Pierre Neuvial

Documents

Publications

	A two-sample tree-based test for hierarchically organized genomic signals Pierre Neuvial , Nathanaël Randriamihamison , Marie Chavent , Sylvain Foissac , Nathalie Vialaneix Journal of the Royal Statistical Society: Series C Applied Statistics, 2024, pp.qlae011. ⟨10.1093/jrsssc/qlae011⟩ Article dans une revue hal-04516167v1
	Post hoc false discovery proportion inference under a Hidden Markov Model Marie Perrot-Dockès , Gilles Blanchard , Pierre Neuvial , Etienne Roquain Test, 2023, ⟨10.1007/s11749-023-00886-7⟩ Article dans une revue hal-03214472v1
	WASCO: A Wasserstein-based Statistical Tool to Compare Conformational Ensembles of Intrinsically Disordered Proteins Javier González-Delgado , Amin Sagar , Christophe Zanon , Kresten Lindorff-Larsen , Pau Bernadó Journal of Molecular Biology, 2023, 435 (14), pp.168053. ⟨10.1016/j.jmb.2023.168053⟩ Article dans une revue hal-04056662v1
	Two-sample goodness-of-fit tests on the flat torus based on Wasserstein distance and their relevance to structural biology Javier González-Delgado , Alberto González-Sanz , Juan Cortés , Pierre Neuvial Electronic Journal of Statistics , 2023, 17 (1), pp.1547-1586. ⟨10.1214/23-EJS2135⟩ Article dans une revue hal-03369795v3
	Powerful and interpretable control of false discoveries in two-group differential expression studies Nicolas Enjalbert-Courrech , Pierre Neuvial Bioinformatics, 2022, ⟨10.1101/2022.03.08.483449⟩ Article dans une revue hal-03601095v2
	Statistical proofs of the interdependence between nearest neighbor effects on polypeptide backbone conformations Javier González-Delgado , Pau Bernadó , Pierre Neuvial , Juan Cortés Journal of Structural Biology, 2022, 214 (4), pp.107907. ⟨10.1016/j.jsb.2022.107907⟩ Article dans une revue hal-03826233v1
	Notip: Non-parametric True Discovery Proportion control for brain imaging Alexandre Blain , Bertrand Thirion , Pierre Neuvial NeuroImage, 2022, 260, pp.119492. ⟨10.1016/j.neuroimage.2022.119492⟩ Article dans une revue hal-03649114v3
	Applicability and interpretability of Ward's hierarchical agglomerative clustering with or without contiguity constraints Nathanaël Randriamihamison , Nathalie Vialaneix , Pierre Neuvial Journal of Classification, 2021, 38, pp.363-389. ⟨10.1007/s00357-020-09377-y⟩ Article dans une revue hal-02294847v2
	Identification of Deregulated Mechanisms Specific to Bladder Cancer Subtypes Magali Champion , Julien Chiquet , Pierre Neuvial , Mohamed Elati , François Radvanyi Journal of Bioinformatics and Computational Biology, 2021, 19 (1), ⟨10.1142/S0219720021400035⟩ Article dans une revue hal-03079966v1
	Post hoc false positive control for structured hypotheses Guillermo Durand , Gilles Blanchard , Pierre Neuvial , Etienne Roquain Scandinavian Journal of Statistics, 2020, 47 (4), pp.1114-1148. ⟨10.1111/sjos.12453⟩ Article dans une revue hal-01829037v3
	Single-Cell Virtual Cytometer allows user-friendly and versatile analysis and visualization of multimodal single cell RNAseq datasets Frédéric Pont , Marie Tosolini , Qing Gao , Marion Perrier , Miguel Madrid-Mencía NAR Genomics and Bioinformatics, 2020, 2 (2), ⟨10.1093/nargab/lqaa025⟩ Article dans une revue hal-02861405v1
	Post hoc confidence bounds on false positives using reference families Gilles Blanchard , Pierre Neuvial , Etienne Roquain Annals of Statistics, 2020, 48 (3), pp.1281-1303. ⟨10.1214/19-AOS1847⟩ Article dans une revue hal-01483585v5
