High-throughput bioinformatics infrastructures for cluster and cloud computing platforms: Scalability of data analysis pipelines using distributed computing; Cross-platform bioinformatics through Docker virtualization; Visualization of genomic data on cloud databases using HTML5 / D3.js and in-browser computing.
Bioinformatics for Next Generation Sequencing (NGS) clinical and personal genomics: NGS analysis pipelines for single-cell RNA-seq, Hi-C, metagenomics, variant discovery, genome assembly; Integrative analysis of variation, expression, chromatin and epigenetic data from TCGA, Encode, 4DN; Metabarcoding for conservation and biodiversity monitoring using environmental DNA (eDNA).
Interdisciplinary research and novel applications of genomic sequencing and bioinformatics: Portable NGS and bioinformatics with Nanopore Minion and Intel Next Units of Computing (NUC); Touch-enabled, mobile computing interfaces for personal genomics and clinical NGS data visualization.
Algorithmic Information Theory, Computability, and Biologically-Inspired Computing:. Emergence, complexity, information content and compressibility of epigenetic networks; Integrating DNA computing with NGS sequencing for reading molecular output with high I/O; Computability and decidability of biologically-inspired and DNA computing models.