Description
The specialized Bioinformatics Platform at ISABIAL provides scientific and technical support for advanced analysis of omics and biological data, both in the field of translational research and in studies with clinical projection.
The platform’s activity focuses on experimental design, analysis, integration, and interpretation of large‑scale datasets generated by next‑generation sequencing (NGS) technologies and other omics approaches. It also operates as a transversal support platform for the institute’s various research groups that require the incorporation of high‑throughput and state‑of‑the‑art technologies into their projects.
The Bioinformatics Platform carries out tasks related to the analysis and management of omics data, as well as the classification and visualization of results—areas in which there is a growing demand from ISABIAL researchers. In addition, the incorporation of dedicated technical support staff, under the supervision of a new scientific lead, has driven organizational changes that make it necessary to update the platform’s definition and its institutional positioning.
Its objectives are:
- To reflect the current and actual organizational structure of the Bioinformatics Platform.
- To provide the unit with its own identity within the ISABIAL website and organizational structure, as an Institutional Support Service.
- To enhance the visibility, accessibility, and understanding of the portfolio of services offered.
Given that the Platform operates with its own objectives, methodologies, and portfolio of services, it is necessary for this autonomy to be reflected both on the institutional website and within the structure of ISABIAL’s support services.
Services of the ISABIAL Bioinformatics Platform
All services include exploratory analyses of files and datasets, batch correction, and the final generation of publication‑quality reports and graphics.
I. Genomics Services
Design and optimization of custom gene panels for targeted sequencing (NGS), tailored to clinical or research objectives, using specialized bioinformatics tools and Bioconductor packages.
Includes:
- Selection of genes and genomic regions of interest.
- Optimization of coverage and specificity.
- Evaluation of target regions.
- Generation of publication‑quality reports and graphics.
2.1. Analysis of Germline and Somatic Variants
Analysis of DNA sequencing data aimed at the identification, annotation, and interpretation of germline and somatic genetic variants in clinical and research studies.
Includes:
- Quality control of reads and samples.
- Detection and annotation of SNVs.
- Identification of INDELs.
- Analysis of somatic variants in oncology studies.
- Filtering and prioritization of variants based on clinical and functional criteria.
2.2. Genetic Association Analysis (GWAS)
Identification of genetic variants associated with complex traits and diseases through large‑scale genomic analyses.
Includes:
- Quality control of genotypic data.
- Genome‑wide association studies (GWAS).
- Statistical analysis of variants associated with phenotypes.
3.1. Infinium MethylationEPIC v2.0 BeadChips
DNA methylation data analysis using Infinium MethylationEPIC v2.0 arrays for the identification of epigenetic patterns associated with biological or clinical conditions.
Includes:
- Quality control and normalization of data.
- Identification of differentially methylated sites and regions.
- Statistical and functional analysis.
3.2. ChIP-Seq
Service aimed at identifying genome‑wide binding sites of modified histones and transcription factors.
Includes:
- Quality control and normalization.
- Peak identifications
- Differential protein–DNA binding analysis.
- Functional annotation.
3.3. ATAC-Seq
Service focused on chromatin accessibility analysis.
Includes:
- Quality control of ATAC‑seq libraries.
- Accessibility assessment: identification of open chromatin regions.
- Differential analysis of open chromatin regions.
II. Transcriptomics Services
4.1. RNA-Seq (Short Reads, Illumina)
Analysis and visualization of gene expression (mRNA, miRNA and other small RNAs).
Includes:
- Experimental design consulting.
- Data quality control and filtering.
- Normalization.
- Identification of differentially expressed genes.
- Functional analysis and biological interpretation.
4.2. RNA-Seq (Long Reads, Nanopore)
Service focused on full‑length transcript analysis, alternative isoforms and complex splicing events.
Includes:
- Experimental design.
- Quality control.
- Full‑length isoform analysis.
- Detection of alternative splicing events.
- Integration with other transcriptomic analyses.
4.3. Single-Cell RNA-Seq (scRNA-Seq)
Single‑cell gene expression analysis for the identification of cellular subpopulations and specific cell states.
Includes:
- Quality control and normalization.
- Clustering celular.
- Identification of cell markers.
Analysis of RNA chemical modifications aimed at the identification and functional interpretation of epitranscriptomic marks.
Includes:
- Identification of RNA modifications (e.g., m⁶A).
- Analysis of Illumina and Nanopore data.
- Integration with RNA‑seq.
III. Cross‑cutting Services
6.1. Extraction of data from specialized repositories.
Download, integration and analysis of public datasets (GEO, SRA, ArrayExpress, BioStudies, Zenodo, among others), including meta‑analysis of public and in‑house data.
6.2. Omics Data Management
- Generation of publication‑quality figures.
- Advanced statistical analysis.
- Support in data protection planning.
- Submission of data and metadata to public repositories.
Development of bespoke bioinformatics analyses tailored to the specific needs of each research project.
Equipment
The Bioinformatics Platform is equipped with computational infrastructure and specialized software for large‑scale omics data analysis, including high‑performance computing resources, secure storage systems, and widely validated bioinformatics tools used in biomedical research.
Networks
