Preprint

  1. Facon B, Hafsi A, Masselière MC de la, Robin S, Massol F, Dubart M, Chiquet J, Frago E, et al.: Joint species distributions reveal the combined effects of host plants, abiotic factors and species competition as drivers of species abundances in fruit flies bioRxiv, 2021
    url
  2. Brault C, Doligez A, LE CUNFF L, COUPEL-LEDRU A, Simonneau T, Chiquet J, This P, Flutre T, et al.: Harnessing multivariate, penalized regression methods for genomic prediction and QTL detection to cope with climate change affecting grapevine, 2021
    url
  3. Lejal E, Chiquet J, Aubert J, Robin S, Estrada-Peña A, Rue O, Midoux C, Mariadassou M, et al.: Temporal patterns in Ixodes ricinus microbial communities: an insight into tick-borne microbe interactions bioRxiv, 2020
    url
  4. Pauvert C, Fort T, Calonnec A, Faivre-d’Arcier J, Chancerel E, Massot M, Chiquet J, Robin S, et al.: Microbial association networks give relevant insights into plant pathobiomes bioRxiv, 2020
    url
  5. Sundqvist M, Chiquet J, Rigaill G: Adjusting the adjusted Rand Index - A multinomial story preprint, 2020
    arXiv url code
  6. Chiquet J, Mariadassou M, Robin S: The Poisson-lognormal model as a versatile framework for the joint analysis of species abundances bioRxiv, 2020
    url
  7. Barbillon P, Chiquet J, Tabouy T: missSBM: An R Package for Handling Missing Values in the Stochastic Block Model preprint, 2019
    arXiv url code

Journal papers

  1. Champion M, Chiquet J, Neuvial P, Elati M, Radvanyi F, Birmelé E: Identification of deregulation mechanisms specific to cancer subtypes Journal of Bioinformatics and Computational Biology 19: 2140003, 2021

