• Courbet G, D’Oria A, Maillard A, Jing L, Pluchon S, Arkoun M, Pateyron S, Paysant Le Roux C, Diquélou S, Ourry A, Trouverie J, Etienne P. (2021) Comparative Omics Analysis of Brassica napus Roots Subjected to Six Individual Macronutrient Deprivations Reveals Deficiency-Specific Genes and Metabolomic Profiles. Int. J. Molecular Sciences 22(21): 11679.
  • Guilcher M, Liehrmann A, Seyman C, Blein T, Rigaill G, Castandet B, Delannoy E. (2021) Full Length Transcriptome Highlights the Coordination of Plastid Transcript Processing. Int. J. Molecular Sciences 22(20): 11297.
  • Lacroix P, Gallopin M, Martin ML (2021) A Comprehensive Review of Variable Selection in High-Dimensional Regression for Molecular Biology.
  • García de la Torre VS, Majorel-Loulergue C, Rigaill GJ, Alfonso-González D, Soubigou-Taconnat L, Pillon Y, Barreau L, Thomine S, Fogliani B, Burtet-Sarramegna V, Merlot S (2021) Wide cross-species RNA-Seq comparison reveals convergent molecular mechanisms involved in nickel hyperaccumulation across dicotyledons. New Phytologist 229: 994-1006.
  • Romano G, Rigaill G, Runge V, Fearnhead P (2021) Detecting abrupt changes in the presence of local fluctuations and autocorrelated noise. J. American Statistical Association;
  • Liehrmann A, Rigaill G, Hocking TD (2021) Increased peak detection accuracy in over-dispersed ChIP-seq data with supervised segmentation models. BMC Bioinformatics 2021 Jun 14;22(1):323;
  • Baudry K, Paysant-Le Roux C, Colella S, Castandet B, Martin-Magniette M-L (2021) Analyzing Multifactorial RNA-Seq Experiments with DicoExpress. J. Vis. Exp. (), e62566;
  • Sow MD, Le Gac A-L, Fichot R, Lanciano S, Delaunay A, Le Jan I, Lesage-Descause M-C, Citerne S, Caius J, Brunaud V, Soubigou-Taconnat L, Cochard H, Segura V, Chaparro C, Grunau C, Daviaud C, Tost J, Brignolas F, Strauss S, Mirouze M, Maury S. (2021) RNAi suppression of DNA methylation affects drought stress response and genome integrity in transgenic poplar. New Phytologist 2021 Jun 15;
  • Deveaux Y, Conde e Silva N, Manicacci D, Le Guilloux M, Brunaud V, Belcram H, Joets J, Soubigou-Taconnat L, Delannoy E, Corti H, Balzergue S, Caius J, Nadot S, Damerval C. (2021) Transcriptome analysis reveals putative target genes of APETALA3-3 during early floral development in Nigella damascena L. Front. Plant Sci. 2021 Jun 4;12:1004.
  • Nguyen TT, Planchard N, Dahan J, Arnal N, Balzergue S, Benamar A, Bertin P, Brunaud V, Dargel-Graffin C, Macherel D, Martin-Magniette ML, Quadrado M, Namy O, Mireau H. (2021) A case of gene fragmentation in plant mitochondria fixed by the selection of a compensatory restorer of fertility-like PPR gene. Mol Biol Evol. 2021 Apr 20:msab115.
  • Fagny M, Kuijjer ML, Stam M, Joëts J, Turc O, Rozière J, Pateyron S, Venon A, Vitte C. (2021) Identification of Key Tissue-Specific, Biological Processes by Integrating Enhancer Information in Maize Gene Regulatory Networks. Front. Genet. 2021 Jan 11;11:606285. PMID: 33505431.
  • De Marco F, Batailler B, Thorpe MR, Razan F, Le Hir R, Vilaine F, Bouchereau A, Martin-Magniette M-L, Eveillard S, Dinant S. (2021) Involvement of SUT1 and SUT2 Sugar Transporters in the Impairment of Sugar Transport and Changes in Phloem Exudate Contents in Phytoplasma-Infected Plants. Int. J. Mol. Sci. 22:745. 
