Magali Richard

CNRS CRCN
95 %
Libre accès
43
Documents
Affiliations actuelles
  • Algorithms, Principles and TheorIes for collaborative Knowledge acquisition And Learning (APTIKAL)
  • Laboratoire d'Informatique de Grenoble (LIG)

Publications

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Publications

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A robust workflow to benchmark deconvolution of multi-omic data

Elise Amblard , Vadim Bertrand , Hugo Barbot , Luis Martin Peña , Slim Karkar et al.

Genome Biology, 2025, 26 (1), pp.429. ⟨10.1186/s13059-025-03897-9⟩

Article dans une revue hal-05444478v1
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hdmax2, an R package to perform high dimension mediation analysis

Florence Pittion , Basile Jumentier , Aurélie Nakamura , Johanna Lepeule , Olivier Francois et al.

Peer Community Journal, 2025

Article dans une revue hal-04658960v6
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Redefining phenotypic intratumor heterogeneity of pancreatic ductal adenocarcinoma: a bottom‐up approach

Marc Hilmi , Flore Delecourt , Jérôme Raffenne , Taib Bourega , Nelson Dusetti et al.

Journal of Pathology, 2025, 265 (4), pp.448-461. ⟨10.1002/path.6398⟩

Article dans une revue hal-04980252v1
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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
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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 Svrcek et al.

Nature Communications, 2023, 14 (1), pp.3459. ⟨10.1038/s41467-023-39026-y⟩

Article dans une revue hal-04164254v1
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Codabench: Flexible, Easy-to-Use and Reproducible Meta-Benchmark Platform

Zhen Xu , Sergio Escalera , Adrien Pavao , Magali Richard , Wei-Wei Tu et al.

Patterns, 2022, 3 (7), pp.100543. ⟨10.1016/j.patter.2022.100543⟩

Article dans une revue hal-03374222v4
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DECONbench: a benchmarking platform dedicated to deconvolution methods for tumor heterogeneity quantification

Clémentine Decamps , Alexis Arnaud , Florent Petitprez , Mira Ayadi , Aurélia Baurès et al.

BMC Bioinformatics, 2021, 22 (1), pp.473. ⟨10.1186/s12859-021-04381-4⟩

Article dans une revue hal-03372668v1
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PenDA, a rank-based method for personalized differential analysis: Application to lung cancer

Magali Richard , Clémentine Decamps , Florent Chuffart , Elisabeth Brambilla , Sophie Rousseaux et al.

PLoS Computational Biology, 2020, 16 (5), pp.e1007869. ⟨10.1371/journal.pcbi.1007869⟩

Article dans une revue inserm-02868566v1
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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 Waguet et al.

BMC Bioinformatics, 2020, 21 (1), ⟨10.1186/s12859-019-3307-2⟩

Article dans une revue hal-03012777v1
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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 Waguet et al.

BMC Bioinformatics, 2020, 21 (1), ⟨10.1186/s12859-019-3307-2⟩

Article dans une revue hal-02997889v1
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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 Boulin et al.

eLife, 2018, 7, ⟨10.7554/eLife.39649⟩

Article dans une revue hal-03369468v1
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Assigning function to natural allelic variation via dynamic modeling of gene network induction

Magali Richard , Florent Chuffart , Hélène Duplus‐bottin , Fanny Pouyet , Martin Spichty et al.

Molecular Systems Biology, 2018, 14 (1), pp.e7803. ⟨10.15252/msb.20177803⟩

Article dans une revue hal-01976613v1
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CRELD1 is an evolutionarily-conserved maturational enhancer of ionotropic acetylcholine receptors

Manuela d'Alessandro , Magali Richard , Christian Stigloher , Vincent Gache , Thomas Boulin et al.

eLife, 2018, 7, ⟨10.7554/eLife.39649⟩

Article dans une revue hal-02009626v1
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Exploiting Single-Cell Quantitative Data to Map Genetic Variants Having Probabilistic Effects

Florent Chuffart , Magali Richard , Daniel Jost , Claire Burny , Hélène Duplus-Bottin et al.

PLoS Genetics, 2016, 12 (8), pp.e1006213. ⟨10.1371/journal.pgen.1006213⟩

Article dans une revue hal-01976590v1
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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
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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
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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 Dusetti et 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
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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 Khochbin et al.

19th International Conference on Systems Biology (ICSB 2018), Oct 2018, Lyon, France

Communication dans un congrès hal-04664879v1
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Retour d'expérience concernant le data challenge épigénétique et médiation à large échelle d'Aussois

Sophie Achard , Dylan Aïssi , Michael Blum , Kevin Caye , Florent Chuffart et al.

CFIES 2017 - Colloque Francophone International sur l’Enseignement de la Statistique, Sep 2017, Grenoble, France

Communication dans un congrès hal-03881657v1

medepir : MEthylation DEconvoluation PIpeline in R

Magali Richard , Clémentine Decamps , Florian Privé , Michael Gb Blum 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 Logiciel hal-04523653v1

hdmax2: R package hdmax2 performs high dimension mediation analysis

Florence Pittion , Magali Richard , Olivier Francois , Basile Jumentier Logiciel hal-04660947v1

decomics: DEConvolution of OMICS data

Slim Karkar , Yuna Blum , Magali Richard Logiciel hal-04661001v1

penda

Magali Richard , Florent Chuffart , Daniel Jost , Clémentine Decamps Logiciel hal-03898939v1

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
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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
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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
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HDMAX2, an R package to perform high dimension mediation analysis

Florence Pittion , Basile Jumentier , Aurélie Nakamura , Johanna Lepeule , Olivier François et al.

COBICA 2024, Mar 2024, Grenoble, France

Poster de conférence hal-04664854v1
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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
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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