A learning-based dual-population optimization algorithm for hybrid seru system scheduling with assembly.

Jie Zheng 0001 University of Pennsylvania, Perelman School of Medicine, Department of Genetics, Philadelphia, PA, USA https://github.com/zhengj2007 https://orcid.org/0000-0002-2999-0103 https://www.wikidata.org/entity/Q90780528 Jie Zheng Jie Zheng 0002 ShanghaiTech University, School of Information Science and Technology, Shanghai, China Nanyang Technological University, School of Computer Engineering, Bioinformatics Research Centre, Singapore A*STAR, Genome Institute of Singapore, Singapore National Institutes of Health, Bethesda, MD, USA University of California Riverside, CA, USA https://orcid.org/0000-0001-6774-9786 https://www.wikidata.org/entity/Q41049421 https://www.researcherid.com/rid/C-1356-2011 https://ieeexplore.ieee.org/author/38238003200 Jie Zheng 0003 郑洁 University of Akron, Department of Chemical and Biomolecular Engineering, OH, USA University of Washington, Seattle, WA, USA http://gozips.uakron.edu/~zhengj/ https://scholar.google.com/citations?user=0popCNUAAAAJ https://orcid.org/0000-0003-1547-3612 https://www.wikidata.org/entity/Q46050359 https://www.researcherid.com/rid/B-5057-2013 Jie Zheng 0004 Tsinghua University, School of Economics and Management, Beijing, China Washington University in Saint Louis, MO, USA https://jzheng.weebly.com/ http://www.sem.tsinghua.edu.cn/en/zhengjie https://orcid.org/0000-0001-9211-2875 https://www.wikidata.org/entity/Q96017450 https://www.researcherid.com/rid/F-9835-2017 https://www.scopus.com/authid/detail.uri?authorId=56532205800 https://d-nb.info/gnd/1070823821 Jie Zheng 0005 Northwest University, School of Information and Technology, Xi'an, China Xidian University, Department of Telecommunications Engineering, Xi'an, China https://orcid.org/0000-0002-4035-8520 https://www.scopus.com/authid/detail.uri?authorId=55676260900 Jie Zheng 0006 University of Bristol, School of Social and Community Medicine, UK MRC Integrative Epidemiology Unit, UK https://orcid.org/0000-0002-6623-6839 https://www.wikidata.org/entity/Q56422689 Jie Zheng 0007 State Key Laboratory of Information Engineering in Surveying, Mapping and Remote Sensing, LIESMARS, Wuhan, China Wuhan University, Collaborative Innovation Center of Geospatial Technology, China Jie Zheng 0008 Tianjin Agricultural University, College of computer and Information Engineering, China https://orcid.org/0000-0001-9777-6371 https://www.wikidata.org/entity/Q130875829 Jie Zheng 0009 Hangzhou Dianzi University, Hangzhou, China Hang Zhou City University, School of Computer and Computing Science, Hangzhou, China https://orcid.org/0009-0002-1253-7297

Yuting Wu Ling Wang 0001 Rui Li 0087 Yuxiang Xu Jie Zheng 0001 A learning-based dual-population optimization algorithm for hybrid seru system scheduling with assembly. 101901 2025 94 Swarm Evol. Comput. https://doi.org/10.1016/j.swevo.2025.101901 db/journals/swevo/swevo94.html#WuWLXZ25 streams/journals/swevo

John Beverley Julie C. Bowker Hollen N. Reischer Rachel A. Mavrovich Regina Hurley Sean Kindya Sam Smith Jie Zheng 0001 Yongqun He Damayanthi Beera William D. Duncan Towards Healthy Aging through Semantic Enrichment. 2025 JOWO https://ceur-ws.org/Vol-4176/phases-2.pdf conf/jowo/2025 db/conf/jowo/jowo2025.html#BeverleyBRMHKSZ25 Finn D. Wilson Matthew Diller Robin McGill Sam Smith Jie Zheng 0001 Clarissa Savluchinske Feio Vieira William D. Duncan John Beverley Yongqun He Modeling of Skills, Abilities, Competences, and Related Dispositions in the Occupation Ontology. 2025 JOWO https://ceur-ws.org/Vol-4176/oss-4.pdf conf/jowo/2025 db/conf/jowo/jowo2025.html#WilsonDMSZVDBH25

