Research

My doctoral thesis, New Insights into Plasmodium Evolution: How Genomics and Evolutionary Biology Contribute to Understanding Malaria, combines genome assembly, phylogenomics and molecular evolution. I generated the first chromosome-level de novo genome assembly of Plasmodium gonderi, a malaria parasite of African monkeys. Phylogenomic analyses with this genome place the common ancestor of Plasmodium vivax within the radiation of Asian primate malarias, supporting an Asian origin for this widespread species. Time-tree analyses also date the origin of the Laverania clade, which includes P. falciparum, to the period of the radiation of its great-ape hosts.

In a companion review I performed the species-tree reconstruction from more than 1,000 genes that frames the deep divergence between the subgenus Plasmodium and Laverania, and the distinct molecular adaptations of each lineage.

I study the diversity of Haemoproteus and related parasites in wildlife. Using complete mitochondrial genomes, we resolved nine parasite lineages in North American owls, including two new to science, and linked a widespread lineage to Haemoproteus syrnii. The data also showed that a presumed single species is a complex of cryptic species.

As a graduate researcher on the NSF-funded project Assessing the systematics and diversity of Haemosporida in African lizards (2022–2026), I developed a machine-learning model to infer haplotypes from target-sequencing data.

During my master’s work at the Universidad Nacional de Colombia (GERPH) I characterized the Haemoproteus columbae apicoplast genome, the first for the genus, and described the complete experimental life cycle of H. columbae in its natural pigeon host and louse-fly vector. For Haemogregarina in Colombian turtles, I assembled the mitochondrial genome from raw reads to design new markers that revealed hidden diversity.

As a graduate researcher on the CDC-funded project Developing an evidence-based molecular surveillance system for mpox (2023–2024; PI: Dr. Ananias A. Escalante), I developed SNP panels for the mpox virus (MPXV) and carried out tip-dating analyses with BEAST2 to support molecular surveillance.

As a bioinformatician I design and implement analysis software. The HmtG-PacBio pipeline uses a variational autoencoder to classify PacBio HiFi long reads from the whole mitochondrial genome, separating distinct parasite haplotypes and species in a single mixed-infection sample. It characterized infections in birds, reptiles and mammals that standard barcoding missed.

Since 2023 I have developed reproducible pathogen-genomics workflows on the Galaxy platform as part of the multi-institutional BRC Analytics / Galaxy Project (Penn State, Temple, Johns Hopkins, UCSC and TACC; NIH-funded). I also write teaching material on pangenomics, phylogenetic model selection and hybrid genome assembly.