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Recent articles

mar, 02/17/2009 - 22:05 — schbath

2010

  • Charbonnier, C., Chiquet, J. and Ambroise, C. (2010). Weighted-LASSO for Structured Network
    Inference from Time Course Data. Statistical Applications in Genetics and Molecular Biology. 9 article
    15. [DOI]

2009

  • Latouche, P., Birmele, E. and Ambroise, C. (2009). Bayesian methods for graph clustering. In Advances in Data Analysis, Data Handling and Business Intelligence. Springer.
  • Martin-Magniette, M.-L. and Taupin, M.-L. (2009). Semi-parametric estimation of the hazard function in a model with covariate measurement error. ESAIM Probability and Statistics. 13 87-114.
  • Schbath, S. and Robin, R. (2009).  How pattern statistics can be useful for DNA motif discovery? In Scan Statistics - Methods and Applications. (J. Glaz, I. Pozdnyakov, and S. Wallenstein, ed.), Statistics for Industry and Technology. Birkhauser.
  • Birmelé, E. (2009). A scale-free graph model based on bipartite graphs. Discrete Applied Mathematics. 157 2267-2284. [DOI]
  • Allman, E. S., Matias, C. and Rhodes, J. A. (2009). Identifiability of parameters in latent structure models with many observed variables. Annals of Statistics. 37 3099-3132. [DOI]
  • Maugis, C., Celeux, G. and Martin-Magniette, M. -L. (2009). Variable selection in model-based clustering: A general variable role modeling. Comput. Stat. Data Anal. 53 3872--3882. [DOI]
  • Schbath, S., Lacroix, V. and Sagot, M.-F. (2009). Assessing the exceptionality of coloured motifs in networks. EURASIP Journal on Bioinformatics and Systems Biology. [DOI]
  • Butucea, C. and Matias, C. and Pouet, C. (2009). Adaptive goodness-of-fit testing from indirect observations. Annales de l'Institut Henri Poincaré. 45 352-372. [DOI]
  • Maugis, C., Martin-Magniette, M. -L., Tamby, J. -P., Renou, J. -P., Lecharny, A., Aubourg, S. and Celeux, G. (2009). Sélection de variables pour la classification par mélanges gaussiens pour prédire la fonction des gènes orphelins. La revue de MODULAD. 40 69-80.
  • Guedj, M., Célisse, A., Robin, S. and Nuel, G. (2009). kerfdr: A semi-parametric kernel-based approach to local FDR estimations. BMC Bioinformatics. 10 [DOI].
  • Teixeira, V.H., Olaso, R., Martin-Magniette, M.-L., Lasbleiz, S., Jacq, L., Oliveira, C.R., Hilliquin, P., Gut, I., Cornelis, F. and Petit-Teixeira, E. (2009). Transcriptome Analysis Describing New Immunity and Defense Genes in Peripheral Blood Mononuclear Cells of Rheumatoid Arthritis Patients. PLoS ONE. 4 e6803. [DOI]
  • Lèbre, S. (2009). Inferring dynamic genetic networks with low order independencies. Statistical Applications in Genetics and Molecular Biology. 8 article 9 [url]
  • Bérard, C., Martin-Magniette, M. -L., To, A., Roudier, F., Colot, V. and Robin, S. (2009). Mélanges gaussiens bidimensionnels pour la comparaison de deux échantillons de chromatine immunoprécipitée. La revue de MODULAD. 40 53-68.
  • Chambaz, A. and Matias, C. (2009). Number of hidden states and memory: a joint order estimation problem for Markov chains with Markov regime. ESAIM Probab. & Stat. 13 38-50. [DOI]
  • Chiquet, J., Smith, A., Grasseau, G., Matias, C. and Ambroise, C. (2009). SIMoNe: Statistical Inference for MOdular NEtworks. Bioinformatics. 25 417--418. [DOI]
  • Elis, S., Blesbois, E., Couty, I., Balzergue, S., Martin-Magniette, M.-L. and Batellier, F. (2009). Identification of germinal disk region derived genes potentially involved in hen fertility. Mol. Reprod. Dev. 76 1043-1055.
  • Ambroise, C. and Chiquet, J. and Matias, C. (2009). Inferring sparse Gaussian graphical models with latent structure. Electronic Journal of Statistics. 3 205-238. [http] 

