Publications

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* Corresponding Author(s)

Names in bold letters: BIIL members

Ongoing papers

Iljung Jin, Jungmin Kim, Mijin Yun, Jae-Ho Cheong*, Hojung Nam*, "Identification of metabolic drug targets via genome-scale metabolic network analysis in EMT-subtype gastric cancer", Submitted.
Dohyun Kim, Hojung Nam*, "SparseSurv: Regularized Cancer Survival Prediction Model Construction Using Weight Pruning", Submitted.

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

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*,

“BayeshERG: A Robust, Reliable, and Interpretable Deep Learning Model for Predicting hERG Channel Blockers",

Briefings in Bioinformatics 2022 Jun 17;bbac211. doi: 10.1093/bib/bbac211.

5. Koon Mook Kang§, Ingoo Lee§, Hojung Nam*, Yong-Chul Kim*,

"AI-Based Prediction of New Binding Site and Virtual Screening for the Discovery of Novel P2X3 Receptor Antagonists",

European Journal of Medicinal Chemistry, 2022 Jul 1;240:114556.

6. Gwangmin Kim†, Eunyoung Kim†, Ohhyeon Kwon†, Seunghwan Jung, Seunghyun Wang, Hojung Nam*, Doheon Lee*,

“CODA 3.0: Integrating heterogeneous assay data for multi-compound drug discovery”,

BMC Bioinformatics, Accepted.

2. Haelee Bae, Hojung Nam*,

"GraphATT-DTA: attention-based novel representation of interaction to predict drug-target binding affinity",

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.

1. Hyunho Kim, Eunyoung Kim, Ingoo Lee, Bongsung Bae, Minsu Park, Hojung Nam*,

"Artificial Intelligence in Drug Discovery: A Comprehensive Review of Data-Driven and Machine Learning Approaches",

Biotechnology and Bioprocess Engineering, 2020;25(6):895-930. doi: 10.1007/s12257-020-0049-y.

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.

Peer Reviewed Journals (2021)