Hasin Rehana Jie Zheng 0001 Leo Yeh Benu Bansal Nur Bengisu Çam Christianah Jemiyo Brett A. McGregor Arzucan Özgür Yongqun He Junguk Hur Cancer Vaccine Adjuvant Name Recognition from Biomedical Literature using Large Language Models. 2025 February abs/2502.09659 CoRR https://doi.org/10.48550/arXiv.2502.09659 db/journals/corr/corr2502.html#abs-2502-09659 streams/journals/corr

Anthony Huffman Xumeng Zhang Meghana Lanka Jie Zheng 0001 Anna Maria Masci Yongqun He Ontological representation, modeling, and analysis of parasite vaccines. 4 2024 December 15 J. Biomed. Semant. 1 https://doi.org/10.1186/s13326-024-00307-0 https://www.wikidata.org/entity/Q130691766 db/journals/biomedsem/biomedsem15.html#HuffmanZLZMH24

Jie Zheng 0001 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 Empowering standardization of cancer vaccines through ontology: enhanced modeling and data analysis. 12 2024 December 15 J. Biomed. Semant. 1 https://doi.org/10.1186/s13326-024-00312-3 db/journals/biomedsem/biomedsem15.html#ZhengLMKHAPGHSSLH24

Yuting Wu Ling Wang 0001 Jingfang Chen 0001 Jie Zheng 0001 Zixiao Pan A reinforcement learning driven two-stage evolutionary optimisation for hybrid seru system scheduling with worker transfer. 3952-3971 2024 62 Int. J. Prod. Res. 11 https://doi.org/10.1080/00207543.2023.2252523 db/journals/ijpr/ijpr62.html#WuWCZP24

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 0001 Jie Zheng 0001 Ling Wang 0001 Meituan's Real-Time Intelligent Dispatching Algorithms Build the World's Largest Minute-Level Delivery Network. 84-101 2024 54 INFORMS J. Appl. Anal. 1 https://doi.org/10.1287/inte.2023.0084 db/journals/interfaces/interfaces54.html#LiangLDLLFZRDCZ24

Hasin Rehana Benu Bansal Nur Bengisu Çam Jie Zheng 0001 Yongqun He Arzucan Özgür Junguk Hur Nested Named Entity Recognition using Multilayer BERT-based Model. 197-206 2024 CLEF (Working Notes) https://ceur-ws.org/Vol-3740/paper-18.pdf conf/clef/2024w db/conf/clef/clef2024w.html#RehanaBC0HOH24 Jie Zheng 0001 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 Empowering Standardization of Cancer Vaccines Through Ontology: Enhanced Modeling and Data Analysis. 2024 ICBO https://jbiomedsem.biomedcentral.com/articles/10.1186/s13326-024-00312-3 conf/icbo/2024 db/conf/icbo/icbo2024.html#0001LMKHAPGHSSL24 John Beverley Robin McGill Sam Smith Jie Zheng 0001 Giacomo De Colle Finn D. Wilson Matthew Diller William D. Duncan William R. Hogan Yongqun He Credentials in the Occupation Ontology. 2024 ICBO https://ceur-ws.org/Vol-3939/paper4.pdf conf/icbo/2024 db/conf/icbo/icbo2024.html#BeverleyMSZCWDD24 Mary Czelusniak Emily Tran Fatima Oudeif Jie Zheng 0001 William D. Duncan Alexander D. Diehl Yongqun He CellCards: Development of a Dynamic Ontology-Derived ETL Pipeline for Automatic Cell Information Extraction and Analysis. 2024 ICBO https://ceur-ws.org/Vol-3939/CELLS_paper1.pdf conf/icbo/2024 db/conf/icbo/icbo2024.html#CzelusniakTOZDD24

John Beverley Robin McGill Sam Smith Jie Zheng 0001 Giacomo De Colle Finn D. Wilson Matthew Diller William D. Duncan William R. Hogan Yongqun He Credentials in the Occupation Ontology. 2024 abs/2405.00186 CoRR https://doi.org/10.48550/arXiv.2405.00186 db/journals/corr/corr2405.html#abs-2405-00186

