Publications

Preprint

Ambroise C, Chiquet J, Guinot F, Szafranski M: Fast Computation of Genome-Metagenome interaction effects preprint
arXiv HAL

@preprint{submitted_interactions,
  title = {{Fast Computation of Genome-Metagenome interaction effects}},
  author = {Ambroise, C. and Chiquet, J. and Guinot, F. and Szafranski, M.},
  journal = {preprint},
  hal = {https://hal.archives-ouvertes.fr/hal-01906069},
  arxiv = {https://arxiv.org/abs/1810.12169}
}

Chiquet J, Mariadassous M, Robin S: Variational inference for sparse network reconstruction from count data submitted to JCGS
arXiv code

@preprint{submitted_jcgs_chiquet,
  author = {Chiquet, J. and Mariadassous, M. and Robin, Stéphane},
  title = {Variational inference for sparse network reconstruction from count data},
  journal = {submitted to JCGS},
  arxiv = {{https://arxiv.org/abs/1806.03120}},
  code = {{https://github.com/jchiquet/PLNmodels}}
}

Tabouy T, Barbillon P, Chiquet J: Variational Inference for Stochastic Block Models from Sampled Data In revision for JASA
arXiv

@preprint{submitted_jrssb_tabouy,
  author = {Tabouy, T. and Barbillon, P. and Chiquet, J.},
  title = {Variational Inference for Stochastic Block Models from Sampled Data},
  journal = {In revision for JASA},
  arxiv = {{https://arxiv.org/abs/1707.04141}}
}

Journal papers

Chiquet J, Mariadassou M, Robin S: Variational inference for probabilistic Poisson PCA Ann Appl Statist 12: 2674–2698, 2018
arXiv url code

@article{2018_AOAS_cmr,
  author = {Chiquet, Julien and Mariadassou, Mahendra and Robin, St\'ephane},
  title = {Variational inference for probabilistic Poisson PCA},
  journal = {Ann. Appl. Statist.},
  fjournal = {Annals of Applied Statistics},
  year = {2018},
  volume = {12},
  number = {4},
  pages = {2674-2698},
  issn = {1932-6157},
  doi = {10.1214/18-AOAS1177},
  sici = {1932-6157(2018)12:4<2674:VIFPPP>2.0.CO;2-S},
  arxiv = {{https://arxiv.org/abs/1703.06633}},
  code = {{https://github.com/jchiquet/PLNmodels}},
  url = {http://dx.doi.org/10.1214/18-AOAS1177}
}

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

@article{2018_sagmb_perrot,
  author = {Perrot, M. and Lévy-Leduc, C. and Chiquet, J. and Sansonnet, L. and Brégère, M. and Étienne, M.-P. and Robin, Stéphane and Genta-Gouve, G.},
  title = {A multivariate variable selection approach for
                    analyzing LC-MS metabolomics data},
  fjournal = {Statistical applications in genetics and molecular
                    biology},
  journal = {SAGMB},
  year = {2018},
  arxiv = {{https://arxiv.org/abs/1704.00076}},
  url = {https://doi.org/10.1515/sagmb-2017-0077},
  code = {https://cran.r-project.org/package=MultiVarSel}
}

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

@article{2018_jmva_perrot,
  author = {Perrot, M. and Lévy-Leduc, C. and Sansonnet, L. and Chiquet, J.},
  title = {Variable selection in multivariate linear models
                    with high-dimensional covariance matrix estimation},
  journal = {J. Multivar. Anal.},
  fjournal = {Journal of Multivariate Analysis},
  volume = {166},
  pages = {78--97},
  year = {2018},
  publisher = {Elsevier},
  arxiv = {{https://arxiv.org/abs/1707.04145}},
  url = {https://doi.org/10.1016/j.jmva.2018.02.006},
  code = {https://cran.r-project.org/package=MultiVarSel}
}

Grandvalet Y, Chiquet J, Ambroise C: Sparsity by Worst-Case Penalties arXiv preprint, 2017
arXiv code

