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Bioinformatics PhD candidate studying gene duplication and lineage-specific gene evolution in Populus through comparative transcriptomics and phylogenetics. Recently working on the robustness of genomic foundation models: parameter-efficient fine-tuning on DNA and RNA language models, and mechanistic interpretability to find where they fail and whether their confidence tracks real biology.

Available Fall 2026. Based in Athens, Georgia. chen.hsieh.uga@gmail.com · GitHub · LinkedIn · Google Scholar

Education

Technical skills

Programming: Python · R · Bash/Shell · JavaScript · C/C++

Deep learning & foundation models: PyTorch · Hugging Face · genomic and RNA language models (Nucleotide Transformer, PlantCAD2, DNABERT2, AIDO.RNA, mRNA-FM, CodonFM) · LoRA · parameter-efficient fine-tuning · embedding extraction, pooling, and frozen probing

Interpretability & robustness: per-layer linear probing · in-silico mutagenesis · per-position importance attribution · decision-depth analysis · black-box adversarial attacks and training · benchmark-validity auditing

Genomics & classical ML: RNA-seq pipelines (STAR, HISAT2, DESeq2, edgeR) · 16S metagenomics (DADA2, QIIME2, SILVA, α/β diversity, MaAsLin2) · comparative transcriptomics · phylogenetics · genome-wide annotation · CRISPR gRNA design · XGBoost and SHAP

Engineering & deployment: Git/GitHub · Docker · CI/CD (GitHub Actions) · Python packaging (PyPI) · REST API · Snakemake · HPC/SLURM · agentic research workflows · Streamlit / R Shiny

Research experience

PhD Dissertation Research — Tsai Lab

Institute of Bioinformatics, University of Georgia · 2020 – present

• Dissertation on lineage-specific genes and the gene-duplication landscape in Populus, using expert-annotated and published case studies as a ground-truth reference set to improve automated analysis pipelines.
• Reprocessed large-scale community RNA-seq data (FASTQ to differential expression) on reproducible, HPC-scalable pipelines; built genome-wide protein structure annotation workflows.
• Modeled ohnolog expression divergence with XGBoost and SHAP under leakage-aware validation (chromosome-held-out cross-validation, permuted-label controls).
• Evaluated seven DNA foundation models (Nucleotide Transformer, PlantCAD2, DNABERT2, AgroNT, HyenaDNA, Grover) on Populus promoter sequences, diagnosing embedding quality and establishing architecture-specific pooling.
• Contributed to VariantDB v3.2 (CRISPR gRNA verification tool) and coexpression analysis of a perennial-specific sulfate transporter subgroup associated with lignification; both published in Tree Physiology (2025).

Adversarial Robustness of Genomic Foundation Models

Algoverse AI Research Program, team research project · 2026

• Built a model-agnostic robustness pipeline (replicate, attack, biological-validity gates, interpret, harden, transfer) across seven classification tasks and six DNA/RNA foundation models (AIDO.RNA-1.6B, Nucleotide Transformer, mRNA-FM, CodonBERT, CodonFM, structRFM).
• Designed constrained black-box adversarial attacks (synonymous, structure-preserving) gated by an independent biological oracle, benchmarked against matched random-edit floors.
• Built a mechanistic interpretability suite (in-silico mutagenesis, activation patching, concept probes, representation geometry); causal patching revealed sparse-but-redundant encoding.
• Delivered LoRA-based defenses that roughly halved attack success. Wrapped the workflow into a modular agentic skill. Submitted to a workshop in August 2026; not yet peer-reviewed.

MSc Research

Department of Horticulture, National Taiwan University · 2017 – 2019

• Comparative transcriptomics of mycorrhiza-enhanced salt tolerance in rice (Frontiers in Plant Science, 2022, co-first author).
• Automated HRM genotyping pipelines for a peach chilling requirement study (IJMS, 2020).