  • Jurdak R, Launay-Avon A, Paysant-Le Roux C, Bailly C. (2021) Retrograde signalling from the mitochondria to the nucleus translates the positive effect of ethylene on dormancy breaking of Arabidopsis thaliana seeds. New Phytologist 229(4):2192-2205.



  • Vittrant B, Bergeron A, Molina OE, Leclercq M,  Légaré X-P, Hovington H, Picard V, Martin-Magniette M-L, Livingstone J, Boutros PC, Collins C, Fradet Y, Droit A (2020) Immune-focused multi-omics analysis of prostate cancer: leukocyte Ig-Like receptors are associated with disease progression. OncoImmunology 9(1): 1851950.
  • Vittrant B, Leclercq M, Martin-Magniette M-L, Collins C, Bergeron A, Fradet Y, Droit A (2020) Identification of a Transcriptomic Prognostic Signature by Machine Learning Using a Combination of Small Cohorts of Prostate Cancer. Front. Genet. 11: 550894.
  • Etienne P, Trouverie J, Haddad C, Arkoun M, Yvin J-C, Caïus J, Brunaud V, Laîné P. (2020) Root Silicon Treatment Modulates the Shoot Transcriptome in Brassica napus L. and in Particular Upregulates Genes Related to Ribosomes and Photosynthesis. Silicon J. (2020). 
  • Soulie M-C, Koka SM, Floch K, Vancostenoble B, Barbe D, Daviere A, Soubigou‐Taconnat L, Brunaud V, Poussereau N, Loisel E, Devallee A, Expert D, Fagard M. (2020) Plant nitrogen supply affects the Botrytis cinerea infection process and modulates known and novel virulence factors. Molecular Plant Pathology 21:1436-1450.
  • Andres-Robin A, Reymond MC, Brunoud G, Martin-Magniette M-L, Monéger F, Scutt CP (2020) Immediate targets of ETTIN suggest a key role for pectin methylesterase inhibitors in the control of Arabidopsis gynecium development. Plant Signal Behav. 15(7):1771937.  
  • Lambert I, Pervent M, Le Queré A, Clément G, Tauzin M, Severac D, Benezech C, Tillard P, Martin-Magniette M-L, Colella S, Lepetit M (2020)  Responses of mature symbiotic nodules to the whole-plant systemic nitrogen signaling, Journal of Experimental Botany, eraa221.
  • Bonnot T, Martre P, Hatte V, Dardevet M, Leroy P, Bénard C, Falagán N, Martin-Magniette M-L, Deborde C, Moing A, Gibon Y, Pailloux M, Bancel E, Ravel C (2020) Omics Data Reveal Putative Regulators of Einkorn Grain Protein Composition under Sulfur Deficiency. Plant Physiology 183(2):501-516.
  • Chardon F, Cueff G, Delannoy E, Aubé F, Lornac A, Bedu M, Gilard F, Pateyron S, Rogniaux H, Gargaros A, Mireau H, Rajjou L, Martin-Magniette M-L, Budar F (2020) The Consequences of a Disruption in Cyto-Nuclear Coadaptation on the Molecular Response to a Nitrate Starvation in Arabidopsis. Plants 9:573.
  • Lambert I, Paysant-Le Roux C, Colella S, Martin-Magniette M-L (2020) DiCoExpress: a tool to process multifactorial RNAseq experiments from quality controls to co-expression analysis through differential analysis based on contrasts inside GLM models. Plant Methods 16:68.
  • Blein T, Balzergue C, Roulé T, Gabriel M, Scalisi L, François T, Sorin C, Christ A, Godon C, Delannoy E, Martin-Magniette M-L, Nussaume L, Hartmann C, Gautheret D, Desnos TM, Crespi M (2020) Landscape of the non-coding transcriptome response of two Arabidopsis ecotypes to phosphate starvation. Plant Physiology May 2020, pp.00446.2020.
  • Chateigner A, Lesage-Descauses M, Rogier O, Jorge V, Leplé J-C, Brunaud V, Paysant-Le Roux C, Soubigou-Taconnat L, Martin-Magniette M-L, Sanchez L, Segura V (2020)  Gene expression predictions and networks in natural populations supports the omnigenic theory. BMC Genomics 21:416.
