@preprint{Facon2020.12.07.414326, author = {Facon, Benoit and Hafsi, Abir and de la Masseli{\`e}re, Maud Charlery and Robin, St{\'e}phane and Massol, Fran{\c c}ois and Dubart, Maxime and Chiquet, Julien and Frago, Enric and Chiroleu, Fr{\'e}d{\'e}ric and Duyck, Pierre-Fran{\c c}ois and Ravign{\'e}, Virginie}, title = {Joint species distributions reveal the combined effects of host plants, abiotic factors and species competition as drivers of species abundances in fruit flies}, elocation-id = {2020.12.07.414326}, year = {2021}, doi = {10.1101/2020.12.07.414326}, publisher = {Cold Spring Harbor Laboratory}, url = {https://www.biorxiv.org/content/early/2021/03/03/2020.12.07.414326}, eprint = {https://www.biorxiv.org/content/early/2021/03/03/2020.12.07.414326.full.pdf}, journal = {bioRxiv} }
@preprint{brault:hal-03113189, title = {{Harnessing multivariate, penalized regression methods for genomic prediction and QTL detection to cope with climate change affecting grapevine}}, author = {Brault, Charlotte and Doligez, Agn{\`e}s and LE CUNFF, Lo{\"i}c and COUPEL-LEDRU, Aude and Simonneau, Thierry and Chiquet, Julien and This, Patrice and Flutre, Timoth{\'e}e}, url = {https://hal.inrae.fr/hal-03113189}, year = {2021}, month = jan, doi = {10.1101/2020.10.26.355420}, hal_id = {hal-03113189}, hal_version = {v1} }
@preprint{Lejal2020.09.26.314179, author = {Lejal, E and Chiquet, J and Aubert, J and Robin, S and Estrada-Pe{\~n}a, A and Rue, O and Midoux, C and Mariadassou, M and Bailly, X and Cougoul, A and Gasqui, P and Cosson, JF and Chalvet-Monfray, K and Vayssier-Taussat, M and Pollet, T}, title = {Temporal patterns in Ixodes ricinus microbial communities: an insight into tick-borne microbe interactions}, elocation-id = {2020.09.26.314179}, year = {2020}, doi = {10.1101/2020.09.26.314179}, publisher = {Cold Spring Harbor Laboratory}, url = {https://www.biorxiv.org/content/early/2020/09/26/2020.09.26.314179}, eprint = {https://www.biorxiv.org/content/early/2020/09/26/2020.09.26.314179.full.pdf}, journal = {bioRxiv} }
@preprint{preprint_pauvert, author = {Pauvert, Charlie and Fort, Tania and Calonnec, Agnès and Faivre-d'Arcier, Julie and Chancerel, Emilie and Massot, Marie and Chiquet, Julien and Robin, Stéphane and Bohan, David A. and Vallance, Jessica and Vacher, Corinne}, title = {Microbial association networks give relevant insights into plant pathobiomes}, elocation-id = {2020.02.21.958033}, year = {2020}, doi = {10.1101/2020.02.21.958033}, publisher = {Cold Spring Harbor Laboratory}, url = {https://www.biorxiv.org/content/early/2020/02/23/2020.02.21.958033}, eprint = {https://www.biorxiv.org/content/early/2020/02/23/2020.02.21.958033.full.pdf}, journal = {bioRxiv} }
@preprint{submitted_MARI, author = {Sundqvist, Martina and Chiquet, Julien and Rigaill, Guillem}, title = {Adjusting the adjusted Rand Index - A multinomial story}, journal = {preprint}, year = {2020}, url = {https://arxiv.org/abs/2011.08708}, arxiv = {{https://arxiv.org/abs/2011.08708}}, code = {{https://github.com/jchiquet/aricode}} }
@preprint{Chiquet2020.10.07.329383, author = {Chiquet, Julien and Mariadassou, Mahendra and Robin, St{\'e}phane}, title = {The Poisson-lognormal model as a versatile framework for the joint analysis of species abundances}, elocation-id = {2020.10.07.329383}, year = {2020}, doi = {10.1101/2020.10.07.329383}, publisher = {Cold Spring Harbor Laboratory}, url = {https://www.biorxiv.org/content/early/2020/10/08/2020.10.07.329383}, eprint = {https://www.biorxiv.org/content/early/2020/10/08/2020.10.07.329383.full.pdf}, journal = {bioRxiv} }
@preprint{submitted_missSBM, author = {Barbillon, Pierre and Chiquet, Julien and Tabouy, Timothée}, title = {missSBM: An R Package for Handling Missing Values in the Stochastic Block Model}, journal = {preprint}, year = {2019}, url = {https://arxiv.org/abs/1906.12201}, arxiv = {{https://arxiv.org/abs/1906.12201}}, code = {{https://github.com/jchiquet/missSBM}} }
PMID: 33653235
HAL url@article{champion_2021, author = {Champion, Magali and Chiquet, Julien and Neuvial, Pierre and Elati, Mohamed and Radvanyi, François and Birmelé, Etienne}, title = {Identification of deregulation mechanisms specific to cancer subtypes}, journal = {Journal of Bioinformatics and Computational Biology}, volume = {19}, number = {01}, pages = {2140003}, year = {2021}, doi = {10.1142/S0219720021400035}, note = {PMID: 33653235}, url = {https://doi.org/10.1142/S0219720021400035}, hal = {https://hal.archives-ouvertes.fr/hal-03079966/file/Paper_Champion_HAL.pdf}, eprint = {https://doi.org/10.1142/S0219720021400035} }
@article{guinot_AMB_2020, title = {{Fast Computation of Genome-Metagenome interaction effects}}, author = {Guinot, Florent and Szafranski, Marie and Chiquet, Julien and Zancarini, Anouk and Le Signor, Christine and Mougel, Christophe and Ambroise, Christophe}, journal = {Algorithms for Molecular Biology}, hal = {{https://hal.archives-ouvertes.fr/hal-01906069}}, arxiv = {{https://arxiv.org/abs/1810.12169}}, url = {http://dx.doi.org/10.1186/s13015-020-00173-2}, code = {{https://github.com/jchiquet/sicomore-pkg}}, year = {2020} }
