Publications

2024

  • Méteignier L-V, Szwarc S, Barunava P, Durand M, Zamar D-L, Williams CB, Gautron N, Dutilleul C, Koudounas K, Lezin E, Perrot T, Oudin A, Pateyron S, Delannoy E, Brunaud V, Lanoue A, Abbasi BH, St-Pierre B, Jensen MK, Papon N, Sun C, Le Pogam-Alluard P, Ling Y, Beniddir MA, Besseau S, Courdavault V. (2024) Harnessing the spatial and transcriptional regulation of monoterpenoid indole alkaloid metabolism in Alstonia scholaris leads to the identification of broad geissoschizine cyclase activities. Plant Physiology and Biochemistry (Nov. 29) 109363.

  • Liehrmann A, Rigaill G. (2024) Ms.FPOP: a fast exact segmentation algorithm with a multiscale penalty. J. Computational and Graphical Statistics, 1-25.

  • Rocher F, Dou S, Philippe G, Martin M.L, Label P, Langin T, Bonhomme L (2024) Integrative systems biology of wheat susceptibility to Fusarium graminearum uncovers a conserved gene regulatory network and identifies master regulators targeted by fungal core effectors. BMC Biol 22, 53.

  • Henchiri H, Rayapuram N, Alhoraibi HM, Caïus J, Paysant-Le Roux C, Citerne S, Hirt H, Colcombet J, Sturbois B, Bigeard J (2024) Integrated multi-omics and genetic analyses reveal molecular determinants underlying Arabidopsis snap33 mutant phenotype. The Plant Journal. Jan 28. Epub ahead of print, PMID: 38281242.

 

2023

  • Martin ML, Pervent M, Lambert I, Colella S, Tancelin M, Severac D, Clément G, Tillard P, Frugier F and Lepetit M. (2023) Localized osmotic stress activates systemic responses to N limitation in Medicago truncatula–Sinorhizobium symbiotic plants. Front. Plant Sci. 14:1288070.

  • Liehrmann A, Delannoy E, Launay-Avon A, Gilbault E, Loudet O, Castandet B, Rigaill G. (2023) DiffSegR: an RNA-seq data driven method for differential expression analysis using changepoint detection. Nucleic Acids Res. Genomics & Bioinformatics 5 (4); lqad098.

  • Djabali Y, Rincent R, Martin ML, Blein-Nicolas M. (2023) Plasticity QTLs specifically contribute to the genotype × water availability interaction in maize. Theor Appl Genet 136, 228.

  • Sundqvist M, Chiquet J, Rigaill G. (2023) Adjusting the adjusted Rand Index: A multinomial story. Computational Statistics 38 (1); 327-347.

  • Rogier O, Chateigner A, Lesage-Descauses MC, Mandin C, Brunaud V, Caius J, Soubigou-Taconnat L, Almeida-Falcon J, Bastien C, Benoit V, Bodineau G, Boizot N, Buret C, Charpentier JP, Déjardin A, Delaunay A, Fichot R, Laine Prade V, Laurans F, Le Jan I, Legac AL, Maury S, Gebreselassie MN, Poursat P, Ridel C, Sanchez L, Jorge V, Segura V. (2023) RNAseq based variant dataset in a black poplar association panel. BMC Res Notes Oct 2; 16(1): 248.

  • Hartasánchez DA, Kiss A, Battu V, Soraru C, Delgado-Vaquera A, Massinon F, Brasó-Vives M, Mollier C, Martin-Magniette M-L, Boudaoud A, Monéger F. (2023) Expression of cell-wall related genes is highly variable and correlates with sepal morphology. Peer Community Journal Vol. 3, e93.

  • Tran HC, Schmitt V, Lama S, Wang C, Launay-Avon A, Bernfur K, Hofmann K, Khan K, Brunaud V, Liehrmann A, Castandet B, Levander F, Rasmusson AG, Mireau H, Delannoy E, Van Aken O. (2023) An mTRAN-mRNA interaction mediates mitochondrial translation initiation in plants. Science 381(6661).

