Guillem Rigaill

Documents

Publications

	Fast tree aggregation for consensus hierarchical clustering: application to multi-omics data analysis Audrey Hulot , Julien Chiquet , Florence Jaffrezic , Guillem Rigaill Statistical Methods for Post-Genomic Data (SMPGD), 2019, Barcelona, Spain Communication dans un congrès hal-02483674v1
	Impact of host partial resistance on the gene expression of Phytophthora capsici: consequences for pepper breeding Véronique Lefebvre , Gaëtan Maillot , Emmanuel Szadkowski , Bernard Caromel , Anne Massire 17. Eucarpia Meeting on Genetics and Breeding of Capsicum and Eggplant (2019), Sep 2019, Avignon, France Communication dans un congrès hal-02735621v1
	Changepoint detection in the presence of outliers and constraints. Guillem Rigaill Journées du GDR Stat et Santé, Oct 2019, Paris, France Communication dans un congrès hal-02961197v1
	A statistical method to detect abrupt changes in trees. Guillem Rigaill Workshop Change Point Detection: Limit Theorems, Algorithms, and Applications in Life Sciences., Jul 2019, Greifswald, Germany Communication dans un congrès hal-02961195v1
	Changepoint detection in the presence of outliers Guillem Rigaill Statistical Scalability Workshop 2018, Apr 2018, Windemere, United Kingdom Communication dans un congrès hal-02961189v1
	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
	Fused-ANOVA : une méthode de clustering en grande dimension Audrey Hulot , Julien Chiquet , Florence Jaffrezic , Guillem Rigaill 50èmes Journées de Statistique, 2018, Palaiseau, France Communication dans un congrès hal-02483532v1
	PeakSeg: constrained optimal segmentation and supervised penalty learning for peak detection in count data Toby Hocking , Guillem Rigaill , Guillaume Bourque ICML 2015, 2015, Lille, France Communication dans un congrès hal-02744063v1
	The Wnt3a targetome in triple-negative breast cancer cell lines Sylvie Maubant , Bruno Tesson , Virginie Maire , Mengliang Ye , Guillem Rigaill 106. Annual Meeting of the American-Association-for-Cancer-Research (AACR), American Association for Cancer Research (AACR). USA., Apr 2015, Philadelphie, United States. 1 p., ⟨10.1158/1538-7445.AM2015-41⟩ Communication dans un congrès hal-02739832v1
	On exact multiple changepoint algorithms. Optimal partitioning and functional pruning Guillem Rigaill Inference for Change-Point and Related Processes, University of Cambridge [UK] (CAM). GBR., Jan 2014, Cambridge, United Kingdom Communication dans un congrès hal-02796353v1
	On exact multiple changepoint algorithms. Optimal partitioning and functional pruning Guillem Rigaill Time Dynamic Change Point Models and its Applications, Georg-August-Universität Göttingen. DEU., Oct 2014, Göttingen, Germany Communication dans un congrès hal-02792281v1
	Partitionnement optimal et élagage fonctionnel pour la détection de ruptures multiples. Application à des données d’Hybridation Génomique Comparative CGH Robert Maidstone , Paul Fearnhead , Guillem Rigaill 46. Journées de Statistique, Société Française de Statistique (SFdS). FRA., Jun 2014, Rennes, France Communication dans un congrès hal-02744132v1
	Weighted fusion penalties for tree inference and its oracle properties Julien Chiquet , Pierre Gutierrez , Guillem Rigaill Workshop MLCB NIPS 2014, Dec 2014, Montréal, Canada Communication dans un congrès hal-01608308v1
	Segmentor3isback : an r package for the fast and exact segmentation of seq-data Alice Cleynen , Michel Koskas , Emilie Lebarbier , Guillem Rigaill , Stéphane Robin The R User Conference, Jun 2013, Albacete, Spain Communication dans un congrès hal-01587007v1
	Learning Sparse Penalties for Change-Point Detection using Max Margin Interval Regression Guillem Rigaill , Toby Dylan Hocking , Francis Bach , Jean-Philippe Vert ICML 2013 - 30 th International Conference on Machine Learning, Supported by the International Machine Learning Society (IMLS), Jun 2013, Atlanta, United States Communication dans un congrès hal-00824075v1
	Fast and parallel algorithm for population-based segmentation of copy-number profiles Guillem Rigaill , Vincent Miele , Franck Picard 10. International Meeting on Computational Intelligence Methods for Bioinformatics and Biostatistics (CIBB), Jun 2013, Nice, France. 275 p., ⟨10.1007/978-3-319-09042-9_18⟩ Communication dans un congrès hal-02742012v1
	Algorithme rapide pour la détection optimale des ruptures Guillem Rigaill 42èmes Journées de Statistique, 2010, Marseille, France, France Communication dans un congrès inria-00494813v1
	Distribution de l'espace des segmentations Guillem Rigaill , Stéphane Robin , Emilie Lebarbier 41èmes Journées de Statistique, SFdS, Bordeaux, 2009, Bordeaux, France, France Communication dans un congrès inria-00386673v1

