Yuna Blum

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Publications

Bimodal silencing of the acinar cell-specific mRNA translation repressor PAIP2B defines a poor prognostic subgroup within the classical pancreatic tumor type

Eulalie Corre , Amandine Alard , Catherine Marbœuf , Charline Lasfargues , Sandra Dailhau et al.

Cancer Letters, 2025, 632, pp.217971. ⟨10.1016/j.canlet.2025.217971⟩

Article dans une revue hal-05235758v1
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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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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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Liver gene expression and its rewiring in hepatic steatosis are controlled by PI3Kα-dependent hepatocyte signaling

Marion Régnier , Arnaud Polizzi , Tiffany Fougeray , Anne Fougerat , Prunelle Perrier et al.

PLoS Biology, 2025, 23 (4), pp.e3003112-e3003112. ⟨10.1371/journal.pbio.3003112⟩

Article dans une revue hal-05063626v1
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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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Preclinical evaluation of CDK4 phosphorylation predicts high sensitivity of pleural mesotheliomas to CDK4/6 inhibition

Sabine Paternot , Eric Raspé , C Meiller , Maxime Tarabichi , Jean-Baptiste Assié et al.

Molecular Oncology, 2024, 18 (4), pp.866-894. ⟨10.1002/1878-0261.13351⟩

Article dans une revue hal-03898858v1
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Cirscan: a shiny application to identify differentially active sponge mechanisms and visualize circRNA-miRNA-mRNA networks

Rose-Marie Fraboulet , Yanis Si Ahmed , Marc Aubry , Sébastien Corre , Marie-Dominique Galibert et al.

BMC Bioinformatics, 2024, 25 (1), pp.53. ⟨10.1186/s12859-024-05668-y⟩

Article dans une revue hal-04540383v1
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Ephrin-B1 regulates the adult diastolic function through a late postnatal maturation of cardiomyocyte surface crests

Clement Karsenty , Celine Guilbeau-Frugier , Gaël Genet , Marie-Helene Seguelas , Philippe Alzieu et al.

eLife, 2023, 12, pp.e80904. ⟨10.7554/eLife.80904⟩

Article dans une revue hal-03944430v1
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Priming therapy by targeting enhancer-initiated pathways in patient-derived pancreatic cancer cells

Nicolas A Fraunhoffer , Aura I Moreno Vega , Analía Meilerman Abuelafia , Marie Morvan , Emilie Lebarbier et al.

EBioMedicine, 2023, 92, pp.104602. ⟨10.1016/j.ebiom.2023.104602⟩

Article dans une revue hal-04100206v1
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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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Genomic Instability and Pro-Tumoral Inflammation are associated with Primary Resistance to Anti-PD1 + Anti-Angiogenesis in Malignant Pleural Mesothelioma

Francois-Xavier Danlos , Matthieu Texier , Bastien Job , Severine Mouraud , Lydie Cassard et al.

Cancer Discovery, 2023, 13 (4), pp.858-879. ⟨10.1158/2159-8290.CD-22-0886⟩

Article dans une revue hal-03972355v1
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Integrative study of diet-induced mouse models of NAFLD identifies PPARα as a sexually dimorphic drug target

Sarra Smati , Arnaud Polizzi , Anne Fougerat , Sandrine Ellero-Simatos , Yuna Blum et al.

Gut, 2022, 71 (4), pp.807-821. ⟨10.1136/gutjnl-2020-323323⟩

Article dans une revue hal-03215969v1
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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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Intratumor CMS Heterogeneity Impacts Patient Prognosis in Localized Colon Cancer

Laetitia Marisa , Yuna Blum , Julien Taieb , Mira Ayadi , Camilla Pilati et al.

Clinical Cancer Research, 2021, 27 (17), pp.4768-4780. ⟨10.1158/1078-0432.CCR-21-0529⟩

Article dans une revue hal-03282346v1
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Multi-site tumor sampling highlights molecular intra-tumor heterogeneity in malignant pleural mesothelioma

Clément Meiller , François Montagne , Theo Hirsch , Stefano Caruso , Julien de Wolf et al.

Genome Medicine, 2021, 13 (1), pp.113. ⟨10.1186/s13073-021-00931-w⟩

Article dans une revue inserm-03289952v1
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Depicting the genetic architecture of pediatric cancers through an integrative gene network approach

Clara Savary , Artem Kim , Alexandra Lespagnol , Virginie Gandemer , Isabelle Pellier et al.

Scientific Reports, 2020, 10 (1), pp.1224. ⟨10.1038/s41598-020-58179-0⟩

Article dans une revue hal-02472258v1
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Genetic alterations of malignant pleural mesothelioma: association to tumor heterogeneity and overall survival Author names

Lisa Quetel , Clément Meiller , Jean-Baptiste Assié , Yuna Blum , Sandrine Imbeaud et al.

