publications

By categories (Preprint, Journal, Book chapters, Theses) in reversed chronological order

An alternative is to check my Google scholar page.

preprint

  1. jss
    Stability Selection and Consensus Clustering in R: The R Package sharp
    Barbara Bodinier, Sabrina Rodrigues, Maryam Karimi, Sarah Filippi, Julien Chiquet, and Marc Chadeau-Hyam
    submitted
  2. bioRxiv
    Microbial association networks give relevant insights into plant pathobiomes
    Charlie Pauvert, Tania Fort, Agnès Calonnec, Julie Faivre-d’Arcier, Emilie Chancerel, Marie Massot, Julien ChiquetStéphane Robin, David A. Bohan, Jessica Vallance, and Corinne Vacher
    2020

journal papers

2023

  1. Bioinformatics
    Automated calibration of consensus weighted distance-based clustering approaches using sharp
    Barbara Bodinier, Sabrina Rodrigues, Maryam Karimi, Sarah Filippi, Julien Chiquet, and Marc Chadeau-Hyam
    Bioinformatics, 2023
  2. Plant Commun.
    Cell specialization and coordination in Arabidopsis leaves upon pathogenic attack revealed by scRNA-seq
    Etienne Delannoy, Bastien Batardiere, Stéphanie Pateyron, Ludivine Soubigou-Taconnat, Julien Chiquet, Jean Colcombet, and Julien Lang
    Plant Communications, 2023
    Focus Issue on Plant Single-Cell Biology
  3. JRSS-C
    Automated calibration for stability selection in penalised regression and graphical models
    Barbara Bodinier, Sarah Filippi, Therese Haugdahl Nøst, Julien Chiquet, and Marc Chadeau-Hyam
    Journal of the Royal Statistical Society Series C: Applied Statistics, 2023

2022

  1. Neurips
    A Probabilistic Graph Coupling View of Dimension Reduction
    Hugues Van Assel, Thibault Espinasse, Julien Chiquet, and Franck Picard
    In Advances in Neural Information Processing Systems, 2022
  2. Comput. Stat.
    Adjusting the adjusted Rand Index - A multinomial story
    Martina Sundqvist, Julien Chiquet, and Guillem Rigaill
    Computational Statistics, 2022
  3. J. Stat. Softw.
    missSBM: An R Package for Handling Missing Values in the Stochastic Block Model
    Pierre BarbillonJulien Chiquet, and Timothée Tabouy
    Journal of Statistical Software, 2022

2021

  1. Adv. Ecol. Res.
    Chapter Nine - Coupling ecological network analysis with high-throughput sequencing-based surveys: Lessons from the next-generation biomonitoring project
    Maxime Dubart, Pascal Alonso, Didac Barroso-Bergada, Nathalie Becker, Kevin Bethune, David A. Bohan, Christophe Boury, Marine Cambon, Elsa Canard, Emilie Chancerel, Julien Chiquet, Patrice David, Natasha de Manincor, Sophie Donnet, Anne Duputié, Benoît Facon, Erwan Guichoux, Tâm Le Minh, Sebastián Ortiz-Martínez, Lucie Piouceau, Ambre Sacco-Martret de Préville, Manuel Plantegenest, Céline Poux, Virginie Ravigné, Stéphane Robin, Marine Trillat, Corinne Vacher, Christian Vernière, and François Massol
    In The Future of Agricultural Landscapes, Part III, 2021
  2. G3
    Harnessing multivariate, penalized regression methods for genomic prediction and QTL detection to cope with climate change affecting grapevine
    Charlotte Brault, Agnès Doligez, Loïc Le Cunff, Aude Coupel-Ledru, Thierry Simonneau, Julien Chiquet, Patrice This, and Timothée Flutre
    G3: Genes|Genomes|Genetics, 2021
  3. Ecol. Lett.
    Joint species distributions reveal the combined effects of host plants, abiotic factors and species competition as drivers of species abundances in fruit flies
    Benoit Facon, Abir Hafsi, Maud Charlery Masselière, Stéphane Robin, François Massol, Maxime Dubart, Julien Chiquet, Enric Frago, Frédéric Chiroleu, Pierre-François Duyck, and Virginie Ravigné
    Ecological Letters, 2021
  4. Microbiome
    Temporal patterns in Ixodes ricinus microbial communities: an insight into tick-borne microbe interactions
    E Lejal, J Chiquet, J Aubert, S Robin, A Estrada-Peña, O Rue, C Midoux, M Mariadassou, X Bailly, A Cougoul, P Gasqui, JF Cosson, K Chalvet-Monfray, M Vayssier-Taussat, and T Pollet
    Microbiome, 2021
  5. Front Ecol Evol
    The Poisson-Lognormal Model as a Versatile Framework for the Joint Analysis of Species Abundances
    Julien ChiquetMahendra Mariadassou, and Stéphane Robin
    Frontiers in Ecology and Evolution, 2021
  6. J. Bio Comp Biol
    Identification of deregulation mechanisms specific to cancer subtypes
    Magali Champion, Julien ChiquetPierre Neuvial, Mohamed Elati, François Radvanyi, and Etienne Birmelé
    Journal of Bioinformatics and Computational Biology, 2021

