- Development of tools to construct and analyze pangenome graphs of any complexity and scale

- Development of a new gap-affine pairwise aligner to align whole eukaryotic chromosomes

- Germline and somatic variants analyses on Whole-Exome sequencing (WES) data: quality control, sample matching, rRNA contamination, read trimming and mapping, variant calling, and functional prediction

- Microsatellite instability (MSI) status on paired tumor-normal and tumor-only WES data

- Variant calling and differential expression analyses on RNA-seq data

- Neoantigen prediction and prioritization by integrating WES data and RNA-seq data

- Analysis of Assay for Transposase-Accessible Chromatin using sequencing (ATAC-seq) data

- Normalization and correlation analysis of transcriptomic microarray data (Affymetrix)

- Proteomic and phosphoproteomic analyses of Reverse Phase Protein microarray (RPPA) data

- Cox modeling and survival analysis on patient cohorts (from TCGA and cBioPortal platforms)

- Basic procedures on High Performance Computing (HPC) machines