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In situ transcriptomic and metabolomic study of the loss of photosynthesis in the leaves of mixotrophic plants exploiting fungi.

Lallemand F, Martin-Magniette ML, Gilard F, Gakière B, Launay-Avon A, Delannoy É, Selosse MA.

Plant J. 2019 Feb 8. doi: 10.1111/tpj.14276. [Epub ahead of print]


Nitrogen Limitation Alters the Response of Specific Genes to Biotic Stress.

Farjad M, Rigault M, Pateyron S, Martin-Magniette ML, Krapp A, Meyer C, Fagard M.

Int J Mol Sci. 2018 Oct 27;19(11). pii: E3364. doi: 10.3390/ijms19113364.


Transcriptome analysis in Hevea brasiliensis latex revealed changes in hormone signalling pathways during ethephon stimulation and consequent Tapping Panel Dryness.

Montoro P, Wu S, Favreau B, Herlinawati E, Labrune C, Martin-Magniette ML, Pointet S, Rio M, Leclercq J, Ismawanto S, Kuswanhadi.

Sci Rep. 2018 May 31;8(1):8483. doi: 10.1038/s41598-018-26854-y.


Corrigendum to "Genetic variability of the phloem sap metabolite content of maize (Zea mays L.) during the kernel-filling period" [Plant Sci. 252 (2016) 347-357].

Yesbergenova-Cuny Z, Dinant S, Martin-Magniette ML, Quilleré I, Armengaud P, Monfalet P, Lea PJ, Hirel B.

Plant Sci. 2018 Jul;272:207. doi: 10.1016/j.plantsci.2018.04.022. Epub 2018 May 3. No abstract available.


Transcriptome reprogramming due to the introduction of a barley telosome into bread wheat affects more barley genes than wheat.

Rey E, Abrouk M, Keeble-Gagnère G, Karafiátová M, Vrána J, Balzergue S, Soubigou-Taconnat L, Brunaud V, Martin-Magniette ML, Endo TR, Bartoš J; International Wheat Genome Sequencing Consortium (IWGSC), Appels R, Doležel J.

Plant Biotechnol J. 2018 Oct;16(10):1767-1777. doi: 10.1111/pbi.12913. Epub 2018 Apr 13.


Combining laser-assisted microdissection (LAM) and RNA-seq allows to perform a comprehensive transcriptomic analysis of epidermal cells of Arabidopsis embryo.

Sakai K, Taconnat L, Borrega N, Yansouni J, Brunaud V, Paysant-Le Roux C, Delannoy E, Martin Magniette ML, Lepiniec L, Faure JD, Balzergue S, Dubreucq B.

Plant Methods. 2018 Feb 3;14:10. doi: 10.1186/s13007-018-0275-x. eCollection 2018.


Altered DNA methylation associated with an abnormal liver phenotype in a cattle model with a high incidence of perinatal pathologies.

Kiefer H, Jouneau L, Campion É, Rousseau-Ralliard D, Larcher T, Martin-Magniette ML, Balzergue S, Ledevin M, Prézelin A, Chavatte-Palmer P, Heyman Y, Richard C, Le Bourhis D, Renard JP, Jammes H.

Sci Rep. 2016 Dec 13;6:38869. doi: 10.1038/srep38869.


Synthetic data sets for the identification of key ingredients for RNA-seq differential analysis.

Rigaill G, Balzergue S, Brunaud V, Blondet E, Rau A, Rogier O, Caius J, Maugis-Rabusseau C, Soubigou-Taconnat L, Aubourg S, Lurin C, Martin-Magniette ML, Delannoy E.

Brief Bioinform. 2018 Jan 1;19(1):65-76. doi: 10.1093/bib/bbw092.


Genetic variability of the phloem sap metabolite content of maize (Zea mays L.) during the kernel-filling period.

Yesbergenova-Cuny Z, Dinant S, Martin-Magniette ML, Quilleré I, Armengaud P, Monfalet P, Lea PJ, Hirel B.