	Fast Online Changepoint Detection via Functional Pruning CUSUM statistics Gaetano Romano , Idris Eckley , Paul Fearnhead , Guillem Rigaill Journal of Machine Learning Research, 2023, 24, 8 p. ⟨10.48550/arXiv.2110.08205⟩ Article dans une revue hal-04190669v1
	gfpop : An R Package for Univariate Graph-Constrained Change-Point Detection Vincent Runge , Toby Dylan Hocking , Gaetano Romano , Fatemeh Afghah , Paul Fearnhead Journal of Statistical Software, 2023, 106 (6), pp.1-39. ⟨10.18637/jss.v106.i06⟩ Article dans une revue hal-04191319v1
	DiffSegR: an RNA-seq data driven method for differential expression analysis using changepoint detection Arnaud Liehrmann , Etienne Delannoy , Alexandra Launay-Avon , Elodie Gilbault , Olivier Loudet NAR Genomics and Bioinformatics, 2023, 5 (4), pp.lqad098. ⟨10.1093/nargab/lqad098⟩ Article dans une revue hal-04282211v1
	Genome-Wide Identification of Key Components of RNA Silencing in Two Phaseolus vulgaris Genotypes of Contrasting Origin and Their Expression Analyses in Response to Fungal Infection Juan Alvarez-Diaz , Manon Richard , Vincent Thareau , Gianluca Teano , Christine Paysant-Le-Roux Genes, 2022, 13 (1), pp.1-19. ⟨10.3390/genes13010064⟩ Article dans une revue hal-04191305v1
	Strive or thrive: Trends in Phytophthora capsici gene expression in partially resistant pepper Gaëtan Maillot , Emmanuel Szadkowski , Anne Massire , Véronique Brunaud , Guillem Rigaill Frontiers in Plant Science, 2022, 13 (980587), pp.1-19. ⟨10.3389/fpls.2022.980587⟩ Article dans une revue hal-03908269v1
	Adjusting the adjusted Rand Index A multinomial story Martina Sundqvist , Julien Chiquet , Guillem Rigaill Computational Statistics, 2022, 38 (1), pp.327-347. ⟨10.1007/s00180-022-01230-7⟩ Article dans une revue hal-03696588v1
	Generalized Functional Pruning Optimal Partitioning (GFPOP) for Constrained Changepoint Detection in Genomic Data Toby Dylan Hocking , Guillem Rigaill , Paul Fearnhead , Guillaume Bourque Journal of Statistical Software, 2022, 101 (10), ⟨10.18637/jss.v101.i10⟩ Article dans une revue hal-04191295v1
	Increased peak detection accuracy in over-dispersed ChIP-seq data with supervised segmentation models Arnaud Liehrmann , Guillem Rigaill , Toby Dylan Hocking BMC Bioinformatics, 2021, 22 (1), ⟨10.1186/s12859-021-04221-5⟩ Article dans une revue hal-03333772v1
	Full Length Transcriptome Highlights the Coordination of Plastid Transcript Processing Marine Guilcher , Arnaud Liehrmann , Chloé Seyman , Thomas Blein , Guillem Rigaill International Journal of Molecular Sciences, 2021, 22 (20), pp.1-15. ⟨10.3390/ijms222011297⟩ Article dans une revue hal-03343771v1
	Wide Cross-species RNA-Seq Comparison Reveals Convergent Molecular Mechanisms Involved in Nickel Hyperaccumulation Across Dicotyledons Vanesa Sanchez Garcia de La Torre , Clarisse Majorel-Loulergue , Guillem J. Rigaill , Dubiel A. Gonzalez , Ludivine Soubigou-Taconnat New Phytologist, 2021, 229 (2), pp.994-1006. ⟨10.1111/nph.16775⟩ Article dans une revue hal-02890477v1
	Relating and comparing methods for detecting changes in mean Paul Fearnhead , Guillem Rigaill Stat, 2020, 9 (1), ⟨10.1002/sta4.291⟩ Article dans une revue hal-02961044v1
	Fast tree aggregation for consensus hierarchical clustering Audrey Hulot , Julien Chiquet , Florence Jaffrezic , Guillem Rigaill BMC Bioinformatics, 2020, 21 (1), ⟨10.1186/s12859-020-3453-6⟩ Article dans une revue hal-02961035v1
	Constrained Dynamic Programming and Supervised Penalty Learning Algorithms for Peak Detection in Genomic Data Toby Dylan Hocking , Guillem Rigaill , Paul Fearnhead , Guillaume Bourque Journal of Machine Learning Research, 2020, 21, pp.1 - 40 Article dans une revue hal-02961069v1
	Detecting Abrupt Changes in the Presence of Local Fluctuations and Autocorrelated Noise Gaetano Romano , Guillem Rigaill , Vincent Runge , Paul Fearnhead Journal of the American Statistical Association, inPress, pp.1-16. ⟨10.1080/01621459.2021.1909598⟩ Article dans une revue hal-02961038v1
	LRP8 is overexpressed in estrogen-negative breast cancers and a potential target for these tumors Virginie Maire , Faisal Mahmood , Guillem Rigaill , Mengliang Ye , Amélie Brisson Cancer Medicine, 2019, 8 (1), pp.325-336. ⟨10.1002/cam4.1923⟩ Article dans une revue hal-02624466v1
	Changepoint detection in the presence of outliers Paul Fearnhead , Guillem Rigaill Journal of the American Statistical Association, 2019, 114 (525), pp.169-183. ⟨10.1080/01621459.2017.1385466⟩ Article dans une revue hal-02622377v1
	Screening populations for copy number variation using genotyping-by-sequencing: a proof of concept using soybean fast neutron mutants Marc-Andre Lemay , Davoud Torkamaneh , Guillem Rigaill , Brian Boyle , Adrian O. Stec BMC Genomics, 2019, 20, pp.634. ⟨10.1186/s12864-019-5998-1⟩ Article dans une revue hal-02625904v1
	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
	Protein arginine methyltransferase 5: A novel therapeutic target for triple-negative breast cancers Mathilde Vinet , Samyuktha Suresh , Virginie Maire , Clarisse Monchecourt , Fariba Nemati Cancer Medicine, 2019, 8 (5), pp.2414-2428. ⟨10.1002/cam4.2114⟩ Article dans une revue hal-02625897v1
	Allele-specific expression and genetic determinants of transcriptomic variations in response to mild water deficit in tomato Elise Albert , Renaud Duboscq , Muriel Latreille , Sylvain Santoni , Matthieu Beukers Plant Journal, 2018, 96 (3), pp.635-650. ⟨10.1111/tpj.14057⟩ Article dans une revue hal-02620940v1
	New efficient algorithms for multiple change-point detection with reproducing kernels Alain Celisse , Guillemette Marot , Pierre-Jean Male , Guillem Rigaill Computational Statistics and Data Analysis, 2018, 128, pp.200-220. ⟨10.1016/j.csda.2018.07.002⟩ Article dans une revue hal-02621669v1
	Homoeologous exchanges cause extensive dosage-dependent gene expression changes in an allopolyploid crop Andrew Lloyd , Aurélien Blary , Delphine Charif , Catherine Charpentier , Joseph Tran New Phytologist, 2018, 217 (1), pp.367-377. ⟨10.1111/nph.14836⟩ Article dans une revue hal-02624624v1
	Fast Tree Inference With Weighted Fusion Penalties Julien Chiquet , Pierre Gutierrez , Guillem Rigaill Journal of Computational and Graphical Statistics, 2017, 26 (1), pp.205 - 216. ⟨10.1080/10618600.2015.1096789⟩ Article dans une revue hal-01597604v1