  • Schweke H, Mucchielli M-H, Sacquin-Mora S, Bei W, Lopes A (2020) Protein Interaction Energy Landscapes are Shaped by Functional and also Non-functional Partners. J. Mol. Biol. 432(4):1183-1198. 
  • Doll NM, Just J, Brunaud V, Caïus J, Grimault A, Depège-Fargeix N, Esteban E, Pasha A, Provart NJ, Ingram GC, Rogowsky PM, Widiez T (2020) Transcriptomics at Maize Embryo/Endosperm Interfaces Identifies a Transcriptionally Distinct Endosperm Subdomain Adjacent to the Embryo Scutellum. Plant Cell 32(4):833-852.
  • Hocking TD, Rigaill G, Fearnhead P, Bourque G (2020) Generalized Functional Pruning Optimal Partitioning (GFPOP) for Constrained Changepoint Detection in Genomic Data. J. Statistical Software.
  • Hocking TD, Rigaill G, Fearnhead P, Bourque G (2020) A log-linear time algorithm for constrained changepoint detection. JMLR 2020 .​
  • Fearnhead P, Rigaill G (2020) Relating and Comparing Methods for  Detecting Changes-in-Mean. Stat 2020; e291.​ 
  • Hulot A, Chiquet J, Jaffrézic F, Rigaill G (2020) Fast tree aggregation for consensus hierarchical clustering. BMC Bioinformatics 21, 120.



  • Ambroise C, Dehman A, Neuvial P, Rigaill G, Vialaneix N (2019) Adjacency-constrained hierarchical clustering of a band similarity matrix with application to genomics. Algorithms Mol. Biol. 14, 22.
  • Lemay M, Torkamaneh D, Rigaill G, Boyle B, Stec A, Stupar R,Belzile F (2019) Screening populations for copy number variation using genotyping-by-sequencing: a proof of concept using soybean fast neutron mutants. BMC Genomics 20, 634.
  • Cuello C, Baldy A, Brunaud V, Joets J, Delannoy E, Jacquemot M-P, Botran L, Griveau Y, Guichard C, Soubigou-Taconnat L, Martin-Magniette M-L, Leroy P, Méchin V, Reymond M, Coursol S (2019) A systems biology approach uncovers a gene co-expression network associated with cell wall degradability in maize. PLoS ONE Dec. 31, 2019 
  • Doll NM, Just J, Brunanud V, Caïus J, Grimault A, Depège-Fargeix N, Esteban E, Pasha A, Provart NJ, Ingram GC, Rogowsky PM, Widiez T. (2019) Transcriptomics at maize embryo/endosperm interfaces identify a novel transcriptionally distinct endosperm sub-domain adjacent to the embryo scutellum (EAS). BioRxiv.
  • Forzani C, Turqueto Duarte G, Van Leene J, Clément G, Huguet S, Paysant-Le Roux C, Mercier R, De Jaeger G, Leprince A-S, Meyer C. (2019) Mutations of the AtYAK1 Kinase Suppress TOR Deficiency in ArabidopsisCell Reports 27(12):3696-3708.
  • Leclercq M, Vittrant B, Martin-Magniette M-L, Scott Boyer M-P, Perin O, Bergeron A, Fradet Y, Droit A. (2019) Large-Scale Automatic Feature Selection for Biomarker Discovery in High-Dimensional OMICs Data. Frontiers in Genetics 10:452
  • C. Boussardon, M.L. Martin-Magniette, B. Godin, A. Benamar, B. Vittrant, S. Citerne, T. Mary-Huard, D. Macherel, L. Rajjou, F. Budar (2019) Novel Cytonuclear Combinations Modify Arabidopsis thaliana Seed Physiology and Vigor. Front. Plant Sci. 05 February 2019
  • V. Maire, F. Mahmood, G. Rigaill, M. Ye, A. Brisson, F. Némati, D. Gentien, G.C. Tucker, S. Roman-Roman, T. Dubois (2019) LRP8 is overexpressed in estrogen-negative breast cancers and a potential target for these tumors. Cancer Medicine 8(1):325-36.
