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members:pneuvial:welcome [2016/06/20 00:42]
Pierre Neuvial
members:pneuvial:welcome [2016/12/07 01:13] (current)
Pierre Neuvial
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 ====== Pierre Neuvial ====== ====== Pierre Neuvial ======
- 
-<WRAP group> 
-<wrap first column> [[http://​biomaths.genopole.fr|{{http://​www.genopole.fr/​newsletter/​evt/​2015_biomaths/​img/​img_01.jpg?​180}}]] </​wrap>​ 
-<wrap second column> CNRS researcher (CR1) \\ 
-Université d'​Évry Val d'​Essonne \\ 
-Laboratoire de Mathématiques et Modélisation d'​Évry (UMR 8071) \\ 
-I.B.G.B.I., 23 Bd. de France, 91037 Évry Cedex \\ 
-☎   +33 1 64 85 35 44 \\ 
-<​Firstname.Lastname@math.cnrs.fr>​ \\ 
-{{:​members:​pneuvial:​cv-neuvial-20160620.pdf|CV as of 2016-06}}\\ 
-[[http://​scholar.google.fr/​citations?​user=V2LO-5wAAAAJ|Google Scholar Citations profile]]\\ 
-</​wrap>​ 
-</​WRAP>​ 
  
 <note important>​ <note important>​
-Conference Statistical analysis of massive genomic data (Evry, Nov 19-20 2015): \\ +In September 2016 I have moved to Institut Mathématique de Toulouse. ​ 
-the **[[http://relaiswebcasting.mediasite.com/​mediasite/​Catalog/​catalogs/​biomathematics2015|videos]]** and **[[evenements:​conferences:​samgd2015|posters]]** are online See also the [[http://biomaths.genopole.fr|SAMGD web page]].+See my current ​[[https://www.math.univ-toulouse.fr/~pneuvial/ 
 +|web page]]
 </​note>​ </​note>​
  
  
-===== Publications ===== 
- 
-++++ Toggle publication list by year| 
-<​btex>​auth:​neuvial</​btex>​ 
-++++ 
- 
-==== Multiple testing ==== 
-Introduction to [[http://​xkcd.com/​1478/​|testing]] and to [[http://​xkcd.com/​882|multiple testing]] (by xkcd) 
-[[http://​www.math-evry.cnrs.fr/​_media/​neuvial_inauguration.pdf|Another introduction (in French)]] 
-    - **Asymptotic Results on Adaptive False Discovery Rate Controlling Procedures Based on Kernel Estimators** (2013). Neuvial, P. //Journal of Machine Learning Research// Vol. 14, pp 1423−1459 [[http://​jmlr.org/​papers/​v14/​neuvial13a.html|[url]]] [[http://​jmlr.org/​papers/​volume14/​neuvial13a/​neuvial13a.pdf|[pdf]]] 
-    - **On False Discovery Rate thresholding for classification under sparsity** (2012). Neuvial, P. and Roquain, E. //Annals of Statistics//​ Vol. 40, No. 5, pp. 2572-2600 [[http://​projecteuclid.org/​DPubS?​service=UI&​version=1.0&​verb=Display&​handle=euclid.aos/​1359987531|[url]]] [[http://​arxiv.org/​pdf/​1106.6147v3.pdf|[pdf]]] 
-    - **Asymptotic properties of false discovery rate controlling procedures under independence **(2008). Neuvial, P. //​Electronic Journal of Statistics//​ Vol. 2 pp. 1065--1110 [[http://​dx.doi.org/​10.1214/​08-EJS207|[url]]] [[http://​projecteuclid.org/​DPubS/​Repository/​1.0/​Disseminate?​view=body&​id=pdfview_1&​handle=euclid.ejs/​1227287693|[pdf]]] [[http://​dx.doi.org/​10.1214/​09-EJS519|[corrigendum]]] 
-==== Statistical methods for DNA copy number analyses ===== 
-{{:​members:​pneuvial:​neuvial_2011-2012_statsingenomics_ecp_copynumber.pdf|Introductory slides (12/2011, Centrale ParisTech)}} 
-    - ** A performance evaluation framework of DNA copy number analysis methods in cancer studies; application to SNP array data segmentation methods** (2015). Pierre-Jean,​ M. and Rigaill, G. and Neuvial, P. //Briefings in Bioinformatics.//​ Vol. 16 No. 4 pp. 600-615 [[http://​arxiv.org/​abs/​1402.7203|[arxiv preprint]]] 