	Independent introductions and admixtures have contributed to adaptation of European maize and its American counterparts Jean-Tristan Brandenburg , Tristan Mary , Guillem Rigaill , Sarah J. Hearne , Hélène Corti PLoS Genetics, 2017, 13 (3), pp.e1006666. ⟨10.1371/journal.pgen.1006666⟩ Article dans une revue hal-01605143v1
	On optimal multiple changepoint algorithms for large data Robert Maidstone , Toby Hocking , Guillem Rigaill , Paul Fearnhead Statistics and Computing, 2017, 27 (2), pp.519-533. ⟨10.1007/s11222-016-9636-3⟩ Article dans une revue hal-01603953v1
	Two interacting PPR proteins are major Arabidopsis editing factors in plastid and mitochondria Damien Guillaumot , Mauricio Lopez Obando , Kévin Baudry , Alexandra Launay-Avon , Guillem Rigaill Proceedings of the National Academy of Sciences of the United States of America, 2017, 114 (33), pp.8877-8882. ⟨10.1073/pnas.1705780114⟩ Article dans une revue hal-01606226v1
	Unraveling the early molecular and physiological mechanisms involved in response to phenanthrene exposure Anne-Sophie Dumas , Ludivine Taconnat , Evangelos Barbas , Guillem Rigaill , Olivier Catrice BMC Genomics, 2016, 17 (1), pp.818. ⟨10.1186/s12864-016-3133-0⟩ Article dans une revue hal-01397859v1
	On coding effects in regularized categorical regression Julien Chiquet , Yves Grandvalet , Guillem Rigaill Statistical Modelling, 2016, 16 (3), pp.228-237. ⟨10.1177/1471082X16644998⟩ Article dans une revue hal-01338164v1
	Synthetic data sets for the identification of key ingredients for RNA-seq differential analysis Guillem Rigaill , Sandrine Balzergue , Véronique Brunaud , Eddy Blondet , Andrea Rau Briefings in Bioinformatics, 2016, 19 (1), pp.65-76. ⟨10.1093/bib/bbw092⟩ Article dans une revue hal-01595551v1
	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
	TIPIN depletion leads to apoptosis in breast cancer cells Céline Baldeyron , Amélie Brisson , Bruno Tesson , Fariba Nemati , Stéphane Koundrioukoff Molecular Oncology, 2015, 9 (8), pp.1580-1598. ⟨10.1016/j.molonc.2015.04.010⟩ Article dans une revue hal-02639424v1
	GEM2Net: from gene expression modeling to -omics networks, a new CATdb module to investigate Arabidopsis thaliana genes involved in stress response Rim Zaag , Jean-Philippe Tamby , Cecile Guichard , Zakia Tariq , Guillem Rigaill Nucleic Acids Research, 2015, 43 (Database issue), pp.D1010-D1017. ⟨10.1093/nar/gku1155⟩ Article dans une revue hal-01137554v1
	Transcriptome analysis of Wnt3a-treated triple-negative breast cancer cells Sylvie Maubant , Bruno Tesson , Virginie Maire , Mengliang Ye , Guillem Rigaill PLoS ONE, 2015, 10 (4), 26 p. ⟨10.1371/journal.pone.0122333⟩ Article dans une revue hal-02639667v1
	Fast and Parallel Algorithm for Population-Based Segmentation of Copy-Number Profiles Guillem Rigaill , Vincent Miele , Franck Picard Lecture Notes in Computer Science, 2014, 8452, pp.248-258 Article dans une revue hal-02045097v1
	Fast estimation of the Integrated Completed Likelihood criterion for change-point detection problems with applications to Next-Generation Sequencing data Alice Cleynen , The Minh Luong , Guillem Rigaill , Gregory Nuel Signal Processing, 2014, 98, pp.233-242. ⟨10.1016/j.sigpro.2013.11.029⟩ Article dans une revue hal-01197622v1
	SegAnnDB: interactive web-based genomic segmentation Toby D. Hocking , Valentina Boeva , Guillem Rigaill , Gudrun Schleiermacher , Isabelle Janoueix-Lerosey Bioinformatics, 2014, 30 (11), pp.1539-1546. ⟨10.1093/bioinformatics/btu072⟩ Article dans une revue hal-01101868v1
	Segmentor3IsBack : an R package for the fast and exact segmentation of Seq-data Alice Cleynen , Michel Koskas , Guillem Rigaill , Stephane Robin Algorithms for Molecular Biology, 2014, 9, 11 p. ⟨10.1186/1748-7188-9-6⟩ Article dans une revue hal-01197619v1
	TTK/hMPS1 is an attractive therapeutic target for triple-negative breast cancer Virginie Maire , Celine Baldeyron , Marion Richardson , Bruno Tesson , Anne Vincent-Salomon PLoS ONE, 2013, 8 (6), ⟨10.1371/journal.pone.0063712⟩ Article dans une revue hal-01190560v1
	Polo-like Kinase 1: A Potential Therapeutic Option in Combination with Conventional Chemotherapy for the Management of Patients with Triple-Negative Breast Cancer Virginie Maire , Fariba Nemati , Marion Richardson , Anne Vincent-Salomon , Bruno Tesson Cancer Research, 2013, 73 (2), pp.813 - 823. ⟨10.1158/0008-5472.CAN-12-2633⟩ Article dans une revue hal-01190661v1
	Genomic instability : a stronger prognostic marker than proliferation for early stage luminal breast carcinomas Anne Vincent-Salomon , Vanessa Benhamo , Eleonore Gravier , Guillem Rigaill , Nadège Gruel PLoS ONE, 2013, 8 (10), ⟨10.1371/journal.pone.0076496⟩ Article dans une revue hal-01219550v1
	Joint segmentation, calling, and normalization of multiple CGH profiles Franck Picard , Mark Hoebeke , Guillem Rigaill , Baba Thiam , Stephane Robin Biostatistics, 2011, 12 (3), pp.413-428. ⟨10.1093/biostatistics/kxq076⟩ Article dans une revue hal-01019859v1
	Oxidative stress promotes myofibroblast differentiation and tumour spreading Aurore Toullec , Damien Gerald , Gilles Despouy , Brigitte Bourachot , Mélissa Cardon EMBO Molecular Medicine, 2010, 2 (6), pp.211-230. ⟨10.1002/emmm.201000073⟩ Article dans une revue hal-02662620v1
	Diaphanous-related formins are required for invadopodia formation and invasion of breast tumor cells Floria Lizarraga , Renaud Poincloux , Marise Romao , Guillaume Montagnac , Gaëlle Le Dez Cancer Research, 2009, 69 (7), pp.2792-2800. ⟨10.1158/0008-5472.CAN-08-3709⟩ Article dans une revue hal-02659942v1
	Genome Alteration Print (GAP): a tool to visualize and mine complex cancer genomic profiles obtained by SNP arrays. Tatiana Popova , Elodie Manié , Dominique Stoppa-Lyonnet , Guillem Rigaill , Emmanuel Barillot Genome Biology, 2009, 10 (11), pp.R128. ⟨10.1186/gb-2009-10-11-r128⟩ Article dans une revue inserm-00663915v1
	Frequent PTEN genomic alterations and activated phosphatidylinositol 3-kinase pathway in basal-like breast cancer cells Bérengère Marty , Virginie Maire , Eleonore Gravier , Guillem Rigaill , Anne Vincent-Salomon Breast Cancer Research, 2008, 10 (6), pp.1-15. ⟨10.1186/bcr2204⟩ Article dans une revue hal-02666624v1
	ITALICS: an algorithm for normalization and DNA copy number calling for Affymetrix SNP arrays Guillem Rigaill , Philippe Hupé , Anna Almeida , Philippe La Rosa , Jean-Philippe Meyniel Bioinformatics, 2008, 24 (6), pp.768-774. ⟨10.1093/bioinformatics/btn048⟩ Article dans une revue hal-02655786v1
	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