  • J. Chiquet, G. Rigaill, M. Sundqvist (2019) A Multiattribute Gaussian Graphical Model for Inferring Multiscale Regulatory Networks: An Application in Breast Cancer. Methods Mol Biol. 1883:143-160. doi: 10.1007/978-1-4939-8882-2_6.
  • F. Lallemand, M.L. Martin-Magniette, F. Gilard, B. Gakière, A. Launay-Avon, E. Delannoy, M.A. Selosse (2019) In situ transcriptomic and metabolomic study of the loss of photosynthesis in the leaves of mixotrophic plants exploiting fungi. Plant J. 98(5): 826-841.

  • Del Prete S, Molitor A, Charif D, Bessoltane N, Soubigou-Taconnat L, Guichard C, Brunaud V, Granier F, Fransz P, Gaudin V. (2019) Extensive nuclear reprogramming and endoreduplication in mature leaf during floral induction. BMC Plant Biology 19:135.

  • Haddad C, Trouverie J, Arkoun M, Yvin J-C, Caïus J, Brunaud V, Laîné P, Etienne P. (2019) Silicon supply affects the root transcriptome of Brassica napus L. Planta 1-7. 
  • Klau S, Martin-Magniette M-L, Boulesteix A-L, Hoffmann S. (2019) Sampling uncertainty versus method uncertainty: A general framework with applications to omics biomarker selection. Biometrical Journal 2019:1– 18.


  • Maubant S, Tahtouh T, Brisson A, Maire V, Némati F, Tesson B, Ye M, Rigaill G, Noizet M, Dumont A, Gentien D, Marty-Prouvost B, de Koning L,Faisal Mahmood S, Decaudin D, Cruzalegui F, Tucker GC, Roman-Roman S, Dubois T (2018) LRP5 regulates the expression of STK40, a new potential target in triple-negative breast cancers. Oncotarget 9:22586-22604.
  • M. Farjad, M. Rigault, S. Pateyron, M.L. Martin-Magniette, A. Krapp, C. Meyer, M. Fagard (2018) Nitrogen limitation alters the response of specific genes to biotic stress. Int. J. Mol. Sci. 19(11):3364. 
  • E. Albert, R. Duboscq, M. Latreille, S. Santoni, M. Beukers, J.P. Bouchet, F. Bitton, J. Gricourt, C. Poncet, V. Gautier, J.M. Jiménez-Gómez, G. Rigaill, M. Causse (2018) Allele-specific expression and genetic determinants of transcriptomic variations in response to mild water deficit in tomato. Plant J. 96(3):635-650.
  • O. Rogier, A. Chateigner, S. Amanzougarene, M.C. Lesage-Descauses, S. Balzergue, V, Brunaud, J. Caius, L. Soubigou-Taconnat, V. Jorge, V. Segura (2018) Accuracy of RNAseq based SNP discovery and genotyping in Populus nigraBMC Genomics 19(1):909
  • P. Montoro, S. Wu, B. Favreau, E. Herlinawati, C. Labrune, M.-L. Martin-Magniette,S. Pointet, M. Rio, J. Leclercq, S. Ismawanto and Kuswanhadi (2018) Transcriptome analysis in Hevea brasiliensis latex revealed changes in hormone signalling pathways during ethephon stimulation and consequent Tapping Panel Dryness. Scientific Reports vol. 8, 8483. :10.1038/s41598-018-26854-y
  • Rey E, Abrouk M, Keeble‐Gagnère G, Karafiátová M, Vrána J, Balzergue S, Soubigou‐Taconnat L, Brunaud V, Martin-Magniette M.L., Endo T.R., Bartoš J, International Wheat Genome Sequencing Consortium, Appels R, Doležel J. (2018) Transcriptome reprogramming due to the introduction of a barley telosome into bread wheat affects more barley genes than wheat. Plant Biotechnology Journal doi :10.1111/pbi.12913
  • Sakai K, Taconnat L, Borrega N, Yansouni J, Brunaud V, Paysant-Le Roux C, Delannoy E, Martin-Magniette M.L, Lepiniec L, Faure J.D, Balzergue S, Dubreucq B.(2018). Combining laser-assisted microdissection (LAM) and RNA-seq allows to perform a comprehensive transcriptomic analysis of epidermal cells of Arabidopsis embryo. Plant Methods, 14:10. doi:10.1186/s13007-018-0275-x.