Yuting Wu Ling Wang 0001 Xinying Zhuang Jing-jing Wang Jing-Fang Chen 0001 Jie Zheng 0001 A cooperative coevolutionary algorithm with problem-specific knowledge for energy-efficient scheduling in <i>seru</i> system. 110663 2023 274 Knowl. Based Syst. https://doi.org/10.1016/j.knosys.2023.110663 db/journals/kbs/kbs274.html#Wu0ZW0Z23

Zixiao Pan Ling Wang 0001 Jie Zheng 0001 Jing-Fang Chen 0001 Xing Wang 0015 A Learning-Based Multipopulation Evolutionary Optimization for Flexible Job Shop Scheduling Problem With Finite Transportation Resources. 1590-1603 2023 December 27 IEEE Trans. Evol. Comput. 6 https://doi.org/10.1109/TEVC.2022.3219238 db/journals/tec/tec27.html#PanWZCW23

Xing Wang 0015 Ling Wang 0001 Shengyao Wang Jize Pan Hao Ren Jie Zheng 0001 Recommending-and-Grabbing: A Crowdsourcing-Based Order Allocation Pattern for On-Demand Food Delivery. 838-853 2023 January 24 IEEE Trans. Intell. Transp. Syst. 1 https://doi.org/10.1109/TITS.2022.3209722 db/journals/tits/tits24.html#WangWWPRZ23

Jie Zheng 0001 Ling Wang 0001 Jingfang Chen 0001 Zi-Xiao Pan Donghui Li Yile Liang Xuetao Ding A Predictive-Reactive Optimization Framework With Feedback-Based Knowledge Distillation for On-Demand Food Delivery. 14841-14857 2023 December 24 IEEE Trans. Intell. Transp. Syst. 12 https://doi.org/10.1109/TITS.2023.3296516 db/journals/tits/tits24.html#ZhengWCPLLD23

Jie Zheng 0001 Ling Wang 0001 Li Wang Shengyao Wang Jingfang Chen 0001 Xing Wang 0015 Solving Stochastic Online Food Delivery Problem via Iterated Greedy Algorithm With Decomposition-Based Strategy. 957-969 2023 53 IEEE Trans. Syst. Man Cybern. Syst. 2 https://doi.org/10.1109/TSMC.2022.3189771 db/journals/tsmc/tsmc53.html#ZhengWWWCW23

Anthony Huffman Edison Ong Timothy Brunson Nasim Sanati Jie Zheng 0001 Anna Maria Masci Guanming Wu Yongqun He Ontology-based Representation and Analysis of Conditional Vaccine Immune Responses Using Omics Data. 1-12 2023 ICBO https://ceur-ws.org/Vol-3603/Paper1.pdf conf/icbo/2023 db/conf/icbo/icbo2023.html#HuffmanOBS0MWH23 John Beverley Sam Smith Matthew Diller William D. Duncan Jie Zheng 0001 John W. Judkins William R. Hogan Robin McGill Damion M. Dooley Yongqun He The Occupation Ontology (OccO): Building a Bridge between Global Occupational Standards. 2023 JOWO https://ceur-ws.org/Vol-3637/paper13.pdf conf/jowo/2023 db/conf/jowo/jowo2023.html#BeverleySDD0JHM23

Yongqun He Hong Yu 0014 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 0001 Anna Maria Masci Liwei Wang 0010 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 0001 A comprehensive update on CIDO: the community-based coronavirus infectious disease ontology. 25 2022 13 J. Biomed. Semant. 1 https://doi.org/10.1186/s13326-022-00279-z https://www.wikidata.org/entity/Q123137905 db/journals/biomedsem/biomedsem13.html#HeYHLNBZPWLOWHT22

Jie Zheng 0001 Ling Wang 0001 Jingfang Chen 0001 Xing Wang 0015 Yile Liang Haining Duan Zixuan Li Xuetao Ding Dynamic multi-objective balancing for online food delivery via fuzzy logic system-based supply-demand relationship identification. 108609 2022 172 Comput. Ind. Eng. Part https://doi.org/10.1016/j.cie.2022.108609 db/journals/candie/candie172.html#ZhengWCWLDLD22

