e-south

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Eric South e-south

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PhD Candidate in the Dunlop Lab, part of the Biological Design Center at Boston University. Aspiring systems, synthetic, and computational biologist.

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e-south/README.md

Eric South

👋 Hey, I'm Eric. I'm building Python tools for DNA sequence design and experimental data workflows.

Current Work

dnadesign

DNA sequence design workspace with modular pipelines for biological design and analysis.

Data companion repository: dnadesign-data
Integrates tools such as dense-arrays and Evo 2

reader

Command-line workbench for experimental data.

Documentation: reader docs
Quickstart: reader quickstart

Prior Work

dense-arrays

Method for designing DNA sequences with densely packed DNA-protein binding motifs.

Paper: Andreani, South, Dunlop (2024), PLOS Computational Biology, "Generating information-dense promoter sequences with optimal string packing"
Package documentation: dunloplab.gitlab.io/dense-arrays

deg2tfbs

Pipeline linking differential expression to transcription factors and candidate binding sites.

Contact

Email: ericjohnsouth@gmail.com
LinkedIn: Eric J. South

Pinned Loading

dense-arrays dense-arrays Public

We introduce a computational technique that efficiently assembles sets of DNA-protein binding sites into dense, contiguous stretches of double-stranded DNA.

Python
dnadesign dnadesign Public

A collection of Python modules and data analysis pipelines, all related to DNA sequence design.

Python
reader reader Public

Command-line workbench for experimental data.

Python
dnadesign-data dnadesign-data Public

This repository contains datasets, such as RegulonDB, EcoCyc, primary literature data.

Python
deg2tfbs deg2tfbs Public

Pipeline for differential expression analysis (DEGs), transcription factor mapping, and TFBS identification.

Python
CIDARLAB/ibis CIDARLAB/ibis Public

Graph-based Datastructure Library for Genetic and Boolean Circuits.

Python 1 2