quasispecies

Viral quasispecies assembly via maximal clique finding. A method to reconstruct viral haplotypes and detect large insertions and deletions from NGS data.

Long-read haplotyping of small sequences with SNP-encoded de Bruijn graphs

Genetic extension to Conway's Game of Life with spatiotemporal and genetic analysis tools.

Reference-guided genomic variant mapping pipeline and intrahost variome atlas for the segmented Influenza A virus (H1N1pdm09), characterizing within-host quasispecies diversity and mutational burdens using deep sequence data.

Containerized Nextflow DSL2 workflow for viral intra-host variant calling (iSNV), quasispecies haplotype reconstruction, and evolutionary selection analysis.

Quantum algorithms for mutation-selection dynamics: formulation, methods, and an assessment of the quantum-classical boundary.

My 2015 dissertation, investigating microscale genomics of yellow fever vaccines.

Repositorio del Trabajo Final de Máster

R package for working with vcf files

quasispecies reconstruction pipeline. Improves Accuracy of Pacbio long read viral RNA sequencing by 15%.