Modeling sample variables with an Experimental Factor Ontology. - James Malone; Ele Holloway; Tomasz Adamusiak; Misha Kapushesky; Jie Zheng 001; Nikolay Kolesnikov; Anna Zhukova; Alvis Brazma; Helen E. Parkinson (Bioinform., 2010)

Modeling biomedical experimental processes with OBI. - Ryan Remy Brinkman; Mélanie Courtot; Dirk Derom; Jennifer Fostel; Yongqun He; Phillip W. Lord; James Malone; Helen E. Parkinson; Björn Peters; Philippe Rocca-Serra; Alan Ruttenberg; Susanna-Assunta Sansone; et al. (J. Biomed. Semant., 2010)

Enriching the Ontology for Biomedical Investigations (OBI) to Improve its Suitability for Web Service Annotations. - Chaitanya Guttula; Alok Dhamanaskar; Rui Wang; John A. Miller 001; Jessica C. Kissinger; Jie Zheng 001; Christian J. Stoeckert Jr. (ICBO, 2011)

Ontology Driven Data Collection for EuPathDB. - Jie Zheng 001; Omar S. Harb; Christian J. Stoeckert Jr. (ICBO, 2011)

AnnotCompute: annotation-based exploration and meta-analysis of genomics experiments. - Jie Zheng 001; Julia Stoyanovich; Elisabetta Manduchi; Junmin Liu; Christian J. Stoeckert Jr. (Database J. Biol. Databases Curation, 2011)

Suggestions for Galaxy Workflow Design Using Semantically Annotated Services. - Alok Dhamanaskar; Michael E. Cotterell; Jie Zheng 001; Jessica C. Kissinger; Christian J. Stoeckert Jr.; John A. Miller 001 (FOIS, 2012)

Ontodog: A Web-based Ontology Community View Generator. - Jie Zheng 001; Zuoshuang Xiang; Christian J. Stoeckert Jr.; Yongqun He (ICBO, 2012)

The Ontology for Parasite Lifecycle (OPL): towards a consistent vocabulary of lifecycle stages in parasitic organisms. - Priti Parikh; Jie Zheng 001; Flora J. Logan-Klumpler; Christian J. Stoeckert Jr.; Christos Louis; Pantelis Topalis; Anna V. Protasio; Amit P. Sheth; Mark Carrington; Matthew Berriman; Satya Sanket Sahoo (J. Biomed. Semant., 2012)

Alignment of Cultured Cell Modeling Across OBO Foundry Ontologies: Key Outcomes, Insights. - Matthew H. Brush; Jie Zheng 001; Yongqun He; Sirarat Sarntivijai; Bjoern Peters; Alexander D. Diehl; Christian J. Stoeckert Jr.; Melissa A. Haendel (ICBO, 2013)

Diagnostic criteria and clinical guidelines standardization to automate case classification. - Mélanie Courtot; Jie Zheng 001; Christian J. Stoeckert Jr.; Ryan Remy Brinkman; Alan Ruttenberg (ICBO, 2013)

Development of an Application Ontology for Beta Cell Genomics Based On the Ontology for Biomedical Investigations. - Jie Zheng 001; Elisabetta Manduchi; Christian J. Stoeckert Jr. (ICBO, 2013)

Modeling a Microbial Community and Biodiversity Assay with OBI and PCO OBO Foundry Ontologies: the Interoperability Gains of a Modular Approach. - Philippe Rocca-Serra; Ramona L. Walls; Jacob Parnell; Rachel Gallery; Jie Zheng 001; Susanna-Assunta Sansone; Alejandra N. González-Beltrán (ICBO, 2014)

OBCS: The Ontology of Biological and Clinical Statistics. - Jie Zheng 001; Marcelline R. Harris; Anna Maria Masci; Yu Lin; Alfred O. Hero III; Barry Smith 001; Yongqun He (ICBO, 2014)

