Guillem Rigaill

88
Documents

Publications

Publications

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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 et al.
NAR Genomics and Bioinformatics, 2023, 5 (4), pp.lqad098. ⟨10.1093/nargab/lqad098⟩
Article dans une revue hal-04282211 v2
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Fast Online Changepoint Detection via Functional Pruning CUSUM statistics

Gaetano Romano , Idris Eckley , Paul Fearnhead , Guillem Rigaill
Journal of Machine Learning Research, 2023, 24, pp.1-36. ⟨10.48550/arXiv.2110.08205⟩
Article dans une revue hal-04190669 v1
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gfpop : An R Package for Univariate Graph-Constrained Change-Point Detection

Vincent Runge , Toby Dylan Hocking , Gaetano Romano , Fatemeh Afghah , Paul Fearnhead et al.
Journal of Statistical Software, 2023, 106 (6), pp.1-39. ⟨10.18637/jss.v106.i06⟩
Article dans une revue hal-04191319 v2
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Strive or thrive: Trends in Phytophthora capsici gene expression in partially resistant pepper

Gaëtan Maillot , Emmanuel Szadkowski , Anne Massire , Véronique Brunaud , Guillem Rigaill et al.
Frontiers in Plant Science, 2022, 13 (980587), pp.1-19. ⟨10.3389/fpls.2022.980587⟩
Article dans une revue hal-03908269 v1
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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-03696588 v1
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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-04191295 v1
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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 et al.
Genes, 2022, 13 (1), pp.1-19. ⟨10.3390/genes13010064⟩
Article dans une revue hal-04191305 v1
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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-03333772 v1
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Full Length Transcriptome Highlights the Coordination of Plastid Transcript Processing

Marine Guilcher , Arnaud Liehrmann , Chloé Seyman , Thomas Blein , Guillem Rigaill et al.
International Journal of Molecular Sciences, 2021, 22 (20), pp.1-15. ⟨10.3390/ijms222011297⟩
Article dans une revue hal-03343771 v1
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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 et al.
New Phytologist, 2021, 229 (2), pp.994-1006. ⟨10.1111/nph.16775⟩
Article dans une revue hal-02890477 v1
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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-02961035 v1
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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, In press, pp.1-16. ⟨10.1080/01621459.2021.1909598⟩
Article dans une revue hal-02961038 v1
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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-02961069 v1

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-02961044 v1
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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 et al.
Cancer Medicine, 2019, 8 (1), pp.325-336. ⟨10.1002/cam4.1923⟩
Article dans une revue hal-02624466 v1
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Protein arginine methyltransferase 5: A novel therapeutic target for triple-negative breast cancers

Mathilde Vinet , Samyuktha Suresh , Virginie Maire , Clarisse Monchecourt , Fariba Nemati et al.
Cancer Medicine, 2019, 8 (5), pp.2414-2428. ⟨10.1002/cam4.2114⟩
Article dans une revue hal-02625897 v1
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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 et al.
BMC Genomics, 2019, 20, pp.634. ⟨10.1186/s12864-019-5998-1⟩
Article dans une revue hal-02625904 v1
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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-02622377 v1
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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-02006331 v2
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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 et al.
The Plant Journal, 2018, 96 (3), pp.635-650. ⟨10.1111/tpj.14057⟩
Article dans une revue hal-02620940 v1

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-02621669 v1

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

Andrew Lloyd , Aurélien Blary , Delphine Charif , Catherine Charpentier , Joseph Tran et al.
New Phytologist, 2018, 217 (1), pp.367-377. ⟨10.1111/nph.14836⟩
Article dans une revue hal-02624624 v1
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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 et al.
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-01606226 v1
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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-01597604 v1
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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 et al.
PLoS Genetics, 2017, 13 (3), pp.e1006666. ⟨10.1371/journal.pgen.1006666⟩
Article dans une revue hal-01605143 v1
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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-01603953 v1

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

Guillem Rigaill , Sandrine Balzergue , Véronique Brunaud , Eddy Blondet , Andrea Rau et al.
Briefings in Bioinformatics, 2016, 19 (1), pp.65-76. ⟨10.1093/bib/bbw092⟩
Article dans une revue hal-01595551 v1

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-01338164 v1
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Unraveling the early molecular and physiological mechanisms involved in response to phenanthrene exposure

Anne-Sophie Dumas , Ludivine Taconnat , Evangelos Barbas , Guillem Rigaill , Olivier Catrice et al.
BMC Genomics, 2016, 17 (1), pp.818. ⟨10.1186/s12864-016-3133-0⟩
Article dans une revue hal-01397859 v1
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Transcriptome analysis of Wnt3a-treated triple-negative breast cancer cells

Sylvie Maubant , Bruno Tesson , Virginie Maire , Mengliang Ye , Guillem Rigaill et al.
PLoS ONE, 2015, 10 (4), 26 p. ⟨10.1371/journal.pone.0122333⟩
Article dans une revue hal-02639667 v1
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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 et al.
Nucleic Acids Research, 2015, 43 (Database issue), pp.D1010-D1017. ⟨10.1093/nar/gku1155⟩
Article dans une revue hal-01137554 v1
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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-00952896 v2