-    - **Stability-based comparison of class discovery methods for array-CGH profiles** (2013). Brito, I. and Hupé, P. and Neuvial, P. and Barillot, E. //PLoS One// Vol. 8 No. 12 pp. e81458 [[http://​www.plosone.org/​article/​info%3Adoi%2F10.1371%2Fjournal.pone.0081458|[paper]]] 
-    - **CalMaTe: A Method and Software to Improve Allele-Specific Copy Number of SNP Arrays for Downstream Segmentation** (2012). Ortiz-Estevez,​ M. and Aramburu, A. and Bengtsson, H. and Neuvial, P. and Rubio, A. //​Bioinformatics//​ Vol. 28 No. 13 pp. 1793-1794 [[http://​bioinformatics.oxfordjournals.org/​content/​28/​13/​1793|[paper]]] [[http://​cran.r-project.org/​web/​packages/​calmate|[R package: calmate]]] [[http://​aroma-project.org/​vignettes/​CalMaTe|[R vignette]]] 
-    - **Parent-specific copy number in paired tumor-normal studies using circular binary segmentation** (2011). Olshen, A.B. et al. //​Bioinformatics//​ Vol. 27 No. 15 pp. 2038-2046 [[http://​bioinformatics.oxfordjournals.org/​content/​27/​15/​2038|[paper]]] [[http://​cran.r-project.org/​web/​packages/​PSCBS|[R package: PSCBS]]] ​ [[http://​aroma-project.org/​vignettes/​PairedPSCBS-lowlevel|[R vignette]]] 
-    - **Statistical analysis of genotyping microarrays in cancer studies** (2011). ​ Neuvial, P. and Bengtsson, H. and Speed, T.P. Book chapter in //Handbook of Statistical Bioinformatics//​. pp. 225-255. Springer. [[http://​hal.archives-ouvertes.fr/​hal-00497273/​en|[paper]]] 
-    - **TumorBoost:​ Normalization of allele-specific tumor copy numbers from a single pair of tumor-normal genotyping microarrays** (2010). Bengtsson, H. and Neuvial, P. and Speed, T.P. //BMC Bioinformatics//​ Vol. 11 No. 1 pp. 245 [[http://​www.biomedcentral.com/​1471-2105/​11/​245|[paper]]] [[http://​aroma-project.org/​vignettes/​tumorboost-highlevel| [R vignette (high-level)]]] [[http://​aroma-project.org/​vignettes/​tumorboost-lowlevel| [R vignette (low-level)]]] Slides: [[http://​aroma-project.org/​share/​presentations/​neuvial,​2010,​CSB,​TumorBoost,​shortTalk.pdf|[short version]]],​[[http://​aroma-project.org/​share/​presentations/​neuvial_20091001_statGen.pdf|[longer version]]] 
-    - **CAPweb: a bioinformatics CGH array Analysis Platform** (2006). Liva, S. et al.// Nucleic Acids Res// Vol. 34(Web Server issue) No. - pp. 477--481 [[http://​dx.doi.org/​10.1093/​nar/​gkl215|[paper]]] 
-    - **Spatial normalization of array-CGH data** (2006). Neuvial, P. and Hupé, P. et al. //BMC Bioinformatics//​ Vol. 7 No. 1 pp. 264 [[http://​www.biomedcentral.com/​1471-2105/​7/​264|[paper]]] 
-    - **VAMP: visualization and analysis of array-CGH, transcriptome and other molecular profiles** (2006). La Rosa, P. et al (2006). //​Bioinformatics//​ Vol. 22 No. 17 pp. 2066--2073 [[http://​bioinformatics.oxfordjournals.org/​cgi/​content/​abstract/​btl359|[paper]]] 
- 
- 
-==== Statistical methods for high-throughput genomic data analyses ===== 
-    - **A model for gene deregulation detection using expression data** //BMC Systems Biology// 9(Suppl 6):S6. Picchetti, T. and Chiquet, J. and Elati, M. and Neuvial, P. and Nicolle, R. and Birmelé, E. [[https://​hal.archives-ouvertes.fr/​hal-01154154v2|[Hal preprint]]]. Presented at the [[http://​www.jsbi.org/​giw-incob2015|GIW/​InCoB 2015]] conference. 