Ontodog: a web-based ontology community view generation tool. - Jie Zheng 001; Zuoshuang Xiang; Christian J. Stoeckert Jr.; Yongqun He (Bioinform., 2014)

CLO: The cell line ontology. - Sirarat Sarntivijai; Yu Lin; Zuoshuang Xiang; Terrence F. Meehan; Alexander D. Diehl; Uma D. Vempati; Stephan C. Schürer; Chao Pang; James Malone; Helen E. Parkinson; Yue Liu; Terue Takatsuki; et al. (J. Biomed. Semant., 2014)

Ontoanimal tools for reusing ontologies, generating and editing ontology terms, and dereferencing ontology terms. - Yongqun He; Jie Zheng 001; Yu Lin (ICBO, 2015)

Ontorat: Automatic generation and editing of ontology terms. - Yongqun He; Jie Zheng 001; Yu Lin (ICBO, 2015)

Modeling a microbial community and biodiversity assay with OBO Foundry ontologies: the interoperability gains of a modular approach. - Philippe Rocca-Serra; Ramona L. Walls; Jacob Parnell; Rachel Gallery; Jie Zheng 001; Susanna-Assunta Sansone; Alejandra N. González-Beltrán (Database J. Biol. Databases Curation, 2015)

Ontorat: automatic generation of new ontology terms, annotations, and axioms based on ontology design patterns. - Zuoshuang Xiang; Jie Zheng 001; Yu Lin; Yongqun He (J. Biomed. Semant., 2015)

EGO: A Biomedical Ontology for Integrative Epigenome Representation and Analysis. - Yongqun He; Zhaohui S. Qin; Jie Zheng 001 (ICBO/BioCreative, 2016)

Ontobull and BFOConvert: Web-based Programs to Support Automatic Ontology Conversion. - Edison Ong; Zuoshuang Xiang; Jie Zheng 001; Barry Smith 001; Yongqun He (ICBO/BioCreative, 2016)

Malaria Study Data Integration and Information Retrieval Based on OBO Foundry Ontologies. - Jie Zheng 001; Jashon Cade; Brian P. Brunk; David S. Roos; Christian J. Stoeckert Jr.; San James; Emmanuel Arinaitwe; Bryan Greenhouse; Grant Dorsey; Steven Sullivan; Jane M. Carlton; Gabriel Carrasco-Escobar; et al. (ICBO/BioCreative, 2016)

OBIB-a novel ontology for biobanking. - Mathias Brochhausen; Jie Zheng 001; David L. Birtwell; Heather Williams; Anna Maria Masci; Helena Judge Ellis; Christian J. Stoeckert Jr. (J. Biomed. Semant., 2016)

VICO: Ontology-based representation and integrative analysis of Vaccination Informed Consent forms. - Yu Lin; Jie Zheng 001; Yongqun He (J. Biomed. Semant., 2016)

The Ontology of Biological and Clinical Statistics (OBCS) for standardized and reproducible statistical analysis. - Jie Zheng 001; Marcelline R. Harris; Anna Maria Masci; Yu Lin; Alfred O. Hero III; Barry Smith 001; Yongqun He (J. Biomed. Semant., 2016)

EuPathDB: the eukaryotic pathogen genomics database resource. - Cristina Aurrecoechea; Ana Barreto; Evelina Y. Basenko; John Brestelli; Brian P. Brunk; Shon Cade; Kathryn Crouch; Ryan Doherty; Dave Falke; Steve Fischer; Bindu Gajria; Omar S. Harb; et al. (Nucleic Acids Res., 2017)

Ontobee: A linked ontology data server to support ontology term dereferencing, linkage, query and integration. - Edison Ong; Zuoshuang Xiang; Bin Zhao; Yue Liu; Yu Lin; Jie Zheng 001; Chris Mungall; Mélanie Courtot; Alan Ruttenberg; Yongqun He (Nucleic Acids Res., 2017)

