Yuna Blum

Publications

Article dans une revue (33)

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 Dailhauet al. Cancer Letters, 2025, 632, pp.217971. ⟨10.1016/j.canlet.2025.217971⟩ Article dans une revue hal-05235758v1
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
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
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 Perrieret al. PLoS Biology, 2025, 23 (4), pp.e3003112-e3003112. ⟨10.1371/journal.pbio.3003112⟩ Article dans une revue hal-05063626v1
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
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 Assiéet al. Molecular Oncology, 2024, 18 (4), pp.866-894. ⟨10.1002/1878-0261.13351⟩ Article dans une revue hal-03898858v1
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 Galibertet al. BMC Bioinformatics, 2024, 25 (1), pp.53. ⟨10.1186/s12859-024-05668-y⟩ Article dans une revue hal-04540383v1
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,Émilie Lebarbieret al. EBioMedicine, 2023, 92, pp.104602. ⟨10.1016/j.ebiom.2023.104602⟩ Article dans une revue hal-04100206v1
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 Alzieuet al. eLife, 2023, 12, pp.e80904. ⟨10.7554/eLife.80904⟩ Article dans une revue hal-03944430v1
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 Cassardet al. Cancer Discovery, 2023, 13 (4), pp.858-879. ⟨10.1158/2159-8290.CD-22-0886⟩ Article dans une revue hal-03972355v1
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
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 Blumet al. Gut, 2022, 71 (4), pp.807-821. ⟨10.1136/gutjnl-2020-323323⟩ Article dans une revue hal-03215969v1
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
Intratumor CMS Heterogeneity Impacts Patient Prognosis in Localized Colon Cancer Laetitia Marisa,Yuna Blum,Julien Taieb,Mira Ayadi,Camilla Pilatiet al. Clinical Cancer Research, 2021, 27 (17), pp.4768-4780. ⟨10.1158/1078-0432.CCR-21-0529⟩ Article dans une revue hal-03282346v1
Multi-site tumor sampling highlights molecular intra-tumor heterogeneity in malignant pleural mesothelioma Clément Meiller,François Montagne,Theo Hirsch,Stefano Caruso,Julien de Wolfet al. Genome Medicine, 2021, 13 (1), pp.113. ⟨10.1186/s13073-021-00931-w⟩ Article dans une revue inserm-03289952v1
Depicting the genetic architecture of pediatric cancers through an integrative gene network approach Clara Savary,Artem Kim,Alexandra Lespagnol,Virginie Gandemer,Isabelle Pellieret al. Scientific Reports, 2020, 10 (1), pp.1224. ⟨10.1038/s41598-020-58179-0⟩ Article dans une revue hal-02472258v1
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 Imbeaudet 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. Pellieret al. Pediatric Blood and Cancer, 2019, 66, pp.S509-S509 Article dans une revue hal-02355731v1
Dissecting heterogeneity in malignant pleural mesothelioma through histo-molecular gradients for clinical applications Yuna Blum,Clément Meiller,Lisa Quetel,Nabila Elarouci,Mira Ayadiet al. Nature Communications, 2019, 10, pp.1333. ⟨10.1038/s41467-019-09307-6⟩ Article dans une revue hal-02090279v1
Stratification of Pancreatic Ductal Adenocarcinomas Based on Tumor and Microenvironment Features Francesco Puleo,Remy Nicolle,Yuna Blum,Jerome Cros,Laetitia Marisaet al. Gastroenterology, 2018, 155 (6), pp.1999+. ⟨10.1053/j.gastro.2018.08.033⟩ Article dans une revue hal-02143548v1
Distinct epigenetic landscapes underlie the pathobiology of pancreatic cancer subtypes Gwen Lomberk,Yuna Blum,Remy Nicolle,Asha Nair,Krutika Satish Gaonkaret al. Nature Communications, 2018, 9 (1), pp.1978. ⟨10.1038/s41467-018-04383-6⟩ Article dans une revue hal-02143535v1
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 Camet al. BMC Genomics, 2018, 19 (1), pp.1-19. ⟨10.1186/s12864-018-4520-5⟩ Article dans une revue hal-01727161v1
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
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 Maignanet al. EMBO Molecular Medicine, 2017, 9 (4), pp.482 - 497. ⟨10.15252/emmm.201606975⟩ Article dans une revue hal-01787567v1
Pancreatic Adenocarcinoma Therapeutic Targets Revealed by Tumor-Stroma Cross-Talk Analyses in Patient-Derived Xenografts Remy Nicolle,Yuna Blum,Laëtitia Marisa,Céline Loncle,Odile Gayetet al. Cell Reports, 2017, 21 (9), pp.2458-2470. ⟨10.1016/j.celrep.2017.11.003⟩ Article dans une revue inserm-01985259v1
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 Franzénet al. G3, 2016, 6 (10), pp.3361-3371. ⟨10.1534/g3.116.033894⟩ Article dans une revue hal-01404133v1
Role of lipid phosphate phosphatase 3 in human aortic endothelial cell function Zahia Touat-Hamici,Henri Weidmann,Yuna Blum,Carole Proust,Hervé Durandet al. Cardiovascular Research, 2016, 112 (3), pp.702 - 713. ⟨10.1093/cvr/cvw217⟩ Article dans une revue hal-01484581v1
Hepatic circadian clock oscillators and nuclear receptors integrate microbiome-derived signals Alexandra Montagner,Agata Korecka,Arnaud Polizzi,Yannick Lippi,Yuna Blumet 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
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 Blumet 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-Bigotet al. Journal of Dairy Science, 2012, 95 (9), pp.4989-5000. ⟨10.3168/jds.2012-5348⟩ Article dans une revue hal-00841015v1
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 Désertet al. BMC Genomics, 2011, 12 (november), pp.8. ⟨10.1186/1471-2164-12-567⟩ Article dans une revue hal-00730144v1
Apports de la génomique fonctionnelle à la cartographie fine de QTL Guillaume Le Mignon,Yuna Blum,Olivier Demeure,Christian Diot,Elisabeth Le Bihan-Duvalet al. INRA Productions Animales, 2010, 23 (4), pp.343-358 Article dans une revue hal-00729443v1