Molecular Oncology, 2020, Epub ahead of print. ⟨10.1002/1878‐0261.12651⟩

Article dans une revue inserm-02490591v1

Deciphering the Genetic Etiology of Pediatric Cancers Through an Integrative Gene Network Approach

C. Savary , A. Kim , A. Lespagnol , V. Gandemer , I. Pellier et al.

Pediatric Blood and Cancer, 2019, 66, pp.S509-S509

Article dans une revue hal-02355731v1
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Dissecting heterogeneity in malignant pleural mesothelioma through histo-molecular gradients for clinical applications

Yuna Blum , Clément Meiller , Lisa Quetel , Nabila Elarouci , Mira Ayadi et al.

Nature Communications, 2019, 10, pp.1333. ⟨10.1038/s41467-019-09307-6⟩

Article dans une revue hal-02090279v1
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Multi-tissue transcriptomic study reveals the main role of liver in the chicken adaptive response to a switch in dietary energy source through the transcriptional regulation of lipogenesis

Colette Désert , Elisabeth Baéza , Meziane Aite , Morgane Boutin , Aurélie Le Cam et al.

BMC Genomics, 2018, 19 (1), pp.1-19. ⟨10.1186/s12864-018-4520-5⟩

Article dans une revue hal-01727161v1

Stratification of Pancreatic Ductal Adenocarcinomas Based on Tumor and Microenvironment Features

Francesco Puleo , Remy Nicolle , Yuna Blum , Jerome Cros , Laetitia Marisa et al.

Gastroenterology, 2018, 155 (6), pp.1999+. ⟨10.1053/j.gastro.2018.08.033⟩

Article dans une revue hal-02143548v1
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Distinct epigenetic landscapes underlie the pathobiology of pancreatic cancer subtypes

Gwen Lomberk , Yuna Blum , Remy Nicolle , Asha Nair , Krutika Satish Gaonkar et al.

Nature Communications, 2018, 9 (1), pp.1978. ⟨10.1038/s41467-018-04383-6⟩

Article dans une revue hal-02143535v1

Multi-omic approaches unveil new therapeutic targets for the treatment of pancreatic cancer

Remy Nicolle , Yuna Blum , Laetitia Marisa , Nelson Dusetti , Juan Iovanna

Médecine/Sciences, 2018, 34 (5), pp.379-382. ⟨10.1051/medsci/20183405003⟩

Article dans une revue hal-02143669v1
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Gene expression profiling of patient‐derived pancreatic cancer xenografts predicts sensitivity to the BET bromodomain inhibitor JQ1: implications for individualized medicine efforts

Benjamin Bian , Martin Bigonnet , Odile Gayet , Céline Loncle , Aurélie Maignan et al.

EMBO Molecular Medicine, 2017, 9 (4), pp.482 - 497. ⟨10.15252/emmm.201606975⟩

Article dans une revue hal-01787567v1
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Pancreatic Adenocarcinoma Therapeutic Targets Revealed by Tumor-Stroma Cross-Talk Analyses in Patient-Derived Xenografts

Remy Nicolle , Yuna Blum , Laëtitia Marisa , Céline Loncle , Odile Gayet et al.

Cell Reports, 2017, 21 (9), pp.2458-2470. ⟨10.1016/j.celrep.2017.11.003⟩

Article dans une revue inserm-01985259v1
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Preservation Analysis of Macrophage Gene Coexpression Between Human and Mouse Identifies PARK2 as a Genetically Controlled Master Regulator of Oxidative Phosphorylation in Humans

Veronica Codoni , Yuna Blum , Mete Civelek , Carole Proust , Oscar Franzén et al.

G3, 2016, 6 (10), pp.3361-3371. ⟨10.1534/g3.116.033894⟩

Article dans une revue hal-01404133v1
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Role of lipid phosphate phosphatase 3 in human aortic endothelial cell function

Zahia Touat-Hamici , Henri Weidmann , Yuna Blum , Carole Proust , Hervé Durand et al.

Cardiovascular Research, 2016, 112 (3), pp.702 - 713. ⟨10.1093/cvr/cvw217⟩

Article dans une revue hal-01484581v1
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Hepatic circadian clock oscillators and nuclear receptors integrate microbiome-derived signals

Alexandra Montagner , Agata Korecka , Arnaud Polizzi , Yannick Lippi , Yuna Blum et al.