Jie Zheng 0001 Ling Wang 0001 Shengyao Wang Jingfang Chen 0001 Xing Wang 0015 Haining Duan Yile Liang Xuetao Ding Modeling stochastic service time for complex on-demand food delivery. 2022 4939-4953 8 Complex Intell. Syst. 6 https://doi.org/10.1007/s40747-022-00719-4 db/journals/comintsys/comintsys8.html#ZhengWWCWDLD22 streams/journals/comintsys

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 0031 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 0001 VEuPathDB: the eukaryotic pathogen, vector and host bioinformatics resource center. 898-911 2022 50 Nucleic Acids Res. D1 https://doi.org/10.1093/nar/gkab929 https://www.wikidata.org/entity/Q112066091 db/journals/nar/nar50.html#AmosABBBBBBBBBC22

Jingfang Chen 0001 Ling Wang 0001 Hao Ren Jize Pan Shengyao Wang Jie Zheng 0001 Xing Wang 0015 An Imitation Learning-Enhanced Iterated Matching Algorithm for On-Demand Food Delivery. 18603-18619 2022 23 IEEE Trans. Intell. Transp. Syst. 10 https://doi.org/10.1109/TITS.2022.3163263 db/journals/tits/tits23.html#ChenWRPWZW22

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 0001 Christian J. Stoeckert Jr. Nicole A. Vasilevsky Ramona L. Walls Jie Zheng 0001 Christopher J. Mungall Bjoern Peters OBO Foundry in 2021: operationalizing open data principles to evaluate ontologies. 2021 2021 Database J. Biol. Databases Curation https://doi.org/10.1093/database/baab069 https://www.wikidata.org/entity/Q112820909 db/journals/biodb/biodb2021.html#JacksonMOVBBCCD21

Randi Vita Jie Zheng 0001 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. Standardization of assay representation in the Ontology for Biomedical Investigations. 2021 2021 Database J. Biol. Databases Curation https://doi.org/10.1093/database/baab040 https://www.wikidata.org/entity/Q112806480 db/journals/biodb/biodb2021.html#VitaZJDOMBSHKBL21

Anthony Huffman Anna Maria Masci Jie Zheng 0001 Nasim Sanati Timothy Brunson Guanming Wu Yongqun He CIDO ontology updates and secondary analysis of host responses to COVID-19 infection based on ImmPort reports and literature. 18 2021 12 J. Biomed. Semant. 1 https://doi.org/10.1186/s13326-021-00250-4 https://www.wikidata.org/entity/Q112684067 db/journals/biomedsem/biomedsem12.html#HuffmanMZSBWH21

Xing Wang 0015 Ling Wang 0001 Shengyao Wang Yang Yu 0005 Jingfang Chen 0001 Jie Zheng 0001 Solving Online Food Delivery Problem via an Effective Hybrid Algorithm with Intelligent Batching Strategy. 340-354 2021 ICIC (2) https://doi.org/10.1007/978-3-030-84529-2_29 conf/icic/2021-2 db/conf/icic/icic2021-2.html#WangWWYCZ21

Jie Zheng 0001 Ling Wang 0001 Jing-jing Wang A cooperative coevolution algorithm for multi-objective fuzzy distributed hybrid flow shop. 105536 2020 194 Knowl. Based Syst. https://doi.org/10.1016/j.knosys.2020.105536 https://www.wikidata.org/entity/Q126328737 db/journals/kbs/kbs194.html#ZhengWW20

Behrouz Shamsaei Szymon Chojnacki Marcin Pilarczyk Mehdi Fazel-Najafabadi Wen Niu Chuming Chen Karen Ross Andrea Matlock Jeremy Muhlich Somchai Chutipongtanate Jie Zheng 0001 John Turner Dusica Vidovic Jake Jaffe Michael J. MacCoss Cathy Wu 0001 Ajay Pillai Avi Ma'ayan Stephan C. Schürer Michal Kouril Mario Medvedovic Jarek Meller piNET: a versatile web platform for downstream analysis and visualization of proteomics data. W85-W93 2020 48 Nucleic Acids Res. Webserver-Issue https://doi.org/10.1093/nar/gkaa436 https://www.wikidata.org/entity/Q95940650 db/journals/nar/nar48.html#ShamsaeiCPFNCRM20

