Jie Zheng

According to our database, Jie Zheng authored at least 64 papers between 2010 and 2024.

Collaborative distances:

• Dijkstra number of four.
• Erdős number of three.

2024

Empowering standardization of cancer vaccines through ontology: enhanced modeling and data analysis.

Jie Zheng, 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, Yongqun He

J. Biomed. Semant., December, 2024

Ontological representation, modeling, and analysis of parasite vaccines.

Anthony Huffman, Xumeng Zhang, Meghana Lanka, Jie Zheng, Anna Maria Masci, Yongqun He

J. Biomed. Semant., December, 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, Jinghua Hao, Ke Xing, Feifan Yin, Renqing He, Yang Sun, Yueqiang Zheng, Yipeng Feng, Zhizhao Sun, Jingfang Chen, Jie Zheng, Ling Wang

INFORMS J. Appl. Anal., 2024

A reinforcement learning driven two-stage evolutionary optimisation for hybrid seru system scheduling with worker transfer.

Yuting Wu, Ling Wang, Jingfang Chen, Jie Zheng, Zixiao Pan

Int. J. Prod. Res., 2024

Credentials in the Occupation Ontology.

John Beverley, Robin McGill, Sam Smith, Jie Zheng, Giacomo De Colle, Finn Wilson, Matthew Diller, William D. Duncan, William R. Hogan, Yongqun He

CoRR, 2024

Nested Named Entity Recognition using Multilayer BERT-based Model.

Hasin Rehana, Benu Bansal, Nur Bengisu Çam, Jie Zheng, Yongqun He, Arzucan Özgür, Junguk Hur

Proceedings of the Working Notes of the Conference and Labs of the Evaluation Forum (CLEF 2024), 2024

2023

A Predictive-Reactive Optimization Framework With Feedback-Based Knowledge Distillation for On-Demand Food Delivery.

Jie Zheng, Ling Wang, Jingfang Chen, Zi-Xiao Pan, Donghui Li, Yile Liang, Xuetao Ding

IEEE Trans. Intell. Transp. Syst., December, 2023

A Learning-Based Multipopulation Evolutionary Optimization for Flexible Job Shop Scheduling Problem With Finite Transportation Resources.

Zixiao Pan, Ling Wang, Jie Zheng, Jing-Fang Chen, Xing Wang

IEEE Trans. Evol. Comput., December, 2023

Recommending-and-Grabbing: A Crowdsourcing-Based Order Allocation Pattern for On-Demand Food Delivery.

Xing Wang, Ling Wang, Shengyao Wang, Jize Pan, Hao Ren, Jie Zheng

IEEE Trans. Intell. Transp. Syst., January, 2023

Solving Stochastic Online Food Delivery Problem via Iterated Greedy Algorithm With Decomposition-Based Strategy.

Jie Zheng, Ling Wang, Li Wang, Shengyao Wang, Jingfang Chen, Xing Wang

IEEE Trans. Syst. Man Cybern. Syst., 2023

A cooperative coevolutionary algorithm with problem-specific knowledge for energy-efficient scheduling in <i>seru</i> system.

Yuting Wu, Ling Wang, Xinying Zhuang, Jing-jing Wang, Jing-Fang Chen, Jie Zheng

Knowl. Based Syst., 2023

The Occupation Ontology (OccO): Building a Bridge between Global Occupational Standards.

John Beverley, Sam Smith, Matthew Diller, William D. Duncan, Jie Zheng, John W. Judkins, William R. Hogan, Robin McGill, Damion M. Dooley, Yongqun He

Proceedings of the Joint Ontology Workshops 2023 Episode IX: The Quebec Summer of Ontology co-located with the 13th International Conference on Formal Ontology in Information Systems (FOIS 2023), 2023

Ontology-based Representation and Analysis of Conditional Vaccine Immune Responses Using Omics Data.