Plant Sci. 2016 Nov;252:347-357. doi: 10.1016/j.plantsci.2016.08.007. Epub 2016 Aug 27. Erratum in: Plant Sci. 2018 Jul;272:207.


Cytonuclear interactions affect adaptive traits of the annual plant Arabidopsis thaliana in the field.

Roux F, Mary-Huard T, Barillot E, Wenes E, Botran L, Durand S, Villoutreix R, Martin-Magniette ML, Camilleri C, Budar F.

Proc Natl Acad Sci U S A. 2016 Mar 29;113(13):3687-92. doi: 10.1073/pnas.1520687113. Epub 2016 Mar 15.


Co-expression analysis of high-throughput transcriptome sequencing data with Poisson mixture models.

Rau A, Maugis-Rabusseau C, Martin-Magniette ML, Celeux G.

Bioinformatics. 2015 May 1;31(9):1420-7. doi: 10.1093/bioinformatics/btu845. Epub 2015 Jan 5.


GEM2Net: from gene expression modeling to -omics networks, a new CATdb module to investigate Arabidopsis thaliana genes involved in stress response.

Zaag R, Tamby JP, Guichard C, Tariq Z, Rigaill G, Delannoy E, Renou JP, Balzergue S, Mary-Huard T, Aubourg S, Martin-Magniette ML, Brunaud V.

Nucleic Acids Res. 2015 Jan;43(Database issue):D1010-7. doi: 10.1093/nar/gku1155. Epub 2014 Nov 11.


Comparing Model Selection and Regularization Approaches to Variable Selection in Model-Based Clustering.

Celeux G, Martin-Magniette ML, Maugis-Rabusseau C, Raftery AE.

J Soc Fr Statistique (2009). 2014;155(2):57-71.


The RNA helicases AtMTR4 and HEN2 target specific subsets of nuclear transcripts for degradation by the nuclear exosome in Arabidopsis thaliana.

Lange H, Zuber H, Sement FM, Chicher J, Kuhn L, Hammann P, Brunaud V, Bérard C, Bouteiller N, Balzergue S, Aubourg S, Martin-Magniette ML, Vaucheret H, Gagliardi D.

PLoS Genet. 2014 Aug 21;10(8):e1004564. doi: 10.1371/journal.pgen.1004564. eCollection 2014 Aug.


Differential gene expression and metabolomic analyses of Brachypodium distachyon infected by deoxynivalenol producing and non-producing strains of Fusarium graminearum.

Pasquet JC, Chaouch S, Macadré C, Balzergue S, Huguet S, Martin-Magniette ML, Bellvert F, Deguercy X, Thareau V, Heintz D, Saindrenan P, Dufresne M.

BMC Genomics. 2014 Jul 25;15:629. doi: 10.1186/1471-2164-15-629.


Functional analysis of Arabidopsis immune-related MAPKs uncovers a role for MPK3 as negative regulator of inducible defences.

Frei dit Frey N, Garcia AV, Bigeard J, Zaag R, Bueso E, Garmier M, Pateyron S, de Tauzia-Moreau ML, Brunaud V, Balzergue S, Colcombet J, Aubourg S, Martin-Magniette ML, Hirt H.

Genome Biol. 2014 Jun 30;15(6):R87. doi: 10.1186/gb-2014-15-6-r87.


Unexpectedly low nitrogen acquisition and absence of root architecture adaptation to nitrate supply in a Medicago truncatula highly branched root mutant.

Bourion V, Martin C, de Larambergue H, Jacquin F, Aubert G, Martin-Magniette ML, Balzergue S, Lescure G, Citerne S, Lepetit M, Munier-Jolain N, Salon C, Duc G.

J Exp Bot. 2014 Jun;65(9):2365-80. doi: 10.1093/jxb/eru124. Epub 2014 Apr 4.


Widespread anti-sense transcription in apple is correlated with siRNA production and indicates a large potential for transcriptional and/or post-transcriptional control.

Celton JM, Gaillard S, Bruneau M, Pelletier S, Aubourg S, Martin-Magniette ML, Navarro L, Laurens F, Renou JP.