Jing-Fang Chen 0001 Shengyao Wang Ling Wang 0001 Jie Zheng 0001 Ying Cha Jinghua Hao Renqing He Zhizhao Sun A Hybrid Differential Evolution Algorithm for the Online Meal Delivery Problem. 1-8 2020 CEC https://doi.org/10.1109/CEC48606.2020.9185792 conf/cec/2020 db/conf/cec/cec2020.html#ChenWWZCHHS20 Jie Zheng 0001 Shengyao Wang Ling Wang 0001 Jingfang Chen 0001 Li Wang Jinghua Hao Renqing He Zhizhao Sun A Two-stage Algorithm for Fuzzy Online Order Dispatching Problem. 1-8 2020 CEC https://doi.org/10.1109/CEC48606.2020.9185858 conf/cec/2020 db/conf/cec/cec2020.html#ZhengWWCWHHS20

Yongqun He Haihe Wang Jie Zheng 0001 Daniel P. Beiting Anna Maria Masci Hong Yu 0014 Kaiyong Liu Jianmin Wu Jeffrey L. Curtis Barry Smith 0001 Alexander V. Alekseyenko Jihad S. Obeid OHMI: the ontology of host-microbiome interactions. 25 2019 10 J. Biomed. Semant. 1 https://doi.org/10.1186/s13326-019-0217-1 https://www.wikidata.org/entity/Q92332757 db/journals/biomedsem/biomedsem10.html#HeWZBMYLWCSAO19

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 0001 Sirarat Sarntivijai Stephan C. Schürer K. Sue O'Shea Alexander D. Diehl OSCI: standardized stem cell ontology representation and use cases for stem cell investigation. 237-247 2019 20-S BMC Bioinform. 5 https://doi.org/10.1186/s12859-019-2723-7 https://www.wikidata.org/entity/Q63846546 db/journals/bmcbi/bmcbi20S.html#HeDCHIOWTSSZSSO19

Edison Ong Peter Sun Kimberly Berke Jie Zheng 0001 Guanming Wu Yongqun He VIO: ontology classification and study of vaccine responses given various experimental and analytical conditions. 704 2019 20-S BMC Bioinform. 21 https://doi.org/10.1186/s12859-019-3194-6 https://www.wikidata.org/entity/Q92182176 db/journals/bmcbi/bmcbi20S.html#OngSBZWH19

Jie Zheng 0001 John Judkins Christian J. Stoeckert Jr. OWLmaker: An Application for Generating OWL Files from Tabular Text. 1-3 2019 ICBO https://ceur-ws.org/Vol-2931/ICBO_2019_paper_54.pdf conf/icbo/2019 db/conf/icbo/icbo2019.html#0001JS19 Sarah Bost Niina Eklund Kaisa Silander Jie Zheng 0001 Christian J. Stoeckert Jr. Mathias Brochhausen Mapping Data Annotated with the Minimum Information About BIobank data Sharing (MIABIS) 2.0 to the Ontology for Biobanking (OBIB). 1-2 2019 ICBO https://ceur-ws.org/Vol-2931/ICBO_2019_paper_52.pdf conf/icbo/2019 db/conf/icbo/icbo2019.html#BostES0SB19 Yongqun He Edison Ong Jennifer Schaub Frederick Dowd John F. O'Toole Anastasios Siapos Christian G. Reich Sarah Seager Ling Wang 0001 Hong Yu 0014 Jie Zheng 0001 Christian J. Stoeckert Jr. Xiaolin Yang Sheng Yang Becky Steck Christopher Park Laura Barisoni Matthias Kretzler Jonathan Himmelfarb Ravi Iyengar Sean D. Mooney OPMI: the Ontology of Precision Medicine and Investigation and its Support for Clinical Data and Metadata Representation and Analysis. 1-10 2019 ICBO https://ceur-ws.org/Vol-2931/ICBO_2019_paper_34.pdf conf/icbo/2019 db/conf/icbo/icbo2019.html#HeOSDOSRS000SYY19 Yongqun He Jie Zheng 0001 Anna Maria Masci Jihad S. Obeid Alignment of the Ontology of Host-Microbiome Interactions (OHMI) High Level Terms with Existing OBO Ontologies. 1 2019 ICBO https://ceur-ws.org/Vol-2931/ICBO_2019_paper_40.pdf conf/icbo/2019 db/conf/icbo/icbo2019.html#HeZMO19