Anthony Huffman, Edison Ong, Timothy Brunson, Nasim Sanati, Jie Zheng, Anna Maria Masci, Guanming Wu, Yongqun He

Proceedings of the International Conference on Biomedical Ontologies 2023 together with the Workshop on Ontologies for Infectious and Immune-Mediated Disease Data Science (OIIDDS 2023) and the FAIR Ontology Harmonization and TRUST Data Interoperability Workshop (FOHTI 2023), Brasília, Brazil, August 28, 2023

2022

An Imitation Learning-Enhanced Iterated Matching Algorithm for On-Demand Food Delivery.

Jingfang Chen, Ling Wang, Hao Ren, Jize Pan, Shengyao Wang, Jie Zheng, Xing Wang

IEEE Trans. Intell. Transp. Syst., 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, Danielle Callan, Lahcen I. Campbell, Mikkel B. Christensen, George K. Christophides, Kathryn Crouch, Kristina Davis, Jeremy D. DeBarry, Ryan Doherty, Yikun Duan, Michael Dunn, Dave Falke, Steve Fisher, Paul Flicek, Brett Fox, Bindu Gajria, Gloria I. Giraldo-Calderón, Omar S. Harb, Elizabeth Harper, Christiane Hertz-Fowler, Mark J. Hickman, Connor Howington, Sufen Hu, Jay C. Humphrey, John Iodice, Andrew R. Jones, John Judkins, Sarah A. Kelly, Jessica C. Kissinger, Dae Kun Kwon, Kristopher Lamoureux, Daniel Lawson, Wei Li, Kallie Lies, Disha Lodha, Jamie Long, Robert M. MacCallum, Gareth Maslen, Mary Ann McDowell, Jaroslaw Nabrzyski, David S. Roos, Samuel S. C. Rund, Stephanie wever Schulman, Achchuthan Shanmugasundram, Vasily Sitnik, Drew Spruill, David Starns, Christian J. Stoeckert Jr., Sheena Shah Tomko, Haiming Wang, Susanne Warrenfeltz, Robert Wieck, Paul A. Wilkinson, Lin Xu, Jie Zheng

Nucleic Acids Res., 2022

Dynamic multi-objective balancing for online food delivery via fuzzy logic system-based supply-demand relationship identification.

Jie Zheng, Ling Wang, Jingfang Chen, Xing Wang, Yile Liang, Haining Duan, Zixuan Li, Xuetao Ding

Comput. Ind. Eng., 2022

A comprehensive update on CIDO: the community-based coronavirus infectious disease ontology.

Yongqun He, Hong Yu, Anthony Huffman, Asiyah Yu Lin, Darren A. Natale, John Beverley, Ling Zheng, Yehoshua Perl, Zhigang Wang, Yingtong Liu, Edison Ong, Yang Wang, Philip Huang, Long Tran, Jinyang Du, Zalan Shah, Easheta Shah, Roshan Desai, Hsin-Hui Huang, Yujia Tian, Eric Merrell, William D. Duncan, Sivaram Arabandi, Lynn M. Schriml, Jie Zheng, Anna Maria Masci, Liwei Wang, Hongfang Liu, Fatima Zohra Smaili, Robert Hoehndorf, Zoë May Pendlington, Paola Roncaglia, Xianwei Ye, Jiangan Xie, Yi-Wei Tang, Xiaolin Yang, Suyuan Peng, Luxia Zhang, Luonan Chen, Junguk Hur, Gilbert S. Omenn, Brian D. Athey, Barry Smith

J. Biomed. Semant., 2022

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, Nasim Sanati, Timothy Brunson, Guanming Wu, Yongqun He

J. Biomed. Semant., 2021

Standardization of assay representation in the Ontology for Biomedical Investigations.

Randi Vita, Jie Zheng, 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, Sagar B. Jain, Marcus C. Chibucos, John Judkins, Michelle G. Giglio, Irene Y. Feng, Gully Burns, Matthew H. Brush, Bjoern Peters, Christian J. Stoeckert Jr.