Selected leadership & projects

Technology Consultant & IT Group Convener

Taiwanese Young Researcher Association (Project TYRA) · Apr 2022 – present

• Built a platform powering a mentor–mentee matching program that grew from 274 to 700+ annual participants across 4 cohorts and facilitated 1,876 researcher connections; organization later partnered with Fulbright Taiwan and government education agencies.
• Deployed an automated event pipeline (Eventbrite API plus scheduling automation) for the weekly seminar series.

Director of Marketing & Communication

PhD Consulting Club, University of Georgia · Jul – Dec 2025

• Tripled club membership across multiple departments; facilitated weekly structured case practice sessions.

Team Leader

Hackathons & startup competitions · 2017 – present

• Led cross-functional teams of up to 5 at HudsonAlpha HATCH (2024, 2025) and the UGA-Bayer Hackathon (2025); delivered working prototypes under 8- to 28-hour constraints, including a plant-based diet planner for astronauts and a corn yield predictor (Snakemake, PyTorch, OpenAI API, Streamlit).
• Built the first Mandarin-language chatbot for plant disease diagnosis (Open Data Innovative Application Contest, Taiwan, 2017); pitched to venture capital panels and secured an NTD$410,000 award.

Publications

Five peer-reviewed publications. Full citations on the publications page.

• Surber et al. (2025), Tree Physiology — sulfate transporter phylogeny, perennial-specific subgroup
• Zhou et al. (2025), Tree Physiology — Populus VariantDB v3.2
• Tuma et al. (2024), Tree Physiology — tonoplast sucrose transport in coppiced poplar
• Hsieh et al. (2022), Frontiers in Plant Science — mycorrhiza-enhanced salt tolerance in rice (co-first author)
• Chou et al. (2020), IJMS — HRM genotyping toolkit for peach chilling requirement

Selected presentations

Talk. Investigating de novo gene birth in Populus. SMBE Satellite Meeting on De Novo Gene Birth, Texas A&M University (2023).

Posters. Characterization of stress-responsive lineage-specific genes in Populus, IUFRO Tree Biotechnology Conference (2024) · Searching for orphan genes in Populus, ASPB Worldwide Summit (2021) · Comparative transcriptome analysis of gibberellin-induced sex determination in bitter gourd, XXX International Horticultural Congress, Istanbul (2018).

Selected open-source tools

Research. slurm-receipt (PyPI): CLI that turns SLURM job history into a compute-cost, energy, and cloud-equivalent report · sapelo2-boilerplate: documented sbatch recipes for eight genomics tools, Snakemake pipelines, and a Claude Code ruleset for GPU/HPC jobs · agentic-research-toolkit: portable agentic research workflows (SKILL.md) written for discovery over confirmation · Biosecurity Atlas: knowledge graph of the biosafety-and-AI research funding landscape aggregated from five public funding and publication APIs.

Creative coding. dna2oiia (PyPI, meme-inspired DNA-to-audio sonification) · bioLOLPython (PyPI, sequence analysis with internet-slang dialects) · Glasshouse, a research greenhouse rendered as a game of Snake · UGA Grad Survivor, a Reigns-style PhD-survival game · slang-capsule, a multilingual timeline of internet slang queryable by year, language, and platform.

More detail on the projects page.

Teaching, mentoring & outreach

Mentored undergraduate researchers in bioinformatics workflows and phenotyping (UGA, 2021–2025) and in genome-wide sequence analysis (NTU, 2017–2018), where the mentee won first prize at the departmental poster competition. Guest lecturer, Methods in Horticultural Research (IV), National Taiwan University: taught RNA-seq analysis to an audience with no computational background; pre-lecture content doubled expected attendance. Elected BIGSA Representative (2022–2023) and organizer of the Institute of Bioinformatics seminar series, hosting Josh Starmer (StatQuest), Robert Edgar (MUSCLE), Ben Langmead (Bowtie/Bowtie2), and Jeffrey Perkel (Nature Technology Editor).

More on the teaching and community page.

Awards & certificates

Government Fellowship for Studying Abroad (est. $150K), Ministry of Education, Taiwan (2019) · Summer Research & Communication Grants, UGA (2021, 2022) · Sci4Pol Certificate, National Science Policy Network (2025).