Scientific Reports, 2016, 6 (1), pp.1-14. ⟨10.1038/srep20127⟩

Article dans une revue hal-01482816v1

Sparse factor model for co-expression networks with an application using prior biological knowledge

Yuna Blum , Magalie Houée-Bigot , David Causeur

Statistical Applications in Genetics and Molecular Biology, 2016, 15 (3), pp.253-272. ⟨10.1515/sagmb-2015-0002⟩

Article dans une revue hal-01340542v1
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Bariatric Surgery Induces Disruption in Inflammatory Signaling Pathways Mediated by Immune Cells in Adipose Tissue: A RNA-Seq Study

Christine Poitou , Claire Perret , François Mathieu , Vinh Truong , Yuna Blum et al.

PLoS ONE, 2015, 10 (5), pp.e0125718. ⟨10.1371/journal.pone.0125718⟩

Article dans une revue hal-01227880v1

Pleiotropic effects of polymorphism of the gene diacylglycerol-O-transferase 1 (DGAT1) in the mammary gland tissue of dairy cows

Núria Mach , Yuna Blum , A. Bannink , David Causeur , M. Houee-Bigot et al.

Journal of Dairy Science, 2012, 95 (9), pp.4989-5000. ⟨10.3168/jds.2012-5348⟩

Article dans une revue hal-00841015v1
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Complex trait subtypes identification using transcriptome profiling reveals an interaction between two QTL affecting adiposity in chicken

Yuna Blum , Guillaume Le Mignon , David Causeur , Olivier Filangi , Colette Désert et al.

BMC Genomics, 2011, 12 (november), pp.8. ⟨10.1186/1471-2164-12-567⟩

Article dans une revue hal-00730144v1
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Apports de la génomique fonctionnelle à la cartographie fine de QTL

Guillaume Le Mignon , Yuna Blum , Olivier Demeure , Christian Diot , Elisabeth Le Bihan-Duval et al.

INRA Productions Animales, 2010, 23 (4), pp.343-358

Article dans une revue hal-00729443v1

Stratification of pleural mesothelioma patients for combined immunotherapy based on sarcomatoid component and tumour microenvironment markers in the IFCT-MAPS2 study

G. Tosato , Y Blum , J-B. Assie , R. Sequeiros , A Langlais et al.

European Lung Cancer Congress (ELCC) 2025, Mar 2025, Paris, France. pp.S151, ⟨10.1016/S1556-0864(25)00432-0⟩

Communication dans un congrès hal-05167693v1

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
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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

Inferring cellular heterogeneity with mixture models for DNA methylation rates

H Barbot , D Causeur , Y Blum , M Richard

Journées de Statistique, Jun 2025, Marseille, France

Communication dans un congrès hal-05489385v1

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
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Cirscan: a shiny application to identify differentially active sponge mechanisms and visualize circRNA-miRNA-mRNA networks

Rose-Marie Fraboulet , Yanis Si Ahmed , Marc Aubry , Sébastien Corre , Marie-Dominique Galibert et al.

JOURNÉES OUVERTES EN BIOLOGIE, INFORMATIQUE ET MATHÉMATIQUES (JOBIM ) 2023, Jun 2023, Diverses villes françaises, France

Communication dans un congrès hal-04286509v1

PACpAInt: a deep learning approach to identify molecular subtypes of pancreatic adenocarcinoma on histology slides

C. Saillard , F. Delecourt , B. Schmauch , O. Moindrot , M. Svrcek et al.

Annual Meeting of the American-Association-for-Cancer-Research (AACR), Apr 2022, New Orleans, United States. pp.Abstract nr 472

Communication dans un congrès hal-04090168v1
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Identification of candidate polymorphism in a QTL region by combining eQTL mapping with NGS data

Pierre-François Roux , Yuna Blum , Colette Désert , Anis Djari , Diane Esquerre et al.

64th Annual Meeting of the European Federation of Animal Science (EAAP), Aug 2013, Nantes, France. pp.300

Communication dans un congrès hal-01019609v1

Sparse factor models for gene co-expression networks.

Yuna Blum , M. Houée , David Causeur

Séminaire de Biostatistiques, Dec 2012, Toulouse (FR), France. non paginé

Communication dans un congrès hal-00841019v1
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Inferring gene networks using a sparse factor model approach, Statistical Learning and Data Science

Yuna Blum , Magali Houée , Chloé Friguet , Sandrine Lagarrigue , David Causeur

Learning and Data Science, May 2012, Florence (IT), Italy

Communication dans un congrès hal-00841017v1
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Transcriptome profiling reveals interaction between two QTL for fatness in chicken

Yuna Blum , Guillaume Le Mignon , Frederique Pitel , David Causeur , Olivier Demeure et al.