Yongqun He Zuoshuang Xiang Jie Zheng 0001 Yu Lin James A. Overton Edison Ong The eXtensible ontology development (XOD) principles and tool implementation to support ontology interoperability. 3:1-3:10 2018 9 J. Biomed. Semant. 1 https://doi.org/10.1186/s13326-017-0169-2 https://www.wikidata.org/entity/Q48252153 db/journals/biomedsem/biomedsem9.html#HeXZLOO18

Francislon S. Oliveira John Brestelli Shon Cade Jie Zheng 0001 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 MicrobiomeDB: a systems biology platform for integrating, mining and analyzing microbiome experiments. D684-D691 2018 46 Nucleic Acids Res. Database-Issue https://doi.org/10.1093/nar/gkx1027 https://www.wikidata.org/entity/Q46268135 db/journals/nar/nar46.html#OliveiraBCZIFAK18

Anna Maria Masci Shannon McCall Alessandro Racioppi Helena Judge Ellis Jihad S. Obeid Barry Smith 0001 Christian J. Stoeckert Jr. Jie Zheng 0001 Standardization of the Histopathology Cancer Report: An Ontological Approach. 2018 ICBO https://ceur-ws.org/Vol-2285/ICBO_2018_paper_10.pdf conf/icbo/2018 db/conf/icbo/icbo2018.html#MasciMREO0S018 Edison Ong Yongqun He Jie Zheng 0001 eXtensible Ontology Development (XOD) using Web-based Ontoanimal Tools. 2018 ICBO https://ceur-ws.org/Vol-2285/ICBO_2018_paper_24.pdf conf/icbo/2018 db/conf/icbo/icbo2018.html#OngH018

Edison Ong Zuoshuang Xiang Bin Zhao Yue Liu Yu Lin Jie Zheng 0001 Chris Mungall Mélanie Courtot Alan Ruttenberg Yongqun He Ontobee: A linked ontology data server to support ontology term dereferencing, linkage, query and integration. D347-D352 2017 45 Nucleic Acids Res. Database-Issue https://doi.org/10.1093/nar/gkw918 https://www.wikidata.org/entity/Q27976541 db/journals/nar/nar45.html#OngXZLLZMCRH17

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 0031 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 0001 EuPathDB: the eukaryotic pathogen genomics database resource. D581-D591 2017 45 Nucleic Acids Res. Database-Issue https://doi.org/10.1093/nar/gkw1105 https://www.wikidata.org/entity/Q37556856 db/journals/nar/nar45.html#AurrecoecheaBBB17

Jie Zheng 0001 Huan Li Qingzhi Liu Yongqun He The Ontology of Biological and Clinical Statistics (OBCS)-based statistical method standardization and meta-analysis of host responses to yellow fever vaccines. 291-301 2017 5 Quant. Biol. 4 https://doi.org/10.1007/s40484-017-0122-5 https://www.wikidata.org/entity/Q112831219 db/journals/quanbio/quanbio5.html#ZhengLLH17

Yu Lin Jie Zheng 0001 Yongqun He VICO: Ontology-based representation and integrative analysis of Vaccination Informed Consent forms. 20 2016 7 J. Biomed. Semant. https://doi.org/10.1186/s13326-016-0062-4 https://www.wikidata.org/entity/Q36815274 db/journals/biomedsem/biomedsem7.html#LinZH16

Mathias Brochhausen Jie Zheng 0001 David L. Birtwell Heather Williams Anna Maria Masci Helena Judge Ellis Christian J. Stoeckert Jr. OBIB-a novel ontology for biobanking. 23 2016 7 J. Biomed. Semant. https://doi.org/10.1186/s13326-016-0068-y https://www.wikidata.org/entity/Q36866845 db/journals/biomedsem/biomedsem7.html#BrochhausenZBWM16