  • A. Lloyd, A. Blary, D. Charif, C. Charpentier, J. Tran, S. Balzergue, E. Delannoy, G. Rigaill, and E. Jenczewski (2018) Homoeologous exchanges cause extensive dosage-dependent gene expression changes in an allopolyploid crop. New Phytologist 217(1):367-377. doi: 10.1111/nph.14836
  • A. Celisse, G. Marot, M. Pierre-Jean, G. Rigaill (2018) New efficient algorithms for multiple change-point detection with reproducing kernels. Computational Statistics & Data Analysis 128:200-20.
  • B. Malbert, G. Rigaill, V. Brunaud, C. Lurin, E. Delannoy (2018) Bioinformatic Analysis of Chloroplast Gene Expression and RNA Posttranscriptional  Maturations Using RNA Sequencing. Methods Mol. Biol. 1829:279-94.



  • A. Canaguier, J. Grimplet, G. Di Gaspero, S. Scalabrin, E. Duchêne, N. Choisne, N. Mohellibi, C. Guichard, S. Rombauts, I. Le Clainche, A. Bérard, A. Chauveau, R. Bounon, C. Rustenholz, M. Morgante, M.-C.Le Paslier, D. Brunel, A.-F. Adam-Blondon (2017) A new version of the grapevine reference genome assembly (12X.v2) and of its annotation (VCost.v3).
  • Martins, S., Montiel-Jorda, A., Cayrel, A., Huguet, S., Paysant Le Roux, C., Ljung, K., Vert, G. (2017). Brassinosteroid signaling-dependent root responses to prolonged elevated ambient temperature. Nature Communications, 8. , doi: 10.1038/s41467-017-00355-4
  • J.-T. Brandenburg, T. Mary-Huard, G. Rigaill, S. J. Hearne, H. Corti, J. Joets, C. Vitte A. Charcosset, S. D. Nicolas, and M. I. Tenaillon (2017) Independent introductions and admixtures have contributed to adaptation of european maize and its american counterparts. PLoS genetics 13(3):e1006666. doi: 10.1371/journal.pgen.1006666.
  • D. Guillaumot, M. Lopez-Obando, K. Baudry, A. Avon, G. Rigaill, A. Falcon de Longevialle, B. Broche, M. Takenaka, R. Berthomé, G. De Jaeger, E. Delannoy, and C. Lurin (2017) Two interacting PPR proteins are major Arabidopsis editing factors in plastid and mitochondria. Proc. Natl. Acad. Sci. USA. 114(33)8877-8882; doi:10.1073/pnas.1705780114
  • R. Maidstone, T. Hocking, G. Rigaill, and P. Fearnhead (2017) On optimal multiple changepoint algorithms for large data. Statistics and Computing 27(2):519-533.
  • J. Chiquet, P. Gutierrez, and G. Rigaill (2017) Fast tree inference with weighted fusion penalties. Journal of Computationnal and Graphical Statistics 26(1):205-216.
  • P. Fearnhead, G.Rigaill (2017) Changepoint Detection in the Presence of Outliers. Journal of the American Statistical Association, 10.1080/01621459.2017.1385466.
  • Tamby J-P., Brunaud V. (2017). FLAGdb++ : A Bioinformatic Environment to Study and Compare Plant Genomes. Methods Mol. Biol. 1533:79-101. doi:10.1007/978-1-4939-6658-5_4.



  • Kiefer H., Jouneau L., Campion E., Rousseau-Ralliard D., Larcher T., Martin-Magniette M-L., Balzergue S., Ledevin M., Prézelin A., Chavatte-Palmer P., Heyman Y., Richard C., Le Bourhis D., J-P. Renard & H. Jammes (2016).. Altered DNA methylation associated with an abnormal liver phenotype in a cattle model with a high incidence of perinatal pathologies. Scientific Reports 6 : 38869. doi:10.1038/srep38869.