Database J. Biol. Databases Curation, 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, Melissa A. Haendel, Suzanna E. Lewis, Darren A. Natale, David Osumi-Sutherland, Alan Ruttenberg, Lynn M. Schriml, Barry Smith, Christian J. Stoeckert Jr., Nicole A. Vasilevsky, Ramona L. Walls, Jie Zheng, Christopher J. Mungall, Bjoern Peters

Database J. Biol. Databases Curation, 2021

Solving Online Food Delivery Problem via an Effective Hybrid Algorithm with Intelligent Batching Strategy.

Xing Wang, Ling Wang, Shengyao Wang, Yang Yu, Jingfang Chen, Jie Zheng

Proceedings of the Intelligent Computing Theories and Application, 2021

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, John Turner, Dusica Vidovic, Jake Jaffe, Michael J. MacCoss, Cathy Wu, Ajay Pillai, Avi Ma'ayan, Stephan C. Schürer, Michal Kouril, Mario Medvedovic, Jarek Meller

Nucleic Acids Res., 2020

A cooperative coevolution algorithm for multi-objective fuzzy distributed hybrid flow shop.

Jie Zheng, Ling Wang, Jing-jing Wang

Knowl. Based Syst., 2020

A Two-stage Algorithm for Fuzzy Online Order Dispatching Problem.

Jie Zheng, Shengyao Wang, Ling Wang, Jingfang Chen, Li Wang, Jinghua Hao, Renqing He, Zhizhao Sun

Proceedings of the IEEE Congress on Evolutionary Computation, 2020

A Hybrid Differential Evolution Algorithm for the Online Meal Delivery Problem.

Jing-Fang Chen, Shengyao Wang, Ling Wang, Jie Zheng, Ying Cha, Jinghua Hao, Renqing He, Zhizhao Sun

Proceedings of the IEEE Congress on Evolutionary Computation, 2020

2019

VIO: ontology classification and study of vaccine responses given various experimental and analytical conditions.

Edison Ong, Peter Sun, Kimberly Berke, Jie Zheng, Guanming Wu, Yongqun He

BMC Bioinform., 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, Sirarat Sarntivijai, Stephan C. Schürer, K. Sue O'Shea, Alexander D. Diehl

BMC Bioinform., 2019

OHMI: the ontology of host-microbiome interactions.

Yongqun He, Haihe Wang, Jie Zheng, Daniel P. Beiting, Anna Maria Masci, Hong Yu, Kaiyong Liu, Jianmin Wu, Jeffrey L. Curtis, Barry Smith, Alexander V. Alekseyenko, Jihad S. Obeid

J. Biomed. Semant., 2019

Alignment of the Ontology of Host-Microbiome Interactions (OHMI) High Level Terms with Existing OBO Ontologies.

Yongqun He, Jie Zheng, Anna Maria Masci, Jihad S. Obeid

Proceedings of the 10th International Conference on Biomedical Ontology (ICBO 2019), Buffalo, New York, USA, July 30, 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, Hong Yu, Jie Zheng, Christian J. Stoeckert Jr., Xiaolin Yang, Sheng Yang, Becky Steck, Christopher Park, Laura Barisoni, Matthias Kretzler, Jonathan Himmelfarb, Ravi Iyengar, Sean D. Mooney

Proceedings of the 10th International Conference on Biomedical Ontology (ICBO 2019), Buffalo, New York, USA, July 30, 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, Christian J. Stoeckert Jr., Mathias Brochhausen

Proceedings of the 10th International Conference on Biomedical Ontology (ICBO 2019), Buffalo, New York, USA, July 30, 2019

OWLmaker: An Application for Generating OWL Files from Tabular Text.

Jie Zheng, John Judkins, Christian J. Stoeckert Jr.

Proceedings of the 10th International Conference on Biomedical Ontology (ICBO 2019), Buffalo, New York, USA, July 30, 2019

2018

MicrobiomeDB: a systems biology platform for integrating, mining and analyzing microbiome experiments.