@article{huot_BMC_2020, author = {Huot, Audrey and Chiquet, Julien and Jaffrezic, Florence and Rigaill, Guillem}, title = {Fast tree aggregation for consensus hierarchical clustering}, journal = {BMC Bioinformatics}, year = {2020}, url = {to appear}, code = {{https://CRAN.R-project.org/package=mergeTrees}} }
@article{mgrandclaudon_tmod, title = {{A Quantitative Multivariate Model of Human Dendritic Cell-T Helper Cell Communication}}, author = {Grandclaudon, Maximilien and Perrot-Dockès, Marie and Trichot, Coline and Mostafa-Abouzid, Omar and Abou-Jaoudé, Wassim and Berger, Frédérique and Hupé, Philippe and Thieffry, Denis and Sansonnet, Laure and Chiquet, Julien and Levy-Leduc, Céline and Soumelis, Vassili}, journal = {Cell}, year = {2019}, url = {http://dx.doi.org/10.2139/ssrn.3353217} }
@inproceedings{2019_ICML_CMR, title = {Variational Inference for sparse network reconstruction from count data}, author = {Chiquet, Julien and Robin, Stephane and Mariadassou, Mahendra}, booktitle = {Proceedings of the 36th International Conference on Machine Learning}, pages = {1162--1171}, year = {2019}, editor = {Chaudhuri, Kamalika and Salakhutdinov, Ruslan}, volume = {97}, series = {Proceedings of Machine Learning Research}, address = {Long Beach, California, USA}, month = {09--15 Jun}, publisher = {PMLR}, code = {{https://github.com/jchiquet/PLNmodels}}, pdf = {http://proceedings.mlr.press/v97/chiquet19a/chiquet19a.pdf}, url = {http://proceedings.mlr.press/v97/chiquet19a.html} }
@article{2019_JASA_TBC, author = {Tabouy, Timothée and Barbillon, Pierre and Chiquet, Julien}, title = {Variational Inference for Stochastic Block Models from Sampled Data}, journal = {Journal of the American Statistical Association}, volume = {0}, number = {ja}, pages = {1-20}, year = {2019}, publisher = {Taylor & Francis}, doi = {10.1080/01621459.2018.1562934}, url = {https://doi.org/10.1080/01621459.2018.1562934}, arxiv = {{https://arxiv.org/abs/1707.04141}}, code = {{https://github.com/jchiquet/missSBM}} }
@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} }
@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} }
@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} }
@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 = {{https://github.com/jchiquet/quadrupen}} }
@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/} }
@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} }
@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} }
@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} }
@incollection{2016_AER_Vacher, title = {Learning ecological networks from next-generation sequencing data}, author = {Vacher, Corinne and Tamaddoni-Nezhad, Alireza and Kamenova, Stefaniya and Peyrard, Nathalie and Moalic, Yann and Sabbadin, Regis and Schwaller, Lo{\"\i}c and Chiquet, Julien and Smith, M Alex and Vallance, Jessica and others}, booktitle = {Advances in Ecological Research}, volume = {54}, pages = {1--39}, year = {2016}, publisher = {Elsevier} }
@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} }
@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} }
@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} }
@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} }
@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} }
@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/} }
@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/} }
@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/} }
@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/} }
@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} }
@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} }
@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} }
@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/} }
@inbook{2019_inbook_chiquet, author = {Chiquet, J. and Rigaill, R. and Sundqvist, M.}, editor = {Sanguinetti, Guido and Huynh-Thu, V{\^a}n Anh}, title = {A Multiattribute Gaussian Graphical Model for Inferring Multiscale Regulatory Networks: An Application in Breast Cancer}, booktitle = {Gene Regulatory Networks: Methods and Protocols}, year = {2019}, publisher = {Springer New York}, pages = {143--160}, isbn = {978-1-4939-8882-2}, doi = {10.1007/978-1-4939-8882-2_6}, url = {https://doi.org/10.1007/978-1-4939-8882-2_6}, code = {https://github.com/jchiquet/multivarNetwork} }
@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} }
@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} }
@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} }
@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/} }
@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/} }
@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} }
@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} }