	Détection de ruptures à partir de méthodes à noyaux Morgane Pierre-Jean , Guillemette Marot , Guillem Rigaill , Alain Celisse United Kingdom, Patent n° : 0000000. 2013 Brevet hal-00943423v1
	Change-point detection with kernel methods : application to DNA copy number signals Morgane Pierre-Jean , Guillemette Marot , Rigaill Guillem , Alain Celisse France, Patent n° : 00000000000000. 2013 Brevet hal-00943413v1

	fst4pg: Genetic Distance Segmentation for Population Genetics Tristan Mary-Huard , Guillem Rigaill 2024, ⟨swh:1:dir:066c394ebf4dceb11cdaa881eba848383d4746a8;origin=https://hal.archives-ouvertes.fr/hal-04499866;visit=swh:1:snp:43f36647203d1f8677274275db14efd82f8accc2;anchor=swh:1:rel:353ee95542e0031d50b4180030898a94a43f5a44;path=/⟩ Logiciel hal-04499866v1
	aricode: Efficient Computations of Standard Clustering Comparison Measures Julien Chiquet , Guillem Rigaill , Martina Sundqvist 2020, ⟨swh:1:dir:5611b0b1a170db175583d4243ec8639e0e846f01;origin=https://hal.archives-ouvertes.fr/hal-04479410;visit=swh:1:snp:e98ee67c94e9d082fcfe9a391e0f933e2a575fe9;anchor=swh:1:rel:a1c2ad44b535c5a6bff2d740d9b0278c3d5a55ba;path=/⟩ Logiciel hal-04479410v1
	mergeTrees: Aggregating Trees Julien Chiquet , Guillem Rigaill , Audrey Hulot 2019, ⟨swh:1:dir:afc2108cf6953ffa4e3b912b6633ced23e817dc7;origin=https://hal.archives-ouvertes.fr/hal-04500072;visit=swh:1:snp:031d57f01a704f13fb222218fbca370a02148249;anchor=swh:1:rel:90c7a9e908b44d5006c0b0b62309dfea7843e76e;path=/⟩ Logiciel hal-04500072v1
	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

