The Computational Biology Platform (CBP) of the Biogipuzkoa HRI provides service to departments of the Donostialdea IHO and the life science community in general. The service transverses all the stages for good research practices, from the experimental design, data analysis, statistical analysis, visualization, preparation of research publication, answers to reviewers and data deposition of omics data in public databases.
The Platform has over 90 publications in high impact journals such as Science (Moore et al, 2015), Nature (Knobloch et al, 2013; Ko et al, 2010; Kim et al, 2009; Kim et al, 2008), Nature Cell Biology (Ohnishi et al, 2014; Esch et al, 2013; Han et al, 2011), Cell (Han et al, 2010; Singhal et al, 2010; Kim et al, 2009), Cell Stem Cell (Rao et al, 2016; Song et al, 2016; Kubaczka et al, 2015; Han et al, 2012; Ko et al, 2009), with a comprehensive list here.
The platform offers data analysis support for both next generation sequencing (NGS) and microarrays:
Next-Generation Sequencing (NGS) data analysis
The Platform has developed workflows and programs to analyze large-scale biological datasets. The analysis includes data quality assessment, comprehensive analysis, results interpretation, communication and presentation in meaningful formats.
The analysis might also involve development of tailored algorithms for some projects.
Some of the various NGS data analyses performed are:
Whole genome sequencing.
cDNA-based whole transcriptome, small RNA discovery and analysis (RNA-Seq).
Sequencing of DNA fragments isolated by chromosome immunoprecipitation (ChIP-Seq) for transcription factor binding site assessment and for chromatin signal analysis.
Discovery of super-enhancers.
Detection of DNA methylation (Meth-Seq) from both Whole Genome Bisulfite Sequencing (WGBS) and Reduced Representation of Bisulfite Sequencing (RRBS).
Variant calling.
Microarray data analysis
The Platform performs data analyses for Affymetrix, Agilent, Illumina, Roche-NimbleGen (among others) microarrays for:
Gene expression.
MicroRNA expression.
DNA methylation.
Copy Number Variation (CNV).
The Computational Biology Platform is specialized in integrating diverse data sets, such as genomics, proteomics, metabolomics and biomedical imaging information.
Research collaboration
The Platform offers project-based collaborations funded through either joint research grants or fee-for-services. Its staff currently participates in multiple research collaborations. The Platform welcomes new collaborations and can work with the customer to apply for joint funding.
The CBP provides collaborative support for large scale multidisciplinary research projects.
