Genomics and phylogenomics of Plasmodium
Reconstructing the evolutionary history of human malaria parasites from high-quality genomes.
Read more →Infectious disease genomics · Evolution · Bioinformatics
Axl S. Cepeda
PhD in Biology (Temple University, 2026) · Visiting Scholar, Escalante Lab
I study the evolution of infectious disease agents, mainly malaria and other haemosporidian parasites, and mpox virus, combining comparative and population genomics, phylogenomics and machine learning. I also build the software that makes those analyses reproducible.
P. falciparum
P. reichenowi
P. gonderi
P. fragile
P. coatneyi
P. knowlesi
P. cynomolgi
P. inui
P. vivax
H. columbae
H. syrnii
Leucocytozoon
CGGCTCCCTGACT-----GACGGGTAGACGAGAATGCTTTCGAACGGTGTCTGCTATAATGGGAGTATCCGCATACCTGCGGGGGCGAATAAA----GACAACCCGTAGTCATACGCCAGGGTCAATGGGGTATG--TGTAGGAGAAAGG
AGGCTCCCTGACTTTCCCGTCAGGTAGACGAGAATGTTATCGAACGGTGTCTGCTATAATGGGAGTATCCGCATACCTGCGGGGGCGAATAAACCGAGACA--CCGGAGTCATACGCCAGG---TAAGGGGTGCGCTTGTTGGAGAAAGG
CAGATTCCTGACCTTCCCGACGGGTAGACGAGATTGCTACCTAACGGTGTCTGCTATAAGGGGAATATCCGCATACGTGCGGGGGCGAATAAACTGAGACAACCC-GAGTCGTACGCCAGGGTCTATGGGG-------GTAGGAGAAAGG
CGGCTCCCAGACTTACCCGACGG-----CGAGAATGCGCTCGAACGGTGTCTGCTATAATGAGAGTATCCGCATACGTGCGGGGGCGAAACTACCGAGTCAACCCGGAGTCCT---CCAGGGTCTA---CGTGCGCTTGTAGGAGAAATG
CGGCTCC-TTACTTTCCCGACGGGTAGACGAGAATGCCAACGAACGGTGTCTGTTCTAACGGAAGTATCCGCA--CCTGCGGGGGCGAACAAACCAAGACAACCC----ACATACTCCAGGGTCCATGGGGTGCGCTTGTGTGAGAAAGG
CCGCTGCC-----TCCCCGACGGGTAGACGAGAATGCCATCGAACGGTGT-TGCTACAATGGGAGTATCCGCATAGCTGGGGGGGCGAATAAACCGAGACAACCCGGAC-----CGCCAGGGGCTATGGGGTGCGCTTGTAGGAGAAAAG
CGGCTCCC---CTTTGCCGACGGGTAGACGAGAGTGATATCGAACGGTGTCTGAT----TGGCG--ATCCGCATTCCTGGGGGGGCGAGTATACCCAGACAACCCGGAGTCATACGCCACGGTCTATGGGGTGGGCTGGTAGGAGAAAGG
CGGGTCCGTGACTTTTCCGTCGGGTAGACGAGAATGCTAGCGAACGGTGTCTGCTA---GGGGAGTATCCGCATAC----GGGGGCGAACAAA----GACAACCCGGAGTCATACGCCAGGGTCTTCGGGGTGCGCTTGTCTGAGAAAGG
CGGCTCCATGACTTTCCCGACGGG--GACGAGAA-----ACGAACGGTGTCTGCTGAAATGGGAGTATCCGGATACCTGCGGGGGCAAACAAACCGAGACAACCCGGAG-----CGCCAGTGTCTATGGGGTGCGCTTGTCGGTGAAAGG
CCGCTGCCTGACTTTACCGACTGGTAGAC-AGAATGATAGCGAACGGTGTCTGTTACAATGGTCGTATCCGCATACCTGCGG---CAACTAGACAGAGACAAACCGGAATCATACGTCAGGGTGCACGGGGTACGCTTG-----GAAAAG
CGGATCCCTGACTTAGCCGA-----AGACGAGAGTGCTATCGAAAGGTGT---CTGTAATGACATTATCCGCATAAGGGCGGTGGCGATCATACTGAGACAACCCGGAGTCATACGCCACGGTCTATGGTGT----TTGTCGGATAAAGG
--GGTCCCTGACCTACCCCCCGGGTAAACGAGAGTGCCATCGAACGGTGTCTGTTTCAATGGGGGTGTC---ATACCTGCGGGGACCACACTACCCA-ACAACCCGGACACATACGCCAGTGTCTGTGAGGTACGCTCGTACGGGAAGCT
CGGCTCCCTGACT-----GACGGGTAGACGAGAATGCTTTCGAACGGTGTCTGCTATAATGGGAGTATCCGCATACCTGCGGGGGCGAATAAA----GACAACCCGTAGTCATACGCCAGGGTCAATGGGGTATG--TGTAGGAGAAAGG
AGGCTCCCTGACTTTCCCGTCAGGTAGACGAGAATGTTATCGAACGGTGTCTGCTATAATGGGAGTATCCGCATACCTGCGGGGGCGAATAAACCGAGACA--CCGGAGTCATACGCCAGG---TAAGGGGTGCGCTTGTTGGAGAAAGG
CAGATTCCTGACCTTCCCGACGGGTAGACGAGATTGCTACCTAACGGTGTCTGCTATAAGGGGAATATCCGCATACGTGCGGGGGCGAATAAACTGAGACAACCC-GAGTCGTACGCCAGGGTCTATGGGG-------GTAGGAGAAAGG