	gfpop : An R Package for Univariate Graph-Constrained Change-Point Detection Vincent Runge , Toby Dylan Hocking , Gaetano Romano , Fatemeh Afghah , Paul Fearnhead 2024 Pré-publication, Document de travail hal-02961088v1
	Geometric-Based Pruning Rules For Change Point Detection in Multiple Independent Time Series Liudmila Pishchagina , Guillem Rigaill , Vincent Runge 2023 Pré-publication, Document de travail hal-04132733v1
	Ms.FPOP: An Exact and Fast Segmentation Algorithm With a Multiscale Penalty Arnaud Liehrmann , Guillem Rigaill 2023 Pré-publication, Document de travail hal-04190673v1
	DiffSegR: An RNA-Seq data driven method for differential expression analysis using changepoint detection Arnaud Liehrmann , Etienne Delannoy , Benoît Castandet , Guillem Rigaill 2023 Pré-publication, Document de travail hal-04190676v1
	Wide cross-species RNA-Seq comparison reveals a highly conserved role for Ferroportins in nickel hyperaccumulation in plants Vanesa S Garcia de La Torre , Clarisse Majorel-Loulergue , Dubiel A Gonzalez , Ludivine Soubigou-Taconnat , Guillem Rigaill 2019 Pré-publication, Document de travail hal-02327677v1
	New efficient algorithms for multiple change-point detection with kernels Alain Celisse , Guillemette Marot , Morgane Pierre-Jean , Guillem Rigaill 2016 Pré-publication, Document de travail hal-01413230v2
	SegAnnot: an R package for fast segmentation of annotated piecewise constant signals Toby Dylan Hocking , Guillem Rigaill 2012 Pré-publication, Document de travail hal-00759129v1

