Publications

Journal articles, preprints, ongoing work, and research software. Google Scholar ↗

Publication list updated November 11, 2026; journal review statuses provided by the author.

Published

2026 · Nature Neuroscience

Massively parallel assessment of gene regulatory activity at human cortical-structure-associated variants

Nana Matoba, Jessica C. McAfee, Oleh Krupa, Alvaro A. Beltran, Jessica L. Bell, Brandon D. Le, Jordan M. Valone, Hyunggyu Min, Gregory E. Crawford, Jesse R. Raab, Hyejung Won, Jason L. Stein.

Published article

Published online September 23, 2026.

2025 · Cell

Massively parallel reporter assay investigates shared genetic variants of eight psychiatric disorders

Sool Lee, Jessica C. McAfee, Jiseok Lee, Alejandro Gomez, Austin T. Ledford, Declan Clarke, Hyunggyu Min, Mark B. Gerstein, Alan P. Boyle, Patrick F. Sullivan, Adriana S. Beltran, Hyejung Won.

Published article

2023 · Scientific Reports

Altered gut microbiota in individuals with episodic and chronic migraine

Dongeun Yong, Hakbae Lee, Hyung-Gyu Min, Kyungnam Kim, Hyun-Seok Oh, Min Kyung Chu.

Published article

2022 · Journal of Functional Foods

Effect of orally administered heat-treated Lactobacillus plantarum LM1004 on the innate immune system: A randomized, placebo-controlled, double-blind study

Won-Young Bae, Hyunggyu Min, So Lim Shin, Tae-Rahk Kim, Hakbae Lee, Minn Sohn, Kyoung Sik Park.

Published article

Preprints

2026 · bioRxiv · Preprint

Polygenic hierarchies of macroscale brain structural organisation

Yuanjun Gu, Amir Ebneabbasi, Yuankai He, Clara Pecci-Terroba, Kuldeep Kumar, Sebastian Jacquemont, Simon Baron-Cohen, HyungGyu Min, Hyejung Won, Edward Bullmore, Rafael Romero-Garcia, Richard A. I. Bethlehem, Varun Warrier.

Preprint

Under revision — Science

2026 · bioRxiv · Preprint

Perturbation of genes linked to common schizophrenia risk variants identifies cilia programs

Jiseok Lee, Hyunggyu Min, Cristine Casingal, Austin T. Ledford, Hannah Lee, Won Ma, Yangzhenyu Gao, Hanqian Mao, Eric S. McCoy, Lei Xing, Cindy Fang, Sang Ho Kwon, Mark J. Zylka, Keri Martinowich, Kristen R. Maynard, Stephanie C. Hicks, E. S. Anton, Hyejung Won.

Preprint · PubMed record

Under revision — Cell

2026 · bioRxiv · Preprint

Systematic Functional Interrogation of Neurodevelopmental Disorder Risk Variants

Alejandro Gomez, Jessica C. McAfee, Hyunggyu Min (co-first author), Tatiana Ulloa Avila, Sean Jones, Jessica L. Bell, Yangzhenyu Gao, Ellen Hu, Haoyue Li, Sool Lee, Ratchell Sadovnik, Zheng Fan, Nan Yang, Adriana S. Beltran, Hyejung Won.

Preprint

Under revision — Neuron

In preparation

Project descriptions below are working summaries, not finalized manuscript titles.

IGVF consortium · First author

In vivo MPRA — Addiction Library

A large-scale in vivo MPRA study testing 12,000 variants from the Addiction Library, prepared as part of the IGVF consortium paper package.

Manuscript in preparation. Target journal: Nature.

PGC consortium · First author · Lead analyst

MPRA meta-analysis

A PGC consortium study integrating 11 MPRA datasets encompassing 130,000 variants tested across 96 replicates. I am leading the analysis as first author.

Manuscript in preparation.

Methods paper · First author

ZiPert

A methods paper on differential expression analysis using negative binomial and zero-inflated count models.

Manuscript in preparation.

Methods paper · First author

Massive Seq Finder (MSF)

A methods paper on fast nearest-reference search for noisy DNA/RNA sequences.

Manuscript in preparation.

Software & Packages

ZiPert

A Python package for differential expression analysis using negative binomial count models, with support for zero inflation and gene-set-level shared dropout.

GitHub ↗

MPRA barcode–element mapping

A pipeline for mapping barcodes to elements from long-read Nanopore sequencing of MPRA libraries. The repository documents its configuration, dependencies, and output tables; it is currently tailored to a specific plasmid configuration.

View the public repository

Massive Seq Finder (MSF)

A fast nearest-reference search tool for noisy DNA/RNA sequences, combining FAISS candidate retrieval with exact Levenshtein verification. Applications include barcode-to-variant mapping, sequence deduplication, and large-scale short-reference assignment.

Repository currently private

Earlier research and study code

• Quantum kernel investigation: notebooks exploring kernel regression and dimension reduction.
• Binary dimension reduction: earlier code repository.
• Convex optimization: earlier code repository.

See my GitHub profile for all public repositories and the Blog & Archive for related notes.