  • Trémulot L, Macadré C, Gal J, Garmier M, Launay-Avon A, Paysant Le Roux C, Ratet P, Noctor G, Dufresne M. (2023) Impact of high atmospheric carbon dioxide on the biotic stress response of the model cereal species Brachypodium distachyon. Frontiers Plant Science Sec. Plant Abiotic Stress, vol.14. doi.org/10.3389/fpls.2023.1237054

  • Durand M, Brehaut V, Clement G, Kelemen Z, Macé J, Feil R, Duville G, Launay-Avon A, Paysant-Le Roux C, Lunn JE, Roudier F, Krapp A. (2023) The Arabidopsis transcription factor NLP2 regulates early nitrate responses and integrates nitrate assimilation with energy and carbon skeleton supply. The Plant Cell 35(5): 1429–1454.

  • Romano G, Eckley IA, Fearnhead P, Rigaill G. (2023)  Fast Online Changepoint Detection via Functional Pruning CuSUM Statistics. J. Machine Learning Res. 24(81): 1−36. ()

  • Runge V, Hocking TD, Romano G, Afghah F, Fearnhead P, Rigaill G. (2023). gfpop: An R Package for Univariate Graph-Constrained Change-Point Detection. J. Statistical Software 106(6): 1–39.

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2022

  • D'Oria A, Courbet G, Billiot B, Jing L, Pluchon S, Arkoun M, Maillard A, Paysant-Le Roux C, Trouverie J, Etienne P, Diquélou S, Ourry A. (2022). Drought specifically downregulates mineral nutrition: Plant ionomic content and associated gene expression. Plant Direct 6(8):e402. doi.org/10.1002/pld3.402

  • Alvarez-Diaz JC, Laugé R, Delannoy E, Huguet S, Paysant-Le Roux C, Gratias A, Geffroy V. (2022) Genome-Wide Transcriptomic Analysis of the Effects of Infection with the Hemibiotrophic Fungus Colletotrichum lindemuthianum on Common Bean. Plants 11(15), 1995.doi.org/10.3390/plants11151995

  • Gosset S, Glatigny A, Gallopin M, Yi Z, Salé M, Mucchielli-Giorgi MH. (2022) APPINetwork: an R package for building and computational analysis of protein-protein interaction networks. PeerJ. Nov 4;10:e14204. doi.org/10.7717/peerj.14204

  • Maillot G, Szadkowski E, Massire A, Brunaud V, Rigaill G, Caromel B, Chadœuf J, Bachellez A, Touhami N, Hein I, Lamour K, Balzergue S, Lefebvre V. (2022) Strive or thrive: Trends in Phytophthora capsici gene expression in partially resistant pepper. Frontiers in Plant Science Nov 21;13:980587. doi.org/10.3389/fpls.2022.980587

  • Damerval C, Claudot C, Le Guilloux M, Conde E Silva N, Brunaud V, Soubigou-Taconnat L, Caïus J, Delannoy E, Nadot S, Jabbour F, Deveaux Y. (2022) Evolutionary analyses and expression patterns of TCP genes in Ranunculales. Frontiers in Plant Science Dec 01;13:1055196. doi.org/10.3389/fpls.2022.1055196

  • Rozière J, Guichard C, Brunaud V, Martin M-L, Coursol S. (2022) A comprehensive map of preferentially located motifs reveals distinct proximal cis-regulatory sequences in plants. Frontiers in Plant Science Oct 12;13:976371. doi.org/10.3389/fpls.2022.976371

  • Hocking TD, Rigaill G, Fearnhead P, Bourque G. (2022) Generalized Functional Pruning Optimal Partitioning (GFPOP) for Constrained Changepoint Detection in Genomic Data. J. Statistical Software 101(10): 1–31. doi.org/10.18637/jss.v101.i10 ()

