Articles from 2009 to 2012

2012

Guergnon, J. and Dalmasso, C. and Broet, P. and Meyer, L. and Westrop, S.J. and Imami, N. and Vicenzi, E. and Morsica, G. and Tinelli, M. and Poma, B.Z. and Goujard, C. and Potard, V. and Gotch, F.M. and Casoli, C. and Cossarizza, A. and others (2012). Single Nucleotide Polymorphism-defined Class-I and Class-III MHC genetic subregions contribute to natural long-term non progression in HIV infection. Journal of Infectious Diseases Vol. 205 No. 5 pp. 718-24

Chiquet, J. and Grandvalet, Y. and Charbonnier, C. (2012). Sparsity with sign-coherent groups of variables via the cooperative-Lasso. The Annals of Applied Statistics Vol. 6 No. 2 pp. 795-830

Acuna, V. and Birmelé, E. and Cottret, L. and Crescenzi, P. and Jourdan, F. and Lacroix, V. and Marchetti-Spaccamela, A. and Marino, A. and Vieira Milreu, P. and Sagot, M.-F. and Stougie, L. (2012). Telling Stories: Enumerating maximal directed acyclic graphs with a constrained set of sources and targets. Theoretical Computer Science Vol. 457 No. 2 pp. 1-9

Didier, G. and Corel, E. and Laprevotte, I. and Grossmann, A. and Devauchelle, C. (2012). Variable length local decoding and alignment-free sequence comparison. Theoretical Computer Science Vol. 00 [DOI]

Ortiz-Estevez, M. and Aramburu, A. and Bengtsson, H. and Neuvial, P. and Rubio, A. (2012). CalMaTe: A Method and Software to Improve Allele-Specific Copy Number of SNP Arrays for Downstream Segmentation. Bioinformatics Vol. 28 No. 13 pp. 1793-1794 [url]

Birmelé, E. (2012). Detecting local network motifs. Electronic Journal of Statistics Vol. 6 pp. 908-933 [url]

Chambaz, A. and Neuvial, P. and van der Laan, M.J. (2012). Estimation of a non-parametric variable importance measure of a continuous exposure.  Electronic Journal of Statistics Vol. 6 pp. 1059-1099 [url]

Jacob, L. and Neuvial, P. and Dudoit, S. (2012). More Power via Graph-Structured Tests for Differential Expression of Gene Networks. Annals of Applied Statistics Vol. 6 No. 2 pp. 561--600 [url]

Bouaziz, M. and Jeanmougin, M. and Guedj, M. (2012). Multiple testing in large-scale genetic studies. Methods Mol Biol. Vol. 888 pp. 213--233 [DOI]

Nicolas, P., Mäder, U., Dervyn,E. et al.(2012). Condition-Dependent Transcriptome Reveals High-Level Regulatory Architecture in Bacillus subtilis. Science vol. 335 no. 6072 pp.1103-1106 [DOI].

Buescher, J.M., Liebermeister, W., ...., Nicolas, P.et al (2012). Global Network Reorganization During Dynamic Adaptations of Bacillus subtilis Metabolism. Science Vol. 335 no. 6072 pp.1099-1103 [DOI].

Fayyaz, A., Launay, G., Schbath, S., Gibrat, J.-F. and Rodolphe, F. (2012) Statistical Significance of Threading Scores. Journal of Computational Biology 19 13-29 [DOI].

Devillers, H. and Schbath, S. (2012) Separating Significant Matches from Spurious Matches in DNA Sequences. Journal of Computational Biology 19 1-12 [DOI].

Arribas-Gil, A. and Matias, C. (2012) A context dependent pair hidden Markov model for statistical alignment. Statistical applications in genetics and molecular biology 11 (1) Article 5 [url].

Dalmasso, M., Aubert, J., Briard-Bion, V., Chuat, V., Deutsch, S.-M., & Even, S., et al. (2012). A temporal -omic study of Propionibacterium freudenreichii CIRM-BIA1T adaptation strategies in conditions mimicking cheese ripening in the cold. PLoS ONE.