Communication dans un congrès (20)

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
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 Langlaiset 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
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
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
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
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
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 Galibertet al. JOURNÉES OUVERTES EN BIOLOGIE, INFORMATIQUE ET MATHÉMATIQUES (JOBIM ) 2023, Jun 2023, Diverses villes françaises, France. pp.53 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. Svrceket 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
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 Esquerreet 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
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
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
Transcriptome profiling reveals interaction between two QTL for fatness in chicken Yuna Blum,Guillaume Le Mignon,Frederique Pitel,David Causeur,Olivier Demeureet 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
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
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-Michelet al. 62. Annual Meeting of the European Association for Animal Production (EAAP), Aug 2011, Stavanger, Norway Communication dans un congrès hal-02748764v1
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

Poster de conférence (7)

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
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
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
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
AnnotQTL: a new tool to gather functional and comparative information on a genomic region Frédéric Lecerf,Anthony Bretaudeau,Olivier Sallou,Colette Désert,Yuna Blumet al. 12. Journées Ouvertes en Biologie, Informatique et Mathématiques, Jun 2011, Paris, France. 2011, JOBIM 2011 Poster de conférence hal-02746728v1
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
Transcriptome profiling reveals interaction between two QTL for fatness in chicken Yuna Blum,Guillaume G. Le Mignon,Colette Désert,Frederique Pitel,David Causeuret 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

Proceedings/Recueil des communications (1)

Benchmarking circRNA Detection Tools from Long-Read Sequencing Using Data-Driven and Flexible Simulation Framework Anastasia Rusakovich,Sebastien Corre,Edouard Cadieu,Rose-Marie Fraboulet,Marie-Dominique Galibertet al. JOBIM, Jul 2025, Bordeaux, France. 2025, ⟨10.1101/2025.04.17.649290⟩ Proceedings/Recueil des communications hal-05402684v1

Pré-publication, Document de travail (6)

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
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
p110α-dependent hepatocyte signaling is critical for liver gene expression and its rewiring in MASLD Marion Régnier,Arnaud Polizzi,Tiffany Fougeray,Anne Fougerat,Prunelle Perrieret al. 2024 Pré-publication, Document de travail hal-04442467v1
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. Svrceket al. 2022 Pré-publication, Document de travail hal-03871989v1
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 Alzieuet al. 2022 Pré-publication, Document de travail hal-03574569v1

Thèse (1)

Analyse génétique d'un caractère complexe à l'aide de données transcriptomiques Yuna Blum Autre. AGROCAMPUS OUEST, 2012. Français. ⟨NNT : ⟩ Thèse tel-02806749v1

Logiciel (1)

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