The Ontology of Biological and Clinical Statistics (OBCS)-based statistical method standardization and meta-analysis of host responses to yellow fever vaccines. - Jie Zheng 001; Huan Li; Qingzhi Liu; Yongqun He (Quant. Biol., 2017)

Standardization of the Histopathology Cancer Report: An Ontological Approach. - Anna Maria Masci; Shannon McCall; Alessandro Racioppi; Helena Judge Ellis; Jihad S. Obeid; Barry Smith 001; Christian J. Stoeckert Jr.; Jie Zheng 001 (ICBO, 2018)

eXtensible Ontology Development (XOD) using Web-based Ontoanimal Tools. - Edison Ong; Yongqun He; Jie Zheng 001 (ICBO, 2018)

The eXtensible ontology development (XOD) principles and tool implementation to support ontology interoperability. - Yongqun He; Zuoshuang Xiang; Jie Zheng 001; Yu Lin; James A. Overton; Edison Ong (J. Biomed. Semant., 2018)

MicrobiomeDB: a systems biology platform for integrating, mining and analyzing microbiome experiments. - Francislon S. Oliveira; John Brestelli; Shon Cade; Jie Zheng 001; John Iodice; Steve Fischer; Cristina Aurrecoechea; Jessica C. Kissinger; Brian P. Brunk; Christian J. Stoeckert Jr.; Gabriel R. Fernandes; David S. Roos; et al. (Nucleic Acids Res., 2018)

OWLmaker: An Application for Generating OWL Files from Tabular Text. - Jie Zheng 001; John Judkins; Christian J. Stoeckert Jr. (ICBO, 2019)

Mapping Data Annotated with the Minimum Information About BIobank data Sharing (MIABIS) 2.0 to the Ontology for Biobanking (OBIB). - Sarah Bost; Niina Eklund; Kaisa Silander; Jie Zheng 001; Christian J. Stoeckert Jr.; Mathias Brochhausen (ICBO, 2019)

OPMI: the Ontology of Precision Medicine and Investigation and its Support for Clinical Data and Metadata Representation and Analysis. - Yongqun He; Edison Ong; Jennifer Schaub; Frederick Dowd; John F. O'Toole; Anastasios Siapos; Christian G. Reich; Sarah Seager; Ling Wang 001; Hong Yu 014; Jie Zheng 001; Christian J. Stoeckert Jr.; et al. (ICBO, 2019)

Alignment of the Ontology of Host-Microbiome Interactions (OHMI) High Level Terms with Existing OBO Ontologies. - Yongqun He; Jie Zheng 001; Anna Maria Masci; Jihad S. Obeid (ICBO, 2019)

OHMI: the ontology of host-microbiome interactions. - Yongqun He; Haihe Wang; Jie Zheng 001; Daniel P. Beiting; Anna Maria Masci; Hong Yu 014; Kaiyong Liu; Jianmin Wu; Jeffrey L. Curtis; Barry Smith 001; Alexander V. Alekseyenko; Jihad S. Obeid (J. Biomed. Semant., 2019)

OSCI: standardized stem cell ontology representation and use cases for stem cell investigation. - Yongqun He; William D. Duncan; Daniel J. Cooper; Jens Hansen; Ravi Iyengar; Edison Ong; Kendal Walker; Omar Tibi; Sam Smith; Lucas M. Serra; Jie Zheng 001; Sirarat Sarntivijai; et al. (BMC Bioinform., 2019)

VIO: ontology classification and study of vaccine responses given various experimental and analytical conditions. - Edison Ong; Peter Sun; Kimberly Berke; Jie Zheng 001; Guanming Wu; Yongqun He (BMC Bioinform., 2019)

A Hybrid Differential Evolution Algorithm for the Online Meal Delivery Problem. - Jing-Fang Chen 001; Shengyao Wang; Ling Wang 001; Jie Zheng 001; Ying Cha; Jinghua Hao; Renqing He; Zhizhao Sun (CEC, 2020)

