Bioinformatic Research Group in Epidemiology
Statistical methods for multi-omics and environmental factors data analysis and integration
At the Bioinformatic Research Group in Epidemiology, we develop statistical methods and software for genomics, transcriptomics and exposomics to be applied in environmental epidemiology. We focus on SNP arrays and next generation sequencing. We are interested in leveraging our expertise in handling both, epidemiological and genomic data, to help translate scientific research into biomedical practice. The group follows open research rules and make every possible effort to make our research reproducible and openly available.
Focusing on
Specific problems we are currently working on include:
Exposomics
Developing statistical methods and tools to deal with 'omic' and exposome data
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Next Generation Sequencing
Developing analysis tools and statistical methods to detect mosaicims and analyze RNA-seq data
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Genomic Inversions
Developing analysis tools and new statistical methods to detect inversions using SNParray data and a...
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CNVs and imputed SNPs
Developing models to incorporate uncertainty in genetic association studies
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Genetic mosaicisms and health
We have developed a new method to detect genetic mosaicisms using SNP array data ([MAD](http://brge....
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Our Team
8 researchers from ISGlobal, 2 external collaborators and 3 Alumni
Combined Pre Doctoral Researcher at BRGE and at Luís Perez-Jurado's lab (UPF) has a background in Biotechnology (BSc from UVic) and in Bioinformatics (MSc from UAB), is working in his PhD Thesis studing structural variants in authism as well as developing new tools to characterize them.
Marcos López
Statistician at the hospital del mar research institute (IMIM) he obtained his PhD in Statistics (fromm UPC) on 2016 and collaborates with the BRGE developing new methods for genomic data analysis and mutliomics analysis.
Isaac Subirana
Pre Doctoral Researcher with a background in Statistics and Mathematics(BScs - UAB) and Omic Data Abalysis (MSc - UVic) is currently working in his PhD in Biomedicine (UPF) studing the integration of genome data with neuroimaging in epidemiologican neuroscientific studies.
Natalia Vilor
Pre Doctoral Researcher with a background in Biochemistry (BSc - UAB) and Bioinformatics (MSc - UPF) is currently working in his PhD in Biomedicine (UPF) about software development for genomic inversions and its effects on human methylome and human transriptome.
Carlos Ruiz-Arenas
Pre Doctoral Researcher at CRG, and with a background in Biotechnology from URV, is collaborating with BRGE throught the Helix Project, where she carries out a study analizing the pre and post natal smoking effects on molecular signatures.
Marta Vives-Usano
Pre Doctoral Researcher with a background in Computer Science (BSc - UAB) and Bioinformatics (MSc -UAB) is currently working in his PhD in Biomedicine (UPF) about software development and data analysis in exposome studies.
Carles Hernandez-Ferrer
Statistician. With a background in Physics (Universidad Nacional de Colombia) and a PhD in Physics (Cambridge University), works in development and implementation of data analysis methods for testing association in polymorphic inversions.
Alejandro Caceres
Associate Research Professor at ISGlobal.
Leading the bioinformatic group in genetic epidemiology (BRGE).
Assistant Professor at the Department of Mathematics at Autonomous University of Barcelona.
Juan R. González
SOFTWARE
We have developed some packages included in Bioconductor and the R project in collaboration with other researches from different institutions. Some of these libraries are related to genetics and other ones to survival analysis with recurrent events. Most of the packages are available at Bioconductor or CRAN. The devel version of these packages are available at our GitHub account (BRGE - https://github.com/isglobal-brge)
eSet_EGCUT_inv.Rdata
June 8, 2020
NameSourceLatest updateeSet_EGCUT350MB08/06/2020
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SNPassoc
October 31, 2017
This package was built when I was working at Xavier Estivill’s lab at Center for Genomic Regulation and it is written in collaboration with Victor Moreno and his colleagues. The R package SN rexposome
August 31, 2017
rexposome is an R package for exposome characterization and exposome-outcome test association. It was developed by Carles Hernandez-Ferrer as part of its PhD project and used in the analysis... CTDquerier
August 31, 2017
The *Comparative Toxicogenomics Database* is a public resource for toxicogenomic information manually curated from the peer-reviewed scientific literature about chemicals, gene and health ou... omicRexposome
August 31, 2017
This R package is built to extend the capabilities of the R package rexposome and to allow to find exposome molecular signatures. This is archived by implementing a limma wrapper that works ... MAD (Mosaic Alteration Detector)
July 31, 2017
This is a joint work with Benjamin Rodriguez-Santiago (qGenomics) and Luis Pérez-Jurado (UPF). MAD is a software tool to detect mosaic events from SNP arrays using BAF and LRR values. The al inveRsion
July 31, 2017
`inveRsion` is an R package for the detection of genetic inversions using SNP-array data. This is a joint collaboration with Alejandro Caceres (ISGlobal) and Suzanne Sindi (Center for Comput... tweeDEseq
July 31, 2017
`tweeDEseq` is an R package for analyzing RNAseq count data. It implements Poisson-Tweedie family of distributions to model count data distribution. This family includes Poisson and Negative...