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Maître de conférences (UEVE)
tel : +33(0)1 64 85 35 43
fax :
Laboratoire Statistique et Génome
UMR CNRS 8071, USC INRA
23 boulevard de France
91037 Évry, France
Google Scientific profile
I am an assistant professor at the University d'Évry, in the south of Paris, working in the "Statistique et Génome" Lab since october 2007, first as a post-doc like fellow, then as an assistant professor since october 2008. I completed my PhD thesis in June 2007 at the University of Technology of Compiègne, under the supervision of Nikolaos Limnios. By this time, I used to work on Markov and Semi-Markov processes with applications to reliability studies.
My work since 2007 at “Statistique et Génome” mainly focuses on Statistical learning (clustering, sparse regression methods, Gaussian graphical models) applied to the analysis of biological networks, microarrays and genomic data in general.
Here is a detailed Vitae (in french, updated january 2012 the 2nd).
Here are my journal papers with associated preprints and slides. If any of these interests you, just ask me for a PDF copy.
Toggle publication list by year
List of publications by chiquet ordered by year
to appear
Journal article
- Sparsity with sign-coherent groups of variables via the cooperative-Lasso
Chiquet, J. and Grandvalet, Y. and Charbonnier, C.
The Annals of Applied Statistics
http://arxiv.org/abs/1103.2697
2011
2010
Journal article
- Weighted-Lasso for Structured Network Inference from Time Course Data
Charbonnier, C. and Chiquet, J. and Ambroise, C.
Statistical Applications in Genetics and Molecular Biology Vol. 9 No. 1
http://www.bepress.com/sagmb/vol9/iss1/art15
2009
Journal article
- Inferring sparse Gaussian graphical models with latent structure
Ambroise, C. and Chiquet, J. and Matias, C.
Electronic Journal of Statistics Vol. 3 pp. 205-238
http://projecteuclid.org/DPubS?service=UI&version=1.0&verb=Display&handle=euclid.ejs/1238078905
- Piecewise deterministic Markov processes applied to fatigue crack growth modelling
Chiquet, J. and Limnios, N. and Eid, M.
Journal of Statistical Planning and Inference Vol. 139 No. 5 pp. 1657-1667
http://dx.doi.org/10.1016/j.jspi.2008.05.034
- SIMoNe: Statistical Inference for MOdular NEtworks
Chiquet, J. and Smith, A. and Grasseau, G. and Matias, C. and Ambroise, C.
Bioinformatics Vol. 25 No. 3 pp. 417-418
http://dx.doi.org/10.1093/bioinformatics/btn637
2008
Journal article
- A Method to Compute the Transition Function of a Piecewise Deterministic Markov Process with Application to Reliability
Chiquet, J. and Limnios, N.
Statistics and Probability Letters Vol. 78 No. 12 pp. 1397-1403
http://dx.doi.org/10.1016/j.spl.2007.12.016
- Modelling and Estimation the Reliability of Stochastic Dynamical Systems with Markovian Switching
Chiquet, J. and Limnios, N. and Eid, M.
Reliabilty Engineering and System Safety Vol. 93 No. 12 pp. 1801-1808
http://dx.doi.org/10.1016/j.ress.2008.03.016
2007
In proceedings
- Modelling the reliability of degradation processes through Markov renewal theory
Chiquet, J. and Limnios, N. and Eid, M.
Proceedings of ESREL - Safety and Reliability Conference
Thesis
- Modélisation et estimation des processus de dégradation avec application en fiabilité des structures
Chiquet, J., Université de Technologie de Compiègne
2006
Journal article
- Estimating stochastic dynamical systems driven by a continuous-time jump Markov process
Chiquet, J. and Limnios, N.
Methodology and Computing in Applied Probability Vol. 8 pp. 431-447
http://dx.doi.org/10.1007/s11009-006-0423-z
In proceedings
- Modeling and Estimating the Reliability of Stochastic Dynamical Systems with markovian switching
Chiquet, J. and Limnios, N. and Eid, M.
