PUBLICATIONS

Under Review

[SCI-E][Co-Author] LAMBDA: A Prophage Detection Benchmark for Genomic Language Models
LAM Lindsey, NL Pershing, K Dufault-Thompson, HJ Gwak, A Habib, A Schindler, A Rakheja, J Round, WZ Stephens, AJ Blaschke, H Sundar, X Jiang

2020 - 2025

[SCI-E][1st Author] DeepCOI: a large language model-driven framework for fast and accurate taxonomic assignment in animal metabarcoding, Genome Biology, 2025, DOI: https://doi.org/10.1186/s13059-025-03861-7 (JCR IF: 9.2)
HJ Gwak, M Rho

[SCI-E][1st Author] Antibiotic Sensitivity and Nasal Microbiome in Patients with Acute Bacterial Rhinosinusitis, The Larngoscope, 2024, DOI: https://doi.org/10.1002/lary.30950 (JCR IF: 2.97)
HJ Gwak, HA Lee, JY Jeong, Y Lee, M Rho, SH Cho

[SCI-E][Co-Author] Skin microbe-dependent TSLP-ILC2 priming axis in early life is co-opted in allergic inflammation, Cell host & Microbe, 2024, DOI: https://doi.org/10.1016/j.chom.2023.12.006 (JCR IF: 30.3)
J Cha, TG Kim, E Bhae, HJ Gwak, Y Ju, YH Choe, IH Jang, Y Jung, S Moon, T Kim, W Lee, JS Park, YW Chung, YM Hyun, GS Hwang, WJ Lee, M Rho, JH Ryu

[SCI-E][1st Author] ViBE: a hierarchical BERT model to identify eukaryotic viruses using metagenome sequencing data, Briefings in Bioinformatics, 2022, DOI: https://doi.org/10.1093/bib/bbac204 (JCR IF: 11.622)
HJ Gwak, M Rho

[SCI-E][Co-Author] Association of microbial dysbiosis with gallbladder diseases identified by bile microbiome profiling, Journal of Korean medical science (JKMS), 2021, DOI: https://doi.org/10.3346/jkms.2021.36.e189 (JCR IF: 1.705)
SJ Choi, Y Kim, J Jeon, HJ Gwak, M Kim, K Kang, Y Kim, J Jeong, YK Jung, KG Lee, HS Choi, DH Jung, SG Lee, Y Lee, SJ Shin, K Jang, M Rho, D Choi

[SCI-E][1st Author] Application of computational approaches to analyze metagenomic data, Journal of Microbiology, 2021, DOI: https://doi.org/10.1007/s12275-021-0632-8 (JCR IF: 2.845)
HJ Gwak, SJ Lee, M Rho

[SCI-E][Co-Author] MegaR: an interactive R package for rapid sample classification and phenotype prediction using metagenome profiles and machine learning, BMC Bioinformatics, 2021, DOI: https://doi.org/10.1186/s12859-020-03933-4 (JCR IF: 3.242)
E Dhungel, Y Mreyoud, HJ Gwak, A Rajeh, M Rho, TH Ahn

[SCI-E][1st Author] Data-Driven Modeling for Species-Level Taxonomy Assignment From 16S rRNA: Application to Human Microbiomes, Frontiers in Microbiology, 2020, DOI: https://doi.org/10.3389/fmicb.2020.570825 (JCR IF: 4.259)
HJ Gwak, M Rho

[SCI-E][1st Author] Functional dynamics of bacterial species in the mouse gut microbiome revealed by metagenomic and metatranscriptomic analysis, PLoS ONE, 2020, DOI: https://doi.org/10.1371/journal.pone.0227886 (JCR IF: 2.776)
YW Chung, HJ Gwak, S Moon, M Rho, JH Ryo