@preprint{report_CSDA_chiquet,
  author = {Grandvalet, Y. and Chiquet, J. and Ambroise, C.},
  title = {Sparsity by Worst-Case Penalties},
  journal = {arXiv preprint},
  year = {2017},
  arxiv = {{http://arxiv.org/abs/1210.2077}},
  code = {{http://r-forge.r-project.org/projects/quadrupen/}}
}

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

@article{2017_EJS_BCLL,
  author = {Brault, Vincent and Chiquet, Julien and L\'evy-Leduc, C\'eline},
  title = {Efficient block boundaries estimation in block-wise constant matrices: An application to HiC data},
  journal = {Electron. J. Statist.},
  fjournal = {Electronic Journal of Statistics},
  year = {2017},
  volume = {11},
  number = {1},
  pages = {1570-1599},
  doi = {10.1214/17-EJS1270},
  arxiv = {{http://arxiv.org/abs/1603.03593}},
  code = {http://cran.r-project.org/web/packages/blockseg/}
}

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

@article{2016_JCGS_Chiquet,
  author = {Chiquet, Julien and Gutierrez, Pierre and Rigaill, Guillem},
  title = {Fast tree inference with weighted fusion penalties},
  journal = {Journal of Computational and Graphical Statistics},
  year = {2017},
  vol = {26},
  pages = {205--216},
  arxiv = {http://arxiv.org/abs/1407.5915},
  code = {https://r-forge.r-project.org/projects/fusedanova/},
  url = {http://dx.doi.org/10.1080/10618600.2015.1096789}
}

Chiquet J, Grandvalet Y, Rigaill G: Categorical regularization: Discussion of article by Tutz and Gertheiss Statistical Modelling: 228–237, 2016
HAL url

@article{2016_SM_Chiquet,
  author = {Chiquet, J. and Grandvalet, Y. and Rigaill, G.},
  title = {Categorical regularization: Discussion of article by Tutz and Gertheiss},
  year = {2016},
  vol = {16},
  pages = {228-237},
  number = {3},
  journal = {Statistical Modelling},
  url = {http://dx.doi.org/10.1177/1471082X16644998},
  hal = {https://hal.archives-ouvertes.fr/hal-01338164}
}

Chiquet J, Mary-Huard T, Robin S: Structured Regularization for conditional Gaussian Graphical Models Statistics and Computing: 789–804, 2016
arXiv url code

@article{2016_SC_Chiquet,
  author = {Chiquet, J. and Mary-Huard, T. and Robin, S.},
  title = {Structured Regularization for conditional {Gaussian} Graphical Models},
  journal = {Statistics and Computing},
  year = {2016},
  vol = {27},
  number = {3},
  pages = {789-804},
  arxiv = {{http://arxiv.org/abs/1403.6168}},
  code = {{http://r-forge.r-project.org/projects/spring-pkg/}},
  url = {http://dx.doi.org/10.1007/s11222-016-9654-1}
}

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

@article{2016_JMVA_Latouche,
  author = {Latouche, Pierre and Mattei, Pierre-Alexandre and Bouveyron, Charles and Chiquet, Julien},
  title = {Combining a Relaxed {EM} Algorithm with {Occam's} Razor for {Bayesian} Variable Selection in High-Dimensional Regression},
  journal = {Journal of Multivariate Analysis},
  year = {2016},
  page = {177-190},
  vol = {146},
  hal = {https://hal.archives-ouvertes.fr/hal-01003395v2},
  code = {http://cran.r-project.org/web/packages/spinyreg/},
  url = {http://dx.doi.org/10.1016/j.jmva.2015.09.004}
}

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

@article{picchetti:hal-01154154,
  title = {{A model for gene deregulation detection using expression data}},
  author = {Picchetti, Thomas and Chiquet, Julien and Elati, Mohamed and Neuvial, Pierre and Nicolle, R{\'e}my and Birmel{\'e}, Etienne},
  journal = {BMC Systems Biology},
  year = {2015},
  vol = {9},
  hal = {https://hal.archives-ouvertes.fr/hal-01154154},
  url = {http://bmcsystbiol.biomedcentral.com/articles/10.1186/1752-0509-9-S6-S6}
}