ESREL 2006 - Safety and Reliability for managing Risks
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Chiquet, J., Smith, A., Grasseau, G., Matias, C., & Ambroise, C. (2009). SIMoNe: Statistical Inference for MOdular NEtworks. Bioinformatics, 25(3), 417-418. final version – web page (with slides)
Chiquet, J., Limnios, N., & Eid, M. (2009). Piecewise deterministic Markov processes applied to fatigue-crack growth modelling. Journal of Statistical Planning and Inference, 139(5), 1657-1667. url Chiquet, J., & Limnios, N. (2008). A Method to Compute the Transition Function of a Piecewise Deterministic Markov Process with Application to Reliability. Statistics and Probability Letters, 78(12), 1397-1403. url Chiquet, J., Limnios, N., & Eid, M. (2008). Modelling and Estimation the Reliability of Stochastic Dynamical Systems with Markovian Switching. Reliabilty Engineering and System Safety, 93(12), 1801-1808. url Chiquet, J., & Limnios, N. (2008). Mathematical methods in survival analysis, reliability and quality of life. In C. Huber, N. Limnios & M. Mesbah & M. Nikulin (Eds.), Wiley/ISTE. url Chiquet, J., & Limnios, N. (2006). Estimating stochastic dynamical systems driven by a continuous-time jump Markov process. Methodology and Computing in Applied Probability, 8, 431-447. url
Réseaux biologiques (2011). Chiquet, J. La gazette des mathématiciens No. 130 pp. 76–82 paper
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M.Sc. (2003). Estimation des températures journalières à l'aide de techniques markoviennes. mémoire
The teaching pages are in french.
Initiation à R (École doctorale GAO, Université d'Évry, intersemestre 2012)
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Camille Charbonnier started her thesis in september, 2009, under the supervision of Christophe Ambroise and myself. She is receiving a 3-year financial support from the french minister of Education and Research. She is working on statistical methods for Gaussian networks inference in a non-iid setting.
Jonathan Plassais started his thesis in october, 2010, under the supervision of Christophe Ambroise and myself. He is working half time at our laboratory, spending the rest of the week at TcLand expression, which supports half of the thesis. He is working on statistical methods to built gene signatures for Rheumatoid Arthritis from heterogeneous genomic data (microarray and SNPs).
LaTeX style-sheet for PhD Thesis
my .emacs
;; ==============================
;; Fichier .emacs: initialisation
;; ==============================
;; -----------------------------------------------------
;; ÉLÉMENTS DE CONFIGURATION STANDARDS
;; -----------------------------------------------------
;; Où aller chercher mes fichiers .el perso
(setq load-path (cons (expand-file-name "~/.emacs.d/") load-path))
;; Position et mise en forme de la fenêtre
(setq default-frame-alist'
((top . 00)
(left . 00)
(width . 85)
(vertical-scroll-bars . nil)))
(menu-bar-mode t)
(tool-bar-mode nil)
;; Font
(set-default-font "DejaVu Sans Mono-12")
;; Couleurs
(require 'color-theme)
(color-theme-ld-dark)
;; Répondre 'y' plutôt que 'yes'.
(defalias 'yes-or-no-p 'y-or-n-p)
;; Langue par défaut et caractères accentués
(setq current-language-environment "French")
;; Gestion du retour à la ligne
(add-hook 'text-mode-hook
(lambda ()
(auto-fill-mode 1)
(setq default-justification 'full)))
;; Pas de retour à la ligne au niveau des caractères : , ; etc.
(defun my-fill-nobreak-predicate ()
(save-match-data
(or (looking-at "[ \t]*[])}»!?;:]")
(looking-at "[ \t]*\\.\\.\\.")
(save-excursion
(skip-chars-backward " \t")
(backward-char 1)
(looking-at "[([{«]")))))
(setq fill-nobreak-predicate 'my-fill-nobreak-predicate)
;; Apparence similaire que le emacs 21.2
(require 'color-theme)
(color-theme-ld-dark)
(tool-bar-mode)
;; Pour que le curseur ne clignote plus
(blink-cursor-mode 0)
;; Reconnaissance syntaxique
(global-font-lock-mode t)
;; Favoris pour la sélection de région
(pc-selection-mode)
(pending-delete-mode t)
(setq transient-mark-mode t)
;; On fixe la longueur d'une tabulation
(setq c-basic-offset 2)
;; Pour avoir l'heure dans la barre d'etat, format 24 heures
(display-time)
(setq display-time-24hr-format t)
;; Actionvation de la molette de la souris
(require 'mwheel)
(mwheel-install)
;; Bips visuels plutôt que sonores
(setq visible-bell t)
;; Recherche non case-sensitive
(setq case-fold-search t)
;; Sauvegarde des fichiers récemment ouverts + création d'un raccourci