A Two-stage Algorithm for Fuzzy Online Order Dispatching Problem. - Jie Zheng 001; Shengyao Wang; Ling Wang 001; Jingfang Chen 001; Li Wang; Jinghua Hao; Renqing He; Zhizhao Sun (CEC, 2020)

A cooperative coevolution algorithm for multi-objective fuzzy distributed hybrid flow shop. - Jie Zheng 001; Ling Wang 001; Jing-jing Wang (Knowl. Based Syst., 2020)

piNET: a versatile web platform for downstream analysis and visualization of proteomics data. - Behrouz Shamsaei; Szymon Chojnacki; Marcin Pilarczyk; Mehdi Fazel-Najafabadi; Wen Niu; Chuming Chen; Karen Ross; Andrea Matlock; Jeremy Muhlich; Somchai Chutipongtanate; Jie Zheng 001; John Turner; et al. (Nucleic Acids Res., 2020)

Solving Online Food Delivery Problem via an Effective Hybrid Algorithm with Intelligent Batching Strategy. - Xing Wang 015; Ling Wang 001; Shengyao Wang; Yang Yu 005; Jingfang Chen 001; Jie Zheng 001 (ICIC (2), 2021)

OBO Foundry in 2021: operationalizing open data principles to evaluate ontologies. - Rebecca C. Jackson; Nicolas Matentzoglu; James A. Overton; Randi Vita; James P. Balhoff; Pier Luigi Buttigieg; Seth Carbon; Mélanie Courtot; Alexander D. Diehl; Damion M. Dooley; William D. Duncan; Nomi L. Harris; et al. (Database J. Biol. Databases Curation, 2021)

Standardization of assay representation in the Ontology for Biomedical Investigations. - Randi Vita; Jie Zheng 001; Rebecca C. Jackson; Damion M. Dooley; James A. Overton; Mark A. Miller; Daniel C. Berrios; Richard H. Scheuermann; Yongqun He; Hande Küçük-McGinty; Mathias Brochhausen; Aisyah Yu Lin; et al. (Database J. Biol. Databases Curation, 2021)

CIDO ontology updates and secondary analysis of host responses to COVID-19 infection based on ImmPort reports and literature. - Anthony Huffman; Anna Maria Masci; Jie Zheng 001; Nasim Sanati; Timothy Brunson; Guanming Wu; Yongqun He (J. Biomed. Semant., 2021)

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)

Dynamic multi-objective balancing for online food delivery via fuzzy logic system-based supply-demand relationship identification. - Jie Zheng 001; Ling Wang 001; Jingfang Chen 001; Xing Wang 015; Yile Liang; Haining Duan; Zixuan Li; Xuetao Ding (Comput. Ind. Eng., 2022)

VEuPathDB: the eukaryotic pathogen, vector and host bioinformatics resource center. - Beatrice Amos; Cristina Aurrecoechea; Matthieu Barba; Ana Barreto; Evelina Y. Basenko; Wojciech Bazant; Robert Belnap; Ann S. Blevins; Ulrike Böhme; John Brestelli; Brian P. Brunk; Mark J. Caddick; et al. (Nucleic Acids Res., 2022)

An Imitation Learning-Enhanced Iterated Matching Algorithm for On-Demand Food Delivery. - Jingfang Chen 001; Ling Wang 001; Hao Ren; Jize Pan; Shengyao Wang; Jie Zheng 001; Xing Wang 015 (IEEE Trans. Intell. Transp. Syst., 2022)

Ontology-based Representation and Analysis of Conditional Vaccine Immune Responses Using Omics Data. - Anthony Huffman; Edison Ong; Timothy Brunson; Nasim Sanati; Jie Zheng 001; Anna Maria Masci; Guanming Wu; Yongqun He (ICBO, 2023)

The Occupation Ontology (OccO): Building a Bridge between Global Occupational Standards. - John Beverley; Sam Smith; Matthew Diller; William D. Duncan; Jie Zheng 001; John W. Judkins; William R. Hogan; Robin McGill; Damion M. Dooley; Yongqun He (JOWO, 2023)