  • 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 M-L., Delannoy E. (2016). Synthetic data sets for the identification of key ingredients for RNA-seq differential analysis. Brief. Bioinformatics 1-12. doi:10.1093/bib/bbw092.
  • Yesbergenova-Cuny Z., Dinant S., Martin-Magniette M-L., Quilleré I., Armengaud P., Monfalet P., Lea PJ., Hirel B. (2016). Genetic variability of the phloem sap metabolite content of maize (Zea mays L.) during the kernel-filling period. Plant Sci. 252:347-357. doi : 10.1016/j.plantsci.2016.08.007.
  • Albert E., Gricourt J., Bertin N., Bonnefoi J., Pateyron S., Tamby J-P., Bitton F., Causse M. (2016). Genotype by watering regime interaction in cultivated tomato : lessons from linkage mapping and gene expression. Theor. Appl. Genet. 129(2):395-418. doi : 10.1007/s00122-015-2635-5.
  • Damiani I., Drain A., Guichard M., Balzergue S., Boscari A., Boyer J-C., Brunaud V., Cottaz S., Rancurel C., Da Rocha M., Fizames C., Fort S., Gaillard I., Danchin EG., Maillol V., Rouached H., Samain E., Su Y., Thouin J., Touraine B., Puppo A., Frachisse J-M., N. Pauly & H. Sentenac (2016). Nod factor effects on root hair-specific transcriptome of Medicago truncatula : focus on plasma membrane transport systems and reactive oxygen species networks. Front. Plant Sci. 7:794. doi : 10.3389/fpls.2016.00794.
  • Bueso E., Muñoz-Bertomeu J., Campos F., Martínez C., Tello C., Martínez-Almonacid I., Ballester P., Simón-Moya M., Brunaud V., Yenush L., C. Ferrándiz & R. Serrano (2016). Arabidopsis COGWHEEL1 links light perception and gibberellins with seed tolerance to deterioration. The Plant Journal 2016 doi : 10.1111/tpj.13220.
  • Roux F., Mary-Huard T., Barillot E., Wenes E., Botran L., Durand S., Villoutreix R., Martin-Magniette M-L., C. Camilleri & F. Budar (2016). Cytonuclear interactions affect adaptive traits of the annual plant Arabidopsis thaliana in the field. Proc. Natl. Acad. Sci. USA 113(13):3687-92.. doi:10.1073/pnas.1520687113.
  • Papastamoulis, P., Martin-Magniette, M.-L., Maugis-Rabusseau, C. (2016). . On the estimation of mixtures of Poisson regression models with large number of components. Computational Statistics and Data Analysis 93:97-106. doi : 10.1016/j.csda.2014.07.005.
  • Plomion C, Aury JM, Amselem J, Alaeitabar T, Barbe V, Belser C, Bergès H, Bodénès C, Boudet N, Boury C, Canaguier A, Couloux A, Da Silva C, Duplessis S, Ehrenmann F, Estrada-Mairey B, Fouteau S, Francillonne N, Gaspin C, Guichard C, Klopp C, Labadie K, Lalanne C, Le Clainche I, Leplé JC, Le Provost G, Leroy T, Lesur I, Martin F, Mercier J, Michotey C, Murat F, Salin F, Steinbach D, Faivre-Rampant P, Wincker P, Salse J, Quesneville H, Kremer A. (2016). Decoding the oak genome : public release of sequence data, assembly, annotation and publication strategies. Mol. Ecol. Resour. 16(1):254-65. doi : 10.1111/1755-0998.12425.

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  • Rigaill G. (2015). A pruned dynamic programming algorithm to recover the best segmentations with 1 to K_max change-points. Journal de la société française de statistique 156(4):180-2015.
  • Hocking T, Rigaill G, Bourque G. (2015). PeakSeg : constrained optimal segmentation and supervised penalty learning for peak detection in count data. In Proceedings of The 32th International Conference on Machine Learning.