	Adjacency-constrained hierarchical clustering of a band similarity matrix with application to Genomics Christophe Ambroise , Alia Dehman , Pierre Neuvial , Guillem Rigaill , Nathalie Vialaneix Algorithms for Molecular Biology, 2019, 14, pp.22. ⟨10.1186/s13015-019-0157-4⟩ Article dans une revue hal-02006331v2
	On the post selection inference constant under restricted isometry properties François Bachoc , Gilles Blanchard , Pierre Neuvial Electronic Journal of Statistics , 2018, 12 (2), ⟨10.1214/18-EJS1490⟩ Article dans une revue hal-03327160v3
	New insight for pharmacogenomics studies from the transcriptional analysis of two large-scale cancer cell line panels (vol 7, 15126, 2016) Benjamin Sadacca , Anne-Sophie Hamy , C. Laurent , Pierre Gestraud , Hélène Bonsang-Kitzis Scientific Reports, 2018, 8, ⟨10.1038/s41598-018-36812-3⟩ Article dans une revue hal-02619813v1
	New insight for pharmacogenomics studies from the transcriptional analysis of two large-scale cancer cell line panels Benjamin Sadacca , Anne-Sophie Hamy-Petit , Cecile Laurent , Pierre Gestraud , Hélène Bonsang-Kitzis Scientific Reports, 2017, 7 (1), pp.15126. ⟨10.1038/s41598-017-14770-6⟩ Article dans une revue hal-01634180v1
	Performance evaluation of DNA copy number segmentation methods Morgane Pierre-Jean , Guillem Rigaill , Pierre Neuvial Briefings in Bioinformatics, 2015, 16 (4), pp.600-615. ⟨10.1093/bib/bbu026⟩ Article dans une revue hal-00952896v2
	A model for gene deregulation detection using expression data Thomas Picchetti , Julien Chiquet , Mohamed Elati , Pierre Neuvial , Rémy Nicolle BMC Systems Biology, 2015, 9, ⟨10.1186/1752-0509-9-S6-S6⟩ Article dans une revue hal-01154154v2
	tmle.npvi: targeted, integrative search of associations between DNA copy number and gene expression, accounting for DNA methylation: Fig. 1. Antoine Chambaz , Pierre Neuvial Bioinformatics, 2015, 31 (18), pp.3054-6. ⟨10.1093/bioinformatics/btv320⟩ Article dans une revue hal-01113680v1
	Performance of a blockwise approach in variable selection using linkage disequilibrium information Alia Dehman , Christophe Ambroise , Pierre Neuvial BMC Bioinformatics, 2015, 16, pp.14. ⟨10.1186/s12859-015-0556-6⟩ Article dans une revue hal-01193074v1
	Asymptotic Results on Adaptive False Discovery Rate Controlling Procedures Based on Kernel Estimators Pierre Neuvial Journal of Machine Learning Research, 2013, 14, pp.1423-1459 Article dans une revue hal-00460677v2
	Stability-Based Comparison of Class Discovery Methods for DNA Copy Number Profiles Isabel Brito , Philippe Hupé , Pierre Neuvial , Emmanuel Barillot PLoS ONE, 2013, 8 (12), ⟨10.1371/journal.pone.0081458⟩ Article dans une revue hal-02643008v1
	Asymptotic Results on Adaptive False Discovery Rate Controlling Procedures Based on Kernel Estimators Pierre Neuvial Journal of Machine Learning Research, 2013, 14, pp.1423 - 1459 Article dans une revue hal-02644679v1
	Subtype and pathway specific responses to anticancer compounds in breast cancer. Laura M Heiser , Anguraj Sadanandam , Wen-Lin Kuo , Stephen C Benz , Theodore C Goldstein Proceedings of the National Academy of Sciences of the United States of America, 2012, 109 (8), pp.2724-9 Article dans une revue hal-01201568v1
	More power via graph-structured tests for differential expression of gene networks Laurent Jacob , Pierre Neuvial , Sandrine Dudoit Annals of Applied Statistics, 2012, 6 (2), pp.561-600. ⟨10.1214/11-AOAS528⟩ Article dans une revue hal-00521097v2
	Estimation of a non-parametric variable importance measure of a continuous exposure Antoine Chambaz , Pierre Neuvial , Mark van Der Laan Electronic Journal of Statistics , 2012, 6, pp.1059-1099. ⟨10.1214/12-EJS703⟩ Article dans une revue hal-00629899v1