  • Thelander M, Landberg K, Muller A, Cloarec G, Cunniffe N, Huguet S, Soubigou-Taconnat L, Brunaud V, Coudert Y. (2022) Apical dominance control by TAR-YUC-mediated auxin biosynthesis is a deep homology of land plants. Current Biology  doi.org/10.1016/j.cub.2022.06.064

  • Schweke H, Mucchielli MH, Chevrollier N, Gosset S, Lopes A. (2022) SURFMAP: A Software for Mapping in Two Dimensions Protein Surface Features. J Chem Inf Model. Apr 11;62(7):1595-1601. doi.org/10.1021/acs.jcim.1c01269

  • Bouré N, Peaucelle A, Goussot M, Adroher B, Soubigou-Taconnat L, Borrega N, Bot C, Tariq Z, Martin-Magniette ML, Pautot V, Laufs P, Arnaud N. (2022) A cell wall-associated gene network shapes leaf boundary domains. Development Jun 1;149(11):dev200359. doi.org/10.1242/dev.200359

  • Alvarez-Diaz JC, Richard MMS, Thareau V, Teano G, Paysant-Le-Roux C, Rigaill G, Pflieger S, Gratias A, Geffroy V. (2022) Genome-Wide Identification of Key Components of RNA Silencing in Two Phaseolus vulgaris Genotypes of Contrasting Origin and Their Expression Analyses in Response to Fungal Infection. Genes 13(1): 64. doi.org/10.3390/genes13010064

  • Decouard B, Bailly M, Rigault M, Marmagne A, Arkoun M, Soulay F, Caïus J, Paysant-Le Roux C, Louahlia S, Jacquard C, Esmaeel Q, Chardon F, Masclaux-Daubresse C, Dellagi A. (2022) Genotypic Variation of Nitrogen Use Efficiency and Amino Acid Metabolism in Barley. Front. Plant Sci. 12. doi.org/10.3389/fpls.2021.807798

  • Boutet S, Barreda L, Perreau F, Totozafy J-C, Mauve C, Gakière B, Delannoy E, Martin-Magniette ML, Monti A, Lepiniec L, Zanetti F, Corso M. (2022) Untargeted metabolomic analyses reveal the diversity and plasticity of the specialized metabolome in seeds of different Camelina sativa genotypes. Plant J. doi.org/10.1111/tpj.15662

  • Rocher F, Alouane T, Philippe G, Martin ML, Label P, Langin T, Bonhomme L. (2022) Fusarium graminearum Infection Strategy in Wheat Involves a Highly Conserved Genetic Program That Controls the Expression of a Core Effectome. Int. J. Molecular Sciences 23(3): 1914; doi.org/10.3390/ijms23031914

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2021

  • Pervent M, Lambert I, Tauzin M, Karouani A, Nigg M, Jardinaud MF, Severac D, Colella S, Martin-Magniette ML, Lepetit M. Systemic control of nodule formation by plant nitrogen demand requires autoregulation-dependent and independent mechanisms. (2021) J Exp Bot. 72(22):7942-7956.

  • Mary-Huard T, Perduca V, Martin-Magniette ML, Blanchard G. (2021) Error rate control for classification rules in multiclass mixture models. Int. J. Biostatistics nov. 29, 2021;

  • 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. doi.org/10.3390/ijms222111679

  • 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. arXiv preprint

  • 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. doi.org/10.1111/nph.16775

  • 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 ML. (2022) 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 ML, 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.