Ambroise, C. and Matias, C. (2012) New consistent and asymptotically normal parameter estimates for random-graph mixture models. Journal of the Royal Statistical Society: Series B. 74, Part 1, 3–35 [url]

Latouche, P. and Birmelé, E. and Ambroise, C. (2012).  Variational Bayesian Inference and Complexity Control for Stochastic Block Models. Statistical Modelling 12(1) 93-115 [url]

2011

Vernoux, T, Brunoud, G, Farcot, E, Morin, V, Van den Daele, H, Legrand, J, Oliva, M, Das, P, Larrieu, A, Wells, D, Guédon, Y, Armitage, L, Picard, F, Guyomarc'h, S, Cellier, C, Parry, G, Koumproglou, R, Doonan, JH, Estelle, M, Godin, C, Kepinski, S, Bennett, M, De Veylder, L, Traas, J (2011). The auxin signalling network translates dynamic input into robust patterning at the shoot apex. Mol. Syst. Biol. 7:508.

Bernardi, D., Cérin, C., Fkaier, H., Jemni, M., & Koskas, M. (2011) Geometrical Interpretation for Data Partitioning on a Grid Architecture. IEEE Press, ISBN 1-4244-0307-3, 355-356.

Cérin, C. and Koskas, M. (2011) Work Stealing Technique and Scheduling on the Critical Path. Third International Computing of Grid and Pervasive Computing.

Li-Thiao-Té, S., Daudin, J.-J., & Robin, S. (2011). Bayesian model averaging for estimating the number of classes. Applications to the total number of species in metagenomics. J. Applied Statis.

Forquin, M., Hébert, A., Roux, A., Aubert, J., Proux, C., & Heilier, J., et al. (2011). Global regulation in response to sulfur availability in the cheese-related bacterium, Brevibacterium aurantiacum. Applied and Environmental Microbiology.

Daudin, J.-J. (2011). A review of statistical models for clustering networks with an application to a PPI network. Journal de la Société Française de Statistique, 152(2), 111-125.

Faivre Rampant, P., Lesur, I., Boussardon, C., Bitton, F., Martin-Magniette, M.-L., & Bodenes, C., et al. (2011). Analysis of BAC end sequences in oak, a keystone forest tree species, providing insight into the composition of its genome. BMC Genomics, 12(1), 292.

Celeux, G., Martin-Magniette, M.-L., Maugis, C., & Raftery, A. E. (2011). Witten, D. M., and Tibshirani, R. (2010), ``A Framework for Feature Selection in Clustering, Journal of the American Statistical Association, 106(493), 383.

Abdelkarim, M., Vintonenko, N., Starzec, A., Robles, A., Aubert, J., & Martin, M.-L., et al. (2011). Invading Basement Membrane Matrix Is Sufficient for MDA-MB-231 Breast Cancer Cells to Develop a Stable In Vivo Metastatic Phenotype. PLoS ONE, 6(8), 23334

Dubois, A., Remay, A., Raymond, O., Balzergue, S., Chauvet, A., & Maene, M., et al. (2011). Genomic Approach to Study Floral Development Genes in Rosa sp. PLoS ONE, 6(12), 28455.

Lédée, N., Munaut, C., Aubert, J., Sérazin, V., Rahmati, M., & Chaouat, G., et al. (2011). Specific and extensive endometrial deregulation is present before conception in IVF/ICSI repeated implantation failures (IF) or recurrent miscarriages. The Journal of Pathology.

Hébert, A., Forquin-Gomez, M.-P., Roux, A., Aubert, J., Junot, C., & Loux, V., et al. (2011). Exploration of sulfur metabolism in the yeast Kluyveromyces lactis. Applied Microbiology and Biotechnology, 91, 1409-1423. [DOI].

Jeanmougin, M. and Guedj, M. and Ambroise, C. (2011) Defining a robust biological prior from Pathway Analysis to drive Network Inference. Journal de la SFdS 152(2) [url].

Bouaziz, M. and Ambroise, C. and Guedj, M. (2011) Accounting for Population Stratification in Practice: a Comparison of the Main Strategies Dedicated to Genome-Wide Association Studies. PLOS one 6(12) e28845 [url].