Jie Zheng 0001 Marcelline R. Harris Anna Maria Masci Yu Lin Alfred O. Hero III Barry Smith 0001 Yongqun He The Ontology of Biological and Clinical Statistics (OBCS) for standardized and reproducible statistical analysis. 53 2016 7 J. Biomed. Semant. https://doi.org/10.1186/s13326-016-0100-2 https://www.wikidata.org/entity/Q28595743 db/journals/biomedsem/biomedsem7.html#ZhengHMLHSH16

Yongqun He Zhaohui S. Qin Jie Zheng 0001 EGO: A Biomedical Ontology for Integrative Epigenome Representation and Analysis. 2016 ICBO/BioCreative https://ceur-ws.org/Vol-1747/IP04_ICBO2016.pdf conf/icbo/2016 db/conf/icbo/icbo2016.html#HeQZ16 Edison Ong Zuoshuang Xiang Jie Zheng 0001 Barry Smith 0001 Yongqun He Ontobull and BFOConvert: Web-based Programs to Support Automatic Ontology Conversion. 2016 ICBO/BioCreative https://ceur-ws.org/Vol-1747/D201_ICBO2016.pdf conf/icbo/2016 db/conf/icbo/icbo2016.html#OngXZSH16 Jie Zheng 0001 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 Malaria Study Data Integration and Information Retrieval Based on OBO Foundry Ontologies. 2016 ICBO/BioCreative https://ceur-ws.org/Vol-1747/IT503_ICBO2016.pdf conf/icbo/2016 db/conf/icbo/icbo2016.html#ZhengCBRSJAGDSC16

Philippe Rocca-Serra Ramona L. Walls Jacob Parnell Rachel Gallery Jie Zheng 0001 Susanna-Assunta Sansone Alejandra N. González-Beltrán Modeling a microbial community and biodiversity assay with OBO Foundry ontologies: the interoperability gains of a modular approach. 2015 2015 Database J. Biol. Databases Curation https://doi.org/10.1093/database/bau132 http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4309925/ https://www.wikidata.org/entity/Q28651313 db/journals/biodb/biodb2015.html#Rocca-SerraWPGZ15

Zuoshuang Xiang Jie Zheng 0001 Yu Lin Yongqun He Ontorat: automatic generation of new ontology terms, annotations, and axioms based on ontology design patterns. 4 2015 6 J. Biomed. Semant. https://doi.org/10.1186/2041-1480-6-4 https://www.wikidata.org/entity/Q35185517 db/journals/biomedsem/biomedsem6.html#XiangZLH15

Yongqun He Jie Zheng 0001 Yu Lin Ontoanimal tools for reusing ontologies, generating and editing ontology terms, and dereferencing ontology terms. 2015 ICBO https://ceur-ws.org/Vol-1515/poster3.pdf conf/icbo/2015 db/conf/icbo/icbo2015.html#HeZL15 Yongqun He Jie Zheng 0001 Yu Lin Ontorat: Automatic generation and editing of ontology terms. 2015 ICBO https://ceur-ws.org/Vol-1515/demo2.pdf conf/icbo/2015 db/conf/icbo/icbo2015.html#HeZL15a

Jie Zheng 0001 Zuoshuang Xiang Christian J. Stoeckert Jr. Yongqun He Ontodog: a web-based ontology community view generation tool. 1340-1342 2014 30 Bioinform. 9 https://doi.org/10.1093/bioinformatics/btu008 https://www.wikidata.org/entity/Q37720705 db/journals/bioinformatics/bioinformatics30.html#ZhengXSH14

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 0001 Christian J. Stoeckert Jr. Bjoern Peters Christopher J. Mungall Thomas E. Carey David J. States Brian D. Athey Yongqun He CLO: The cell line ontology. 37 2014 5 J. Biomed. Semant. https://doi.org/10.1186/2041-1480-5-37 https://www.wikidata.org/entity/Q28650204 db/journals/biomedsem/biomedsem5.html#SarntivijaiLXMDVSPMPLTSMNBHZSPMCSAH14