	Stability-based comparison of class discovery methods for DNA copy number profiles. Isabel Brito , Philippe Hupé , Pierre Neuvial , Emmanuel Barillot PLoS ONE, 2012, 8 (12), pp.e81458 Article dans une revue hal-01201580v1
	On false discovery rate thresholding for classification under sparsity Pierre Neuvial , Etienne Roquain Annals of Statistics, 2012, 40 (5), pp.Vol. 40, No. 5, 2572-2600. ⟨10.1214/12-AOS1042⟩ Article dans une revue hal-00604427v3
	CalMaTe: a method and software to improve allele-specific copy number of SNP arrays for downstream segmentation Maria Ortiz-Estevez , Ander Aramburu , Henrik Bengtsson , Pierre Neuvial , Angel Rubio Bioinformatics, 2012, 28 (13), pp.1793-1794. ⟨10.1093/bioinformatics/bts248⟩ Article dans une revue hal-01200761v1
	Parent-specific copy number in paired tumor–normal studies using circular binary segmentation Adam B Olshen , Henrik Bengtsson , Pierre Neuvial , Paul T Spellman , Richard A Olshen Bioinformatics, 2011, 27 (15), pp.2038-2046. ⟨10.1093/bioinformatics/btr329⟩ Article dans une revue hal-01200750v1
	Statistiques et Génome Franck Picard , S. Schbath , E. Lebarbier , Pierre Neuvial , J. Chiquet Gazette des Mathématiciens, 2011, 130, pp.1-32 Article dans une revue hal-00698143v1
	Integrated genomic analyses of ovarian carcinoma. The Cancer Genome Atlas Research Network , Pierre Neuvial Nature, 2011, 474 (7353), pp.609-15 Article dans une revue hal-01201577v1
	TumorBoost: Normalization of allele-specific tumor copy numbers from a single pair of tumor-normal genotyping microarrays Henrik Bengtsson , Pierre Neuvial , Terence P Speed BMC Bioinformatics, 2010, pp.245. ⟨10.1186/1471-2105-11-245⟩ Article dans une revue hal-01199777v1
	Identification of a CpG island methylator phenotype that defines a distinct subgroup of glioma. Houtan Noushmehr , Daniel Weisenberger , Kristin Diefes , Heidi Phillips , Kanan Pujara Cancer Cell, 2010, 17 (5), pp.510-22. ⟨10.1016/j.ccr.2010.03.017⟩ Article dans une revue hal-01201573v1
	High-resolution mapping of DNA breakpoints to define true recurrences among ipsilateral breast cancers M. Bollet , N. Servant , Pierre Neuvial , C. Decraene , I. Lebigot JNCI: Journal of the National Cancer Institute, 2008, 100 (1), pp.48-58. ⟨10.1093/jnci/djm266⟩ Article dans une revue hal-00204833v1
	Asymptotic Properties of False Discovery Rate Controlling Procedures Under Independence Pierre Neuvial Electronic Journal of Statistics , 2008, 2, pp.1065-1110. ⟨10.1214/08-EJS20⟩ Article dans une revue hal-00286066v1
	LICORN: learning cooperative regulation networks from gene expression data. Mohamed Elati , Pierre Neuvial , Monique Bolotin-Fukuhara , Emmanuel Barillot , François Radvanyi Bioinformatics, 2007, 23 (18), pp.2407-14. ⟨10.1093/bioinformatics/btm352⟩ Article dans une revue hal-00192537v1
	Spatial normalization of array-CGH data. Pierre Neuvial , Philippe Hupé , Isabel Brito , Stéphane Liva , Elodie Manié BMC Bioinformatics, 2006, 7, pp.264. ⟨10.1186/1471-2105-7-264⟩ Article dans une revue inserm-00089910v1
	VAMP: Visualization and analysis of array-CGH, transcriptome and other molecular profiles Philippe La Rosa , Eric Viara , Philippe Hupé , Gaëlle Pierron , Stéphane Liva Bioinformatics, 2006, 22 (17), pp.2066-2073. ⟨10.1093/bioinformatics/btl359⟩ Article dans une revue hal-01199867v1
	CAPweb: a bioinformatics CGH array Analysis Platform Stéphane Liva , Philippe Hupé , Pierre Neuvial , Isabel Brito , Eric Viara Nucleic Acids Research, 2006, 34 (W), pp.477-481. ⟨10.1093/nar/gkl215⟩ Article dans une revue hal-01199870v1

