Magali Richard CNRS CRCN

Identifiants chercheurs

IdHAL :

magali-richard

ORCID :

0000-0003-3165-3218

IdRef :

168149184

ResearcherID :

http://www.researcherid.com/rid/AAY-9412-2020

Publications

Communication dans un congrès (10)

Inferring cellular heterogeneity with mixture models for DNA methylation rates (SMPGD 2026) Hugo Barbot,David Causeur,Yuna Blum,Magali Richard SMPGD 2026, Jan 2026, Grenoble, France Communication dans un congrès hal-05489490v1
Inferring cellular heterogeneity with mixture models for DNA methylation rates Hugo Barbot,David Causeur,Yuna Blum,Magali Richard JdS, Jun 2025, Marseille, France Communication dans un congrès hal-05065027v1
Multi-omic statistical inference of cellular heterogeneity - IGDR SCAN 26/03/2025 Hugo Barbot,David Causeur,Yuna Blum,Magali Richard IGDR SCAN, Mar 2025, Rennes (CHU), France Communication dans un congrès hal-05065011v1
Multi-omic statistical inference of cellular heterogeneity - JOBIM 2024 Hugo Barbot,David Causeur,Yuna Blum,Magali Richard JOBIM 2024, Jun 2024, Toulouse, France Communication dans un congrès hal-04664788v1
Multi-omic statistical inference of cellular heterogeneity - JdS 2024 Hugo Barbot,David Causeur,Yuna Blum,Magali Richard JdS 2024, May 2024, Bordeaux, France Communication dans un congrès hal-04664748v1
Redefining phenotypic heterogeneity of pancreatic ductal adenocarcinoma: A bottom-up approach Marc Hilmi,Flore Delecourt,Jerôme Rafenne,Taib Bourega,Nelson Dusettiet al. AACR Special Conference in Cancer Research: Pancreatic Cancer; 2023 Sep 27-30; Boston, Massachusetts., Sep 2023, Boston, United States. pp.B064-B064, ⟨10.1158/1538-7445.panca2023-b064⟩ Communication dans un congrès hal-04456752v1
PenDA, a rank-based method for personalized differential analysis: Application to lung cancer Clémentine Decamps,Magali Richard,Daniel Jost Journées Ouvertes en Biologie, Informatique et Mathématiques (JOBIM2021), Jul 2021, Paris, France Communication dans un congrès hal-04664892v1
codabench, a web-plateform to organize scientific competitions Florent Chuffart,Anne-Catherine Letournel,Isabelle Guyon,Magali Richard JOBIM2024, Jun 2024, Toulouse, France Communication dans un congrès hal-04664118v1
PenDA, a rank-based method for Personalized Differential Analysis: application to lung cancer Magali Richard,Florent Chuffart,Clémentine Decamps,Sophie Rousseaux,Saadi Khochbinet al. 19th International Conference on Systems Biology (ICSB 2018), Oct 2018, Lyon, France Communication dans un congrès hal-04664879v1
Retour d'expérience concernant le data challenge épigénétique et médiation à large échelle d'Aussois Sophie Achard,Dylan Aïssi,Michael Blum,Kevin Caye,Florent Chuffartet al. CFIES 2017 - Colloque Francophone International sur l’Enseignement de la Statistique, Sep 2017, Grenoble, France Communication dans un congrès hal-03881657v1

Pré-publication, Document de travail (5)