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2020

  • Vittrant B, Bergeron A, Molina OE, Leclercq M,  Légaré X-P, Hovington H, Picard V, Martin-Magniette ML, 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 ML, 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. doi.org/10.3389/fgene.2020.550894

  • Etienne P, Trouverie J, Haddad C, Arkoun M, Yvin JC, 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 MC, 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 ML, 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 ML, Colella S, Lepetit M. (2020)  Responses of mature symbiotic nodules to the whole-plant systemic nitrogen signaling, Journal of Experimental Botany, eraa221. doi.org/10.1093/jxb/eraa221

  • Bonnot T, Martre P, Hatte V, Dardevet M, Leroy P, Bénard C, Falagán N, Martin-Magniette ML, 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. doi.org/10.1104/pp.19.00842

  • 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 ML, 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 ML. (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. doi.org/10.1186/s13007-020-00611-7

  • Blein T, Balzergue C, Roulé T, Gabriel M, Scalisi L, François T, Sorin C, Christ A, Godon C, Delannoy E, Martin-Magniette ML, 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 JC, Brunaud V, Paysant-Le Roux C, Soubigou-Taconnat L, Martin-Magniette ML, Sanchez L, Segura V. (2020)  Gene expression predictions and networks in natural populations supports the omnigenic theory. BMC Genomics 21:416. doi.org/10.1186/s12864-020-06809-2

  • Schweke H, Mucchielli MH, 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) Constrained Dynamic Programming and Supervised Penalty Learning Algorithms for Peak Detection in Genomic Data. JMLR 21(87); 1-40. (arXiv:1703.03352)

  • Fearnhead P, Rigaill G. (2020) Relating and Comparing Methods for  Detecting Changes-in-Mean. Stat 2020; e291. doi.org/10.1002/sta4.291​ 

  • Hulot A, Chiquet J, Jaffrézic F, Rigaill G. (2020) Fast tree aggregation for consensus hierarchical clustering. BMC Bioinformatics 21, 120. doi.org/10.1186/s12859-020-3453-6

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2019

  • 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. doi.org/10.1186/s13015-019-0157-4

  • 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. doi.org/10.1186/s12864-019-5998-1

  • Cuello C, Baldy A, Brunaud V, Joets J, Delannoy E, Jacquemot M-P, Botran L, Griveau Y, Guichard C, Soubigou-Taconnat L, Martin-Magniette ML, 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. doi.org/10.1101/799338

  • Forzani C, Turqueto Duarte G, Van Leene J, Clément G, Huguet S, Paysant-Le Roux C, Mercier R, De Jaeger G, Leprince AS, Meyer C. (2019) Mutations of the AtYAK1 Kinase Suppress TOR Deficiency in Arabidopsis. Cell Reports 27(12):3696-3708. doi.org/10.1016/j.celrep.2019.05.074

  • Leclercq M, Vittrant B, Martin-Magniette ML, Scott Boyer MP, 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

  • Boussardon C, Martin-Magniette ML, Godin B, Benamar A, Vittrant B, Citerne S, Mary-Huard T, Macherel D, Rajjou L, Budar F. (2019) Novel Cytonuclear Combinations Modify Arabidopsis thaliana Seed Physiology and Vigor. Front. Plant Sci. 05 February 2019

  • Maire V, Mahmood F, Rigaill G, Ye M, Brisson A, Némati F, Gentien D, Tucker GC, Roman-Roman S, Dubois T. (2019) LRP8 is overexpressed in estrogen-negative breast cancers and a potential target for these tumors. Cancer Medicine 8(1):325-36.

  • Chiquet J, Rigaill G, Sundqvist G. (2019) A Multiattribute Gaussian Graphical Model for Inferring Multiscale Regulatory Networks: An Application in Breast Cancer. Methods Mol Biol. 1883:143-160.

  • Lallemand F, Martin-Magniette ML, Gilard F, Gakière B, Launay-Avon A, Delannoy E, Selosse MA. (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. doi.org/10.1002/bimj.201800309

  • Fearnhead P, Rigaill G. (2019) Changepoint Detection in the Presence of Outliers. J. American Statistical Association 114(525);169-183.  doi.org/10.1080/01621459.2017.1385466

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2018

  • 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. doi.org/10.18632/oncotarget.25187

  • Farjad M, Rigault M, Pateyron S, Martin-Magniette M-L, Krapp A, Meyer C, Fagard M. (2018) Nitrogen limitation alters the response of specific genes to biotic stress. Int. J. Mol. Sci. 19(11):3364. 