New Phytol. 2014 Jul;203(1):287-99. doi: 10.1111/nph.12787. Epub 2014 Apr 1.


Salmonella enterica flagellin is recognized via FLS2 and activates PAMP-triggered immunity in Arabidopsis thaliana.

Garcia AV, Charrier A, Schikora A, Bigeard J, Pateyron S, de Tauzia-Moreau ML, Evrard A, Mithöfer A, Martin-Magniette ML, Virlogeux-Payant I, Hirt H.

Mol Plant. 2014 Apr;7(4):657-74. doi: 10.1093/mp/sst145. Epub 2013 Nov 6.


MultiChIPmixHMM: an R package for ChIP-chip data analysis modeling spatial dependencies and multiple replicates.

Bérard C, Seifert M, Mary-Huard T, Martin-Magniette ML.

BMC Bioinformatics. 2013 Sep 9;14:271. doi: 10.1186/1471-2105-14-271.


A gene-phenotype network based on genetic variability for drought responses reveals key physiological processes in controlled and natural environments.

Rengel D, Arribat S, Maury P, Martin-Magniette ML, Hourlier T, Laporte M, Varès D, Carrère S, Grieu P, Balzergue S, Gouzy J, Vincourt P, Langlade NB.

PLoS One. 2012;7(10):e45249. doi: 10.1371/journal.pone.0045249. Epub 2012 Oct 8.


A light-regulated genetic module was recruited to carpel development in Arabidopsis following a structural change to SPATULA.

Reymond MC, Brunoud G, Chauvet A, Martínez-Garcia JF, Martin-Magniette ML, Monéger F, Scutt CP.

Plant Cell. 2012 Jul;24(7):2812-25. doi: 10.1105/tpc.112.097915. Epub 2012 Jul 31.


Expression variation in connected recombinant populations of Arabidopsis thaliana highlights distinct transcriptome architectures.

Cubillos FA, Yansouni J, Khalili H, Balzergue S, Elftieh S, Martin-Magniette ML, Serrand Y, Lepiniec L, Baud S, Dubreucq B, Renou JP, Camilleri C, Loudet O.

BMC Genomics. 2012 Mar 27;13:117. doi: 10.1186/1471-2164-13-117.


Mutations in the Arabidopsis homolog of LST8/GβL, a partner of the target of Rapamycin kinase, impair plant growth, flowering, and metabolic adaptation to long days.

Moreau M, Azzopardi M, Clément G, Dobrenel T, Marchive C, Renne C, Martin-Magniette ML, Taconnat L, Renou JP, Robaglia C, Meyer C.

Plant Cell. 2012 Feb;24(2):463-81. doi: 10.1105/tpc.111.091306. Epub 2012 Feb 3.


Genomic approach to study floral development genes in Rosa sp.

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.

PLoS One. 2011;6(12):e28455. doi: 10.1371/journal.pone.0028455. Epub 2011 Dec 14.


Analysis of BAC end sequences in oak, a keystone forest tree species, providing insight into the composition of its genome.

Faivre Rampant P, Lesur I, Boussardon C, Bitton F, Martin-Magniette ML, Bodénès C, Le Provost G, Bergès H, Fluch S, Kremer A, Plomion C.

BMC Genomics. 2011 Jun 6;12:292. doi: 10.1186/1471-2164-12-292.


Integrative epigenomic mapping defines four main chromatin states in Arabidopsis.

Roudier F, Ahmed I, Bérard C, Sarazin A, Mary-Huard T, Cortijo S, Bouyer D, Caillieux E, Duvernois-Berthet E, Al-Shikhley L, Giraut L, Després B, Drevensek S, Barneche F, Dèrozier S, Brunaud V, Aubourg S, Schnittger A, Bowler C, Martin-Magniette ML, Robin S, Caboche M, Colot V.

EMBO J. 2011 May 18;30(10):1928-38. doi: 10.1038/emboj.2011.103. Epub 2011 Apr 12.


Unsupervised classification for tiling arrays: ChIP-chip and transcriptome.

