My current research interests center on developing and applying computational methods to genomic data analyses. With my educational and research background in discrete mathematics and computer science, I am fascinated by the complexity of biological systems that, in some cases, the most powerful algorithms and computational resources are unable to overcome. During my postdoctoral training at the University of Kentucky, I have intensively worked with genomic data from key vertebrate groups, specifically salamanders, lampreys, and hagfish. My research includes investigations into programmed DNA elimination, structural variation, inter- and intraspecific variation, sex determination, repetitive genomic content and epigenetic. Driven by the need for the development of efficient integrative solutions, my methods leverage parallel and high-performance computing alongside careful parametrization of existing computational tools to deliver robust and timely results. My goal is to provide a coherent and systematic approach for data analysis starting from quality control of sequencing data, re-iteration of critical stages of pipelines, and finishing with comprehensive biological interpretation of computational outcomes.
To advance studies of complex vertebrate genomes, I have strived to more directly tackle the “inconvenient” portions of a genome – variable and repetitive regions. Lately, with the successful development of high-quality salamander assemblies, my research focus has shifted toward more translational work on regeneration. Currently, I am advancing two major research lines that complement each other: the investigation of molecular processes at the cell-population level using single-cell analysis of gene expression and chromatin accessibility, and the identification, classification, and characterization of conserved regulatory elements that enable robust functional genomic analyses of tissue regeneration and other traits that uniquely empower salamander models in biological research. Recent developments in these projects have allowed me to confirm that many conserved elements overlap with active chromatin marks, validating that they correspond to cis-regulatory sequences and revealing several thousand that are utilized during regeneration.