Francislon S. Oliveira, John Brestelli, Shon Cade, Jie Zheng, John Iodice, Steve Fischer, Cristina Aurrecoechea, Jessica C. Kissinger, Brian P. Brunk, Christian J. Stoeckert Jr., Gabriel R. Fernandes, David S. Roos, Daniel P. Beiting

Nucleic Acids Res., 2018

The eXtensible ontology development (XOD) principles and tool implementation to support ontology interoperability.

Yongqun He, Zuoshuang Xiang, Jie Zheng, Yu Lin, James A. Overton, Edison Ong

J. Biomed. Semant., 2018

eXtensible Ontology Development (XOD) using Web-based Ontoanimal Tools.

Edison Ong, Yongqun He, Jie Zheng

Proceedings of the 9th International Conference on Biological Ontology (ICBO 2018), 2018

Standardization of the Histopathology Cancer Report: An Ontological Approach.

Anna Maria Masci, Shannon McCall, Alessandro Racioppi, Helena Judge Ellis, Jihad S. Obeid, Barry Smith, Christian J. Stoeckert Jr., Jie Zheng

Proceedings of the 9th International Conference on Biological Ontology (ICBO 2018), 2018

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, Huan Li, Qingzhi Liu, Yongqun He

Quant. Biol., 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, Chris Mungall, Mélanie Courtot, Alan Ruttenberg, Yongqun He

Nucleic Acids Res., 2017

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, Mark Heiges, Christiane Hertz-Fowler, Sufen Hu, John Iodice, Jessica C. Kissinger, Cris Lawrence, Wei Li, Deborah F. Pinney, Jane A. Pulman, David S. Roos, Achchuthan Shanmugasundram, Fatima Silva-Franco, Sascha Steinbiss, Christian J. Stoeckert Jr., Drew Spruill, Haiming Wang, Susanne Warrenfeltz, Jie Zheng

Nucleic Acids Res., 2017

2016

The Ontology of Biological and Clinical Statistics (OBCS) for standardized and reproducible statistical analysis.

Jie Zheng, Marcelline R. Harris, Anna Maria Masci, Yu Lin, Alfred O. Hero III, Barry Smith, Yongqun He

J. Biomed. Semant., 2016

VICO: Ontology-based representation and integrative analysis of Vaccination Informed Consent forms.

Yu Lin, Jie Zheng, Yongqun He

J. Biomed. Semant., 2016

OBIB-a novel ontology for biobanking.

Mathias Brochhausen, Jie Zheng, David L. Birtwell, Heather Williams, Anna Maria Masci, Helena Judge Ellis, Christian J. Stoeckert Jr.

J. Biomed. Semant., 2016

Malaria Study Data Integration and Information Retrieval Based on OBO Foundry Ontologies.

Jie Zheng, 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, Dionicia Gamboa, Paula Maguina-Mercedes, Joseph Vinetz

Proceedings of the Joint International Conference on Biological Ontology and BioCreative, 2016

Ontobull and BFOConvert: Web-based Programs to Support Automatic Ontology Conversion.

Edison Ong, Zuoshuang Xiang, Jie Zheng, Barry Smith, Yongqun He

Proceedings of the Joint International Conference on Biological Ontology and BioCreative, 2016

EGO: A Biomedical Ontology for Integrative Epigenome Representation and Analysis.

Yongqun He, Zhaohui S. Qin, Jie Zheng

Proceedings of the Joint International Conference on Biological Ontology and BioCreative, 2016

2015

Ontorat: automatic generation of new ontology terms, annotations, and axioms based on ontology design patterns.

Zuoshuang Xiang, Jie Zheng, Yu Lin, Yongqun He

J. Biomed. Semant., 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, Susanna-Assunta Sansone, Alejandra N. González-Beltrán

Database J. Biol. Databases Curation, 2015

Ontorat: Automatic generation and editing of ontology terms.

Yongqun He, Jie Zheng, Yu Lin

Proceedings of the International Conference on Biomedical Ontology, 2015

Ontoanimal tools for reusing ontologies, generating and editing ontology terms, and dereferencing ontology terms.