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

@article{2014_Science_Chaloub,
  author = {Chaloub, B. and Denoeud, F. and Liu, S. and Parkin, S. and Tang, H. and X., Wang and Chiquet, J. and {76 more}},
  title = {Early allopolyploid evolution in the post-neolithic
                    {Brassica} napus oilseed genome},
  journal = {Science},
  year = {2014},
  vol = {345},
  number = {6199},
  page = {950--953},
  url = {http://www.sciencemag.org/content/345/6199/950}
}

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

@article{2013_NP_Chiquet,
  author = {Chelaifa, H. and Chagué, V. and Chalabi, S. and Mestiri, I. and Arnaud, D. and Deffains, D. and Lu, Y. and Belcram, H. and Huteau, V. and Chiquet, J. and Coriton, O. and Just, J. and Jahier, J. and Chalhoub, B.},
  title = {Prevalence of gene expression additivity in genetically
                    stable wheat allohexaploids},
  journal = {New Phytologist},
  volume = {197},
  number = {3},
  issn = {1469-8137},
  pages = {730--736},
  year = {2013},
  url = {http://onlinelibrary.wiley.com/doi/10.1111/nph.12108/full}
}

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

@article{2012_AAS_chiquet,
  author = {Chiquet, J. and Grandvalet, Y. and Charbonnier, C.},
  title = {Sparsity in sign-coherent groups of variables via
                    the cooperative-Lasso},
  journal = {The Annals of Applied Statistics},
  year = {2012},
  volume = {6},
  number = {2},
  pages = {795--830},
  arxiv = {http://arxiv.org/abs/1103.2697},
  url = {http://projecteuclid.org/euclid.aoas/1339419617},
  slides = {http://www.slideshare.net/jchiquet/sparsity-with-signcoherent-groups-of-variables-via-the-cooperativelasso}
}

Chiquet J, Grandvalet Y, Ambroise C: Inferring multiple graphical models Statistics and Computing 21: 537–553, 2011
arXiv url slides code

@article{2011_SC_Chiquet,
  author = {Chiquet, J. and Grandvalet, Y. and Ambroise, C.},
  title = {Inferring multiple graphical models},
  journal = {Statistics and Computing},
  year = {2011},
  volume = {21},
  number = {4},
  pages = {537--553},
  arxiv = {http://arxiv.org/abs/0912.4434},
  url = {http://dx.doi.org/10.1007/s11222-010-9191-2},
  slides = {http://www.slideshare.net/jchiquet/multitask-learning-for-ggm},
  code = {http://cran.r-project.org/web/packages/simone/}
}

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

@article{2010_SAGMB_Chiquet,
  author = {Charbonnier, C. and Chiquet, J. and Ambroise, C.},
  title = {Weighted-Lasso for structured network
                    inference from time course data},
  journal = {Statistical Applications in Genomics and Molecular Biology},
  year = {2010},
  volume = {9},
  arxiv = {http://arxiv.org/abs/0910.1723},
  url = {https://doi.org/10.2202/1544-6115.1519},
  slides = {http://www.slideshare.net/jchiquet/weighted-lasso-for-network-inference},
  code = {http://cran.r-project.org/web/packages/simone/}
}

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

@article{2009_EJS_Chiquet,
  author = {Ambroise, C. and Chiquet, J. and Matias, C.},
  title = {Inferring sparse {Gaussian} graphical models with
                    latent structure},
  journal = {Electronic Journal of Statistics},
  year = {2009},
  volume = {3},
  pages = {205--238},
  arxiv = {http://arxiv.org/abs/0810.3177},
  url = {http://projecteuclid.org/DPubS?service=UI&version=1.0&verb=Display&handle=euclid.ejs/1238078905},
  slides = {http://www.slideshare.net/jchiquet/gaussian-graphical-models-with-latent-structure},
  code = {http://cran.r-project.org/web/packages/simone/}
}