-    - **tmle.npvi:​ targeted, integrative search of associations between DNA copy number and gene expression, accounting for DNA methylation** //​Bioinformatics (Application Note)// Vol. 31(18):​3054-6. Chambaz, A. and Neuvial, P.  [[https://​hal.archives-ouvertes.fr/​hal-01113680|[Hal preprint]]][[http://​cran.r-project.org/​web/​packages/​tmle.npvi/​index.html|[R package: tmle.npvi]]] 
-    - **Performance of a Blockwise Approach in Variable Selection using Linkage Disequilibrium Information** (2015), Dehman, A. and Ambroise, C. and Neuvial, P. //BMC Bioinformatics//​ [[http://​www.biomedcentral.com/​1471-2105/​16/​148|[url]]][[http://​www.math-evry.cnrs.fr/​publications/​logiciels|[R package: BALD]]] 
-    - **Estimation of a non-parametric variable importance measure of a continuous exposure** (2012). Chambaz, A. and Neuvial, P. and van der Laan, M.J. //​Electronic journal of Statistics//​ Vol. 6 pp 1059-1099 [[http://​projecteuclid.org/​DPubS?​service=UI&​version=1.0&​verb=Display&​handle=euclid.ejs/​1340369355|[paper]]] {{:​members:​pneuvial:​neuvial_201203_tmle.npvi_fr.pdf|[extended abstract (in French)]}}{{:​members:​pneuvial:​neuvial_20120829_mas2012_clermont.pdf|[slides (08/​2012)]}} 
-    - **More Power via Graph-Structured Tests for Differential Expression of Gene Networks** (2012). Jacob, L. and Neuvial, P. and Dudoit, S. //Annals of Applied Statistics//​ Vol. 6 No. 2 pp 561–600 ​ [[http://​projecteuclid.org/​DPubS?​service=UI&​version=1.0&​verb=Display&​handle=euclid.aoas/​1339419608|[url]]] ​ {{:​members:​pneuvial:​aoas528.pdf|[pdf]}} [[http://​www.bioconductor.org/​packages/​release/​bioc/​html/​DEGraph.html|[Bioconductor package: DEGraph]]] {{:​members:​pneuvial:​neuvial_20120127_smpgd_pathwaytesting.pdf|[slides (01/​2012)]}} 
-    - **LICORN: LearIng COoperative Regulation Networks** (2008). Elati, M. and Neuvial, P. and Bolotin-Fukuhara,​ M. and Barillot, E. and Radvanyi, F. and Rouveirol, C. //​Bioinformatics//​ Vol. 23 No. 18 pp. 2407--2414. [[http://​bioinformatics.oxfordjournals.org/​content/​23/​18/​2407|[paper]]] 
-==== Applications to cancer research ==== 
-    - **Subtype and pathway specific responses to anticancer compounds in breast cancer** (2012). Heiser, L. M. et al. //PNAS// [[http://​www.pnas.org/​content/​109/​8/​2724.abstract|[paper]]] 
-    - **Integrated Genomic Analyses of Ovarian Carcinoma** (2011). The Cancer Genome Atlas Network. Nature Vol. 474 No. 7353 pp. 609--615 ​ [[http://​dx.doi.org/​10.1038/​nature10166|[paper]]] 
-    - **Identification of a CpG Island Methylator Phenotype that Defines a Distinct Subgroup of Glioma** (2010). Noushmehr, H. et al. //Cancer cell// Vol. 17 No. 5 pp. 510--522 [[http://​www.cell.com/​cancer-cell/​abstract/​S1535-6108(10)00108-X|[paper]]] 
-    - **High-resolution mapping of DNA breakpoints to define true recurrences among ipsilateral breast cancers** (2008). Bollet, M. et al. //J Natl Cancer Inst// Vol. 100 No. 1 pp. 48--58 [[http://​jnci.oxfordjournals.org/​cgi/​content/​abstract/​100/​1/​48|[paper]]] 
- 
-==== General audience ==== 
-    - **Vers une médecine personnalisée grâce à la recherche en génomique** (2013). Neuvial, P. Variances Vol. 48 pp 31--33 {{:​members:​pneuvial:​papers/​neuvial13variances.pdf|[paper]}} 
-    - **Tests multiples en génomique** (2011). ​ Neuvial, P.  //La gazette des mathématiciens//​ No. 130 pp. 71--76 [[http://​smf4.emath.fr/​Publications/​Gazette/​2011/​130/​smf_gazette_130_71-76.pdf|[paper]]] 
-    - **Problématiques statistiques à l'​heure de la post-génomique** (2009). Neuvial, P. and Bourguignon,​ P.-Y. //​Variances//​ Vol. 35 pp. 56--60 {{variances.pdf|[paper]}} 
- 
- 
-===== PhD students ===== 
- 
-  * Guillermo Durand (2015-): "​Multiple testing for structured biological data". Co-supervised with [[http://​etienne.roquain.free.fr|Etienne Roquain]]. Funded by Université Paris 6. 
