Research

My research projects focus on better understanding the biological heterogeneity underlying cancers and complex traits though multi-omic integration and network inference.

Statistical and bioinformatics analysis of high throughput data

Heterogeneity in biological datasets using matrix factorization approaches; Multi-omic integration using unsupervised clustering approaches and multiple factor analysis approaches; Regulatory network inference; System genetics using GWAS/linkage analysis.

Biological contexts

Human diseases:  cancers (CIT program) / metabolic diseases using mouse models / human cohorts (during my postdoc at the Jake Lusis Laboratory in 2014).; Agronomy:  adiposity  in meat chickens (during my thesis, 2009-2012). Pig carcasses calibration (during 2013).

My projects mainly focus on Malignant Pleural Mesothelioma, Pancreatic cancer, Leukemia and Melanoma.

List of publications

Peer-reviewed articles:

Brevets internationaux

  • Blum, Y., Dusetti N., Giovannini M., Gilabert M., Iovanna J., Nicolle R., Turrini O. “Method for determining a reference tumor aggressiveness molecular gradient for a pancreatic ductal adenocarcinoma“. International Patent: Application number: EP20305052.1 (2020)
  • Blum Y., Dusetti N., Giovannini M., Gilabert M., Iovanna J., Nicolle R., Turrini O. “Method for determining a reference tumor aggressiveness molecular gradient for a pancreatic ductal adenocarcinoma“. International Patent: WO2020216722A1 (2020)

Large audience articles:

  • Nicolle R., Blum Y., Marisa L., Dusetti N. & Iovanna J. Des approches multi-omiques dévoilent de nouvelles cibles thérapeutiques pour le traitement du cancer du pancréas. Médecine Science, n° 5, vol. 34, mai (2018)
  • Le Mignon G., Blum Y., Demeure O., Diot C., Le Roy P. & Lagarrigue S. Contribution of functional genomics to the fine mapping of QTL. Inra Prod. Anim., 23 (4), 343-358 (2010)

Conference article:

  • Blum Y., Monziols M., Causeur D. & Daumas G. Recalibrage de la principale méthode de classement des carcasses de porcs en France. Journées Rech. Porcine, 46, 39-44, (2014)

Grants and awards

Funding

  • 2022 Ligue Contre le Cancer – Grand Ouest. Long-read sequencing for extensive profiling of circRNAs associated with acquired resistance to BRAFi in melanoma. (Principal investigator, 25k€)
  • 2021–2024 MIC, ACACIA: Artificial Intelligence on multi-omic data to study cancer heterogeneity and develop clinical grade classifiers. (co-investigator, 315k€ total, administered amount: 47k€).
  • 2020 European funding – EIT Health, COMETH: Benchmarking of computational methods (co-leader, 630k€).
  • 2018–2021 Grant PAIR pancreas INCa, project EpiShift, (co-investigator, 530kE total, administered amount: 120k€).

Awards

  • 2018  Best Investigator award, iMig international Conference, Ottawa, Canada,
  • 2018 First prize, Data Challenge on signal deconvolution, Aussois (CNRS),
  • 2010–2019 #4 Best poster awards, (ESMO conference, Barcelona, 2019 ; SysBioCancer workshop, Paris, 2019 ; BioNetVisa, Strasbourg, 2014 ; Yoshi Suzuki award ISAG conference, Edinburgh, 2010)

Communications

Oral communications 

International conferences

  • Blum Y. A web-application for clinicians: towards a better characterization of tumors. Bioengineering and Medtech against Cancer, Flash presentation and Round Table, Online conference, October 24, 2020
  •  Blum Y, Meiller C. …, de Reyniès A, Jaurand MC and Jean D -Molecular subtypes characterization of Malignant Pleural Mesothelioma and deconvolution approach for prognostic assessment., iMig, Ottawa Canada, 2-5 May 2018 website
  •  Blum Y, Renier A, Elarouci N, …, de Reyniès A, Jaurand MC and Jean D – Multi-Omics integration for Malignant Pleural Mesothelioma subtypes characterization, iMig, Birmingham UK, 1-4 May 2016 website
  • Blum Y, Houée M, Friguet C, Lagarrigue S & Causeur D, Sparse factor models for gene co-expression networks, BioNetVisa part of ECCB conference, Strasbourg, 7th Sept 2014 (Flash presentation)
  • Blum Y, Houée-Bigot M, Lagarrigue S & Causeur D – The R package FANet: sparse Factor Analysis model for high dimensional gene co-expression Networks , useR 2014, UCLA Los Angeles, June 30- July 3 2014
  • Blum Y, Houée-Bigot M & Causeur D – Sparse factor models for gene co-expression networks, Statistical Methods for Post-Genomic Data, Amsterdam, 24-25 January 2013
  • Blum Y, Houée M, Friguet C, Lagarrigue S & Causeur D. Inferring gene networks using a sparse factor model approach, Statistical Learning and Data Science, Florence, Italy, 7-9 May 2012.
  • Blum Y, Demeure O., Désert C., Guillou H., Bertrand-Michel J., Filangi O., Le Roy P., Causeur D., Lagarrigue S. Integrating QTL controlling fatness, lipid metabolites and gene expressions to genetically dissect the adiposity complex trait in a meat chicken cross. 62nd Annual Meeting EAAP. August 2011, Norway
  • Blum Y, Le Mignon G, Causeur D, Pitel F,  Demeure O, Filangi O, Le Roy P,Lagarrigue S – Transcriptome profiling reveals interaction between two QTL for fatness in chicken. The 15th QTL-MAS workshop, Rennes, 19-20 May 2011. Website
  • Blum Y, Friguet C, Lagarrigue S & Causeur D. Inferring gene networks using a sparse factor model approach: application in a lipid metabolism study, International Biometric Society Channel Network, Bordeaux, 11-13 April 2011. Website
  • Blum Y, Lagarrigue S  &  Causeur D– A factor model to analyze heterogeneity in gene expression in a context of QTL characterization. International Society for Animal Genetics, Edinburgh, 26-30 July 2010. Program Website
  • Blum Y, Friguet C, Lagarrigue S & Causeur D – Inférence sur réseaux géniques par Analyse en Facteurs. SFdS Marseille, 25-28 May 2010. Program Website
  • Blum Y, Lagarrigue S  &  Causeur D– A factor model to analyze heterogeneity in gene expression in a context of QTL mapping. 8th workshop « Statistical Methods for Post-Genomic Data» Luminy, Marseille, 14-15 January 2010. Program Website