(add-to-list 'load-path "~/.emacs.d/lisp/recent")
(require 'recentf)
(recentf-mode 1)
(defun recentf-open-files-compl ()
(interactive)
(let* ((all-files recentf-list)
(tocpl (mapcar (function
(lambda (x) (cons (file-name-nondirectory x) x))) all-files))
(prompt (append '("File name: ") tocpl))
(fname (completing-read (car prompt) (cdr prompt) nil nil)))
(find-file (cdr (assoc-ignore-representation fname tocpl)))))
(global-set-key "\C-x\C-l" 'recentf-open-files-compl)
(require 'ido)
(ido-mode t)
;; -----------------------------------------------------
;; COMMANDES AucTeX / LaTeX
;; -----------------------------------------------------
(require 'tex-site)
(require 'font-latex)
(setq TeX-save-query nil)
;; Choix des programmes de visualition selon le fichier de sortie
(setq TeX-output-view-style (quote (("^pdf$" "." "evince %o") )))
;; Pour voir les les équations compilées directes dans emacs
;; (load "preview-latex.el" nil t t)
;; -----------------------------------------------------
;; CORRECTEUR ISPELL
;; -----------------------------------------------------
;: Dictionnaire francais
(setq-default ispell-program-name "aspell")
;; Empèche Ispell de vérifier le contenu de certaines commandes
(setq ispell-tex-skip-alists
(list
(append (car ispell-tex-skip-alists)
'(("\\\\cite" ispell-tex-arg-end)
("\\\\nocite" ispell-tex-arg-end)
("\\\\includegraphics" ispell-tex-arg-end)
("\\\\figScale" ispell-tex-arg-end)
("\\\\author" ispell-tex-arg-end)
("\\\\ref" ispell-tex-arg-end)
("\\\\eqref" ispell-tex-arg-end)
("\\\\label" ispell-tex-arg-end)
))
(cadr ispell-tex-skip-alists)))
;; Empèche Ispell de vérifier le contenu des citation natbib
(eval-after-load "ispell"
'(let ((list (car ispell-tex-skip-alists)))
(add-to-list 'list '("\\\\cite[tp]" ispell-tex-arg-end))
(setcar ispell-tex-skip-alists list))
)
;; Quelques commandes additionnelles du mode LaTeX
(add-hook 'LaTeX-mode-hook
(function
(lambda ()
(add-to-list 'TeX-command-list
(list "PDFLaTeX" "pdflatex %s.tex"
'TeX-run-command nil t))
(add-to-list 'TeX-command-list
(list "Acroread" "acroread %s.pdf"
'TeX-run-command nil t))
(add-to-list 'TeX-command-list
(list "XPDF" "xpdf -g 1280x1600 -z width %s.pdf"
'TeX-run-command nil t))
(add-to-list 'TeX-command-list
(list "Clean" "nettoyage"
'TeX-run-command nil t))
(add-to-list 'TeX-command-list
(list "Evince" "evince %s.pdf"
'TeX-run-command nil t))
(TeX-PDF-mode)
;gestion de la table matière et autre...
(reftex-mode)
;; Corrrection à la volée syntaxique
(flyspell-mode)
;; dictionnaire évitant les erreurs d'accents
(ispell-change-dictionary "francais")
)))
;; Aller à la prochaine erreur LaTeX
(global-set-key [f11] 'TeX-next-error) ; goto next found
; LaTeX error
(global-set-key [f12] 'next-error) ; goto next found lacheck
; error (run Check first)
;; mode Python
;; (autoload 'python-mode "python-mode" "Python editing mode." t)
;; Afficher la 'parenthèse correspondante'
(require 'paren)
(show-paren-mode t)
;; Parenthesage automatique
(defun brace-insert (sta stb stc)
(if (= (preceding-char) sta )
(insert stb)
(insert stc)
(backward-char 1)
)
)
(defun curly-braces () (interactive "*") (brace-insert ?\\ "{" "{}"))
(defun round-braces () (interactive "*") (brace-insert ?\\ "(" "()"))
(defun square-braces () (interactive "*") (brace-insert ?\\ "[" "[]"))
(defun dollar-braces () (interactive "*") (brace-insert ?\\ "$" "$$"))
(defun guillemet-braces () (interactive "*") (brace-insert ?\\ "«" "«»"))
(defun One-line-up () (interactive) (scroll-down 1))
(defun One-line-down () (interactive) (scroll-up 1))
(defun left-right () (interactive "*")
(insert "\\right")
(backward-char 7)
(insert "\\left")
(forward-char 1)
)
(global-set-key "{" 'curly-braces)
(global-set-key "(" 'round-braces)
(global-set-key "[" 'square-braces)
(global-set-key [(?«)] 'guillemet-braces)
(global-set-key "\C-\\" 'left-right)
(setq inhibit-startup-screen t)
(setq x-select-enable-clipboard t)
;; Copier / colelr vers d'autres applications
(setq selection-coding-system 'compound-text-with-extensions)
;; utf-8
(setq locale-coding-system 'utf-8)
(set-selection-coding-system 'utf-8)
(prefer-coding-system 'utf-8)
;;; impression avec la couleur
(autoload 'psprint "psprint")
(autoload 'psprint-all "psprint-all")
(global-set-key [f8 ?i] 'psprint)
(global-set-key [f8 ?p] 'psprint-all)
(setq delete-old-versions t)
(setq confirm-kill-emacs 'yes-or-no-p)
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