Bérard C, Martin-Magniette ML, Brunaud V, Aubourg S, Robin S.

Stat Appl Genet Mol Biol. 2011 Nov 1;10(1). pii: /j/sagmb.2011.10.issue-1/1544-6115.1692/1544-6115.1692.xml. doi: 10.2202/1544-6115.1692.


Comparative transcriptomics of drought responses in Populus: a meta-analysis of genome-wide expression profiling in mature leaves and root apices across two genotypes.

Cohen D, Bogeat-Triboulot MB, Tisserant E, Balzergue S, Martin-Magniette ML, Lelandais G, Ningre N, Renou JP, Tamby JP, Le Thiec D, Hummel I.

BMC Genomics. 2010 Nov 12;11:630. doi: 10.1186/1471-2164-11-630.


Brain transcriptional stability upon prion protein-encoding gene invalidation in zygotic or adult mouse.

Chadi S, Young R, Le Guillou S, Tilly G, Bitton F, Martin-Magniette ML, Soubigou-Taconnat L, Balzergue S, Vilotte M, Peyre C, Passet B, Béringue V, Renou JP, Le Provost F, Laude H, Vilotte JL.

BMC Genomics. 2010 Jul 22;11:448. doi: 10.1186/1471-2164-11-448.


Transcriptome analysis describing new immunity and defense genes in peripheral blood mononuclear cells of rheumatoid arthritis patients.

Teixeira VH, Olaso R, Martin-Magniette ML, Lasbleiz S, Jacq L, Oliveira CR, Hilliquin P, Gut I, Cornelis F, Petit-Teixeira E.

PLoS One. 2009 Aug 27;4(8):e6803. doi: 10.1371/journal.pone.0006803.


Identification of germinal disk region derived genes potentially involved in hen fertility.

Elis S, Blesbois E, Couty I, Balzergue S, Martin-Magniette ML, Batellier F, Govoroun MS.

Mol Reprod Dev. 2009 Nov;76(11):1043-55. doi: 10.1002/mrd.21062.


Variable selection for clustering with Gaussian mixture models.

Maugis C, Celeux G, Martin-Magniette ML.

Biometrics. 2009 Sep;65(3):701-9. doi: 10.1111/j.1541-0420.2008.01160.x. Epub 2009 Feb 4.


ChIPmix: mixture model of regressions for two-color ChIP-chip analysis.

Martin-Magniette ML, Mary-Huard T, Bérard C, Robin S.

Bioinformatics. 2008 Aug 15;24(16):i181-6. doi: 10.1093/bioinformatics/btn280.


Genome-scale Arabidopsis promoter array identifies targets of the histone acetyltransferase GCN5.

Benhamed M, Martin-Magniette ML, Taconnat L, Bitton F, Servet C, De Clercq R, De Meyer B, Buysschaert C, Rombauts S, Villarroel R, Aubourg S, Beynon J, Bhalerao RP, Coupland G, Gruissem W, Menke FL, Weisshaar B, Renou JP, Zhou DX, Hilson P.

Plant J. 2008 Nov;56(3):493-504. doi: 10.1111/j.1365-313X.2008.03606.x. Epub 2008 Sep 18.


Differential gene expression of the honey bee Apis mellifera associated with Varroa destructor infection.

Navajas M, Migeon A, Alaux C, Martin-Magniette M, Robinson G, Evans J, Cros-Arteil S, Crauser D, Le Conte Y.

BMC Genomics. 2008 Jun 25;9:301. doi: 10.1186/1471-2164-9-301.


Normalization for triple-target microarray experiments.

Martin-Magniette ML, Aubert J, Bar-Hen A, Elftieh S, Magniette F, Renou JP, Daudin JJ.

BMC Bioinformatics. 2008 Apr 28;9:216. doi: 10.1186/1471-2105-9-216.


Search for the genes involved in oocyte maturation and early embryo development in the hen.

Elis S, Batellier F, Couty I, Balzergue S, Martin-Magniette ML, Monget P, Blesbois E, Govoroun MS.