	Statistical and algorithmic developments for the analysis of Triple Negative Breast Cancers Guillem Rigaill Applications [stat.AP]. AgroParisTech, 2010. English. ⟨NNT : 2010AGPT0066⟩ Thèse pastel-00593939v1

	A Multiattribute Gaussian Graphical Model for Inferring Multiscale Regulatory Networks: An Application in Breast Cancer Julien Chiquet , Guillem Rigaill , Martina Sundqvist Gene Regulatory Networks, pp.143-160, 2019, ⟨10.1007/978-1-4939-8882-2_6⟩ Chapitre d'ouvrage hal-02961121v1
	Bioinformatic analysis of chloroplast gene expression and RNA posttranscriptional maturations using RNA Sequencing Bastien Malbert , Guillem Rigaill , Véronique Brunaud , Claire Lurin , Etienne Delannoy Plastids, 1829, Humana Press Inc., pp.16, 2018, Methods in Molecular Biology, 978-1-4939-8654-5; 978-1-4939-8653-8. ⟨10.1007/978-1-4939-8654-5_19⟩ Chapitre d'ouvrage hal-02788517v1
	Exact posterior distributions over the segmentation space and model selection for multiple change-point detection problems Guillem Rigaill , Stephane Robin Proceedings of COMPSTAT'2010: 19th International Conference on Computational StatisticsParis France, August 22-27, 2010 Keynote, Invited and Contributed Papers, Springer - Verlag, 2010, 978-3-7908-2603-6. ⟨10.1007/978-3-7908-2604-3_57⟩ Chapitre d'ouvrage hal-01197523v1

