Alex Sweeten

alex.sweeten

nih.gov

Alex is a PhD student at Johns Hopkins University, supervised by Michael Schatz and Adam Phillippy. Alex recieved a Bachelor’s degree with a Joint Major in Computer Science and Molecular Biology & Biochemistry from Simon Fraser University in 2017, and a Master’s Degree in Computer Science in 2019. Before starting his PhD, Alex worked as a software developer at Canada’s Michael Smith Genome Science Centre.

Software

AniAnn's is a tandem repeat annotation and masking tool which can infer repeat structure across whole chromosomes without sequence alignment.

ModDotPlot is a dotplot visualization tool, built for scalability to visualizae large tandem repeats across whole chromosomes.

Publications

A complete diploid human genome benchmark for personalized genomics

Cell, August 6, 2026

AniAnn's: alignment-free annotation of tandem repeat arrays using fast average nucleotide identity estimates

Bioinformatics, August 4, 2026

Sweeten A, Schatz MC, Phillippy AM

Origin and evolution of acrocentric chromosomes in human and great apes

bioRxiv, December 23, 2025

Solar SJ, Hebbar P, Gomes de Lima L, Sweeten A, Rhie A, Potapova T, de Gennaro L, Guarracino A, Kim J, Pickett BD, Paten B, Wilson MA, Koren S, Garrison E, Eichler EE, Ventura M, Gerton JL, Phillippy AM

Contributions of the Petabyte Scale Sequence Search Codeathon toward efforts to scale sequence-based searches on SRA

arXiv, May 9, 2025

Ghosh P … Sweeten A … Brister JR