu, D, Delledonne, M, Pezzotti, M, Lecharny, A, Scarpelli, C,
Artiguenave, F, Pè, ME, Valle, G, Morgante, M, Caboche, M,
Adam-Blondon, AF, Weissenbach, J, Quétier, F, Wincker, P
(2007). The grapevine genome sequence suggests ancestral
hexaploidization in major angiosperm phyla. Nature, 449,
7161:463-7.
Gauthier, JP, Legeai, F, Zasadzinski, A, Rispe, C, Tagu, D
(2007). AphidBase: a database for aphid genomic resources.
Bioinformatics, 23, 6:783-4.
Lamoureux, D, Bernole, A, Le Clainche, I, Tual, S, Thareau, V,
Paillard, S, Legeai, F, Dossat, C, Wincker, P, Oswald, M,
Merdinoglu, D, Vignault, C, Delrot, S, Caboche, M, Chalhoub, B,
Adam-Blondon, AF (2006). Anchoring of a large set of markers
onto a BAC library for the development of a draft physical map of the
grapevine genome. Theor. Appl. Genet., 113, 2:344-56.
Sabater-Muñoz, B, Legeai, F, Rispe, C, Bonhomme, J,
Dearden, P, Dossat, C, Duclert, A, Gauthier, JP, Ducray, DG, Hunter,
W, Dang, P, Kambhampati, S, Martinez-Torres, D, Cortes, T, Moya, A,
Nakabachi, A, Philippe, C, Prunier-Leterme, N, Rahbé, Y,
Simon, JC, Stern, DL, Wincker, P, Tagu, D (2006). Large-scale
gene discovery in the pea aphid Acyrthosiphon pisum (Hemiptera).
Genome Biol., 7, 3:R21.
Tagu, D, Prunier-Leterme, N, Legeai, F, Gauthier, JP,
Duclert, A, Sabater-Muñoz, B, Bonhomme, J, Simon, JC (2004).
Annotated expressed sequence tags for studies of the regulation of
reproductive modes in aphids. Insect Biochem. Mol. Biol.,
34, 8:809-22.
Small, I, Peeters, N, Legeai, F, Lurin, C (2004).
Predotar: A tool for rapidly screening proteomes for N-terminal
targeting sequences. Proteomics, 4, 6:1581-90.
Nicot, N, Chiquet, V, Gandon, B, Amilhat, L, Legeai, F,
Leroy, P, Bernard, M, Sourdille, P (2004). Study of simple
sequence repeat (SSR) markers from wheat expressed sequence tags
(ESTs). Theor. Appl. Genet., 109, 4:800-5.
Samson, D, Legeai, F, Karsenty, E, Reboux, S, Veyrieras,
JB, Just, J, Barillot, E (2003). GénoPlante-Info (GPI):
a collection of databases and bioinformatics resources for plant
genomics. Nucleic Acids Res., 31, 1:179-82.
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