    PMID: 33653235

    HAL url
  2. Guinot F, Szafranski M, Chiquet J, Zancarini A, Le Signor C, Mougel C, Ambroise C: Fast Computation of Genome-Metagenome interaction effects Algorithms for Molecular Biology, 2020
    arXiv HAL url code
  3. Huot A, Chiquet J, Jaffrezic F, Rigaill G: Fast tree aggregation for consensus hierarchical clustering BMC Bioinformatics, 2020
    url code
  4. Grandclaudon M, Perrot-Dockès M, Trichot C, Mostafa-Abouzid O, Abou-Jaoudé W, Berger F, Hupé P, Thieffry D, et al.: A Quantitative Multivariate Model of Human Dendritic Cell-T Helper Cell Communication Cell, 2019
    url
  5. Chiquet J, Robin S, Mariadassou M: Variational Inference for sparse network reconstruction from count data, in: Chaudhuri K, Salakhutdinov R (eds) Proceedings of the 36th International Conference on Machine Learning.Vol 97. Proceedings of Machine Learning Research. Long Beach, California, USA: PMLR, 2019, pp. 1162–1171.
    url code
  6. Tabouy T, Barbillon P, Chiquet J: Variational Inference for Stochastic Block Models from Sampled Data Journal of the American Statistical Association 0: 1–20, 2019
    arXiv url code
  7. Chiquet J, Mariadassou M, Robin S: Variational inference for probabilistic Poisson PCA Ann Appl Statist 12: 2674–2698, 2018
    arXiv url code
  8. Perrot M, Lévy-Leduc C, Chiquet J, Sansonnet L, Brégère M, Étienne M-P, Robin S, Genta-Gouve G, et al.: A multivariate variable selection approach for analyzing LC-MS metabolomics data SAGMB, 2018
    arXiv url code
  9. Perrot M, Lévy-Leduc C, Sansonnet L, Chiquet J: Variable selection in multivariate linear models with high-dimensional covariance matrix estimation J Multivar Anal 166: 78–97, 2018
    arXiv url code
  10. Grandvalet Y, Chiquet J, Ambroise C: Sparsity by Worst-Case Penalties arXiv preprint, 2017
    arXiv code
  11. Brault V, Chiquet J, Lévy-Leduc C: Efficient block boundaries estimation in block-wise constant matrices: An application to HiC data Electron J Statist 11: 1570–1599, 2017
    arXiv code
  12. Chiquet J, Gutierrez P, Rigaill G: Fast tree inference with weighted fusion penalties Journal of Computational and Graphical Statistics: 205–216, 2017
    arXiv url code
  13. Chiquet J, Grandvalet Y, Rigaill G: Categorical regularization: Discussion of article by Tutz and Gertheiss Statistical Modelling: 228–237, 2016
    HAL url
  14. Chiquet J, Mary-Huard T, Robin S: Structured Regularization for conditional Gaussian Graphical Models Statistics and Computing: 789–804, 2016
    arXiv url code
  15. Vacher C, Tamaddoni-Nezhad A, Kamenova S, Peyrard N, Moalic Y, Sabbadin R, Schwaller Loı̈c, Chiquet J, et al.: Learning ecological networks from next-generation sequencing data, in: Advances in Ecological Research.Vol 54. Elsevier, 2016, pp. 1–39.
  16. Latouche P, Mattei P-A, Bouveyron C, Chiquet J: Combining a Relaxed EM Algorithm with Occam’s Razor for Bayesian Variable Selection in High-Dimensional Regression Journal of Multivariate Analysis: 177–190, 2016
    HAL url code
  17. Picchetti T, Chiquet J, Elati M, Neuvial P, Nicolle R, Birmelé E: A model for gene deregulation detection using expression data BMC Systems Biology, 2015
    HAL url
  18. Chaloub B, Denoeud F, Liu S, Parkin S, Tang H, X. W, Chiquet J, 76 more, et al.: Early allopolyploid evolution in the post-neolithic Brassica napus oilseed genome Science: 950–953, 2014
    url
  19. Chelaifa H, Chagué V, Chalabi S, Mestiri I, Arnaud D, Deffains D, Lu Y, Belcram H, et al.: Prevalence of gene expression additivity in genetically stable wheat allohexaploids New Phytologist 197: 730–736, 2013
    url
  20. Chiquet J, Grandvalet Y, Charbonnier C: Sparsity in sign-coherent groups of variables via the cooperative-Lasso The Annals of Applied Statistics 6: 795–830, 2012
    arXiv url slides
  21. Chiquet J, Grandvalet Y, Ambroise C: Inferring multiple graphical models Statistics and Computing 21: 537–553, 2011
    arXiv url slides code
  22. Charbonnier C, Chiquet J, Ambroise C: Weighted-Lasso for structured network inference from time course data Statistical Applications in Genomics and Molecular Biology 9, 2010
    arXiv url slides code
  23. Ambroise C, Chiquet J, Matias C: Inferring sparse Gaussian graphical models with latent structure Electronic Journal of Statistics 3: 205–238, 2009
    arXiv url slides code
  24. Chiquet J, Smith A, Grasseau G, Matias C, Ambroise C: SIMoNe: Statistical Inference for MOdular NEtworks Bioinformatics 25: 417–418, 2009
    url code
  25. Chiquet J, Limnios N, Eid M: Piecewise deterministic Markov processes applied to fatigue crack growth modelling Journal of Statistical Planning and Inference 139: 1657–1667, 2009
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  26. Chiquet J, Limnios N: A method to compute the transition function of a piecewise deterministic Markov process Statistics and Probability Letters 78: 1397–1403, 2008
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  27. Chiquet J, Limnios N, Eid M: Modelling and Estimating Stochastic Dynamical Systems with Markovian Switching Reliability Engineering and System Safety 93: 1801–1808, 2008
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  28. Chiquet J, Limnios N: Estimating stochastic dynamical systems driven by a continuous-time jump Markov process Methodology and Computing in Applied Probability 8: 431–447, 2006
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Book chapter

  1. Chiquet J, Rigaill R, Sundqvist M: A Multiattribute Gaussian Graphical Model for Inferring Multiscale Regulatory Networks: An Application in Breast Cancer, in: Sanguinetti G, Huynh-Thu VA (eds) Gene Regulatory Networks: Methods and Protocols. Springer New York, 2019, pp. 143–160.
    url code
  2. Jeanmoungin M, Charbonnier C, Guedj M, Chiquet J: Probabilistic graphical models dedicated to applications in genetics, genomics and postgenomics, in: 2014.
    url
  3. Chiquet J, Limnios N: Stochastic Reliability and Maintenance Modeling, in: Vol 9. Springer Series in Reliability Engineering. Springer, 2013.
    url
  4. Chiquet J, Limnios N: Mathematical methods in survival analysis, reliability and quality of life, in: Wiley/ISTE, 2008.
    url
  1. Chiquet J: Statistique et génome: réseaux biologiques La gazette des mathématiciens 130: 76–82, 2011
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Thesis

  1. Chiquet J: Contributions to sparse methods for complex data analysis, 2015
    url
  2. Chiquet J: Modélisation et estimation des processus de dégradation avec application en fiabilité des structures, 2007
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  3. Chiquet J: Estimation des températures journalières à l’aide de techniques markoviennes, 2003
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