  • Albert E, Duboscq R, Latreille M, Santoni S, Beukers M, Bouchet JP, Bitton F, Gricourt J, Poncet C, Gautier V, Jiménez-Gómez JM, Rigaill G, Causse M. (2018) Allele-specific expression and genetic determinants of transcriptomic variations in response to mild water deficit in tomato. Plant J. 96(3):635-650.

  • Rogier O, Chateigner A, Amanzougarene S, Lesage-Descauses MC, Balzergue S, Brunaud V, Caius J, Soubigou-Taconnat L, Jorge V, Segura V. (2018) Accuracy of RNAseq based SNP discovery and genotyping in Populus nigra.  BMC Genomics 19(1):909

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

  • 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, 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 16(10).

  • 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. (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.

  • Lloyd A, Blary A, Charif D, Charpentier C, Tran J, Balzergue S, Delannoy E, Rigaill G, Jenczewski E. (2018) Homoeologous exchanges cause extensive dosage-dependent gene expression changes in an allopolyploid crop. New Phytologist 217(1):367-377.

  • Celisse A, Marot G, Pierre-Jean M, Rigaill G. (2018) New efficient algorithms for multiple change-point detection with reproducing kernels. Computational Statistics & Data Analysis 128:200-20. doi.org/10.1016/j.csda.2018.07.002

  • Malbert B, Rigaill G, Brunaud V, Lurin C, Delannoy E. (2018) Bioinformatic Analysis of Chloroplast Gene Expression and RNA Posttranscriptional  Maturations Using RNA Sequencing. Methods Mol. Biol. 1829:279-94.

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 2017

  • Canaguier A, Grimplet J, Di Gaspero G, Scalabrin S, Duchêne E, Choisne N, Mohellibi N, Guichard C, Rombauts S, Le Clainche I, Bérard A, Chauveau A, Bounon R, Rustenholz C, Morgante M, Le Paslier MC, Brunel D, Adam-Blondon AF. (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

  • Brandenburg JT, Mary-Huard T, Rigaill G, Hearne SJ, Corti H, Joets J, Vitte C, Charcosset A, Nicolas SD, Tenaillon MI. (2017) Independent introductions and admixtures have contributed to adaptation of european maize and its american counterparts. PLoS genetics 13(3):e1006666.

  • Guillaumot D, Lopez-Obando M, Baudry K, Avon A, Rigaill G, Falcon de Longevialle A, Broche B, Takenaka M, Berthomé R, De Jaeger G, Delannoy E, Lurin C. (2017) Two interacting PPR proteins are major Arabidopsis editing factors in plastid and mitochondria. Proc. Natl. Acad. Sci. USA. 114(33)8877-8882;

  • Maidstone R, Hocking T, Rigaill G, Fearnhead P. (2017) On optimal multiple changepoint algorithms for large data. Statistics and Computing 27(2):519-533.

  • Chiquet J, Gutierrez P, Rigaill G. (2017) Fast tree inference with weighted fusion penalties. Journal of Computationnal and Graphical Statistics 26(1):205-216.

  • Tamby JP, Brunaud V. (2017). FLAGdb++ : A Bioinformatic Environment to Study and Compare Plant Genomes. Methods Mol. Biol. 1533:79-101.

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2016

  • Kiefer H, Jouneau L, Campion E, 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. (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.

  • 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. (2016) Synthetic data sets for the identification of key ingredients for RNA-seq differential analysis. Brief. Bioinformatics 1-12.

  • Yesbergenova-Cuny Z, Dinant S, Martin-Magniette ML, 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.