Chiquet J, Smith A, Grasseau G, Matias C, Ambroise C: SIMoNe: Statistical Inference for MOdular NEtworks Bioinformatics 25: 417–418, 2009
url code

@article{2009_BI_Chiquet,
  author = {Chiquet, J. and Smith, A. and Grasseau, G. and Matias, C. and Ambroise, C.},
  title = {{SIMoNe: Statistical Inference for MOdular NEtworks}},
  journal = {Bioinformatics},
  year = {2009},
  volume = {25},
  number = {3},
  pages = {417--418},
  url = {http://dx.doi.org/10.1093/bioinformatics/btn637},
  code = {http://cran.r-project.org/web/packages/simone/}
}

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
url

@article{2009_JSPI_Chiquet,
  author = {Chiquet, J. and Limnios, N. and Eid, M.},
  title = {Piecewise deterministic {Markov} processes applied to
                    fatigue crack growth modelling},
  journal = {Journal of Statistical Planning and Inference},
  year = {2009},
  volume = {139},
  number = {5},
  pages = {1657--1667},
  url = {http://dx.doi.org/10.1016/j.jspi.2008.05.034}
}

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
url

@article{2008_SPL_Chiquet,
  author = {Chiquet, J. and Limnios, N.},
  title = {A method to compute the transition function of a
                    piecewise deterministic {Markov} process},
  journal = {Statistics and Probability Letters},
  year = {2008},
  volume = {78},
  number = {12},
  pages = {1397--1403},
  url = {http://dx.doi.org/10.1016/j.spl.2007.12.016}
}

Chiquet J, Limnios N, Eid M: Modelling and Estimating Stochastic Dynamical Systems with Markovian Switching Reliability Engineering and System Safety 93: 1801–1808, 2008
url

@article{2008_RESS_Chiquet,
  author = {Chiquet, J. and Limnios, N. and Eid, M.},
  title = {Modelling and Estimating Stochastic Dynamical
                    Systems with {Markovian} Switching},
  journal = {Reliability Engineering and System  Safety},
  year = {2008},
  volume = {93},
  number = {12},
  pages = {1801--1808},
  url = {http://dx.doi.org/10.1016/j.ress.2008.03.016}
}

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
url

@article{2006_MCAP_Chiquet,
  author = {Chiquet, J. and Limnios, N.},
  title = {Estimating stochastic dynamical systems driven by a
                    continuous-time jump {Markov} process},
  journal = {Methodology and Computing in Applied Probability},
  year = {2006},
  volume = {8},
  pages = {431--447},
  url = {http://www.springerlink.com/content/e8736480p20271l3/}
}

Book chapter

Chiquet J, Rigaill R, Sundqvist M: Gene Regulatory Networks: Methods and Protocols (Guido Sanguinetti and Vân Anh Huynh-Thu, eds.)), in: Springer Science+Business Media, LLC, part of Springer Nature, 2019.
url code

@inbook{chatpter_multggm,
  author = {Chiquet, J. and Rigaill, R. and Sundqvist, M.},
  chapter = {A multiattribute Gaussian graphical model for
                    inferring multiscale regulatory networks: an
                    application in breast cancer},
  title = {Gene Regulatory Networks: Methods and Protocols
                    (Guido Sanguinetti and Vân Anh Huynh-Thu, eds.))},
  year = {2019},
  publisher = {Springer Science+Business Media, LLC, part of Springer Nature},
  url = {https://doi.org/10.1007/978-1-4939-8882-2_6},
  code = {https://github.com/jchiquet/multivarNetwork}
}

Vacher A C. Tamaddoni-Nezhad, Kamenova S, Peyrard N, Schwaller L, Julien Chiquet J, Smith MA, Vallance J, Moalic Y, et al.: Advances in Ecological Research, in: 2016.