BMC Genomics. 2008 Feb 29;9:110. doi: 10.1186/1471-2164-9-110.


Transcriptional and metabolic adjustments in ADP-glucose pyrophosphorylase-deficient bt2 maize kernels.

Cossegal M, Chambrier P, Mbelo S, Balzergue S, Martin-Magniette ML, Moing A, Deborde C, Guyon V, Perez P, Rogowsky P.

Plant Physiol. 2008 Apr;146(4):1553-70. doi: 10.1104/pp.107.112698. Epub 2008 Feb 20.


Systemic signaling of the plant nitrogen status triggers specific transcriptome responses depending on the nitrogen source in Medicago truncatula.

Ruffel S, Freixes S, Balzergue S, Tillard P, Jeudy C, Martin-Magniette ML, van der Merwe MJ, Kakar K, Gouzy J, Fernie AR, Udvardi M, Salon C, Gojon A, Lepetit M.

Plant Physiol. 2008 Apr;146(4):2020-35. doi: 10.1104/pp.107.115667. Epub 2008 Feb 20.


Genome-wide interacting effects of sucrose and herbicide-mediated stress in Arabidopsis thaliana: novel insights into atrazine toxicity and sucrose-induced tolerance.

Ramel F, Sulmon C, Cabello-Hurtado F, Taconnat L, Martin-Magniette ML, Renou JP, El Amrani A, Couée I, Gouesbet G.

BMC Genomics. 2007 Dec 5;8:450.


Analysis of CATMA transcriptome data identifies hundreds of novel functional genes and improves gene models in the Arabidopsis genome.

Aubourg S, Martin-Magniette ML, Brunaud V, Taconnat L, Bitton F, Balzergue S, Jullien PE, Ingouff M, Thareau V, Schiex T, Lecharny A, Renou JP.

BMC Genomics. 2007 Nov 2;8:401.


CATdb: a public access to Arabidopsis transcriptome data from the URGV-CATMA platform.

Gagnot S, Tamby JP, Martin-Magniette ML, Bitton F, Taconnat L, Balzergue S, Aubourg S, Renou JP, Lecharny A, Brunaud V.

Nucleic Acids Res. 2008 Jan;36(Database issue):D986-90. Epub 2007 Oct 16.


Arabidopsis TFL2/LHP1 specifically associates with genes marked by trimethylation of histone H3 lysine 27.

Turck F, Roudier F, Farrona S, Martin-Magniette ML, Guillaume E, Buisine N, Gagnot S, Martienssen RA, Coupland G, Colot V.

PLoS Genet. 2007 Jun;3(6):e86. Epub 2007 Apr 17.


Genome-wide expression profiling of the host response to root-knot nematode infection in Arabidopsis.

Jammes F, Lecomte P, de Almeida-Engler J, Bitton F, Martin-Magniette ML, Renou JP, Abad P, Favery B.

Plant J. 2005 Nov;44(3):447-58.


Answer to the comments of K. Dobbin, J. Shih and R. Simon on the paper 'Evaluation of the gene-specific dye-bias in cDNA microarray experiments'.

Martin-Magniette ML, Aubert J, Cabannes E, Daudin JJ.

Bioinformatics. 2005 Jul 15;21(14):3065. Epub 2005 Jun 7. No abstract available.


Evaluation of the gene-specific dye bias in cDNA microarray experiments.

Martin-Magniette ML, Aubert J, Cabannes E, Daudin JJ.

Bioinformatics. 2005 May 1;21(9):1995-2000. Epub 2005 Feb 2.


Genome-wide analysis of Arabidopsis pentatricopeptide repeat proteins reveals their essential role in organelle biogenesis.

Lurin C, Andrés C, Aubourg S, Bellaoui M, Bitton F, Bruyère C, Caboche M, Debast C, Gualberto J, Hoffmann B, Lecharny A, Le Ret M, Martin-Magniette ML, Mireau H, Peeters N, Renou JP, Szurek B, Taconnat L, Small I.

Plant Cell. 2004 Aug;16(8):2089-103. Epub 2004 Jul 21.

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