How to organise a scientific competition to benchmark methods and algorithms in computational biology? Nicolas Homberg,Lucie Lamothe,Elise Amblard,Hugo Barbot,Morgane Térézolet al. 2026 Pré-publication, Document de travail hal-05445539v2
Group lasso based selection for high-dimensional mediation analysis Allan Jérolon,Flora Alarcon,Florence Pittion,Magali Richard,Olivier Françoiset al. 2025 Pré-publication, Document de travail hal-04710663v2
HDMAX2-surv: high-dimensional mediation analysis of survival data with application to pancreatic cancer Florence Pittion,Elise Amblard,Emilie Devijver,Adeline Samson,Nelle Varoquauxet al. 2026 Pré-publication, Document de travail hal-05262669v1
A robust workflow to benchmark deconvolution of multi-omic data Elise Amblard,Vadim Bertrand,Luis Martin Pena,Slim Karkar,Florent Chuffartet al. 2024 Pré-publication, Document de travail hal-04773934v1
AI Competitions and Benchmarks, Practical issues: Proposals, grant money, sponsors, prizes, dissemination, publicity Magali Richard,Yuna Blum,Justin Guinney,Gustavo Stolovitzky,Adrien Pavão 2024 Pré-publication, Document de travail hal-04342074v1

Article dans une revue (17)

A robust workflow to benchmark deconvolution of multi-omic data Elise Amblard,Vadim Bertrand,Hugo Barbot,Luis Martin Peña,Slim Karkaret al. Genome Biology, 2025, 26 (1), pp.429. ⟨10.1186/s13059-025-03897-9⟩ Article dans une revue hal-05444478v1
hdmax2, an R package to perform high dimension mediation analysis Florence Pittion,Basile Jumentier,Aurélie Nakamura,Johanna Lepeule,Olivier Francoiset al. Peer Community Journal, 2025 Article dans une revue hal-04658960v6
Redefining phenotypic intratumor heterogeneity of pancreatic ductal adenocarcinoma: a bottom‐up approach Marc Hilmi,Flore Delecourt,Jérôme Raffenne,Taib Bourega,Nelson Dusettiet al. Journal of Pathology, 2025, 265 (4), pp.448-461. ⟨10.1002/path.6398⟩ Article dans une revue hal-04980252v1
DECOMICS, a shiny application for unsupervised cell type deconvolution and biological interpretation of bulk omic data Slim Karkar,Ashwini Sharma,Carl Herrmann,Yuna Blum,Magali Richard Bioinformatics Advances, 2024, 4 (1), pp.vbae136. ⟨10.1093/bioadv/vbae136⟩ Article dans une revue hal-04660629v2
Pacpaint: a histology-based deep learning model uncovers the extensive intratumor molecular heterogeneity of pancreatic adenocarcinoma Charlie Saillard,Flore Delecourt,Benoit Schmauch,Olivier Moindrot,Magali Svrceket al. Nature Communications, 2023, 14 (1), pp.3459. ⟨10.1038/s41467-023-39026-y⟩ Article dans une revue hal-04164254v1
Codabench: Flexible, Easy-to-Use and Reproducible Meta-Benchmark Platform Zhen Xu,Sergio Escalera,Adrien Pavao,Magali Richard,Wei-Wei Tuet al. Patterns, 2022, 3 (7), pp.100543. ⟨10.1016/j.patter.2022.100543⟩ Article dans une revue hal-03374222v4
DECONbench: a benchmarking platform dedicated to deconvolution methods for tumor heterogeneity quantification Clémentine Decamps,Alexis Arnaud,Florent Petitprez,Mira Ayadi,Aurélia Baurèset al. BMC Bioinformatics, 2021, 22 (1), pp.473. ⟨10.1186/s12859-021-04381-4⟩ Article dans une revue hal-03372668v1