@inbook{2016_inbook_vacher,
  author = {Vacher, C. Tamaddoni-Nezhad, A. and Kamenova, S. and Peyrard, N. and Schwaller, L. and Julien Chiquet, J. and Smith, M.A. and Vallance, J. and Moalic, Y. and Sabbadin, R. and Fievet, V. and Jakuschkin, B. and Bohan, D.A.},
  title = {Advances in Ecological Research},
  chapter = {Learning Ecological Networks from Next-Generation Sequencing Data},
  year = {2016}
}

Jeanmoungin M, Charbonnier C, Guedj M, Chiquet J: Probabilistic graphical models dedicated to applications in genetics, genomics and postgenomics, in: 2014.
url

@inbook{2014_inbook_jeanmougin,
  author = {Jeanmoungin, M. and Charbonnier, C. and Guedj, M. and Chiquet, J.},
  title = {Probabilistic graphical models dedicated to
                    applications in genetics, genomics and postgenomics},
  chapter = {Network inference in breast cancer with Gaussian
                    graphical models and extensions},
  year = {2014},
  url = {http://ukcatalogue.oup.com/product/9780198709022.do}
}

Chiquet J, Limnios N: Stochastic Reliability and Maintenance Modeling, in: Vol 9. Springer Series in Reliability Engineering. Springer, 2013.
url

@inbook{2013_Springer_Chiquet,
  author = {Chiquet, J. and Limnios, N.},
  title = {Stochastic Reliability and Maintenance Modeling},
  chapter = {Dynamical systems with semi-{markovian} perturbations
                    and their use in structural reliability},
  series = {Springer Series in Reliability Engineering},
  volume = {9},
  publisher = {Springer},
  year = {2013},
  url = {http://www.springer.com/engineering/production+engineering/book/978-1-4471-4970-5}
}

Chiquet J, Limnios N: Mathematical methods in survival analysis, reliability and quality of life, in: Wiley/ISTE, 2008.
url

@inbook{2008_Wiley_Chiquet,
  author = {Chiquet, J. and Limnios, N.},
  title = {Mathematical methods in survival analysis,
                    reliability and quality of life},
  chapter = {Reliability of stochastic dynamical systems applied
                    to fatigue crack growth modelling},
  publisher = {Wiley/ISTE},
  year = {2008},
  url = {http://eu.wiley.com/WileyCDA/WileyTitle/productCd-1848210108,subjectCd-ST80.html}
}

Popular science

Chiquet J: Statistique et génome: réseaux biologiques La gazette des mathématiciens 130: 76–82, 2011
url

@article{2011_gazette_chiquet,
  author = {Chiquet, J.},
  title = {Statistique et génome: réseaux biologiques},
  journal = {La gazette des mathématiciens},
  year = {2011},
  volume = {130},
  pages = {76--82},
  url = {http://smf4.emath.fr/en/Publications/Gazette/2011/130/}
}

Thesis

Chiquet J: Contributions to sparse methods for complex data analysis, 2015
url

@hdrthesis{2015_hdr_chiquet,
  author = {Chiquet, J.},
  title = {Contributions to sparse methods for complex data analysis},
  school = {Université d'Évry Val-d'Essonne},
  year = {2015},
  url = {https://tel.archives-ouvertes.fr/tel-01288976/}
}

Chiquet J: Modélisation et estimation des processus de dégradation avec application en fiabilité des structures, 2007
url

@phdthesis{2007_thesis_chiquet,
  author = {Chiquet, J.},
  title = {Modélisation et estimation des processus de
                    dégradation avec application en fiabilité des
                    structures},
  school = {Université de Technologie de Compiègne},
  year = {2007},
  url = {http://tel.archives-ouvertes.fr/tel-00165782}
}

Chiquet J: Estimation des températures journalières à l’aide de techniques markoviennes, 2003
url

@mastersthesis{2003_msc_chiquet,
  author = {Chiquet, J.},
  title = {Estimation des températures journalières à l'aide de
                    techniques markoviennes},
  school = {Université de Technologie de Compiègne},
  year = {2003},
  url = {http://julien.cremeriefamily.info/doc/master_thesis.pdf}
}