Yongqun He, Jie Zheng, Yu Lin

Proceedings of the International Conference on Biomedical Ontology, 2015

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, Kaoru Saijo, Hiroshi Masuya, Yukio Nakamura, Matthew H. Brush, Melissa A. Haendel, Jie Zheng, Christian J. Stoeckert Jr., Bjoern Peters, Christopher J. Mungall, Thomas E. Carey, David J. States, Brian D. Athey, Yongqun He

J. Biomed. Semant., 2014

Ontodog: a web-based ontology community view generation tool.

Jie Zheng, Zuoshuang Xiang, Christian J. Stoeckert Jr., Yongqun He

Bioinform., 2014

OBCS: The Ontology of Biological and Clinical Statistics.

Jie Zheng, Marcelline R. Harris, Anna Maria Masci, Yu Lin, Alfred O. Hero III, Barry Smith, Yongqun He

Proceedings of the 5th International Conference on Biomedical Ontology, 2014

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, Susanna-Assunta Sansone, Alejandra N. González-Beltrán

Proceedings of the 5th International Conference on Biomedical Ontology, 2014

2013

Development of an Application Ontology for Beta Cell Genomics Based On the Ontology for Biomedical Investigations.

Jie Zheng, Elisabetta Manduchi, Christian J. Stoeckert Jr.

Proceedings of the 4th International Conference on Biomedical Ontology, 2013

Diagnostic criteria and clinical guidelines standardization to automate case classification.

Mélanie Courtot, Jie Zheng, Christian J. Stoeckert Jr., Ryan Remy Brinkman, Alan Ruttenberg

Proceedings of the 4th International Conference on Biomedical Ontology, 2013

Alignment of Cultured Cell Modeling Across OBO Foundry Ontologies: Key Outcomes, Insights.

Matthew H. Brush, Jie Zheng, Yongqun He, Sirarat Sarntivijai, Bjoern Peters, Alexander D. Diehl, Christian J. Stoeckert Jr., Melissa A. Haendel

Proceedings of the 4th International Conference on Biomedical Ontology, 2013

2012

The Ontology for Parasite Lifecycle (OPL): towards a consistent vocabulary of lifecycle stages in parasitic organisms.

Priti Parikh, Jie Zheng, 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

Ontodog: A Web-based Ontology Community View Generator.

Jie Zheng, Zuoshuang Xiang, Christian J. Stoeckert Jr., Yongqun He

Proceedings of the 3rd International Conference on Biomedical Ontology (ICBO 2012), 2012

Suggestions for Galaxy Workflow Design Using Semantically Annotated Services.

Alok Dhamanaskar, Michael E. Cotterell, Jie Zheng, Jessica C. Kissinger, Christian J. Stoeckert Jr., John A. Miller

Proceedings of the Formal Ontology in Information Systems, 2012

2011

AnnotCompute: annotation-based exploration and meta-analysis of genomics experiments.

Jie Zheng, Julia Stoyanovich, Elisabetta Manduchi, Junmin Liu, Christian J. Stoeckert Jr.

Database J. Biol. Databases Curation, 2011

Ontology Driven Data Collection for EuPathDB.

Jie Zheng, Omar S. Harb, Christian J. Stoeckert Jr.

Proceedings of the 2nd International Conference on Biomedical Ontology, 2011

Enriching the Ontology for Biomedical Investigations (OBI) to Improve its Suitability for Web Service Annotations.

Chaitanya Guttula, Alok Dhamanaskar, Rui Wang, John A. Miller, Jessica C. Kissinger, Jie Zheng, Christian J. Stoeckert Jr.

Proceedings of the 2nd International Conference on Biomedical Ontology, 2011

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, Larisa N. Soldatova, Christian J. Stoeckert Jr., Jessica A. Turner, Jie Zheng, et al.

J. Biomed. Semant., 2010

Modeling sample variables with an Experimental Factor Ontology.

James Malone, Ele Holloway, Tomasz Adamusiak, Misha Kapushesky, Jie Zheng, Nikolay Kolesnikov, Anna Zhukova, Alvis Brazma, Helen E. Parkinson

Bioinform., 2010