A graph-theoretic modeling on GO space for biological interpretation of gene clusters. - Sung Geun Lee; Junguk Hur; Yang Seok Kim (Bioinform., 2004)

SciMiner: web-based literature mining tool for target identification and functional enrichment analysis. - Junguk Hur; Adam D. Schuyler; David J. States; Eva L. Feldman (Bioinform., 2009)

Identification of fever and vaccine-associated gene interaction networks using ontology-based literature mining. - Junguk Hur; Arzucan Özgür; Zuoshuang Xiang; Yongqun He (J. Biomed. Semant., 2012)

Updates on the web-based VIOLIN vaccine database and analysis system. - Yongqun He; Rebecca Racz; Samantha Sayers; Yu Lin; Thomas E. Todd; Junguk Hur; Xinna Li; Mukti Patel; Boyang Zhao; Monica Chung; Joseph Ostrow; Andrew Sylora; et al. (Nucleic Acids Res., 2014)

Extension of the Interaction Network Ontology for Literature Mining of Gene-gene Interaction Networks from Sentences with Multiple Interaction Keywords. - Arzucan Özgür; Junguk Hur; Yongqun He (BDM2I@ISWC, 2015)

GLASS: a comprehensive database for experimentally validated GPCR-ligand associations. - Wallace K. B. Chan; Hongjiu Zhang; Jianyi Yang 002; Jeffrey R. Brender; Junguk Hur; Arzucan Özgür; Yang Zhang 040 (Bioinform., 2015)

Development and application of an interaction network ontology for literature mining of vaccine-associated gene-gene interactions. - Junguk Hur; Arzucan Özgür; Zuoshuang Xiang; Yongqun He (J. Biomed. Semant., 2015)

Ignet: A Centrality and INO-based Web System for Analyzing and Visualizing Literature-mined Networks. - Arzucan Özgür; Junguk Hur; Zuoshuang Xiang; Edison Ong; Dragomir R. Radev; Yongqun He (ICBO/BioCreative, 2016)

The Interaction Network Ontology-supported modeling and mining of complex interactions represented with multiple keywords in biomedical literature. - Arzucan Özgür; Junguk Hur; Yongqun He (BioData Min., 2016)

Ontology-based collection, representation and analysis of drug-associated neuropathy adverse events. - Abra Guo; Rebecca Racz; Junguk Hur; Yu Lin; Zuoshuang Xiang; Lili Zhao; Jordan Rinder; Guoqian Jiang; Qian Zhu 003; Yongqun He (J. Biomed. Semant., 2016)

Extracting Adverse Drug Reactions using Deep Learning and Dictionary Based Approaches. - Mert Tiftikci; Arzucan Özgür; Yongqun He; Junguk Hur (TAC, 2017)

Ontology-based literature mining of E. coli vaccine-associated gene interaction networks. - Junguk Hur; Arzucan Özgür; Yongqun He (J. Biomed. Semant., 2017)

Ontology-based literature mining and class effect analysis of adverse drug reactions associated with neuropathy-inducing drugs. - Junguk Hur; Arzucan Özgür; Yongqun He (J. Biomed. Semant., 2018)

A 2018 workshop: vaccine and drug ontology studies (VDOS 2018). - Junguk Hur; Cui Tao; Yongqun He (BMC Bioinform., 2019)

Machine learning-based identification and rule-based normalization of adverse drug reactions in drug labels. - Mert Tiftikci; Arzucan Özgür; Yongqun He; Junguk Hur (BMC Bioinform., 2019)

Pathway crosstalk perturbation network modeling for identification of connectivity changes induced by diabetic neuropathy and pioglitazone. - Guillermo de Anda-Jáuregui; Kai Guo; Brett A. McGregor; Eva L. Feldman; Junguk Hur (BMC Syst. Biol., 2019)

Correction to: Pathway crosstalk perturbation network modeling for identification of connectivity changes induced by diabetic neuropathy and pioglitazone. - Guillermo de Anda-Jáuregui; Kai Guo; Brett A. McGregor; Eva L. Feldman; Junguk Hur (BMC Syst. Biol., 2019)

Identification of Casiopeina II-gly secondary targets through a systems pharmacology approach. - Guillermo de Anda-Jáuregui; Jesús Espinal-Enríquez; Junguk Hur; Sergio Antonio Alcalá-Corona; Lena Ruiz-Azuara; Enrique Hernández-Lemus (Comput. Biol. Chem., 2019)

CIDO: The Community-Based Coronavirus Infectious Disease Ontology. - Yongqun He; Hong Yu 014; Edison Ong; Yang Wang; Yingtong Liu; Anthony Huffman; Hsin-Hui Huang; John Beverley; Asiyah Yu Lin; William D. Duncan; Sivaram Arabandi; Jiangan Xie; et al. (ICBO/ODLS, 2020)

GBMPSO: Hybrid Gradient Boosting Machines with Particle Swarm Optimization in Cell Segmentation Data. - Temidayo Adeluwa; Eunjin Kim; Junguk Hur (SSCI, 2021)

COVID-19 vaccine design using reverse and structural vaccinology, ontology-based literature mining and machine learning. - Anthony Huffman; Edison Ong; Junguk Hur; Adonis D'mello; Hervé Tettelin; Yongqun He (Briefings Bioinform., 2022)

A comprehensive update on CIDO: the community-based coronavirus infectious disease ontology. - Yongqun He; Hong Yu 014; Anthony Huffman; Asiyah Yu Lin; Darren A. Natale; John Beverley; Ling Zheng; Yehoshua Perl; Zhigang Wang; Yingtong Liu; Edison Ong; Yang Wang; et al. (J. Biomed. Semant., 2022)

Evaluation of GPT and BERT-based models on identifying protein-protein interactions in biomedical text. - Hasin Rehana; Nur Bengisu Çam; Mert Basmaci; Yongqun He; Arzucan Özgür; Junguk Hur (CoRR, 2023)

Nested Named Entity Recognition using Multilayer BERT-based Model. - Hasin Rehana; Benu Bansal; Nur Bengisu Çam; Jie Zheng 001; Yongqun He; Arzucan Özgür; Junguk Hur (CLEF (Working Notes), 2024)

Cancer Vaccine Adjuvant Name Recognition from Biomedical Literature using Large Language Models. - Hasin Rehana; Jie Zheng 001; Leo Yeh; Benu Bansal; Nur Bengisu Çam; Christianah Jemiyo; Brett A. McGregor; Arzucan Özgür; Yongqun He; Junguk Hur (CoRR, 2025)