PenDA, a rank-based method for personalized differential analysis: Application to lung cancer Magali Richard,Clémentine Decamps,Florent Chuffart,Elisabeth Brambilla,Sophie Rousseauxet al. PLoS Computational Biology, 2020, 16 (5), pp.e1007869. ⟨10.1371/journal.pcbi.1007869⟩ Article dans une revue inserm-02868566v1
Guidelines for cell-type heterogeneity quantification based on a comparative analysis of reference-free DNA methylation deconvolution software Clémentine Decamps,Florian Privé,Raphael Bacher,Daniel Jost,Arthur Waguetet al. BMC Bioinformatics, 2020, 21 (1), ⟨10.1186/s12859-019-3307-2⟩ Article dans une revue hal-02997889v1
Guidelines for cell-type heterogeneity quantification based on a comparative analysis of reference-free DNA methylation deconvolution software Clémentine Decamps,Florian Privé,Raphael Bacher,Daniel Jost,Arthur Waguetet al. BMC Bioinformatics, 2020, 21 (1), ⟨10.1186/s12859-019-3307-2⟩ Article dans une revue hal-03012777v1
Genomics of cellular proliferation in periodic environmental fluctuations Jérôme Salignon,Magali Richard,Etienne Fulcrand,Hélène Duplus‐bottin,Gaël Yvert Molecular Systems Biology, 2018, 14 (3), pp.e7823. ⟨10.15252/msb.20177823⟩ Article dans une revue hal-02009632v1
CRELD1 is an evolutionarily-conserved maturational enhancer of ionotropic acetylcholine receptors Manuela d'Alessandro,Magali Richard,Christian Stigloher,Vincent Gache,Thomas Boulinet al. eLife, 2018, 7, ⟨10.7554/eLife.39649⟩ Article dans une revue hal-03369468v1
Assigning function to natural allelic variation via dynamic modeling of gene network induction Magali Richard,Florent Chuffart,Hélène Duplus‐bottin,Fanny Pouyet,Martin Spichtyet al. Molecular Systems Biology, 2018, 14 (1), pp.e7803. ⟨10.15252/msb.20177803⟩ Article dans une revue hal-01976613v1
CRELD1 is an evolutionarily-conserved maturational enhancer of ionotropic acetylcholine receptors Manuela d'Alessandro,Magali Richard,Christian Stigloher,Vincent Gache,Thomas Boulinet al. eLife, 2018, 7, ⟨10.7554/eLife.39649⟩ Article dans une revue hal-02009626v1
Exploiting Single-Cell Quantitative Data to Map Genetic Variants Having Probabilistic Effects Florent Chuffart,Magali Richard,Daniel Jost,Claire Burny,Hélène Duplus-Bottinet al. PLoS Genetics, 2016, 12 (8), pp.e1006213. ⟨10.1371/journal.pgen.1006213⟩ Article dans une revue hal-01976590v1
How does evolution tune biological noise? Magali Richard,Gaël Yvert Frontiers in Genetics, 2014, ⟨10.3389/fgene.2014.00374⟩ Article dans une revue ensl-01224442v1
Biosynthesis of ionotropic acetylcholine receptors requires the evolutionarily conserved ER membrane complex Magali Richard,Thomas Boulin,Valérie Robert,Janet Richmond,Jean-Louis Bessereau Proceedings of the National Academy of Sciences of the United States of America, 2013, 110 (11), pp.E1055-E1063. ⟨10.1073/pnas.1216154110⟩ Article dans une revue hal-03369480v1