2008

  • Martin-Magniette, M.-L., Mary-Huard, T., Bérard, C. and Robin, S. (2008). ChIPmix: mixture model of regressions for two-color ChIP-chip analysis. Bioinformatics. 24 i181-186. [DOI]
  • Robin, S. and Stevanov, V. (2008). Simultaneous occurrences of runs in independent Markov chains. Methodology and Computing in Applied Probability. 11 267-275 [DOI]
  • Lebre, S. and Bourguignon, P.-Y. (2008). An EM algorithm for estimation in the Mixture Transition Distribution Model. Journal of Statistical Computation and Simulation. 78 713-729. [url]
  • Martin, J., Regad, L., Etchebest, C. and Camproux, A. (2008b). Taking advantage of local structure descriptors to analyze interresidue contacts in protein structures and protein complexes. Proteins. 73 672-689.
  • Mercier, R., Petit, M.-A., Schbath, S., Robin, S., El Karoui, M., Boccard, F. and Espeli, O. (2008). The MatP/matS site specific system organizes the Terminus region of the E. coli chromosome into a Macrodomain. Cell. 1-11. [ DOI ]
  • Butucea, C., Matias, C. and Pouet, C. (2008). Adaptivity in convolution models with partially known noise distribution. Electronic Journal of Statistics. 2 897-915.
  • Nicolas, P., Mondot, S., Achaz, G., Bouchenot, C., Bernardet, J.-F. and Duchaud, E. (2008). Population structure of the fish-pathogenic bacterium Flavobacterium psychrophilum. Appl. Environ. Microbiol. 74 3702-3709. [ DOI ]
  • Giraud, C. (2008). Estimation of Gaussian graphs by model selection. Electronic Journal of Statistics. 2 542-563.
  • Vergne, N. and Abadi, M. (2008). Poisson approximation for search of rare words in DNA sequences. ALEA. 4 223-244. [ .pdf ]
  • Vergne, N. (2008). Drifting Markov Models with Polynomial Drift and Applications to DNA Sequences. Statistical Applications in Genetics Molecular Biology. 7 1. [ http ]
  • Mary-Huard, T., Aubert, J., Mansouri-Attia, N., Sandra, O. and Daudin, J.-J. (2008). Statistical methodology for the analysis of dye-switch microarray experiments. BMC Bioinformatics. 9 98.
  • Martin, J., Regad, L., Lecornet, H. and Camproux, A.-C. (2008a). Structural deformation upon protein-protein interaction: a structural alphabet approach. BMC Structural Biology. 8 12.
  • Miele, V., Vaillant, C., D'Aubenton, Y., Thermes, C. and Grange, T. (2008). Dna physical properties determine nucleosome occupancy from yeast to fly. Nucleic Acids Research. 36 3746-3756.
  • Zanghi, H., Ambroise, C. and Miele, V. (2008). Fast online graph clustering via erdös-rényi mixture. Pattern Recognition. 3592-3599.
  • Nuel, G. (2008b). Pattern markov chains: optimal Markov chain embedding through deterministic finite automata. J. App. Proba. 226-243.
  • Nuel, G. (2008a). Cumulative distribution function of a geometric poisson distribution. J. Stat. Comp. and Sim. 385-394.
  • Rodolphe, F., Martin, J. and Della-Chiesa, E. (2008). Theoretical description of chromosome architecture after multiple back-crossing. Theoretical Population Biology. 289-299.
  • Aguileta, G., Marthey, S., Chiapello, H., Lebrun, M.-H., Rodolphe, F., Fournier, E., Gendrault-Jacquemard, A. and Giraud, T. (2008). Assessing the performance of single-copy genes for recovering robust phylogenies. Systematic Biology. 613-627. [ DOI ]
  • Daudin, J. and Mary-Huard, T. (2008). Estimation of the conditional risk in classification : The swapping method. Comp. Stat. Data Anal. 3220-3232. [ DOI ]
  • Celisse, A. and Robin, S. (2008). Nonparametric density estimation by explicit leave-p-out cross-validation. Comput. Statist. Data Analysis. 2350-68.