A cooperative coevolutionary algorithm with problem-specific knowledge for energy-efficient scheduling in seru system. - Yuting Wu; Ling Wang 001; Xinying Zhuang; Jing-jing Wang; Jing-Fang Chen 001; Jie Zheng 001 (Knowl. Based Syst., 2023)

Solving Stochastic Online Food Delivery Problem via Iterated Greedy Algorithm With Decomposition-Based Strategy. - Jie Zheng 001; Ling Wang 001; Li Wang; Shengyao Wang; Jingfang Chen 001; Xing Wang 015 (IEEE Trans. Syst. Man Cybern. Syst., 2023)

Recommending-and-Grabbing: A Crowdsourcing-Based Order Allocation Pattern for On-Demand Food Delivery. - Xing Wang 015; Ling Wang 001; Shengyao Wang; Jize Pan; Hao Ren; Jie Zheng 001 (IEEE Trans. Intell. Transp. Syst., 2023)

A Learning-Based Multipopulation Evolutionary Optimization for Flexible Job Shop Scheduling Problem With Finite Transportation Resources. - Zixiao Pan; Ling Wang 001; Jie Zheng 001; Jing-Fang Chen 001; Xing Wang 015 (IEEE Trans. Evol. Comput., 2023)

A Predictive-Reactive Optimization Framework With Feedback-Based Knowledge Distillation for On-Demand Food Delivery. - Jie Zheng 001; Ling Wang 001; Jingfang Chen 001; Zi-Xiao Pan; Donghui Li; Yile Liang; Xuetao Ding (IEEE Trans. Intell. Transp. Syst., 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)

Credentials in the Occupation Ontology. - John Beverley; Robin McGill; Sam Smith; Jie Zheng 001; Giacomo De Colle; Finn Wilson; Matthew Diller; William D. Duncan; William R. Hogan; Yongqun He (ICBO, 2024)

CellCards: Development of a Dynamic Ontology-Derived ETL Pipeline for Automatic Cell Information Extraction and Analysis. - Mary Czelusniak; Emily Tran; Fatima Oudeif; Jie Zheng 001; William D. Duncan; Alexander D. Diehl; Yongqun He (ICBO, 2024)

A reinforcement learning driven two-stage evolutionary optimisation for hybrid seru system scheduling with worker transfer. - Yuting Wu; Ling Wang 001; Jingfang Chen 001; Jie Zheng 001; Zixiao Pan (Int. J. Prod. Res., 2024)

Meituan's Real-Time Intelligent Dispatching Algorithms Build the World's Largest Minute-Level Delivery Network. - Yile Liang; Haocheng Luo; Haining Duan; Donghui Li; Hongsen Liao; Jie Feng; Jiuxia Zhao; Hao Ren; Xuetao Ding; Ying Cha; Qingte Zhou; Chenqi Situ; et al. (INFORMS J. Appl. Anal., 2024)

Ontological representation, modeling, and analysis of parasite vaccines. - Anthony Huffman; Xumeng Zhang; Meghana Lanka; Jie Zheng 001; Anna Maria Masci; Yongqun He (J. Biomed. Semant., 2024)

Empowering standardization of cancer vaccines through ontology: enhanced modeling and data analysis. - Jie Zheng 001; Xingxian Li; Anna Maria Masci; Hayleigh Kahn; Anthony Huffman; Eliyas Asfaw; Yuanyi Pan; Jinjing Guo; Virginia He; Justin Song; Andrey I. Seleznev; Asiyah Yu Lin; et al. (J. Biomed. Semant., 2024)

A learning-based dual-population optimization algorithm for hybrid seru system scheduling with assembly. - Yuting Wu; Ling Wang 001; Rui Li 087; Yuxiang Xu; Jie Zheng 001 (Swarm Evol. Comput., 2025)

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)