Local workshops/seminars

  • Blum Y. Genetic and epigenetic regulations in cancer,  online, May 5, 2022, HDR 
  • Blum Y. Inter and intra-tumor molecular heterogeneity assessment for clinical applications: illustration in several cancer types. IGDR seminar Rennes, October 11, 2019
  • Blum Y. Unravelling cancer heterogeneity through molecular deconvolution approaches. Workshop SysBioCancer, Paris, September 23-28, 2019 (Flash presentation)
  • Blum Y. Dissecting molecular heterogeneity in cancer and clinical applications. TIMC-IMAG seminar Grenoble, September 19, 2019
  • Blum Y & Nicolle R. The CIT classifications. International PDA consensus meeting, MSKCC New York, June 22, 2019
  • Blum Y, Meiller C…de Reyniès A,  Jaurand MC and Jean D. Molecular subtypes characterization of Malignant Pleural Mesothelioma and deconvolution approach for prognostic assessment. Journées francophones sur le mésothéliome CHI Créteil, 15-16 november 2017
  • Blum Y, Remy Nicolle,  SMAP: a tool for patient-derived xenografts sequencing data analysis, CIT Seminars, Ligue Nationale Contre le Cancer, Paris, 5 october 2017
  • Civelek M & Blum Y –  Mining Bayesian and Co-expression Networks for CAD genes, CAD genomics Network Leducq Grant, Munich Germany, 14th February 2014.
  • Blum Y, Houée M & Causeur D – Sparse factor models for gene co-expression networks. Séminaire NETBIO, Paris, 11-12 September 2013.
  • Blum Y, Houée M & Causeur D – Sparse factor models for gene co-expression networks. Séminaire de Biostatistiques, UPS Toulouse, 11th December 2012.
  • Blum Y, Houée M & Causeur D – Inférence de réseaux de co-expression génique. 10ème Journée Biogenouest, IRISA Rennes, 30th November 2012.
  • Blum Y, Revisiting BxD F2 db/db cross data taking into account the heterogeneity in gene expression
    for QTL and eQTL analyses, Jake Lusis Lab, UCLA (Los Angeles, US), 12th April 2012.
  • Blum Y, Houée M, Friguet C, Lagarrigue S & Causeur D- Inférence de réseaux de gènes à partir de données transcriptomiques. Séminaire de Biologie Intégrative et Genomique dans le Grand Ouest, Auray, 7-9 November 2011.
  • Blum Y, Lagarrigue S., Causeur D. Genetic analysis of a complex trait using transcriptomic data: contribution of gene regulatory network modeling. Séminaire des Doctorants du Département de Génétique Animale INRA, Pornichet, 5-6 April 2011.
  • Blum Y, Lagarrigue S  &  Causeur D – Analyse génétique de caractères complexes, IFR140 Génétique Fonctionnelle, Agronomie et Santé, Rennes, 1srt December, 2010.
  • Blum Y, Lagarrigue S  &  Causeur D – Caractérisation fonctionnelle d’un QTL par prise en compte de la dépendance génique, Journée des Doctorants de Rennes & Brest en Biologie-Santé, Rennes, June 2010.

