Eric South e-south

Eric J. South

Systems, synthetic, and computational biologist at Boston University's Biological Design Center.
PhD candidate in the Dunlop Lab.

dnadesign A modular bioinformatics toolkit for designing sequence libraries, assembling DNA constructs, running sequence models, and analyzing their outputs.	dense-arrays Designs DNA sequences with densely packed protein-binding sites using optimal string packing across both strands.
reader Ingests instrument files and experiment metadata, applies specified transformations, and produces validated records, plots, exports, and notebooks.	motif-balance Designs DNA libraries that balance transcription-factor motif preferences, with alternative binding-site arrangements and sequence variants for testing biological function.
hop-design Plans construction of degenerate DNA hairpins for sequence-to-function studies, preserving the experimental stem and specifying oligonucleotides and modeled processing steps.

2024: "Generating information-dense promoter sequences with optimal string packing" (co-first author). PLOS Computational Biology.
2024: "A molecular toolkit of cross-feeding strains for engineering synthetic yeast communities". Nature Microbiology.
2023: "Spontaneously established syntrophic yeast communities improve bioproduction" (co-first author). Nature Chemical Biology.
2022: "Transcriptional Tuning of Mevalonate Pathway Enzymes to Identify the Impact on Limonene Production in Escherichia coli" (co-first author). ACS Omega.