15th European workshop on QTL mapping and marker assisted selection (QTLMAS), May 2011, Rennes (FR), France. 1 p

Communication dans un congrès hal-00841016v1

Genetic analysis of a complex trait using transcriptomic data: contribution of gene regulatory network modeling

Yuna Blum , Magalie Houée , Chloé Friguet , Sandrine Lagarrigue , David Causeur

XX. Conference of the plant & animal genome (PAG), Jan 2012, San Diego, United States. 1 p

Communication dans un congrès hal-00841103v1

Inférence de réseaux de co-expression génique

Yuna Blum , M. Houée , David Causeur

10ème Journée Biogenouest, Nov 2012, Rennes (FR), France. non paginé

Communication dans un congrès hal-00841018v1

Effect of the gene diacylglycerol-O-transferase 1 (DGAT1) polymorphism on the global expression pattern of genes in the mammary gland tissue of dairy cows

Núria Mach , Yuna Blum , David Causeur , Sandrine Lagarrigue , M. A. Smits

62. Annual Meeting of the European Federation of Animal Science (EAAP), Aug 2011, Stavanger, Norway

Communication dans un congrès hal-02747109v1
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Integrating QTL controlling fatness, lipid metabolites and gene expressions to genetically dissect the adiposity complex trait in a meat chicken cross

Yuna Blum , Olivier O. Demeure , Colette Désert , Hervé Guillou , J Bertrand-Michel et al.

62. Annual Meeting of the European Association for Animal Production (EAAP), Aug 2011, Stavanger, Norway

Communication dans un congrès hal-02748764v1
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Inférence sur réseaux géniques par Analyse en Facteurs

Yuna Blum , Chloé Friguet , Sandrine Lagarrigue , David Causeur

42èmes Journées de Statistique, 2010, Marseille, France, France

Communication dans un congrès inria-00494802v1

A factor model to analyze heterogeneity in gene expression in a context of QTL mapping

Yuna Blum , Sandrine Lagarrigue , David Causeur

8th workshop " Statistical Methods for Post-Genomic Data ", Jan 2010, Marseille, France

Communication dans un congrès hal-00459362v1

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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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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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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deconvPDAC : a quantifier of PDAC tumor cellular heterogeneity

Yasmina Kermezli , Lucie Lamothe , Jerome Cros , Magali Richard , Yuna Blum

Journées Ouvertes en Biologie, Informatique et Mathématiques (JOBIM 2024), Jun 2024, Toulouse, France.

Poster de conférence hal-04669313v1
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AnnotQTL: a new tool to gather functional and comparative information on a genomic region

Frédéric Lecerf , Anthony Bretaudeau , Olivier Sallou , Colette Désert , Yuna Blum et al.

12. Journées Ouvertes en Biologie, Informatique et Mathématiques, Jun 2011, Paris, France. 2011, JOBIM 2011

Poster de conférence hal-02746728v1
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A factor model to analyse heterogeneity in gene expression in a context of QTL characterization

Yuna Blum , Sandrine Lagarrigue , David Causeur

XXXII International Conference on Animal Genetics (ISAG), Jul 2010, Edinburgh, United Kingdom. 2010, Proceedings of the 32nd International Conference on Animal Genetics

Poster de conférence hal-02754275v1
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Transcriptome profiling reveals interaction between two QTL for fatness in chicken

Yuna Blum , Guillaume G. Le Mignon , Colette Désert , Frederique Pitel , David Causeur et al.

XXXII International Conference on Animal Genetics (ISAG), Jul 2010, Edinburgh, United Kingdom. 2010, Proceedings of the 32nd International Conference on Animal Genetics

Poster de conférence hal-02754276v1
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How to organise a scientific competition to benchmark methods and algorithms in computational biology?

Nicolas Homberg , Lucie Lamothe , Elise Amblard , Hugo Barbot , Morgane Térézol et al.

2026

Pré-publication, Document de travail hal-05445539v2
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A robust workflow to benchmark deconvolution of multi-omic data

Elise Amblard , Vadim Bertrand , Luis Martin Pena , Slim Karkar , Florent Chuffart et al.

2024

Pré-publication, Document de travail hal-04773934v1
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p110α-dependent hepatocyte signaling is critical for liver gene expression and its rewiring in MASLD

Marion Régnier , Arnaud Polizzi , Tiffany Fougeray , Anne Fougerat , Prunelle Perrier et al.

2024

Pré-publication, Document de travail hal-04442467v1
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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

PACpAInt: a deep learning approach to identify molecular subtypes of pancreatic adenocarcinoma on histology slides

C. Saillard , F. Delecourt , B. Schmauch , O. Moindrot , M. Svrcek et al.

2022

Pré-publication, Document de travail hal-03871989v1
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Crest maturation at the cardiomyocyte surface contributes to a new late postnatal development stage that controls the diastolic function of the adult heart

Clément Karsenty , Céline Guilbeau-Frugier , Gaël Genet , Marie-Hélène Seguelas , Philippe Alzieu et al.

2022

Pré-publication, Document de travail hal-03574569v1