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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> | ||
- | ++++ |