Computational Identification of De-Centric Genetic Regulatory Relationships from Functional Genomic Data. - Zongliang Yue; Ping Wan; Zhan Xie; Jake Y. Chen (ISBRA, 2014)

SLDR: a computational technique to identify novel genetic regulatory relationships. - Zongliang Yue; Ping Wan; Hui Huang 007; Zhan Xie; Jake Yue Chen (BMC Bioinform., 2014)

PAGER: constructing PAGs and new PAG-PAG relationships for network biology. - Zongliang Yue; Madhura M. Kshirsagar; Thanh Nguyen 005; Chayaporn Suphavilai; Michael T. Neylon; Liugen Zhu; Timothy Ratliff; Jake Yue Chen (Bioinform., 2015)

DMAP: a connectivity map database to enable identification of novel drug repositioning candidates. - Hui Huang 007; Thanh Nguyen 005; Sara Ibrahim; Sandeep Shantharam; Zongliang Yue; Jake Y. Chen (BMC Bioinform., 2015)

Towards constructing "Super Gene Sets" regulatory networks. - Jake Y. Chen; Zongliang Yue; Michael T. Neylon; Thanh Nguyen 005; Nafisa Bulsara; Itika Arora; Timothy Ratliff (BIBM, 2016)

Repositioning drugs by targeting network modules: a Parkinson's disease case study. - Zongliang Yue; Itika Arora; Eric Y. Zhang; Vincent Laufer; S. Louis Bridges; Jake Y. Chen (BMC Bioinform., 2017)

PAGER 2.0: an update to the pathway, annotated-list and gene-signature electronic repository for Human Network Biology. - Zongliang Yue; Qi Zheng; Michael T. Neylon; Minjae Yoo; Jimin Shin; Zhiying Zhao; Aik Choon Tan; Jake Y. Chen (Nucleic Acids Res., 2018)

"Super Gene Set" Causal Relationship Discovery from Functional Genomics Data. - Zongliang Yue; Michael T. Neylon; Thanh Nguyen 005; Timothy Ratliff; Jake Y. Chen (IEEE ACM Trans. Comput. Biol. Bioinform., 2018)

BEERE: a web server for biomedical entity expansion, ranking and explorations. - Zongliang Yue; Christopher D. Willey; Anita B. Hjelmeland; Jake Y. Chen (Nucleic Acids Res., 2019)

WIPER: Weighted in-Path Edge Ranking for biomolecular association networks. - Zongliang Yue; Thanh Nguyen 005; Eric Zhang; Jianyi Zhang; Jake Y. Chen (Quant. Biol., 2019)

PAGER-CoV-Run: An online interactive analytical platform for COVID-19 functional genomic downstream analysis. - Zongliang Yue; Nishant Batra; Hui-Chen Hsu; John Mountz; Jake Y. Chen (AMIA, 2021)

Statistical Enrichment Analysis of Samples: A General-Purpose Tool to Annotate Metadata Neighborhoods of Biological Samples. - Thanh Nguyen 005; Samuel Bharti; Zongliang Yue; Christopher D. Willey; Jake Y. Chen (Frontiers Big Data, 2021)

Corrigendum: Statistical Enrichment Analysis of Samples: A General-Purpose Tool to Annotate Metadata Neighborhoods of Biological Samples. - Thanh Nguyen 005; Samuel Bharti; Zongliang Yue; Christopher D. Willey; Jake Y. Chen (Frontiers Big Data, 2021)

PAGER-CoV: a comprehensive collection of pathways, annotated gene-lists and gene signatures for coronavirus disease studies. - Zongliang Yue; Eric Zhang; Clark Xu; Sunny Khurana; Nishant Batra; Son Do Hai Dang; James J. Cimino; Jake Y. Chen (Nucleic Acids Res., 2021)

DEMA: a distance-bounded energy-field minimization algorithm to model and layout biomolecular networks with quantitative features. - Zhenyu Weng; Zongliang Yue; Yuesheng Zhu; Jake Yue Chen (Bioinform., 2022)

WINNER: A network biology tool for biomolecular characterization and prioritization. - Thanh Nguyen 005; Zongliang Yue; Radomir Slominski; Robert S. Welner; Jianyi Zhang; Jake Y. Chen (Frontiers Big Data, 2022)

Handwriting Anomalies and Learning Disabilities through Recurrent Neural Networks and Geometric Pattern Analysis. - Vasileios Alevizos; Sabrina Edralin; Akebu Simasiku; Dimitra Malliarou; Antonis Messinis; George A. Papakostas; Clark Xu; Zongliang Yue (CoRR, 2024)

Logarithmic Positional Partition Interval Encoding. - Vasileios Alevizos; Nikitas Gerolimos; Sabrina Edralin; Clark Xu; Akebu Simasiku; Georgios Priniotakis; George A. Papakostas; Zongliang Yue (CoRR, 2024)

Integrating Artificial Open Generative Artificial Intelligence into Software Supply Chain Security. - Vasileios Alevizos; George A. Papakostas; Akebu Simasiku; Dimitra Malliarou; Antonis Messinis; Sabrina Edralin; Clark Xu; Zongliang Yue (CoRR, 2024)

PAGER-scFGA: unveiling cell functions and molecular mechanisms in cell trajectories through single-cell functional genomics analysis. - Fengyuan Huang; Robert S. Welner; Jake Y. Chen; Zongliang Yue (Frontiers Bioinform., 2024)

Systematic Review on Sustainable Design Thinking Through Biomimetic Approach. - Vasileios Alevizos; Nikitas Gerolimos; Sabrina Edralin; Clark Xu; Akebu Simasiku; Georgios Priniotakis; George A. Papakostas; Zongliang Yue (ICAIIC, 2025)

Optimizing Carbon Footprint in ICT through Swarm Intelligence with Algorithmic Complexity. - Vasileios Alevizos; Nikitas Gerolimos; Sabrina Edralin; Clark Xu; Akebu Simasiku; Georgios Priniotakis; George A. Papakostas; Zongliang Yue (CoRR, 2025)

Autonomous Decision-Making Enhancing Natural Disaster Management through Open World Machine Learning: A Systematic Review. - Nikitas Gerolimos; Vasileios Alevizos; Sabrina Edralin; Clark Xu; Georgios Priniotakis; George A. Papakostas; Zongliang Yue (Hum. Centric Intell. Syst., 2025)