Bérard, C., Martin-Magniette, M.-L., Brunaud, V., Aubourg, S. and Robin, S. (2011) Unsupervised Classification for Tiling Arrays: ChIP-chip and Transcriptome. Statistical Applications in Genetics and Molecular Biology 10 [url].

Olshen, A.B. and Bengtsson, H. and Neuvial, P. and Spellman, P.T. and Olshen, R.A. and Seshan, V.E. (2011) Parent-specific copy number in paired tumor-normal studies using circular binary segmentation. Bioinformatics 27 (15):2038-2046 [url]

Moghaddam, A.M.B. and Roudier, F. and Seifert, M. and Bérard, C. and Martin-Magniette, M.L. and Ashtiyani, R.K. and Houben, A. and Colot, V. and Mette, M.F. (2011) Additive inheritance of histone modifications in Arabidopsis thaliana intra-specific hybrids. The Plant Journal.

Chaouat, G. and Rodde, N. and Petitbarat, M. and Bulla, R. and Rahmati, M. and Dubanchet, S. and Zourbas, S. and Bataillon, I. and Coqué, N. and Hennuy, B. and Martal, J. and Munaut, C. and Aubert, J. and Sérazin, V. and Steffen, T. and Jensenius, JC. and Foidart, JM. and Sandra, O. and Tedesco, F. and Lédée, N. (2011) An insight into normal and pathological pregnancies using large-scale microarrays: lessons from microarray. Journal of Reproductive Immunology. [DOI]

Maugis, C. and Celeux, G. and Martin-Magniette, M.-L. (2011) Variable selection in model-based discriminant analysis. Journal of Multivariate Analysis. [DOI]

Roudier, F. and Ahmed, I. and Bérard, C. and Sarazin, A. and Mary-Huard, T. and al. (2011) Integrative epigenomic mapping defines four main chromatin states in Arabidopsis. The EMBO Journal. 30, 1928-1938. [DOI]

Wurmser, F. and Ogereau, D. and Mary-Huard, T. and Loriod, B. and Joly, D. and Montchamp-Moreau, C. (2011) Population transcriptomics: insights from Drosophila simulans, Drosophila sechellia and their hybrids. Genetica.

Stefanov, V.T. and Robin, S. and Schbath, S. (2011) Occurrence of structured motifs in random sequences: Arbitrary number of boxes. Discr. Appli. Math.

Rigaill, R. and Lebarbier, E. and Robin, S. (2011) Exact posterior distributions and model selection criteria for multiple change-point detection problems. Stat. comput.

Picard, F. and Lebarbier, E. and Hoebecke, M. and Thiam, B. and Robin, S. (2011) Joint segmentation, calling and normalization of multiple CGH profiles. Biostatistics.

Picard, F. and Lebarbier, E. and Budinska, E. and Robin, S. (2011) Joint segmentation of multivariate Gaussian processes using mixed linear models. CSDA. 55(2): 1160-1170.

Gazal, S. and Daudin, J.-J. and Robin, S. (2011) Accuracy of variational estimates for random graph mixture models. J. Comput. Comput. Simul.

Brlek, S. and Koskas, M. and Provençal, X. (2011) A linear time and space algorithm for detecting path intersection. Theoretical Computer Science.

Latouche, P. and Birmele, E. and Ambroise, C. (2011) Overlapping Stochastic Block Models with Application to the French Political Blogosphere. Annals of Applied Statistics. 5(1), 309-336.