CGGCTCCCAGACTTACCCGACGG-----CGAGAATGCGCTCGAACGGTGTCTGCTATAATGAGAGTATCCGCATACGTGCGGGGGCGAAACTACCGAGTCAACCCGGAGTCCT---CCAGGGTCTA---CGTGCGCTTGTAGGAGAAATG
CGGCTCC-TTACTTTCCCGACGGGTAGACGAGAATGCCAACGAACGGTGTCTGTTCTAACGGAAGTATCCGCA--CCTGCGGGGGCGAACAAACCAAGACAACCC----ACATACTCCAGGGTCCATGGGGTGCGCTTGTGTGAGAAAGG
CCGCTGCC-----TCCCCGACGGGTAGACGAGAATGCCATCGAACGGTGT-TGCTACAATGGGAGTATCCGCATAGCTGGGGGGGCGAATAAACCGAGACAACCCGGAC-----CGCCAGGGGCTATGGGGTGCGCTTGTAGGAGAAAAG
CGGCTCCC---CTTTGCCGACGGGTAGACGAGAGTGATATCGAACGGTGTCTGAT----TGGCG--ATCCGCATTCCTGGGGGGGCGAGTATACCCAGACAACCCGGAGTCATACGCCACGGTCTATGGGGTGGGCTGGTAGGAGAAAGG
CGGGTCCGTGACTTTTCCGTCGGGTAGACGAGAATGCTAGCGAACGGTGTCTGCTA---GGGGAGTATCCGCATAC----GGGGGCGAACAAA----GACAACCCGGAGTCATACGCCAGGGTCTTCGGGGTGCGCTTGTCTGAGAAAGG
CGGCTCCATGACTTTCCCGACGGG--GACGAGAA-----ACGAACGGTGTCTGCTGAAATGGGAGTATCCGGATACCTGCGGGGGCAAACAAACCGAGACAACCCGGAG-----CGCCAGTGTCTATGGGGTGCGCTTGTCGGTGAAAGG
CCGCTGCCTGACTTTACCGACTGGTAGAC-AGAATGATAGCGAACGGTGTCTGTTACAATGGTCGTATCCGCATACCTGCGG---CAACTAGACAGAGACAAACCGGAATCATACGTCAGGGTGCACGGGGTACGCTTG-----GAAAAG
CGGATCCCTGACTTAGCCGA-----AGACGAGAGTGCTATCGAAAGGTGT---CTGTAATGACATTATCCGCATAAGGGCGGTGGCGATCATACTGAGACAACCCGGAGTCATACGCCACGGTCTATGGTGT----TTGTCGGATAAAGG
--GGTCCCTGACCTACCCCCCGGGTAAACGAGAGTGCCATCGAACGGTGTCTGTTTCAATGGGGGTGTC---ATACCTGCGGGGACCACACTACCCA-ACAACCCGGACACATACGCCAGTGTCTGTGAGGTACGCTCGTACGGGAAGCT
Genomes produced or improved in my research
01
Research lines
Diversity of haemosporidian and related blood parasites
Birds, reptiles and mammals as hosts: species limits, cryptic diversity and life cycles.
Read more →Molecular surveillance and evolution of mpox virus
Genomic tools to track the transmission and evolution of mpox virus.
Read more →Computational methods and machine-learning tools
Pipelines and models in Python and R that turn genomic data into reproducible biological results.
Read more →02
All publications →Recent publications
- 2026
New Insights into Plasmodium Evolution: How Genomics and Evolutionary Biology Contribute to Understanding Malaria
Cepeda, A. S.
PhD dissertation, Temple UniversityPhD thesis
- 2025
Haemoproteus syrnii and other haemosporidians infecting owls from North America
Pacheco, M. A., Miller, E. A., Harl, J., Ferreira, F. C., Cepeda, A. S., Valkiūnas, G., Beckerman, S., Oswald, M., Mateus-Pinilla, N. E., Escalante, A. A.
Malaria Journal, 24, 365DOI: 10.1186/s12936-025-05612-2
- 2024
A new long-read mitochondrial-genome protocol (PacBio HiFi) for haemosporidian parasites: a tool for population and biodiversity studies
Pacheco, M. A., Cepeda, A. S., Miller, E. A., Beckerman, S., Oswald, M., London, E., Mateus-Pinilla, N. E., Escalante, A. A.
Malaria Journal, 23(1), 134DOI: 10.1186/s12936-024-04961-8
- 2024
The genome of Plasmodium gonderi: insights into the evolution of human malaria parasites
Cepeda, A. S., Mello, B., Pacheco, M. A., Luo, Z., Sullivan, S. A., Carlton, J. M., Escalante, A. A.
Genome Biology and Evolution, 16(2), evae027DOI: 10.1093/gbe/evae027