PhD Candidate · UC San Diego · Expected 2027
Evolutionary biologist and bioinformatician building computational tools for population genomics and phylogenomics: from genome skimming to eDNA for biodiversity monitoring.
Models genome repetitiveness, coverage, and sequencing error to compute accurate k-mer-based genomic distances from low-coverage genome skims. Published in Genome Biology (2026).
Read paper →Reference-free population genomics with diploid genome skims — extending the genome skimming framework to explicitly model heterozygosity for accessible nucleotide diversity estimation. Preprint Available in BioRxiv 2026.
Read paper →Expectation-maximization approach enabling phylogenetic dating under a categorical rate model, improving accuracy of divergence time estimation. Systematic Biology (2024).
Read paper →Collaboration with the Field Museum and Minderoo Foundation to improve detection of environmental DNA for population health tracking and marine species conservation.
ReSkmer: modeling repeats allows k-mer-based alignment-free methods to calculate population genomic distances
Genome Biology
doi →Expectation-maximization enables phylogenetic dating under a categorical rate model
Systematic Biology, 73(5): 823–838
doi →Updated Skmer Improves Reference- and Alignment-Free Population Genomics
Genome Skimming Symposium @ Botany · Palm Springs, CA
Genome Skimming Workshop
Field Museum, Grainger Bioinformatics Center · Chicago, IL
2023
Field Museum Grainger Bioinformatics Center Fellow
2022
San Diego Match Fellowship
2022
UCSD Sloan Scholar — University Center of Exemplary Mentoring
2021
NIH Minority Biomedical Research Support — Initiative for Maximizing Student Development
2021
USDA Hispanic Serving Institutions Program Grant
I'm a PhD Candidate in Bioinformatics & Systems Biology at UC San Diego, working in the Mirarab Lab. My research focuses on building reference-free, alignment-free genomic tools that make population genomics accessible without expensive references and high coverage, and modeling how complex genome characteristics (such as repetitiveness and diploidy) interact with and bias the Jaccard Index.
I am also in active collaboration with the Field Museum and the Minderoo Foundation to develop environmental DNA methods for population monitoring and conservation.
Sampling Salvia brandegeei · Santa Rosa Island