Allman, E.S. and Matias, C. and Rhodes, J.A. (2011) Parameter identifiability in a class of random graph mixture models. Journal of Statistical Planning and Inference. 141(5), 1719-1736. [DOI]

Dalmasso, C. and Broët, P. (2011) Detection of chromosomal abnormalities using high resolution arrays in clinical cancer research. Journal of Biomedical Informatics. [DOI]

Broet, P. and Dalmasso, C. and Tan, E.H. and Alifano, M. and Zhang, S.L. and Wu, J. and Lee, M.H. and Regnard, J.F. and Lim, W.T. and Koong, H.N. and Agasthian, T. and Miller, L. and Camilleri-Broet, S. and Tan, P. (2011). Genomic Profiles Specific to Patient Ethnicity in Lung Adenocarcinoma. Clinical Cancer Research, 17(11), 3542-50

Chiquet, J., Grandvalet, Y. and Ambroise, C. (2010) Inferring multiple graphical structures, Statistics and Computing. 21(4), 537-553. [http]

Schbath, S. and Hoebeke, M. (2011). R'MES: a tool to find motifs with a significantly unexpected frequency in biological sequences. In  Advances in genomic sequence analysis and pattern discovery (L. Elnitski, O. Piontkivska, and L. Welch, eds.). Science, Engineering, and Biology Informatics, vol. 7. World Scientific. [http]

2010

Chadi, S. and Young, R.l and Le Guillou, S. and Tilly, G. and Bitton, F. and Martin-Magniette, M.-L. and Soubigou-Taconnat, L. and Balzergue, S. and Vilotte, M. and Peyre, C. and Passet, B. and Beringue, V. and Renou, J.-P. and Le Provost, F. and Laude, H. and Vilotte, J.-L. (2010) Brain transcriptional stability upon prion protein-encoding gene invalidation in zygotic or adult mouse. BMC Genomics. 11(1), 448. [DOI]

Cohen, D. and Bogeat Triboulot, M.B. and Tisserant, E. and Balzergue, S. and Martin Magniette, M.-L. and Lelandais, G. and Ningre, N. and Renou, J.-P. and Tamby, J.-P. and Le Thiec, D. and Hummel, I. (2010) Comparative transcriptomics of drought responses in Populus: a meta-analysis of genome-wide expression profiling in mature leaves and root apices across two genotypes. BMC Genomics. [DOI]

Pitschi, F. and Devauchelle, C. and Corel, E. (2010) Automatic detection of anchor points for multiple sequence alignment. BMC Bioinformatics. 11, 445. [DOI]

Corel, E. and Pitschi, F. and Laprevotte, I. and Grasseau, G. and Didier, G. and Devauchelle, C. (2010) MS4 - Multi-Scale Selector of Sequence Signatures: An alignment-free method for classification of biological sequences. BMC Bioinformatics. 11, 406. [DOI]

Jeanmougin, M. and de Reynies, A. and Marisa, L. and Paccard, C. and Nuel, G. and Guedj, M. (2010). Should We Abandon the t-Test in the Analysis of Gene Expression Microarray Data: A Comparison of Variance Modeling Strategies. PLoS ONE 5(9), e12336. [DOI]

Zanghi, H. and Picard, F. and Miele, V. and Ambroise, C. (2010) Strategies for Online Inference of Network Mixture. Annals of Applied Statistics. 4(2), 687-714.

Célisse, A. and Robin, S. (2010). A cross-validation based estimation of the proportion of true null hypotheses. J. Statist. Planing Infer., 140, 3132-47.

Devillers, H., Chiapello, H., Schbath, S. and El Karoui, M. (2010). Assessing the robustness of complete bacterial genome segmentations. In RECOMB-CG 2010, (E. Tannier, ed.). Lecture Notes in Bioinformatics. 6398 173-187.

Mariadassou, M., Robin, S., and Vacher, C. (2010). Uncovering structure in valued graphs: a variational approach. Ann. Appl. Statist., 4(2), 715-42.

Daudin, J. J., Pierre, L., and Vacher, C. (2010). Model for Heterogeneous Random Networks Using Continuous Latent Variables and an Application to a Tree–Fungus Network. Biometrics. [DOI]

Forquin, MP. and Hébert, A. and Roux, A. and Aubert, J. and Proux, C. and Heilier, JF. and Landaud, S. and Junot, C. and Bonnarme, P. and Martin-Verstraete, I. (2010). Global regulation in response to sulfur availability in the cheese-related bacterium, Brevibacterium aurantiacum. Applied and Environmental Microbiology. [DOI]

