====== Pierre Neuvial ======

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  * photo: {pierre.neuvial.jpg?20x25}
  * statut: CNRS research associate (CR2) {{members:pneuvial:cv-neuvial-20111212.pdf| CV as of 2011-12}}
  * mel: pierre.neuvial.png
  * tel: +33 1 64 85 35 44
  * fax: +33 1 64 85 36 01
)#

===== Publications =====
[[http://scholar.google.fr/citations?user=V2LO-5wAAAAJ|Google Scholar Citations profile]]
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==== Multiple testing ====
[[http://imgs.xkcd.com/comics/significant.png|An introduction (by xkcd)]] [[http://www.math-evry.cnrs.fr/_media/neuvial_inauguration.pdf|Another introduction (in French)]]
    - **On False Discovery Rate thresholding for classification under sparsity** (preprint). Neuvial, P. and Roquain, E. [[http://hal.archives-ouvertes.fr/hal-00604427|[preprint]]]
    - **Intrinsic bounds and false discovery rate control in multiple testing problems** (preprint). Neuvial, P. [[http://arxiv.org/abs/1003.0747|[preprint]]]
    - **Asymptotic properties of false discovery rate controlling procedures under independence **(2008). Neuvial, P. //Electron. J. Stat.// Vol. 2 pp. 1065--1110 [[http://dx.doi.org/10.1214/08-EJS207|[paper]]] [[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)}}
    - **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://cran.r-project.org/web/packages/aroma.cn|[R package: aroma.cn]]] [[http://aroma-project.org/vignettes/tumorboost-highlevel| [R vignette]]]
    - **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 =====
    - **Estimation of a non-parametric variable importance measure of a continuous exposure** (preprint). Chambaz, A. and Neuvial, P. and van der Laan, M.J. [[http://hal.archives-ouvertes.fr/hal-00629899|[preprint]]]
    - **More Power via Graph-Structured Tests for Differential Expression of Gene Networks** (to appear). Jacob, L. and Neuvial, P. and Dudoit, S. //Annals of Applied Statistics// [[http://www.e-publications.org/ims/submission/index.php/AOAS/user/submissionFile/8652?confirm=b67b9b50|[preprint]]] [[http://www.bioconductor.org/packages/release/bioc/html/DEGraph.html|[Bioconductor package: DEGraph]]]
    - **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** (2011). Heiser, L. M. et al. //PNAS// [[http://www.pnas.org/content/early/2011/10/13/1018854108.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]]]

==== Vulgarisation (popular science) ====
    - **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]}}


===== Teaching (in French, mostly) =====
==== 2011-2012 ====
=== Démarches statistiques (I) ===
TD du cours de [[http://stat.genopole.cnrs.fr/~mtaupin|Marie-Luce Taupin]] en [[http://www.univ-evry.fr/fr/formation/l_offre_de_formation/master_mention_sciences_du_genome_et_des_organismes_m1_tronc_commun.html|Master 1 SGO]] (Sciences du génome et des organismes) de l'[[http://www.univ-evry.fr|Université d'Évry]].

=== Analyse statistique de séquences biologiques et données de puces à ADN ===
Cours de Master M2 [[http://www.bibs.u-psud.fr|BIBS]] (Orsay), avec [[http://stat.genopole.cnrs.fr/~bprum|Bernard Prum]].\\
Les {{:members:pneuvial:neuvial_2011-2012_bibs_copyNumber.pdf|transparents}} de la partie "nombre de copies d'ADN".

=== Introduction aux méthodes statistiques en biologie moléculaire ===
Cours en troisième année (6h) à l'[[http://www.ensae.fr|ENSAE]], avec  [[http://stat.genopole.cnrs.fr/~cmatias|Catherine Matias]].\\
Les {{:members:pneuvial:neuvial_ensae_2011-2012_methstatgenomique.pdf|transparents}}.\\
NB: Dans la partie "tests multiples", l'accent est mis sur les résultats de statistique asymptotique.


=== Analyse statistique de données génomiques; applications en cancérologie ===
Séminaire professionnel (3h) à l'[[http://ensai.com|ENSAI]] (Rennes).\\
Les {{:members:pneuvial:neuvial_20111129_ensai.pdf|transparents}}.\\
NB: Version condensée où l'accent est mis sur les applications.

=== Statistical methods for genomic data analysis ===
Cours en deuxième année (6h) à [[http://www.ecp.fr|Centrale Paris]]\\
NB: En anglais.


===== Links =====
==== Software ====
  * [[http://aroma-project.org]]: An open-source R framework for your microarray analysis, by Henrik Bengtsson et al.

==== Co-authors ====
  * Henrik Bengtsson, University of California at San Francisco, Epidemiology & Biostatistics
  * [[http://www.math-info.univ-paris5.fr/~chambaz|Antoine Chambaz]], Université Paris Descartes, MAP5
  * [[http://cbio.ensmp.fr/~ljacob|Laurent Jacob]], University of California at Berkeley, Statistics
  * [[http://etienne.roquain.free.fr|Etienne Roquain]], Université Paris Diderot, LPMA.