	Vers une médecine personnalisée grâce à la recherche en génomique Pierre Neuvial 2013 Autre publication scientifique hal-01201657v1
	Tests multiples en génomique Pierre Neuvial 2011, No. 130 pp. 71-76 Autre publication scientifique hal-01201629v1
	Problématiques statistiques à l'heure de la post-génomique Pierre Neuvial , Pierre-Yves Bourguignon 2009 Autre publication scientifique hal-01201651v1

	Classification ascendante hiérarchique, contrainte d'ordre : conditions d'applicabilité, interprétabilité des dendrogrammes Nathanaël Randriamihamison , Pierre Neuvial , Nathalie Vialaneix Conférence sur l'Apprentissage Automatique (CAp 2019), Jul 2019, Toulouse, France. , 2019 Poster de conférence hal-02786174v1
	Adjacency-constrained hierarchical clustering of a band similarity matrix with application to genomics Christophe Ambroise , Alia Dehman , Pierre Neuvial , Guillem Rigaill , Nathalie Vialaneix Statistical Methods for Post Genomic Data (SMPGD 2019), Jan 2019, Barcelona, Spain. 2019 Poster de conférence hal-02790995v1

	False Discovery Proportion control for aggregated Knockoffs Alexandre Blain , Bertrand Thirion , Olivier Grisel , Pierre Neuvial NeurIPS 2023 – 37th Conference on Neural Information Processing Systems, Dec 2023, New Orleans, United States. ⟨10.48550/arXiv.2310.10373⟩ Communication dans un congrès hal-04250621v1
	Identification of deregulated transcription factors involved in subtypes of cancers Magali Champion , Julien Chiquet , Pierre Neuvial , Mohamed Elati , François Radvanyi Proceedings of the 12th International Conference on Bioinformatics and Computational Biology, Mar 2020, SAN FRANCISCO, United States. pp.1--10, ⟨10.29007/v7qj⟩ Communication dans un congrès hal-01516892v2
	Analyse différentielle de données Hi-C via la Classification Ascendante Hiérarchique sous Contrainte de Contiguïté Nathanaël Randriamihamison , Marie Chavent , Sylvain Foissac , Nathalie Vialaneix , Pierre Neuvial 52èmes Journées de Statistiques de la SFdS, Société Française de Statistique, May 2020, Nice, France. pp.655-660 Communication dans un congrès hal-02892664v1
	Classification ascendante hiérarchique, contrainte d'ordre : conditions d'applicabilité, interprétabilité des dendrogrammes Nathanaël Randriamihamison , Pierre Neuvial , Nathalie Vialaneix 51èmes Journées de Statistique de la SFdS, Jun 2019, Nancy, France Communication dans un congrès hal-02734011v1
	Adjacency-constrained hierarchical clustering of a band similarity matrix with application to genomics Christophe Ambroise , Alia Dehman , Michel Koskas , Pierre Neuvial , Guillem Rigaill Journée Régionale de Bioinformatique et Biostatistique, Génopole Toulouse, Dec 2018, Toulouse, France Communication dans un congrès hal-02788245v1

	Contributions to statistical inference from genomic data Pierre Neuvial Statistics [math.ST]. Université Toulouse III Paul Sabatier, 2020 HDR tel-02969229v1

	Comprendre l'organisation spatiale de l'ADN à l'aide de la statistique Pierre Neuvial , Sylvain Foissac , Nathalie Vialaneix Martina Knoop, Stéphane Blanc, Mokrane Bouzeghoub. L’Interdisciplinarité, CNRS Editions, pp.178-182, 2023 Chapitre d'ouvrage hal-03930070v1
	On agnostic post hoc approaches to false positive control Gilles Blanchard , Pierre Neuvial , Etienne Roquain Xinping Cui, Thorsten Dickhaus, Ying Ding, Jason C. Hsu. Handbook of Multiple Comparisons, Chapman & Hall/CRC, 2021, Handbooks of Modern Statistical Methods, 9780367140670 Chapitre d'ouvrage hal-02320543v2
	Statistical analysis of Single Nucleotide Polymorphism microarrays in cancer studies Pierre Neuvial , Henrik Bengtsson , Terence Paul Speed Handbook of Statistical Bioinformatics, 2011, Springer Handbooks of Computational Statistics, 978-3-642-16344-9. ⟨10.1007/978-3-642-16345-6_11⟩ Chapitre d'ouvrage hal-00497273v1

	Selective inference after convex clustering with $\ell_1$ penalization François Bachoc , Cathy Maugis , Pierre Neuvial 2023 Pré-publication, Document de travail hal-04200062v1
	Post-clustering Inference under Dependency Javier González-Delgado , Juan Cortés , Pierre Neuvial 2023 Pré-publication, Document de travail hal-04250364v1

	adjclust: Adjacency-Constrained Clustering of a Block-Diagonal Similarity Matrix (R package, available on CRAN) Pierre Neuvial , Christophe Ambroise , Shubham Chaturvedi , Alia Dehman , Michel Koskas 2017 Logiciel hal-02791370v1

	Contributions to the statistical analysis of microarray data. Pierre Neuvial Life Sciences [q-bio]. Université Paris-Diderot - Paris VII, 2009. English. ⟨NNT : ⟩ Thèse tel-00433045v1