Logiciel (5)

medepir : MEthylation DEconvoluation PIpeline in R Magali Richard,Clémentine Decamps,Florian Privé,Michael Gb Blum 2025, ⟨swh:1:dir:efd827b7099bac94dab11520f6e5f77d2990ef90;origin=https://github.com/bcm-uga/medepir;visit=swh:1:snp:52844a39c5dafa3e89447e3a12266b2e3a0be444;anchor=swh:1:rev:2fdd8d6a151cdadf42884f32c3f4bf69527cb9bd⟩ Logiciel hal-04979641v1
ptlmapper: Useful genetic tool allowing to discriminate individuals by comparing the distribution of their phenotype and to map the genetic loci responsible for specific distributions Florent Chuffart,Magali Richard,Daniel Jost,Gael Yvert 2024, ⟨swh:1:dir:fdb7c18c6cc1da4e23be844d76960975de7d58b4;origin=https://github.com/fchuffar/ptlmapper;visit=swh:1:snp:b5ad098a35fef37940d0859e1c93d62daef2b508;anchor=swh:1:rev:c5068be2f281eab0e315cdfca29f1d5278d97617⟩ Logiciel hal-04523653v1
hdmax2: R package hdmax2 performs high dimension mediation analysis Florence Pittion,Magali Richard,Olivier Francois,Basile Jumentier 2024, ⟨swh:1:dir:2104ab22c7a823c80352569346b3787eeda32cd6;origin=https://github.com/bcm-uga/hdmax2;visit=swh:1:snp:0d86431f5a14de2dbe7681c2cef29f30a8292c91;anchor=swh:1:rev:69a04407810a5559a464dcb6ec512effd5ace588⟩ Logiciel hal-04660947v1
decomics: DEConvolution of OMICS data Slim Karkar,Yuna Blum,Magali Richard 2024, ⟨swh:1:dir:c0fcb31492397ae5ecfed04ed8f51e4f3bfafa70;origin=https://gitlab.in2p3.fr/Magali.Richard/decomics;visit=swh:1:snp:b68305bea69e3160c83aaccc906dd63246b9a1bf;anchor=swh:1:rev:50a6a6cf42d94b2b891e75fef206a7e8ef9d0fee⟩ Logiciel hal-04661001v1
penda Magali Richard,Florent Chuffart,Daniel Jost,Clémentine Decamps 2020, ⟨swh:1:dir:e8496e082b5c3c62500d2e4c728f5db659e6be30;origin=https://github.com/bcm-uga/penda;visit=swh:1:snp:e4dcc1ca19c558baceaa2efa17e924a697494398;anchor=swh:1:rev:5dd5dd268b3cb511d044200105a1270ca0f56d60⟩ Logiciel hal-03898939v1

Poster de conférence (6)

Evaluation of linear modeling assumptions in a simulation context for deconvolution of multi-omic data Elouan Deffains,Hugo Barbot,David Causeur,Yuna Blum,Magali Richard Journée de Biologie In Silico de Rennes, Nov 2025, Rennes, France. Poster de conférence hal-05489405v1
The backstage of the third Health Data Challenge: Introducing an Organizational Template and Custom, Temporary and Local Codabench Instances. Nicolas Homberg,Magali Richard,Florent Chuffart Jobim 2024, Jun 2024, Toulouse, France. ⟨10.1016/j.patter.2022.100543⟩ Poster de conférence hal-04664469v1
Simulation of data-driven multi-omic benchmark data for cellular deconvolution methods evaluation Hugo Barbot,David Causeur,Yuna Blum,Magali Richard IGDR PhD symposium, Nov 2024, Rennes (Campus de Beaulieu), France. 2024 Poster de conférence hal-04790951v1
HDMAX2, an R package to perform high dimension mediation analysis Florence Pittion,Basile Jumentier,Aurélie Nakamura,Johanna Lepeule,Olivier Françoiset al. COBICA 2024, Mar 2024, Grenoble, France Poster de conférence hal-04664854v1
Multi-omic statistical inference of cellular heterogeneity - COBICA 2024 Hugo Barbot,David Causeur,Yuna Blum,Magali Richard cobica2024 : Computational Biology of Cancer 2024, Mar 2024, Grenoble, France Poster de conférence hal-04664694v1
THEMA: Identification of molecular mechanisms by which Tumor HEterogeneity influences disease outcome: high-dimension Mediation Analysis Florence Pittion,Olivier François,Magali Richard 31st Annual Intelligent Systems For Molecular Biology and 22nd Annual European Conference on Computational Biology (ISCM/ECCB 2023), Jul 2023, Lyon, France. ISCM/ECCB 2023 Proceedings Poster de conférence hal-04667942v1

HDR (1)

An investigation of tumor heterogeneity based on computational approaches Magali Richard Cancer. Université Grenoble - Alpes, 2022 HDR tel-04664124v1