  • Albert E, Gricourt J, Bertin N, Bonnefoi J, Pateyron S, Tamby JP, 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.

  • Damiani I, Drain A, Guichard M, Balzergue S, Boscari A, Boyer JC, 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 JM, Pauly N, Sentenac H. (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. .

  • Bueso E, Muñoz-Bertomeu J, Campos F, Martínez C, Tello C, Martínez-Almonacid I, Ballester P, Simón-Moya M, Brunaud V, Yenush L, Ferrándiz C, Serrano R. (2016) Arabidopsis COGWHEEL1 links light perception and gibberellins with seed tolerance to deterioration. The Plant Journal 2016

  • Roux F, Mary-Huard T, Barillot E, Wenes E, Botran L, Durand S, Villoutreix R, Martin-Magniette ML, Camilleri C, Budar F. (2016) Cytonuclear interactions affect adaptive traits of the annual plant Arabidopsis thaliana in the field. Proc. Natl. Acad. Sci. USA 113(13):3687-92.

  • Papastamoulis P, Martin-Magniette ML, 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.

  • 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.

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2015

  • 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.

  • 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. .

  • Martínez F, Arif A, Nebauer SG, 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.

  • 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.

  • 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.

  • 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.

 

2014

  • 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.

  • 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. (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.

  • Hocking TD, 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.

  • 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. (2014) Unexpectedly low nitrogen acquisition and absence of root architecture adaptation to nitrate supply in a Medicago truncatula highly branched root mutant. J Exp Bot. 65(9): 2365-80.

  • Celton JM, Gaillard S, Bruneau M, Pelletier S, Aubourg S, Martin-Magniette ML, Navarro L, Laurens F, Renou JP. (2014) Widespread anti-sense transcription in apple is correlated with siRNA production and indicates a large potential for transcriptional and/or post-transcriptional control. New Phytol. 203(1): 287-99.

  • 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. (2014) Salmonella enterica flagellin is recognized via FLS2 and activates PAMP-triggered immunity in Arabidopsis thaliana. Mol. Plant. 7(4): 657-74.

 

2013

  • Bueso E, Munoz-Bertomeu J, Campos F, Brunaud V, Martinez L, Sayas E, Ballester P, Yenush L, Serrano R. (2013) Arabidopsis thaliana HOMEOBOX 25 uncovers a role for gibberellins in seed longevity. Plant Physiol.164(2): 999-1010.

  • Houel C, Martin-Magniette M.-L., Nicolas S.D, LacombeT, Le Cunff L, Franck D, Torregrosa L, Conéjéro G, Lalet S, This P, Adam-Blondon AF. (2013) Genetic variability of berry size in the grapevine (Vitis vinifera L.). Australian Journal of Grape and Wine Research, 19 (2): 208–220.

  • Volant S, Bérard C, Martin-Magniette ML, Robin S. (2013) Hidden Markov Models with mixtures as emission distributions. Stat. Comput., 2013.

  • Rigaill G, Hocking T, Vert JP, Bach F. (2013) Learning Sparse Penalties for Change-point Detection using Max Margin Interval Regression. Proceedings of the 30 th International Conference on Machine Learning, Atlanta, Georgia, USA. Journal of Machine Learning Research W&CP volume 28.

  • Ronde JJ, Rigaill G, Rottenberg S, Rodenhuis S, Wessels LF. (2013) Identifying subgroup markers in heterogeneous populations. Nucleic Acids Res. 41(21): e200. (pas affilié URGV)

  • Vincent-Salomon A, Benhamo V, Gravier E, Rigaill G, Gruel N, Robin S, de Rycke Y, Mariani O, Pierron G, Gentien D, Reyal F, Cottu P, Fourquet A, Rouzier R, Sastre-Garau X, Delattre O. (2013) Genomic instability: a stronger prognostic marker than proliferation for early stage luminal breast carcinomas. PLoS One. 8(10): e76496. (pas affilié URGV)

 

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