Research

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

Statistical and bioinformatics analysis of high throughput data*

Multi-omic integration using clustering approaches; Regulatory network inference; System genetics using GWAS/linkage analysis; Heterogeneity in biological datasets using factor analysis approaches

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

Biological contexts

Human diseases:  cancer (CIT program) / metabolic syndrome using mouse models (during my postdoc at the Jake Lusis Laboratory in 2014).; Agronomy:  adiposity  in meat chickens and milk production in dairy cows (during my thesis, 2009-2012). Pig carcasses calibration (during 2013).

I am currently working on projects on Malignant Pleural Mesothelioma, Pancreatic cancer, and lung cancer.

List of publications

International Journals:

  • Nicolle, R., Raffenne, J., …, Blum, Y.  and Cros J. Prognostic Biomarkers in Pancreatic Cancer: Avoiding Errata When Using
    the TCGA Dataset. Cancers, in press 

French Journals:

 

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
  • 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 (Flash presentation).
  • 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
  • Mach N., Blum Y, Smits M., Causeur D., Lagarrigue S. – 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. 62nd Annual Meeting EAAP. August 2011, Norway
  • Houée M., Friguet C., Lagarrigue S., Blum Y., Causeur D. Large-scale significance testing of high-thoroughput Data with FAMT. ASMDA 2011 Conference, Rome, 7-10 June 2011
  • 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

 

Local workshops/seminars

  • 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:

  • Blum Y*, et al  – 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 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

  • First Award, Data Challenge on signal deconvolution, Aussois (CNRS), 2018
  • Best Investigator Award, iMig international Conference, Canada, 2018
  • Best Poster Award, BioNetVisa, Strasbourg, 2014
  • Mobility Grant from Rennes Metropole (4 months), 2012
  • Travel Grant, International Society for Animal Genetics, Edinburgh, 26-30 July 2010.
  • Best Poster Award (Yoshi Suzuki award), International Society for Animal Genetics, Edimbourg, 2010

Scientific activities

  • Co-organizer of the SIB working group (Statistics for Integrative Biology) which organizes regular seminars.
  • Member of the organizing committee for the 6th edition of the International Conference CARME at Rennes in Feb. 2011 (140 participants).
  • Member of the organizing committee for the 13th edition Seminar of the INRA Animal Genetics Phd students at Pornichet in April 2010 (71 participants).

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