San Raffaele Telethon Institute for Gene Therapy
The Bioinformatics Core supports SR-Tiget researchers in addressing a wide variety of biological questions by analysing and interpreting data coming from high-throughput sequencing technologies. The Core provides matrix supervision to bioinformaticians of different labs and its activities are fully integrated with the expertise and technologies of the OSR Center for Omics Sciences, which also provides to the team a shared computational facility for the analysis of sequencing data. With expertise ranging from biology to computer science, this team provides contributions in several aspects of the different projects, from experimental design to manuscript preparation. All the activities of the Core are built on a constant and collaborative setting that allows bioinformaticians to take part actively in the production and interpretation of research findings.
The Bioinformatics Core uses state-of-the-art computational approaches to perform quality control, analysis, integration, and interpretation of datasets in genomics (Whole Genome Sequencing, Whole Exome Sequencing, Target Resequencing, CRISPR knockout screening, Barcode Sequencing, Genome Editing, Clonal Tracking experiments), epigenomics (Whole Bisulfite Genome Sequencing, Reduced Representation Bisulfite Sequencing, ATAC-Sequencing, single-cell ATAC-seq, ChIP-Sequencing, High-Throughput Chromatin Conformation Capture), transcriptomics (bulk RNA-seq, single-cell RNA-seq, spatial single-cell RNA-seq, feature barcoding, TCR/BCR repertoire profiling, tracking of barcodes), proteomics, and metabolomics. Several statistical and modelling approaches have also been tested and implemented to integrate data from these different experimental technologies, making multi-omics data accessible to researchers. The Core has developed automatic data analysis workflows for different omics experiments, which can be easily tailored to the specific project requirements. Particular importance has been given to provide reproducibility of processed data, using structured pipelines and controlled working environments, in agreement with the FAIR (Findable, Accessible, Interoperable, and Re-usable) guiding principles of Bioinformatics. The team has also experience in coding custom scripts, in designing new algorithms, and developing applications to solve emerging problems. The Core has capacity of realizing databases and web tools for data management and visualization, as well as knowledge in high-performance computing for scaling applications while dealing with Big Data challenges.
The Bioinformatics Core supports SR-Tiget researchers at different levels, from basic bioinformatics services to full-stack scientific collaborations. Core activities include:
- Consultation on experimental design of high-throughput projects
- Data quality assessment and coordination with the sequencing facility
- Setup and development of automated data analysis pipelines for common assays
- Custom and on-demand development of bioinformatics tools and visualization toolkits
- Data analysis, integration, and interpretation using statistical models
- Design and implementation of databases and web applications
- Customization and high-performance scaling of software tools and pipelines
- Data mining of published datasets, correlation, and integration of results
- Assistance with the preparation of manuscripts and grant proposals