-  * Benjamin Sadacca (2013-): "​Tumoral microenvironment and treatment response in breast cancers"​. Co-supervised with [[http://​www.institut-curie.org/​research/​residual-tumour-and-treatment-response|Fabien Reyal]]. Funded by Institut Curie. 
-  * Morgane Pierre-Jean (2013-): "​Statistical methods for the analysis of structured genomic data". Funded by École doctorale GAO, University of Évry. 
-  * Alia Dehman (2012-2015/​12/​9):​ "​Structured sparse regression for Genome-Wide Association Studies"​. Co-supervised with [[[members:​cambroise:​welcome|Christophe Ambroise]]. Funded by École doctorale GAO, University of Évry. 
- 
- 
-===== Teaching===== 
- 
-2015-2016 
- 
-  * [[members:​pneuvial:​teaching:​isg|Programming for Genomics]]. [[http://​www.univ-evry.fr|Université d'​Evry]],​ Master 2 Ingénierie Statistique pour la Génomique (ISG) 
-  * {{:​members:​pneuvial:​teaching:​neuvial_2015_methstatgenomique_dsa.pdf|Statistique en grande dimension et génomique: segmentation de données de nombres de copies d'ADN en cancérologie}}. Formation [[http://​www.institutdesactuaires.com/​gene/​main.php?​base=943|Data science pour l'​actuariat]] à l'​[[http://​www.institutdesactuaires.com|Institut des Actuaires]],​ décembre 2015.  
- 
-2014-2015 (in French) 
- 
-  * [[members:​pneuvial:​demstat|Démarche Statistique I]]. [[http://​www.univ-evry.fr|Université d'​Evry]],​ Master 1 mention SGO 
-  * [[members:​pneuvial:​teaching:​bibs|Analyse statistique des données génomiques]] (a.k.a. "​ASBDE"​). Université Paris Sud, Master 2 [[http://​www.bibs.u-psud.fr|BIBS]] 
-  * [[members:​pneuvial:​teaching:​ensae|Introduction aux méthodes statistiques en biologie moléculaire]]. [[http://​www.ensae.fr|ENSAE]] ParisTech, troisième année. Avec  [[http://​cmatias.perso.math.cnrs.fr|Catherine Matias]].\\ 
- 
-===== Software ===== 
-<​html><​a href="​http://​depsy.org/​person/​331501">​ 
-    <img src="​http://​depsy.org/​api/​person/​331501/​badge.svg">​ 
-</​a></​html>​(essentially driven by the contributions of [[http://​www.epibiostat.ucsf.edu/​epidem/​personnel/​hbengtsson.html|Henrik Bengtsson]]) 
-  * [[http://​aroma-project.org]]:​ An open-source R framework for your microarray analysis, by Henrik Bengtsson et al. 
-  * R package [[logiciels:​bald|BALD]] 
-  * R package [[logiciels:​jointseg|jointseg]] 
-  * R package [[logiciels:​tmle.npvi|tmle.npvi]] 
-Other [[publications:​logiciels|software from LaMME]] 
- 
-===== Some co-authors ===== 
-  * [[http://​www.epibiostat.ucsf.edu/​epidem/​personnel/​hbengtsson.html|Henrik Bengtsson]],​ University of California at San Francisco, Epidemiology & Biostatistics. 
-  * [[http://​www.math-info.univ-paris5.fr/​~chambaz|Antoine Chambaz]], Université Paris Ouest Nanterre, Modal'​X. 
-  * [[http://​lbbe.univ-lyon1.fr/​-Jacob-Laurent-.html|Laurent Jacob]], Laboratoire de Biométrie et Biologie Évolutive, Lyon. 
-  * [[http://​etienne.roquain.free.fr|Etienne Roquain]], Université Pierre et Marie Curie, LPMA. 
- 
-++++ my .screenrc| 
- 
-<​code>​ 
-verbose on 
- 
-# visual bell 
-vbell on 
- 
-# startup message 
-startup_message off 
- 
-# increase default scrollback 
-defscrollback 10000 
- 
-# customization of the screen window 
-caption always "​%{wk}%h %=%c" 
-hardstatus alwayslastline "​%{=b}%{G}Screen(s):​ %{w}%-Lw%n%f* %t%{-}%{w}%+Lw%=%{G}Connected \ 
-to %H" 
- 
- 
-# default programs 
-screen -t bash 
-screen -t emacs emacs 
-screen -t R R 
-screen -t htop htop 
-</​code>​ 
-++++ 
members/pneuvial/welcome.txt · Last modified: 2016/12/07 01:13 by Pierre Neuvial

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