2020

  1. Algo Mol Biol
    Fast Computation of Genome-Metagenome interaction effects
    Florent Guinot, Marie Szafranski, Julien Chiquet, Anouk Zancarini, Christine Le Signor, Christophe Mougel, and Christophe Ambroise
    Algorithms for Molecular Biology, 2020
  2. BMC Bioinfo
    Fast tree aggregation for consensus hierarchical clustering
    Audrey Hulot, Julien Chiquet, Florence Jaffrezic, and Guillem Rigaill
    BMC Bioinformatics, 2020

2019

  1. Cell
    A Quantitative Multivariate Model of Human Dendritic Cell-T Helper Cell Communication
    Maximilien Grandclaudon, Marie Perrot-Dockès, Coline Trichot, Omar Mostafa-Abouzid, Wassim Abou-Jaoudé, Frédérique Berger, Philippe Hupé, Denis Thieffry, Laure Sansonnet, Julien Chiquet, Céline Levy-Leduc, and Vassili Soumelis
    Cell, 2019
  2. ICML
    Variational Inference for sparse network reconstruction from count data
    Julien Chiquet, Stephane Robin, and Mahendra Mariadassou
    In Proceedings of the 36th International Conference on Machine Learning, 09–15 jun 2019
  3. JASA
    Variational Inference for Stochastic Block Models from Sampled Data
    Timothée Tabouy, Pierre Barbillon, and Julien Chiquet
    Journal of the American Statistical Association, 09–15 jun 2019

2018

  1. Ann Appl Stat
    Variational inference for probabilistic Poisson PCA
    Julien ChiquetMahendra Mariadassou, and Stéphane Robin
    Ann. Appl. Statist., 09–15 jun 2018
  2. SAGMB
    A multivariate variable selection approach for analyzing LC-MS metabolomics data
    M. Perrot, C. Lévy-LeducJulien Chiquet, L. Sansonnet, M. Brégère, M.-P. Étienne, Stéphane Robin, and G. Genta-Gouve
    SAGMB, 09–15 jun 2018
  3. JMVA
    Variable selection in multivariate linear models with high-dimensional covariance matrix estimation
    M. Perrot, C. Lévy-Leduc, L. Sansonnet, and Julien Chiquet
    J. Multivar. Anal., 09–15 jun 2018

2017

  1. arXiv
    Sparsity by Worst-Case Penalties
    Y. GrandvaletJulien Chiquet, and C. Ambroise
    09–15 jun 2017
  2. EJS
    Efficient block boundaries estimation in block-wise constant matrices: An application to HiC data
    Vincent Brault, Julien Chiquet, and Céline Lévy-Leduc
    Elec. J. Statist., 09–15 jun 2017
  3. JCGS
    Fast tree inference with weighted fusion penalties
    Julien Chiquet, Pierre Gutierrez, and Guillem Rigaill
    Journal of Computational and Graphical Statistics, 09–15 jun 2017

2016

  1. Stat Model
    Categorical regularization: Discussion of article by Tutz and Gertheiss
    Julien ChiquetY. Grandvalet, and G. Rigaill
    Statistical Modelling, 09–15 jun 2016
  2. Stat Comput
    Structured Regularization for conditional Gaussian Graphical Models
    Julien ChiquetT. Mary-Huard, and S. Robin
    Statistics and Computing, 09–15 jun 2016
  3. Adv Ecol Res
    Learning ecological networks from next-generation sequencing data
    Corinne Vacher, Alireza Tamaddoni-Nezhad, Stefaniya Kamenova, Nathalie Peyrard, Yann Moalic, Regis Sabbadin, Loı̈c Schwaller, Julien Chiquet, M Alex Smith, Jessica Vallance, and  others
    In Advances in Ecological Research, 09–15 jun 2016
  4. JMVA
    Combining a Relaxed EM Algorithm with Occam’s Razor for Bayesian Variable Selection in High-Dimensional Regression
    Pierre Latouche, Pierre-Alexandre Mattei, Charles Bouveyron, and Julien Chiquet
    Journal of Multivariate Analysis, 09–15 jun 2016

