Author
University of MichiganORCID 0000-0002-2999-0103Unclaimed ORCID profile · follow to get notified of new preprints
10 papers
Recent·Most cited
Yongqun Oliver He, Anthony Huffman, Jie Zheng, Anna Maria Masci, Yu Lin, Barry Smith
The paper uses Vaccine Ontology to model immune biomarkers, profiles, and responses, enhancing classification and analysis of vaccine-induced immunity.
Journal of Biomedical Semantics · Jun 27, 2026Peer-reviewedImmunology
Jie Zheng, Yu Lin, Anthony Huffman, Anna Maria Masci, Rebecca Racz, Guanming Wu, Kallan Roan, Edison Ong, Sirarat Sarntivijai, Jie Hu, Eliyas K. Asfaw, Hayleigh Kahn, Xingxian Li, Xumeng Zhang, Joshua Monickaraj, , Yongqun Oliver He
The paper introduces the Vaccine Ontology (VO), a standardized framework for representing vaccines and related data, enhancing data integration and AI research.
Scientific Data · Apr 30, 2026Peer-reviewedBioinformatics
Jie Zheng, Elisabetta Manduchi, Christian J. Stoeckert
The paper describes the development of a beta cell genomics application ontology (BCGO) based on the Ontology for Biomedical Investigations, validated through data annotation, queries, and automated classification.
bioRxiv · Aug 18, 2025 · PreprintBioinformatics
Feng-Yu Yeh, Matthew Asato, Jie Zheng, Yongqun Oliver He
This paper develops VaxKG, a vaccine knowledge graph integrating VIOLIN and VO, enabling complex queries and LLM-powered chat systems for vaccine information.
bioRxiv · Jul 15, 2025 · PreprintBioinformatics
Yuanyi Pan, Warren Manuel, Rashmie Abeysinghe, Jie Zheng, Alexander Davydov, Qi Yang, Yu Lin, Licong Cui, Yongqun Oliver He
The paper maps CVX vaccine codes to the Vaccine Ontology using semi-automated and manual methods, achieving full coverage and improving semantic vaccine classification.
bioRxiv · Jul 15, 2025 · PreprintBioinformatics
Yongqun Oliver He, Laura M. C. Barisoni, Avi Z. Rosenberg, Peter N. Robinson, Alexander D. Diehl, Yichao Chen, Jimmy Phuong, Jens Hansen, Bruce W. Herr, Katy Börner, Nikki Bonevich, Ghida Arnous, Saketh Boddapati, Jie Zheng, Fadhl Alakwaa, , the Kidney Precision Medicine Project
The paper uses ontologies to integrate clinical, pathological, and molecular kidney data for precision medicine analysis.
bioRxiv · Apr 1, 2024 · PreprintBioinformatics
Rebecca Jackson, Nicolas Matentzoglu, James A. Overton, Randi Vita, James P. Balhoff, Pier Luigi Buttigieg, Seth Carbon, Mélanie Courtot, Alexander D. Diehl, Damion Dooley, William D. Duncan, Nomi L. Harris, Melissa Anne Haendel, Suzanna Lewis, Darren A. Natale, , Bjoern Peters
The paper describes how the OBO Foundry formalized its principles into operational rules and implemented automated checks to evaluate ontology compliance, improving interoperability and quality.
Database · Oct 1, 2021Peer-reviewedBioinformatics
Behrouz Shamsaei, Szymon Chojnacki, Marcin Pilarczyk, Mehdi Fazel Najafabadi, Wen Niu, Chuming Chen, Karen E. ROSS, Andrea D. Matlock, Jeremy L. Muhlich, Somchai Chutipongtanate, Jie Zheng, John Turner, Dušica Vidović, Jacob D. Jaffe, Michael J. MacCoss, , Jarek Meller
piNET is a web platform for analyzing and visualizing proteomics data, including PTMs, by connecting them to biological knowledge and LINCS signatures.
Nucleic Acids Research · May 27, 2020Peer-reviewedBioinformatics
Chengfeng Xiao, Danna Hull, Shuang Qiu, Joanna Yeung, Jie Zheng, Taylor Barwell, R. Meldrum Robertson, Laurent Seroude
This study shows that overexpressing hsp70 in Drosophila melanogaster does not extend longevity or stress resistance, except for a reduction in male lifespan with ubiquitous expression.
G3 Genes Genomes Genetics · Oct 17, 2019Peer-reviewedGenetics
Taylor Barwell, Brian DeVeale, Luc Poirier, Jie Zheng, Frederique Seroude, Laurent Seroude
This study constructs and characterizes Tet-off GAL80 transgenes to enable temporal control of GAL4 activity in adult Drosophila, showing age and sex-dependent effects on repression.
PeerJ · Dec 14, 2017Peer-reviewedGenetics