TIPIN depletion leads to apoptosis in breast cancer cells

Céline Baldeyron , Amélie Brisson , Bruno Tesson , Fariba Nemati , Stéphane Koundrioukoff et al.
Molecular Oncology, 2015, 9 (8), pp.1580-1598. ⟨10.1016/j.molonc.2015.04.010⟩
Article dans une revue hal-02639424 v1
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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-01197622 v1
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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-01197619 v1
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SegAnnDB: interactive web-based genomic segmentation

Toby D. Hocking , Valentina Boeva , Guillem Rigaill , Gudrun Schleiermacher , Isabelle Janoueix-Lerosey et al.
Bioinformatics, 2014, 30 (11), pp.1539-1546. ⟨10.1093/bioinformatics/btu072⟩
Article dans une revue hal-01101868 v1

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-02045097 v1
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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 et al.
PLoS ONE, 2013, 8 (10), ⟨10.1371/journal.pone.0076496⟩
Article dans une revue hal-01219550 v1
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TTK/hMPS1 is an attractive therapeutic target for triple-negative breast cancer

Virginie Maire , Celine Baldeyron , Marion Richardson , Bruno Tesson , Anne Vincent-Salomon et al.
PLoS ONE, 2013, 8 (6), ⟨10.1371/journal.pone.0063712⟩
Article dans une revue hal-01190560 v1

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 et al.
Cancer Research, 2013, 73 (2), pp.813 - 823. ⟨10.1158/0008-5472.CAN-12-2633⟩
Article dans une revue hal-01190661 v1
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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-01019859 v1
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Oxidative stress promotes myofibroblast differentiation and tumour spreading

Aurore Toullec , Damien Gerald , Gilles Despouy , Brigitte Bourachot , Mélissa Cardon et al.
EMBO Molecular Medicine, 2010, 2 (6), pp.211-230. ⟨10.1002/emmm.201000073⟩
Article dans une revue hal-02662620 v1
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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 et al.
Genome Biology, 2009, 10 (11), pp.R128. ⟨10.1186/gb-2009-10-11-r128⟩
Article dans une revue inserm-00663915 v1

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 et al.
Cancer Research, 2009, 69 (7), pp.2792-2800. ⟨10.1158/0008-5472.CAN-08-3709⟩
Article dans une revue hal-02659942 v1
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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 et al.
Breast Cancer Research, 2008, 10 (6), pp.1-15. ⟨10.1186/bcr2204⟩
Article dans une revue hal-02666624 v1

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 et al.
Bioinformatics, 2008, 24 (6), pp.768-774. ⟨10.1093/bioinformatics/btn048⟩
Article dans une revue hal-02655786 v1

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

M. Bollet , N. Servant , Pierre Neuvial , C. Decraene , I. Lebigot et al.
JNCI: Journal of the National Cancer Institute, 2008, 100 (1), pp.48-58. ⟨10.1093/jnci/djm266⟩
Article dans une revue hal-00204833 v1
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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 et al.
13e Rencontres de Phytopathologie - Mycologie, Journées Jean Chevaugeon, Sep 2022, Aussois (France), France
Poster de conférence hal-04133322 v1
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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-02790995 v1
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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-04440537 v1

Transcriptomic regulation in pepper during the interaction with Phytophthora capsici.

Gaëtan Maillot , Emmanuel Szadkowski , Anne Massire , Jean-Paul Bouchet , Veronique Brunaud et al.
16th Eucarpia Capsicum and Eggplant Meeting, Sep 2016, Kecskemét, Hungary
Poster de conférence hal-03551784 v1
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Transcriptomic regulation in pepper during the interaction with <em>Phytophthora capsici</em>

Gaëtan Maillot , Emmanuel Szadkowski , Anne Massire , Jean-Paul Bouchet , Veronique Brunaud et al.
16. Eucarpia Capsicum and Eggplant Meeting, Sep 2016, Kecskemét, Hungary. 2016
Poster de conférence hal-02799453 v1
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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-01601843 v1

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 et al.
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-01189748 v1

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-02483674 v1

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 et al.
17. Eucarpia Meeting on Genetics and Breeding of Capsicum and Eggplant (2019), Sep 2019, Avignon, France
Communication dans un congrès hal-02735621 v1

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-02961195 v1

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-02961197 v1
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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-02483532 v1

Changepoint detection in the presence of outliers

Guillem Rigaill
Statistical Scalability Workshop 2018, Apr 2018, Windemere, United Kingdom
Communication dans un congrès hal-02961189 v1

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

Christophe Ambroise , Alia Dehman , Michel Koskas , Pierre Neuvial , Guillem Rigaill et al.
Journée Régionale de Bioinformatique et Biostatistique, Génopole Toulouse, Dec 2018, Toulouse, France
Communication dans un congrès hal-02788245 v1

The Wnt3a targetome in triple-negative breast cancer cell lines

Sylvie Maubant , Bruno Tesson , Virginie Maire , Mengliang Ye , Guillem Rigaill et al.
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-02739832 v1

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-02744063 v1

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-02796353 v1

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-02792281 v1

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-02744132 v1

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-01608308 v1

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-02742012 v1

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-01587007 v1

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-00824075 v1
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Algorithme rapide pour la détection optimale des ruptures

Guillem Rigaill
42èmes Journées de Statistique, 2010, Marseille, France, France
Communication dans un congrès inria-00494813 v1
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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-00386673 v1