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An introduction (by xkcd) Another introduction (in French)

1. 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 [url] [pdf]
2. Asymptotic Results on Adaptive False Discovery Rate Controlling Procedures Based on Kernel Estimators (preprint). Neuvial, P. [HAL preprint] [(older version)]
3. Asymptotic properties of false discovery rate controlling procedures under independence (2008). Neuvial, P. Electronic Journal of Statistics Vol. 2 pp. 1065–1110 [url] [pdf] [corrigendum]

Introductory slides (12/2011, Centrale ParisTech)

1. 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 [paper] [R package: calmate] [R vignette]
2. 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 [paper] [R package: PSCBS] [R vignette]
3. 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. [paper]
4. 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 [paper] [R vignette (high-level)] [R vignette (low-level)]
5. CAPweb: a bioinformatics CGH array Analysis Platform (2006). Liva, S. et al. Nucleic Acids Res Vol. 34(Web Server issue) No. - pp. 477–481 [paper]
6. Spatial normalization of array-CGH data (2006). Neuvial, P. and Hupé, P. et al. BMC Bioinformatics Vol. 7 No. 1 pp. 264 [paper]
7. 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 [paper]

1. 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 [paper] [extended abstract (in French)][slides (08/2012)]
2. 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 [url] [pdf] [Bioconductor package: DEGraph] [slides (01/2012)]
3. 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. [paper]

1. Subtype and pathway specific responses to anticancer compounds in breast cancer (2012). Heiser, L. M. et al. PNAS [paper]
2. Integrated Genomic Analyses of Ovarian Carcinoma (2011). The Cancer Genome Atlas Network. Nature Vol. 474 No. 7353 pp. 609–615 [paper]
3. 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 [paper]
4. 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 [paper]

1. Tests multiples en génomique (2011). Neuvial, P. La gazette des mathématiciens No. 130 pp. 71–76 [paper]
2. Problématiques statistiques à l'heure de la post-génomique (2009). Neuvial, P. and Bourguignon, P.-Y. Variances Vol. 35 pp. 56–60 [paper]

Cours (24h) de Master M2 BIBS (Orsay).
Les transparents de l'ensemble du cours, et par chapitre:

• nombre de copies d'ADN
• tests multiples
• classification

Cours (8h) en troisième année à l'ENSAE, avec Catherine Matias.
Les transparents.
NB: Dans la partie “tests multiples”, l'accent est mis sur les résultats de statistique asymptotique.

• From the lab
• R package jointSeg:

install.packages("jointSeg", repos="http://R-Forge.R-project.org")

• http://aroma-project.org: An open-source R framework for your microarray analysis, by Henrik Bengtsson et al.

• Henrik Bengtsson, University of California at San Francisco, Epidemiology & Biostatistics
• Antoine Chambaz, Université Paris Ouest Nanterre, Modal'X
• Laurent Jacob, University of California at Berkeley, Statistics
• Etienne Roquain, Université Paris Diderot, LPMA.

my .screenrc

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"