Vacher, C. and Daudin, J.J. and Piou, D. and  Desprez-Loustau, M.L. (2010) Ecological integration of alien species into a tree-parasitic fungus network. Biological Invasions. 12(9). 3249-3259. [http]

Reynaud-Bouret, P. and Schbath, S. (2010). Adaptive estimation for Hawkes' processes; Application to genome analysis. Annals of Statistics. 38 (5) 2781-2822. [ DOI ]

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]

Aguileta, G., Lengelle, J., Marthey, S., Chiapello, H., Rodolphe, F., Gendrault, A., Yockteng, R., Vercken, E., Devier, B., Wincker, P., Dossat, C., Cruaud, C., Couloux, A. and Giraud, T. (2010). Genes under positive selection in non-model species: Examples of genes involved in host specialization in pathogens. Molecular Ecology. 19 (2) 292-306.

Zanghi, H., Volant, S. and Ambroise, C. (2010). Clustering based on random graph model embedding vertex features.Pattern Recognition Letters. 31(9)  830-83.  

2009

Grelaud,A., Robert,C. P., Marin,J.-M., Rodolphe,F., Taly,J.-F.  (2009). ABC likelihood-free methods for model choice in Gibbs random fields. Bayesian Analysis. 4 317—336.

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.

Mary-Huard, T. and Robin, S. (2009). Tailored Aggregation for Classification. IEEE Trans. Pattern Anal. and Machine Intel. 21(8).

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, eds.), 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.

Maugis, C. and Celeux, G. and Martin-Magniette, M.-L. (2009). Variable Selection for Clustering with Gaussian Mixture Models. Biometrics. 65. 701-709.

Nicolas, P.  and Leduc, A.  and Robin, S.  and Rasmussen, S.  and Jarmer, H.  and Bessieres, P. (2009). Transcriptional landscape estimation from tiling array data using a model of signal shift and drift. Bioinformatics. 25. 2341-2347.

Picard, F. and Miele, V. and Daudin, J.-J. and Cottret, L. and Robin, S. (2009). Deciphering the connectivity structure of biological networks using MixNet. BMC Bioinformatics. [http]

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]

S. Robin and V. T. Stefanov (2009). Simultaneous Occurrences of Runs in Independent Markov Chains. Methodology and Computing in Applied Probability. 11(2). 267-275.

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.

Teixeira, V. H. and Olaso, R. and Martin-Magniette, M.-L. andLasbleiz, S. and Jacq, L. and Oliveira, C. R. and Hilliquin, P. and Gut, I. and 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. 8(4). [DOI]

Mansouri-Attia, N. and Aubert, J. and Reinaud, P. and Giraud-Delville, C. and Taghouti, G. and Galio, L. and Everts, R.E. and Degrelle, S. and Richard, C. and Hue, I. and Yang, X. and Tian, X.C. and Lewin, H.A. and Renard, J.-P. and
Sandra, O. (2009). Gene expression profiles of bovine caruncular and intercaruncular endometrium
at implantation. Physiological Genomics. 39(1). 14-27. [http]

Mansouri-Attia, N. and Sandra, O. and  Aubert, J. and Degrelle, S. and Everts, R.E. and Giraud-Delville, C. and Heyman, Y. and  Galio, L. and Hue, I. and Yang, X. and Tian, X.C. and Lewin, H. A. and Renard, J.-P. (2009). Endometrium as an early sensor of in vitro embryo manipulation technologies. PNAS. [DOI]

Faucon, F. and Rebours, E. and Bevilacqua, C. and Helbling, J.-C. and Aubert, J. and Makhzami, S. and Dhorne-Pollet, S. and Robin,S. and Martin, P. (2009). Terminal differentiation of goat mammary tissue during pregnancy requires the expression of genes involved in immune functions. Physiological Genomics. 40. 61-82. [http]

Elis, S. and Blesbois, E. and Couty, I. and Balzergue, S. and Martin-Magniette, M.-L. and Batellier, F. (2009). Identification of germinal disk region derived genes potentially involved in hen fertility. Mol. Reprod. Dev. 76(11)

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]