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;

*RNAseq, MethylomeChIP-Seq, miRnome, SNPMetabolome, microbiome

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, and lung cancer.

List of publications

Peer-reviewed articles:

Large audience articles:

  • Blum Y., Jaurand M.C., De Reyniès A. & Jean D. Unraveling the cellular heterogeneity of malignant pleural mesothelioma through a deconvolution approach. Molecular & cellular oncology, 6(4), 1610322 (2019)
  • 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. Porcine46, 39-44, (2014)

Communications

Oral communications 

International conferences

  •  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. 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 YLagarrigue S  &  Causeur D – Analyse génétique de caractères complexes, IFR140 Génétique Fonctionnelle, Agronomie et Santé, Rennes, 1srt December, 2010.
  • Blum YLagarrigue 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:

  • 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 YUnravelling 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, BostonUSA, 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 EWha 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.

Awards and grants

  • European grant, project COMETH, co-leader with Magali Richard,(630KE), 2019-2021
  • Best poster award, ESMO conference, Barcelona, 2019
  • Best poster award, SysBioCancer workshop, Paris, 2019
  • First Award, Data Challenge on signal deconvolution, Aussois (CNRS), 2018
  • Best Investigator award, iMig international Conference, Canada, 2018
  • Grant PAIR pancreas INCa, project EpiShift, co-investigator, (530kE), 2018-2021
  • Best poster award, BioNetVisa, Strasbourg, 2014
  • International mobility grant, from Rennes Metropole: 4 months at UCLA, 2012
  • Best Poster award (Yoshi Suzuki award), ISAG conference, Edinburgh, 2010

Scientific activities

  • 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. (website)
  • 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.
  • 2015-2017: organization with Ayadi M. of local seminars on Cancer genomics at the French League Against Cancer, Paris. (website)
  • 2012-2013: organization with Lebras Y. and Ouedraogo M. of the INRA PhD student Seminar (13th edition). 71 participants.

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