Biostatistics and Bioinformatics Unit

The Unit provides resources and personnel specialized in the analysis of phenotypegenotype associations, the identification of biomarkers, the analysis of gene expression microarray data, real time PCR analysis, the functional analysis of differential expression results, and those obtained by next  generation sequencing, etc.

A project control web application has been developed for storing and processing data and monitoring samples pertaining to different nutrition research projects. This application, designed by the IMDEA Food Institute and which uses open source software, can store and manage a large volume of phenotype and genotype data. It also holds anthropometric, medical and biochemical data, as well as validated nutritional questionnaires that can be filled in on-line (greatly facilitating data entry). The recruitment process can also be managed using this application.

The entire system dissociates/anonymises all data in keeping with Spanish privacy legislation (Ley Orgánica 15/1999 de 13 de diciembre de Protección de Datos de Carácter Personal). The Unit organizes specialized training courses and collaborates with the postgraduate program of the Universidad Autónoma de Madrid. Heatmap representing the level of expression of the most differentially expressed genes between two experimental conditions.

Members

Dr. Gonzalo Colmenarejo Sánchez
Senior Biostatistician

Roberto Martín Hernández
Bioinformatic, predoctoral researcher

Dr. Gonzalo Colmenarejo Sánchez

  Senior Biostatistician

Gonzalo Colmenarejo got his PhD in the Biophysics area in the Complutense University of Madrid. Then was a postdoctoral researcher in the Chemistry Department of University of California at Berkeley. He joined GlaxoWellcome (later GlaxoSmithKline) R&D center in Tres Cantos, Spain, where he stayed more than 17 years. There he developed multiple statistical and machine learning models to predict biological activity form molecular structure, and was a statistical and data analysis support for a multidisciplinary and international group of biologists, biochemists, medicinal chemists and pharmacologists. He specialized in the massive data analysis of cellular and biochemical high-throughput screens (HTS), and processed more than 100 campaigns of multiple target classes, screening technologies and therapeutic areas, were he increased the number and quality of hits there obtained. He developed new theoretical methods for the prioritization of compounds in HTS campaigns, as well as automated chemical pattern extraction from sets of molecules. He co-leaded the Screening Analytics Investment Area of GlaxoSmithKline, an international team devoted to finding new approaches to the analysis of HTS. He is (co)author of > 30 scientific publications in peer-reviewed journals and book chapters.

Email: gonzalo.colmenarejo@imdea.org 
Phone:  +34 91 727 81 00, ext. 510 

Roberto Martín Hernández

Bioinformatics scientist, predoctoral researcher

Roberto Martín Hernández obtained his Master’s Degree of Science in Biochemistry and Biotechnologies at the Université Paul Sabatier (Toulouse, France). He worked as a trainee scientist at Bayer CropScience division (Lyon, France) developing enzymatic assays for high throughput applications. In March 2008 he joined the Computers Architecture Department of the Universidad Complutense de Madrid (Spain) and started to work in the statistical analysis of biological data generated by high throughput technologies. Afterwards he joined the R&D Department of the bioinformatics startup  integromics (Madrid, Spain), where he continued working on massive data analysis generated by transcriptomics and genomics platforms, and he contributed to the development of professional software packages which are still commercialized.

He joined the IMDEA Food research Institute on May 2012. With an 8 years’ experience in bioinformatics and computational biology, he has co-authored more than 25 original research articles published in international journals. His scientific interests focus on data mining, data integration and deep learning. In addition he is completing the UAM (Madrid) PhD program in Nutrition science as a part-time student. 

Email: roberto.martin@imdea.org
Phone:  +34 91 727 81 00, ext. 510 

                                  

most relevant publications
  • Science. 2019 Aug 30;365(6456). pii: eaau1682. doi: 10.1126/science.aau1682. Validation of the protein kinase PfCLK3 as a multistage cross-species malarial drug target. Alam MM1, Sanchez-Azqueta A2, Janha O2, Flannery EL3, Mahindra A4, Mapesa K4, Char AB5, Sriranganadane D6, Brancucci NMB7, Antonova-Koch Y8, Crouch K1, Simwela NV1, Millar SB1, Akinwale J9, Mitcheson D10, Solyakov L9, Dudek K9, Jones C9, Zapatero C11, Doerig C12, Nwakanma DC13, Vázquez MJ11, Colmenarejo G14, Lafuente-Monasterio MJ11, Leon ML11, Godoi PHC6, Elkins JM15, Waters AP1, Jamieson AG4, Álvaro EF11, Ranford-Cartwright LC5, Marti M1, Winzeler EA8, Gamo FJ11, Tobin AB.
  • Colmenarejo, G.; Lozano-Arias, S.; González-Cortés, C.; Calvo, D.; Sánchez-García, J.; Presa-Matilla, J.L.; Leroy, D.; Rodrigues, J. Predicting transmission blocking potential of anti-malarial compounds in the mosquito feeding as-say using Plasmodium falciparum male gamete inhibition assay. (2018) Sci. Rep. 8, 7764. DOI: 10.1038/s41598-018-26125-w.
  • Norcliffe, J.L..; Mina, J.G.; Alvarez-Ruiz, E.; Cantizani-Perez, J.; de Dios-Anton, F.; Colmenarejo, G.; Gonzalez del-Valle, S.; Marco, M.; Fiandor, J.; Martín, J.; Steel, P.; Denny, P. Iden-tifying inhibitors of the Leishmania inositol phosphoryl-ceramide synthase with antiprotozoal activity using a yeast-based assay and ultra-high throughput screening platform. (2018) Sci. Rep. 8, 3938. DOI: 10.1038/s41598-018-22063-9.
  • Martín-Hernández R, Reglero G, Dávalos A. Data mining of nutrigenomics experiments: Identification of a cancerprotective gene signature. Journal of Functional Foods (2018), 42, 380-386. doi: 10.1016/j.jff.2018.01.021.
  • Costa-Machado LF, Martín-Hernández R, Sánchez-Luengo MA, Hess K, Vales-Villamarin C, Barradas M, Lynch C, de la Nava D, Diaz-Ruiz A, de Cabo R, Cañamero M, Martinez L, Sánchez-Carbayo M, Herranz D, Serrano M, Fernández-Marcos PJ. Sirt1 protects from K-Ras-driven lung carcino-génesis. EMBO reports (2018)19:e43879. DOI: 10.15252/embr.20164387.
main research grants

NutrigenomeDB


http://www.nutrigenomedb.org/


NutriGenomeDB is a web-based application that hosts manually curated gene sets, defined from gene expression signatures of 61 nutrigenomics studies performed on microarray platforms and publicly available in GEO database. The application is based on two main modules: 1) a data browse module allowing the exploration of gene expression data across experiments through interactive visualizations, and 2) a phenotype centered analysis module allowing the comparison of external gene expression signatures, aimed at finding potential connections among phenotypes and food compounds. NutrigenomeDB tool can be helpful to generate new research hypothesis with the aim of contributing to the field of precision nutrition, improving future functional foods formulations and further investigate the molecular mechanisms that confer healthy properties to specific dietary components.

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