Pierre Neuvial

Publications

A two-sample tree-based test for hierarchically organized genomic signals

Post hoc false discovery proportion inference under a Hidden Markov Model

WASCO: A Wasserstein-based Statistical Tool to Compare Conformational Ensembles of Intrinsically Disordered Proteins

Two-sample goodness-of-fit tests on the flat torus based on Wasserstein distance and their relevance to structural biology

Powerful and interpretable control of false discoveries in two-group differential expression studies

Statistical proofs of the interdependence between nearest neighbor effects on polypeptide backbone conformations

Notip: Non-parametric True Discovery Proportion control for brain imaging

Applicability and interpretability of Ward's hierarchical agglomerative clustering with or without contiguity constraints

Identification of Deregulated Mechanisms Specific to Bladder Cancer Subtypes

Post hoc false positive control for structured hypotheses

Single-Cell Virtual Cytometer allows user-friendly and versatile analysis and visualization of multimodal single cell RNAseq datasets

Post hoc confidence bounds on false positives using reference families

Adjacency-constrained hierarchical clustering of a band similarity matrix with application to Genomics

On the post selection inference constant under restricted isometry properties

New insight for pharmacogenomics studies from the transcriptional analysis of two large-scale cancer cell line panels (vol 7, 15126, 2016)

New insight for pharmacogenomics studies from the transcriptional analysis of two large-scale cancer cell line panels

Performance evaluation of DNA copy number segmentation methods

A model for gene deregulation detection using expression data

tmle.npvi: targeted, integrative search of associations between DNA copy number and gene expression, accounting for DNA methylation: Fig. 1.

Performance of a blockwise approach in variable selection using linkage disequilibrium information

Asymptotic Results on Adaptive False Discovery Rate Controlling Procedures Based on Kernel Estimators

Stability-Based Comparison of Class Discovery Methods for DNA Copy Number Profiles

Asymptotic Results on Adaptive False Discovery Rate Controlling Procedures Based on Kernel Estimators

Subtype and pathway specific responses to anticancer compounds in breast cancer.

More power via graph-structured tests for differential expression of gene networks

Estimation of a non-parametric variable importance measure of a continuous exposure

Stability-based comparison of class discovery methods for DNA copy number profiles.

On false discovery rate thresholding for classification under sparsity

CalMaTe: a method and software to improve allele-specific copy number of SNP arrays for downstream segmentation

Parent-specific copy number in paired tumor–normal studies using circular binary segmentation

Statistiques et Génome

Integrated genomic analyses of ovarian carcinoma.

TumorBoost: Normalization of allele-specific tumor copy numbers from a single pair of tumor-normal genotyping microarrays

Identification of a CpG island methylator phenotype that defines a distinct subgroup of glioma.

High-resolution mapping of DNA breakpoints to define true recurrences among ipsilateral breast cancers

Asymptotic Properties of False Discovery Rate Controlling Procedures Under Independence

LICORN: learning cooperative regulation networks from gene expression data.

Spatial normalization of array-CGH data.

VAMP: Visualization and analysis of array-CGH, transcriptome and other molecular profiles

CAPweb: a bioinformatics CGH array Analysis Platform

Vers une médecine personnalisée grâce à la recherche en génomique

Tests multiples en génomique

Problématiques statistiques à l'heure de la post-génomique

Classification ascendante hiérarchique, contrainte d'ordre : conditions d'applicabilité, interprétabilité des dendrogrammes

Adjacency-constrained hierarchical clustering of a band similarity matrix with application to genomics

False Discovery Proportion control for aggregated Knockoffs

Identification of deregulated transcription factors involved in subtypes of cancers

Analyse différentielle de données Hi-C via la Classification Ascendante Hiérarchique sous Contrainte de Contiguïté

Classification ascendante hiérarchique, contrainte d'ordre : conditions d'applicabilité, interprétabilité des dendrogrammes

Adjacency-constrained hierarchical clustering of a band similarity matrix with application to genomics

Contributions to statistical inference from genomic data

Comprendre l'organisation spatiale de l'ADN à l'aide de la statistique

On agnostic post hoc approaches to false positive control

Statistical analysis of Single Nucleotide Polymorphism microarrays in cancer studies

Selective inference after convex clustering with $\ell_1$ penalization

Post-clustering Inference under Dependency

adjclust: Adjacency-Constrained Clustering of a Block-Diagonal Similarity Matrix (R package, available on CRAN)

Contributions to the statistical analysis of microarray data.