2015

  1. BMC Syst Biol
    A model for gene deregulation detection using expression data
    Thomas Picchetti, Julien Chiquet, Mohamed Elati, Pierre Neuvial, Rémy Nicolle, and Etienne Birmelé
    BMC Systems Biology, 09–15 jun 2015

2014

  1. Science
    Early allopolyploid evolution in the post-neolithic Brassica napus oilseed genome
    B. Chaloub, F. Denoeud, S. Liu, S. Parkin, H. Tang, Wang X., Julien Chiquet, and  76 more
    Science, 09–15 jun 2014

2013

  1. New Phytol
    Prevalence of gene expression additivity in genetically stable wheat allohexaploids
    H. Chelaifa, V. Chagué, S. Chalabi, I. Mestiri, D. Arnaud, D. Deffains, Y. Lu, H. Belcram, V. Huteau, Julien Chiquet, O. Coriton, J. Just, J. Jahier, and B. Chalhoub
    New Phytologist, 09–15 jun 2013

2012

  1. Ann Appl Stat
    Sparsity in sign-coherent groups of variables via the cooperative-Lasso
    Julien ChiquetY. Grandvalet, and C. Charbonnier
    The Annals of Applied Statistics, 09–15 jun 2012

2011

  1. Stat Comput
    Inferring multiple graphical models
    Julien ChiquetY. Grandvalet, and C. Ambroise
    Statistics and Computing, 09–15 jun 2011

2010

  1. SAGMB
    Weighted-Lasso for structured network inference from time course data
    C. Charbonnier, Julien Chiquet, and C. Ambroise
    Statistical Applications in Genomics and Molecular Biology, 09–15 jun 2010

2009

  1. EJS
    Inferring sparse Gaussian graphical models with latent structure
    C. AmbroiseJulien Chiquet, and C. Matias
    Electronic Journal of Statistics, 09–15 jun 2009
  2. Bioinformatics
    SIMoNe: Statistical Inference for MOdular NEtworks
    Julien Chiquet, A. Smith, G. Grasseau, C. Matias, and C. Ambroise
    Bioinformatics, 09–15 jun 2009
  3. JSPI
    Piecewise deterministic Markov processes applied to fatigue crack growth modelling
    Julien ChiquetN. Limnios, and M. Eid
    Journal of statistical planning and inference, 09–15 jun 2009

2008

  1. Stat Prob Lett
    A method to compute the transition function of a piecewise deterministic Markov process
    Julien Chiquet, and N. Limnios
    Statistics & Probability Letters, 09–15 jun 2008
  2. RESS
    Modelling and Estimating Stochastic Dynamical Systems with Markovian Switching
    Julien ChiquetN. Limnios, and M. Eid
    Reliability Engineering System Safety, 09–15 jun 2008

2006

  1. MCAP
    Estimating stochastic dynamical systems driven by a continuous-time jump Markov process
    Julien Chiquet, and N. Limnios
    Methodology and Computing in Applied Probability, 09–15 jun 2006

book chapters

  1. Statistical Approaches for Hidden Variables in Ecology
    Julien Chiquet, Marie-Josée Cros, Mahendra Mariadassou, Nathalie Peyrard, and Stéphane Robin
    2022
  2. A Multiattribute Gaussian Graphical Model for Inferring Multiscale Regulatory Networks: An Application in Breast Cancer
    J. Chiquet, R. Rigaill, and M. Sundqvist
    2019
  3. Probabilistic graphical models dedicated to applications in genetics, genomics and postgenomics
    M. Jeanmoungin, C. Charbonnier, M. Guedj, and J. Chiquet
    2014
  4. Stochastic Reliability and Maintenance Modeling
    J. Chiquet, and N. Limnios
    2013
  5. Mathematical methods in survival analysis, reliability and quality of life
    J. Chiquet, and N. Limnios
    2008

theses

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