Eric J. South
ericjohnsouth@gmail.com | Boston, MA | ericsouth.com
Summary
Systems, synthetic, and computational biologist combining laboratory assays, bioinformatics, machine learning, and open-source software development to design biological sequences and evaluate their function, drawing on experience in genetic circuit design, protein engineering, and high-throughput screening.
Technical Skills
- Experimental Biology: Experimental design and assay development; genetic circuit and biosensor design; DNA assembly, cloning, transformation, and conjugation; bacterial, yeast, and mammalian cell culture; protein purification; automated liquid handling; flow cytometry and plate-reader assays; ELISA and Western blotting; amplicon sequencing (NGS); anaerobic gas fermentation
- Computational Biology: Regulatory DNA design; structure-guided protein design (ProteinMPNN); transcription-factor binding-site design; genetic-circuit modeling; active learning for experimental selection; latent-space analysis of sequence representations (Evo2); RNA–protein structural analysis
- Scientific Software & Data: Python, R, shell scripting, and Git; package and API/CLI development; experimental data ingestion, validation, and analysis pipelines; dependency and environment management (uv, pixi); automated testing, linting, and CI (GitHub Actions); agent tooling and workflow automation
Research Experience
Boston University, Dunlop Lab / Biological Design Center Sept. 2020 — Present
PhD Research
- Developed a dense-array algorithm to compile transcription-factor binding sites into synthetic promoters; integrated foundation-model representations and experimental feedback in a closed-loop active learning pipeline to target distinct gene-expression responses across conditions.
- Engineered modular scientific software for DNA design and assembly, multi-motif sequence optimization, computational hairpin construction planning, and experimental data integration and analysis.
- Combined structure-guided reverse-transcriptase design, engineered retron lnRNAs, and functional assays to investigate intracellular gene regulation.
LanzaTech, Synthetic Biology & Host Strain Engineering Team Summer 2022 — Fall 2022
Engineering Biology Research Consortium Intern
- Contributed genetic tools for gas-fermenting strains through pooled DNA-library design, massively parallel reporter assays, next-generation sequencing, and biosensor development.
Imperial College London / The Francis Crick Institute 2018 — 2020
MRes Student / Postgraduate Researcher
- Implemented a high-throughput workflow using laboratory robotics to screen hundreds of yeast cultures in parallel and identify metabolic cross-feeding communities.
SRI International, Center for Macromolecular Bioscience 2017 — 2018
Student Associate
- Analyzed peptide drug-candidate binding and internalization in mammalian cell lines using flow cytometry and Western blotting to support tissue-specific cancer drug delivery; also supervised two interns.
James Madison University, School of Integrated Sciences 2014 — 2017
REU Undergraduate Researcher
- Purified ubiquitin-like proteins from E. coli using size-exclusion and ion-exchange chromatography to support biochemical characterization of the human Uba1 enzyme.
Education
Boston University, Boston, Massachusetts, USA Started Sept. 2020
PhD Candidate - Molecular Biology, Cell Biology, and Biochemistry (MCBB)
Advisors: Mary J. Dunlop
Thesis: “Molecular Sequence Design for Cellular Gene Regulation”
Imperial College London, London, England, UK Sept. 2018 — Sept. 2019
Master of Research - Systems & Synthetic Biology; Graduated first in class
Advisors: Rodrigo Ledesma-Amaro, Markus Ralser
Thesis: “A Screening Platform to Identify Synthetic Microbial Communities”
James Madison University, Harrisonburg, Virginia, USA May 2018
Bachelor of Science - Biotechnology; GPA: 3.72; Magna Cum Laude
Publications
, . 2026. Manuscripts in preparation
- Specification-driven experimental search for multistate promoter behavior
- Balanced inverse design of fixed-length DNA sequences from multiple motif models
- Designing oligonucleotide processing routes for DNA hairpin construction
; [*Co-first]. PLoS Comput Biol (2024), 20(7): e1012276
, , , , , . Nat Microbiol (2024), 9: 848–863
; [*Co-first]. Nat Chem Biol (2023), 19(8): 951–961
; [*Co-first]. ACS Omega (2022), 7(22): 18331–18338
Teaching, Mentoring & Leadership
Teaching Fellow, BU BE 209: Molecular Cell Biology & Biotechnology
(Fall 2023) | 39 students | evaluation 4.53/5.00; (Spring 2021) | 45 students | evaluation 4.92/5.00
Chair & Organizer, Gordon Research Seminar: Synthetic Biology (2027): PhD/postdoc meeting
BU mentoring: Mentored three graduate rotation students individually (2022–Present); Supervised five BME undergraduates developing a CNN image-processing pipeline for microbial viability assays.
Mentorship Organizer, BU BDC (2022–2024): Linked dozens of PhD mentees and biotech mentors.
Industry Liaison, EBRC (2021–2023): Organized biotech business and data-infrastructure panels.
Outreach Manager, Science Entrepreneur Club (2018–2019): Co-organized a biotech startup pitch competition with Merck Accelerator.
President, JMU Student Biotechnology Association (2017–2018): Planned an eight-month program with six facility tours, six guest speakers, and five networking events.
Presentations, Training & Honors
Posters: Gordon Research Conferences—Synthetic Biology (2023, 2025) and Microbial Stress Response (2024); BU BDC Symposium (2023); SEED (2022)
SynbiCITE 4-Day MBA, Imperial College Incubator, Entrepreneurship and pitching workshop (2018)
NIH T32 Trainee in Synthetic Biology & Biotechnology, Boston University (2021–2026)
Excellence in Biotechnology Leadership Award, JMU (2018): Was recognized for student-organization work, program marketing, and peer instruction.