	Impact de la résistance partielle du piment sur l'expression des gènes de Phytophthora capsici : conséquences pour la création variétale Véronique Lefebvre , Anne Massire , Gaëtan Maillot , Emmanuel Szadkowski , Bernard Caromel 13e Rencontres de Phytopathologie - Mycologie, Journées Jean Chevaugeon, Sep 2022, Aussois (France), France Poster de conférence hal-04133322v1
	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
	PO-435 Proteomic classification of triple negative breast cancer Martina Sundqvist , Leanne de Koning , Guillem Rigaill , Tristan Dubois , Julien Chiquet 25th Biennial Congress of the European Association for Cancer Research, Jun 2018, Amsterdam, Netherlands. ESMO Open, 3, pp.A402, 2018, ⟨10.1136/esmoopen-2018-EACR25.946⟩ Poster de conférence hal-04440537v1
	Transcriptomic regulation in pepper during the interaction with Phytophthora capsici. Gaëtan Maillot , Emmanuel Szadkowski , Anne Massire , Jean-Paul Bouchet , Veronique Brunaud 16th Eucarpia Capsicum and Eggplant Meeting, Sep 2016, Kecskemét, Hungary Poster de conférence hal-03551784v1
	Transcriptomic regulation in pepper during the interaction with Phytophthora capsici Gaëtan Maillot , Emmanuel Szadkowski , Anne Massire , Jean-Paul Bouchet , Veronique Brunaud 16. Eucarpia Capsicum and Eggplant Meeting, Sep 2016, Kecskemét, Hungary. 2016 Poster de conférence hal-02799453v1
	A fast homotopy algorithm for a large class of weighted classification problems Pierre Gutierrez , Guillem Rigaill , Julien Chiquet MLCB NIPS 2013, Oct 2013, South Lake Thao, United States. 2013 Poster de conférence hal-01601843v1
	Integrative approaches for the identification of therapeutic targets in basal-like breast cancer from multi-level molecular data B. M. Tesson , Guillem Rigaill , D. Gentien , S. Roman-Roman , F. Cruzalegui 22. Biennial Congress of the European Association for Cancer Research, Jul 2012, Barcelone, Spain. Elsevier Science LTD, European Journal of Cancer, 48 (Suppl. 5), 2012, European Journal of Cancer Poster de conférence hal-01189748v1

	Quelques développements statistiques et algorithmiques pour l’analyse de données génomiques Guillem Rigaill Statistiques [math.ST]. Université Paris Saclay, 2020 HDR tel-02955535v1

Guillem Rigaill

Publications

Fast tree aggregation for consensus hierarchical clustering: application to multi-omics data analysis

Impact of host partial resistance on the gene expression of Phytophthora capsici: consequences for pepper breeding

Changepoint detection in the presence of outliers and constraints.

A statistical method to detect abrupt changes in trees.

Changepoint detection in the presence of outliers

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

Fused-ANOVA : une méthode de clustering en grande dimension

PeakSeg: constrained optimal segmentation and supervised penalty learning for peak detection in count data

The Wnt3a targetome in triple-negative breast cancer cell lines

On exact multiple changepoint algorithms. Optimal partitioning and functional pruning

On exact multiple changepoint algorithms. Optimal partitioning and functional pruning

Partitionnement optimal et élagage fonctionnel pour la détection de ruptures multiples. Application à des données d’Hybridation Génomique Comparative CGH

Weighted fusion penalties for tree inference and its oracle properties

Segmentor3isback : an r package for the fast and exact segmentation of seq-data

Learning Sparse Penalties for Change-Point Detection using Max Margin Interval Regression

Fast and parallel algorithm for population-based segmentation of copy-number profiles

Algorithme rapide pour la détection optimale des ruptures

Distribution de l'espace des segmentations

Fast Online Changepoint Detection via Functional Pruning CUSUM statistics

gfpop : An R Package for Univariate Graph-Constrained Change-Point Detection

DiffSegR: an RNA-seq data driven method for differential expression analysis using changepoint detection

Genome-Wide Identification of Key Components of RNA Silencing in Two Phaseolus vulgaris Genotypes of Contrasting Origin and Their Expression Analyses in Response to Fungal Infection

Strive or thrive: Trends in Phytophthora capsici gene expression in partially resistant pepper

