Genopole Evry


Accueil > Recherche > Interactions Biotiques > Equipe ML Martin-Magniette


Réseaux Génomiques

Publications 2017

- 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). Genomics Data, 14:56-62

- Damien Guillaumot, Mauricio Lopez-Obando, Kevin Baudry, Alexandra Avon, Guillem Rigaill, Andéol Falcon de Longevialle, Benjamin Broche, Mizuki Takenaka, Richard Berthomé, Geert De Jaeger, Etienne Delannoy, and Claire Lurin (2017) Two interacting PPR proteins are major Arabidopsis editing factors in plastid and mitochondria. Proc Natl Acad Sci U S A. 114 (33) 8877-8882 ; doi:10.1073/pnas.1705780114

- Paul Fearnhead, Guillem 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 in Molecular Biology 1533:79-101. doi:10.1007/978-1-4939-6658-5_4.


Publications 2016

- 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 Bioinform. 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 U S A. 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.


Publications 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. 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.


Publications 2014

- Rigaill G, Miele V, and 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 Genomics15:629. 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.

- 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. doi : 10.1093/jxb/eru124.

- 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. doi : 10.1111/nph.12787.

- 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. doi : 10.1093/mp/sst145.


Publications 2013

- Bueso E, Munoz-Bertomeu J, Campos F, Brunaud V, Martinez L, Sayas E, Ballester P, Yenush L, and Serrano R (2013). ARABIDOPSIS THALIANA HOMEOBOX 25 uncovers a role for gibberellins in seed longevity Plant Physiol.164(2):999-1010. doi : 10.1104/pp.113.232223.

- 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 A-F. (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 M.-L., and Robin S. (2013). "Hidden Markov Models with mixtures as emission distributions," Stat. Comput., 2013.

- Rigaill G, Hocking T, Vert J-P, and Francis 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. doi : 10.1093/nar/gkt845. (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. doi : 10.1371/journal.pone.0076496. (pas affilié urgv)