Publications
Click: Google Scholar Citation Page
* Corresponding Author(s)
Names in bold letters: BIIL members
1. Iljung Jin, Songyeon Lee, Martin Schmuhalek, Hojung Nam*,
Briefings in Bioinformatics, Volume 26, Issue 1, January 2025, bbae717.
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Selected as RECOMB 2025 Highlights Track (acceptance rate of 18.9%).
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Media covered: 동아일보 and +20 daily newspapers, KBS, YTN Science news.
2. Hyunho Kim, Bonsung Bae, Minsu Park, Yewon Shin, Trey Ideker*, Hojung Nam*,
"G2D-Diff: A genotype-to-drug diffusion model for generation of tailored anti-cancer small molecules",
Under revision.
3. Dongok Nam, Hojung Nam*,
"ICAN-PPII: Interpretable cross-attention network for predicting protein-protein interaction inhibitors",
Under review.
4. Songyeon Lee, Hojung Nam*,
"KG-SLomics: Cancer Type-Specific Synthetic Lethality Prediction Using Knowledge Graph and Multiomics Integrated Graph Neural Network",
Under review.
5. Hansol Lee, Juntae Park, Daehun Bae, Hojung Nam*,
"AMP-LoRAgen: Generation of species-aware antimicrobial peptides using GPT and Low-Rank Adaptation",
Under review.
6. Daehun Bae†, Minsang Kim†, Jiwon Seo*, Hojung Nam*,
"AI-Guided Discovery and Optimization of Antimicrobial Peptides Through Species-Aware Language Model",
Submitted.
Peer Reviewed Conferences & Journals (2025)
Peer Reviewed Conferences & Journals (2024)
1. Haelee Bae, Hojung Nam*,
"A Deep Learning Approach for RNA-Compound Interaction Prediction with Binding Site Interpretability",
NeurIPS 2024 Workshop on AI for New Drug Modalities (Spotlight), Dec 2024
Peer Reviewed Journals (2023)
1. Hansol Lee, Songyeon Lee, Ingoo Lee, Hojung Nam*,
"AMP-BERT: Prediction of Antimicrobial Peptide Function Based on a BERT Model",
Protein Science. 2023; 32(1):e4529. https://doi.org/10.1002/pro.4529
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Media covered: 조선비즈 and +10 daily newspapers, YTN Science news.
2. Haelee Bae, Hojung Nam*,
Biomedicines. 2023, 11(1), 67.
3. Bongsung Bae, Haelee Bae, Hojung Nam*,
"LOGICS: Learning optimal generative distribution for designing de novo chemical structures",
Journal of Cheminformatics 2023 Sep 7;15(1):77. doi: 10.1186/s13321-023-00747-3.
4. In Seok Yang, Insu Jang, Jin Ok Yang, Jinhyuk Choi, Min-Seo Kim, Ka-Kyung Kim, Byung-Joon Seung, Jae-Ho Cheong, Jung-Hyang Sur, Hojung Nam, Byungwook Lee, Junho Kim, Sangwoo Kim,
"CanISO: a database of genomic and transcriptomic variations in domestic dog (Canis lupus familiaris)",
BMC Genomics. 2023 Oct 13;24(1):613. doi: 10.1186/s12864-023-09655-0.
Peer Reviewed Journals (2022)
1. Ingoo Lee, Hojung Nam*,
"Sequence-based prediction of protein binding regions and drug–target interactions",
Journal of Cheminformatics. 2022 Feb 8;14(1):5. doi: 10.1186/s13321-022-00584-w.
2. Eunyoung Kim, Hojung Nam*,
"DeSIDE-DDI: Interpretable prediction of drug-drug interactions using drug-induced gene expressions",
Journal of Cheminformatics. 2022 Mar 4;14(1):9. doi: 10.1186/s13321-022-00589-5.
3. Songyeon Lee, Byung-Joon Seung, In Seok Yang, Jueun Lee, Taewoong Ha, Hee-Myung Park, Jae-Ho Cheong, Sangwoo Kim, Jung-Hyang Sur, Geum-Sook Hwang*, Hojung Nam*,
"1H NMR based urinary metabolites profiling dataset of canine mammary tumor",
Scientific Data. volume 9, Article number: 132 (2022).
4. Hyunho Kim, Minsu Park, Ingoo Lee, Hojung Nam*,
Briefings in Bioinformatics 2022 Jun 17;bbac211. doi: 10.1093/bib/bbac211.
5. Koon Mook Kang§, Ingoo Lee§, Hojung Nam*, Yong-Chul Kim*,
European Journal of Medicinal Chemistry, 2022 Jul 1;240:114556.
1. Hyunho Kim, Eunyoung Kim, Ingoo Lee, Bongsung Bae, Minsu Park, Hojung Nam*,
Biotechnology and Bioprocess Engineering, 2020;25(6):895-930. doi: 10.1007/s12257-020-0049-y.
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2022 BBE Best Article Awarded
2. Iljung Jin, Hojung Nam*,
"HiDRA: Hierarchical Network for Drug Response Prediction with Attention",
J. Chem. Inf. Model. 2021 Aug 23;61(8):3858-3867. doi: 10.1021/acs.jcim.1c00706.