  • Baldeyron C, Brisson A, Tesson B, Némati F, Koundrioukoff S, Saliba E, De Koning L, Martel E, Ye M, Rigaill G, Meseure D, Nicolas A, Gentien D, Decaudin D, Debatisse M, Depil S, Cruzalegui F, Pierré A, Roman-Roman S, Tucker GC, Dubois T. (2015). TIPIN depletion leads to apoptosis in breast cancer cells. Mol. Oncol. 9(8):1580-98. doi : 10.1016/j.molonc.2015.04.010..
  • Maubant S, Tesson B, Maire V, Ye M, Rigaill G, et al. (2015). Transcriptome Analysis of Wnt3a-Treated Triple-Negative Breast Cancer Cells. PLoS ONE 10(4):e0122333. doi : 10.1371/journal.pone.0122333.
  • Martínez F., Arif A., Nebauer S.G., Bueso E., Ali R., Montesinos C., Brunaud V., Muñoz-Bertomeu J., Serrano R. (2015). A fungal transcription factor gene is expressed in plants from its own promoter and improves drought tolerance. Planta. 242(1):39-52. doi : 10.1007/s00425-015-2285-5.
  • Danquah A, de Zelicourt A, Boudsocq M, Neubauer J ,Frey NFD, Leonhardt N, Pateyron S, Gwinner F, Tamby JP, Ortiz-Masia D, Marcote MJ,Hirt H, Colcombet J. (2015). Identification and characterization of an ABA-activated MAP kinase cascade in Arabidopsis thaliana. Plant J. 82(2):232-44. doi : 10.1111/tpj.12808.
  • Rau A, Maugis-Rabusseau C, Martin-Magniette ML, Celeux G. (2015). Co-expression analysis of high-throughput transcriptome sequencing data with Poisson mixture models. Bioinformatics. 31(9):1420-7. doi : 10.1093/bioinformatics/btu845.
  • 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. (2015). GEM2Net : from gene expression modeling to -omics networks, a new CATdb module to investigate Arabidopsis thaliana genes involved in stress response. Nucleic Acids Res. 43(Database issue):D1010-7. doi : 10.1093/nar/gku1155.



  • Rigaill G, Miele V, Picard F (2014). Fast and Parallel Algorithm for Population-Based Segmentation of Copy-Number Profiles. Computational Intelligence Methods for Bioinformatics and Biostatistics. Springer International Publishing, 2014. 248-258.
  • 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.(2014). Differential gene expression and metabolomic analyses of Brachypodium distachyon infected by deoxynivalenol producing and non-producing strains of Fusarium graminearum. BMC Genomics 15:629. doi : 10.1186/1471-2164-15-629.
  • Lange H, Zuber H, Sement F. M., Chicher J., Kuhn L., Hammann P, Brunaud V, Bérard C, Bouteiller N, Balzergue S, Aubourg S, Martin-Magniette M.-L., Vaucheret H., Gagliardi D. (2014). The RNA Helicases AtMTR4 and HEN2 Target Specific Subsets of Nuclear Transcripts for Degradation by the Nuclear Exosome in Arabidopsis thaliana. PloS genetics 10(8):e1004564.
  • Pierre-Jean M, Rigaill G, Neuvial P. (2014). Performance evaluation of DNA copy number segmentation methods. Briefings in Bioinformatics Advanced Access 2014
  • Cleynen A, The Minh L, Rigaill G, and Nuel G. (2014). Fast estimation of the Integrated Completed Likelihood criterion for change-point detection problems with applications to Next-Generation Sequencing data. Signal Processing 98 : 233-242.
  • Cleynen A, Koskas M, Lebarbier E, Rigaill G, and Robin S (2014). Segmentor3IsBack : an R package for the fast and exact segmentation of Seq-data. Algorithms for Molecular Biology 9 : 6. doi : 10.1186/1748-7188-9-6.
  • Hocking T D., Boeva V, Rigaill G, Schleiermacher G, Janoueix-Lerosey I, Delattre O, Richer W, Bourdeaut F, Suguro M, Seto M, Bach F, Vert JP (2014). SegAnnDB : interactive Web-based genomic segmentation. Bioinformatics 30, 11 : 1539-1546.
  • 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. (2014). Functional analysis of Arabidopsis immune-related MAPKs uncovers a role for MPK3 as negative regulator of inducible defenses. Genome Biol. 15(6):R87.
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