  • Picard, F., Daudin, J.-J. and Robin, S. (2008b). A mixture model for random graphs. Stat. Comput. 173-183.
  • Touzain, F., Schbath, S., Debled-Rennesson, I., Aigle, B., Leblond, P. and Kucherov, G. (2008). SIGffRid: a tool to search for σ factor binding sites in bacterial genomes using comparative approach and biologically driven statistics. BMC Bioinformatics. 9:73 1-23. [ http ]
  • Picard, F., Daudin, J.-J., Koskas, M., Schbath, S. and Robin, S. (2008a). Assessing the exceptionality of network motifs. J. Comp. Biol. 15:1 1-20. [ http ]
  • Touyar, N., Schbath, S., Cellier, D. and Dauchel, H. (2008). Poisson approximation for the number of repeats in a Markov chain model. J. Appl. Prob. 45 440-455.
  • Guedj, M., Nuel, G. and Prum, B. (2008). A note on allelic tests in case-control association studies. Annals of Human Genetics. 407-409.
  • Elis, Sebastien and Batellier, Florence and Couty, Isabelle and Balzergue, Sandrine and Martin-Magniette, Marie-Laure and Monget, Philippe and Blesbois, Elisabeth and Govoroun, Marina. (2008). Search for the genes involved in oocyte maturation and early embryo development in the hen. BMC Genomics. 9 1471-2164. [DOI]
  • Martin-Magniette, Marie-Laure and Aubert, Julie and Bar-Hen, Avner and Elftieh, Samira and Magniette, Frederic and Renou, Jean-Pierre and Daudin, Jean-Jacques. (2008). Normalization for triple-target microarray experiments. BMC Bioinformatics. 9 1471-2105. [DOI]
  • Navajas, M and Migeon, A and Alaux, C and Martin-Magniette, ML and Robinson, GE and Evans, JD and Cros-Arteil, S and Crauser, D and Le Conte, Y. (2008). Differential gene expression of the honey bee Apis mellifera associated with Varroa destructor infection. BMC Genomics. 9 1471-2164. [DOI]
  • Cossegal, Magalie and Chambrier, Pierre and Mbelo, Sylvie and Balzergue, Sandrine and Martin-Magniette, Marie-Laure and Moing, Annick and Deborde, Catherine and Guyon, Virginie and Perez, Pascual and Rogowsky, Peter. (2008). Transcriptional and Metabolic Adjustments in ADP-Glucose Pyrophosphorylase-Deficient bt2 Maize Kernels. Plant Physiol. 146 1553-1570. [DOI]
  • Ruffel, Sandrine and Freixes, Sandra and Balzergue, Sandrine and Tillard, Pascal and Jeudy, Christian and Martin-Magniette, Marie Laure and van der Merwe, Margaretha J. and Kakar, Klementina and Gouzy, Jerome and Fernie, Alisdair R. and Udvardi, Michael and Salon, Christophe and Gojon, Alain and Lepetit, Marc. (2008). Systemic Signaling of the Plant Nitrogen Status Triggers Specific Transcriptome Responses Depending on the Nitrogen Source in Medicago truncatula. Plant Physiol. 146 2020-2035. [DOI]
  • Gagnot, Séverine and tamby, Jean-Philippe and Martin-Magniette, Marie-Laure and Bitton, Frédérique and Taconnat, Ludivine and Balzergue, Sandrine and Aubourg, Sébastien and Renou, Jean-Pierre and Lecharny Alain and Brunaud Véronique. (2008). CATdb: a public access to Arabidopsis transcriptome data from the URGV-CATMA platform. Nucleic Acids Research. 36 D986-D990.
  • BENHAMED, M and MARTIN-MAGNIETTE, ML and TACONNAT, L and BITTON, F and SERVET, C and De Clercq, Rebecca and De Meyer, Bj\"o{}rn and Buysschaert, Caroline and Rombauts, Stephane and Villarroel-Mandiola, Raimundo and AUBOURG, S and BEYNON, J and BHALERAO, RP and COUPLAND, G and GRUISSEM, W and MENKE, FLH and WEISSHAAR, B and RENOU, JP and ZHOU, DX and Hilson, Pierre. (2008). Genome-scale Arabidopsis promoter array identifies targets of the histone acetyltransferase GCN5. PLANT JOURNAL. 56 493--504.