Adjusting the adjusted Rand Index A multinomial story

Generalized Functional Pruning Optimal Partitioning (GFPOP) for Constrained Changepoint Detection in Genomic Data

Increased peak detection accuracy in over-dispersed ChIP-seq data with supervised segmentation models

Full Length Transcriptome Highlights the Coordination of Plastid Transcript Processing

Wide Cross-species RNA-Seq Comparison Reveals Convergent Molecular Mechanisms Involved in Nickel Hyperaccumulation Across Dicotyledons

Relating and comparing methods for detecting changes in mean

Fast tree aggregation for consensus hierarchical clustering

Constrained Dynamic Programming and Supervised Penalty Learning Algorithms for Peak Detection in Genomic Data

Detecting Abrupt Changes in the Presence of Local Fluctuations and Autocorrelated Noise

LRP8 is overexpressed in estrogen-negative breast cancers and a potential target for these tumors

Changepoint detection in the presence of outliers

Screening populations for copy number variation using genotyping-by-sequencing: a proof of concept using soybean fast neutron mutants

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

Protein arginine methyltransferase 5: A novel therapeutic target for triple-negative breast cancers

Allele-specific expression and genetic determinants of transcriptomic variations in response to mild water deficit in tomato

New efficient algorithms for multiple change-point detection with reproducing kernels

Homoeologous exchanges cause extensive dosage-dependent gene expression changes in an allopolyploid crop

Fast Tree Inference With Weighted Fusion Penalties

Independent introductions and admixtures have contributed to adaptation of European maize and its American counterparts

On optimal multiple changepoint algorithms for large data

Two interacting PPR proteins are major Arabidopsis editing factors in plastid and mitochondria

Unraveling the early molecular and physiological mechanisms involved in response to phenanthrene exposure

On coding effects in regularized categorical regression

Synthetic data sets for the identification of key ingredients for RNA-seq differential analysis

Performance evaluation of DNA copy number segmentation methods

TIPIN depletion leads to apoptosis in breast cancer cells

GEM2Net: from gene expression modeling to -omics networks, a new CATdb module to investigate Arabidopsis thaliana genes involved in stress response

Transcriptome analysis of Wnt3a-treated triple-negative breast cancer cells

Fast and Parallel Algorithm for Population-Based Segmentation of Copy-Number Profiles

Fast estimation of the Integrated Completed Likelihood criterion for change-point detection problems with applications to Next-Generation Sequencing data

SegAnnDB: interactive web-based genomic segmentation

Segmentor3IsBack : an R package for the fast and exact segmentation of Seq-data

TTK/hMPS1 is an attractive therapeutic target for triple-negative breast cancer

Polo-like Kinase 1: A Potential Therapeutic Option in Combination with Conventional Chemotherapy for the Management of Patients with Triple-Negative Breast Cancer

Genomic instability : a stronger prognostic marker than proliferation for early stage luminal breast carcinomas

Joint segmentation, calling, and normalization of multiple CGH profiles

Oxidative stress promotes myofibroblast differentiation and tumour spreading

Diaphanous-related formins are required for invadopodia formation and invasion of breast tumor cells

Genome Alteration Print (GAP): a tool to visualize and mine complex cancer genomic profiles obtained by SNP arrays.

Frequent PTEN genomic alterations and activated phosphatidylinositol 3-kinase pathway in basal-like breast cancer cells

ITALICS: an algorithm for normalization and DNA copy number calling for Affymetrix SNP arrays

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

Détection de ruptures à partir de méthodes à noyaux

Change-point detection with kernel methods : application to DNA copy number signals

fst4pg: Genetic Distance Segmentation for Population Genetics

aricode: Efficient Computations of Standard Clustering Comparison Measures

mergeTrees: Aggregating Trees

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

gfpop : An R Package for Univariate Graph-Constrained Change-Point Detection

Geometric-Based Pruning Rules For Change Point Detection in Multiple Independent Time Series

Ms.FPOP: An Exact and Fast Segmentation Algorithm With a Multiscale Penalty

DiffSegR: An RNA-Seq data driven method for differential expression analysis using changepoint detection

Wide cross-species RNA-Seq comparison reveals a highly conserved role for Ferroportins in nickel hyperaccumulation in plants

New efficient algorithms for multiple change-point detection with kernels

SegAnnot: an R package for fast segmentation of annotated piecewise constant signals