Posters:

  • Fraboulet R, Corre S, Galibert MD, Blum Y. cirscan: a Shiny application to decipher circRNA-miRNA-mRNA  networks from multi-level transcriptomic data, JOBIM, Rennes, July 5 – July 8, 2022 (presenter R. Fraboulet)
  • Fraboulet R, Corre S, Galibert MD, Blum Y. Decoding the RNA regulatory network to identify microRNA mechanisms involving circular RNA, JOBIM, Online, July 6 – July 9, 2021 (presenter R. Fraboulet)
  • Moreno Vega A, Lebarbier E, Mary-Huart T, Iovanna J, Blum Y. Nicolle R.  Switching resistant to sensitive phenotype of PDAC by targeting the epigenome, CompuSysBioCancer , Paris, June30 – July 3, 2021 (presenter A. Moreno Vega)
  • Decamps C, […], Blum Y*, Richard M*. DECONbench: a benchmarking platform dedicated to deconvolution methods for tumor heterogeneity quantification. JOBIM, Online, June30 – July 3, 2020
  • Blum Y, Job S, […] Brambilla E & De Reyniès A. From tumor transcriptomes to underlying cell type proportions to better predict prognosis and response to treatments. ESMO, Barcelona, Sept.27 – Oct. 1, 2019
  • Blum Y. Unravelling cancer heterogeneity through molecular deconvolution approaches. Workshop SysBioCancer, Paris, September 23-28, 2019
  • Blum Y, Lomberk G, Nicolle R, […], Iovanna J & Urrutia R. Epigenetic landscapes of pancreatic ductal adenocarcinoma. AACR pancreas, Boston USA, September 21-24, 2018
  • Nicolle R*, Blum Y*, Marisa L* … de Reyniès A, Iovanna J, Dusetti N – Multiomics assessment of the cancer and stromal compartments of patient-derived pancreatic xenografts reveals clinically-relevant subtypes and novel targeted therapies, AACR Washington USA, April 1-5 2017
  • Nicolle R*, Blum Y*, Marisa L* … de Reyniès A, Iovanna J, Dusetti N – Multi-omics characterization of PDAC subtypes using PDX reveals that epigenetic but not genetic analysis permit a clinically relevant classification, AACR Pancreas, , Orlando USA, May 12-15, 2016
  • Nicolle R*,Blum Y*, Marisa L* … de Reyniès A, Iovanna J, Dusetti N – Pancreatic cancer cell drives stroma composition, AACR Pancreas, Orlande USA, May 12-15, 2016.
  • Nicolle R, Blum Y, Marisa L … de Reyniès A, Iovanna J, Dusetti N – Genomic profiling of patient-derived xenografts with pancreatic adenocarcinoma : evaluation of the PACAomics trial pilot phase,Pancreatic Cancer Symposium, Marseille, October 28-30 2015.
  •  Org E, Wha J Joo J, Blum Y, … Laakso M, Eskin E and  Lusis AJ –  Genomic Interactions between host geneticsand diet affect gut microbiota and influence metabolic traits in mouse and human. American Association of Human Genetics, San Diego, October 18-22, 2014.
  • Blum Y, Houée M, Friguet C, Lagarrigue S & Causeur D, Sparse factor models for gene co-expression networks, BioNetVisa workshop, Strasbourg, 7th Sept 2014
  • Blum Y, Houée M, Friguet C, Lagarrigue S & Causeur D- Genetic analysis of a complex trait using transcriptomic data: contribution of gene regulatory network modeling. Session “Genes and pathways” Plant&Animal Genome XX, San Diego CA USA, 14-18 January 2012.
  • Blum Y– Modélisation de réseaux de gènes : apport dans le déterminisme génétique de caractères complexes. Séminaire des Thésards du Département de Génétique Animale INRA, Pornichet, 6-7 April 2010.
  • Blum Y, Lagarrigue S  &  Causeur D– A factor model to analyze heterogeneity in gene expression in a context of QTL characterization. International Society for Animal Genetics, Edinburgh, 26-30 July 2010.
  • Blum Y, Le Mignon G, Causeur D, Pitel F,  Demeure O, Filangi O, Le Roy P,Lagarrigue S – Transcriptome profiling reveals interaction between two QTL for fatness in chicken. International Society for Animal Genetics, Edinburgh, 26-30 July 2010.

Scientific activities

  • 2022-2026: Internal member of the Expertise Committee of the Ligue Nationale Contre le Cancer.
  • 2022-2027: Elected member of the laboratory council of the IGDR Institute.
  • 2019  Co-leading with Richard M. the organization of an International Data Challenge on Deconvolution Methods in Cancer, Aussois CNRS (2nd edition). 40 participants, 7 countries. https://cancer-heterogeneity.github.io/data_challenge_2019.html
  • 2018 Conception of a scientific animation on Cancer Genomics for the large audience, Cité des Sciences, Paris, Centenary of the French League Against Cancer event: https://yuna-blum.com/miscellaneous/
  • 2015 – 2017  Co-organization with Ayadi M. of local seminars on Cancer genomics at the French League Against Cancer, Paris: http://cit.ligue-cancer.net/language/fr/seminaires/
  • 2012 – 2013  Co-coordination with Houee M. and Causeur D. of the Statistics for Integrative Biology (SIB) working group: http://sibgroup.wordpress.com/

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