Philippe Rocca-Serra Ramona L. Walls Jacob Parnell Rachel Gallery Jie Zheng 0001 Susanna-Assunta Sansone Alejandra N. González-Beltrán Modeling a Microbial Community and Biodiversity Assay with OBI and PCO OBO Foundry Ontologies: the Interoperability Gains of a Modular Approach. 64 2014 ICBO https://ceur-ws.org/Vol-1327/icbo2014_paper_20.pdf conf/icbo/2014 db/conf/icbo/icbo2014.html#Rocca-SerraWPGZ14 Jie Zheng 0001 Marcelline R. Harris Anna Maria Masci Yu Lin Alfred O. Hero III Barry Smith 0001 Yongqun He OBCS: The Ontology of Biological and Clinical Statistics. 65 2014 ICBO https://ceur-ws.org/Vol-1327/icbo2014_paper_21.pdf conf/icbo/2014 db/conf/icbo/icbo2014.html#ZhengHMLHSH14 Jie Zheng 0001 Elisabetta Manduchi Christian J. Stoeckert Jr. Development of an Application Ontology for Beta Cell Genomics Based On the Ontology for Biomedical Investigations. 62-67 2013 ICBO https://ceur-ws.org/Vol-1060/icbo2013_submission_31.pdf conf/icbo/2013 db/conf/icbo/icbo2013.html#ZhengMS13 Mélanie Courtot Jie Zheng 0001 Christian J. Stoeckert Jr. Ryan Remy Brinkman Alan Ruttenberg Diagnostic criteria and clinical guidelines standardization to automate case classification. 101-104 2013 ICBO https://ceur-ws.org/Vol-1060/icbo2013_submission_57.pdf conf/icbo/2013 db/conf/icbo/icbo2013.html#CourtotZSBR13 Matthew H. Brush Jie Zheng 0001 Yongqun He Sirarat Sarntivijai Bjoern Peters Alexander D. Diehl Christian J. Stoeckert Jr. Melissa A. Haendel Alignment of Cultured Cell Modeling Across OBO Foundry Ontologies: Key Outcomes, Insights. 120 2013 ICBO https://ceur-ws.org/Vol-1060/icbo2013_submission_68.pdf conf/icbo/2013 db/conf/icbo/icbo2013.html#BrushZHSPDSH13

Priti Parikh Jie Zheng 0001 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 The Ontology for Parasite Lifecycle (OPL): towards a consistent vocabulary of lifecycle stages in parasitic organisms. 5 2012 3 J. Biomed. Semant. https://doi.org/10.1186/2041-1480-3-5 https://www.wikidata.org/entity/Q36368053 db/journals/biomedsem/biomedsem3.html#ParikhZLSLTPSCBS12

Alok Dhamanaskar Michael E. Cotterell Jie Zheng 0001 Jessica C. Kissinger Christian J. Stoeckert Jr. John A. Miller 0001 Suggestions for Galaxy Workflow Design Using Semantically Annotated Services. 29-42 2012 FOIS https://doi.org/10.3233/978-1-61499-084-0-29 conf/fois/2012 db/conf/fois/fois2012.html#DhamanaskarCZKSM12 Jie Zheng 0001 Zuoshuang Xiang Christian J. Stoeckert Jr. Yongqun He Ontodog: A Web-based Ontology Community View Generator. 2012 ICBO https://ceur-ws.org/Vol-897/poster_13.pdf conf/icbo/2012 db/conf/icbo/icbo2012.html#ZhengXSH12

Jie Zheng 0001 Julia Stoyanovich Elisabetta Manduchi Junmin Liu Christian J. Stoeckert Jr. AnnotCompute: annotation-based exploration and meta-analysis of genomics experiments. 2011 2011 Database J. Biol. Databases Curation https://doi.org/10.1093/database/bar045 http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3244265/ https://www.wikidata.org/entity/Q35628293 db/journals/biodb/biodb2011.html#ZhengSMLS11

Chaitanya Guttula Alok Dhamanaskar Rui Wang John A. Miller 0001 Jessica C. Kissinger Jie Zheng 0001 Christian J. Stoeckert Jr. Enriching the Ontology for Biomedical Investigations (OBI) to Improve its Suitability for Web Service Annotations. 2011 ICBO https://ceur-ws.org/Vol-833/paper37.pdf conf/icbo/2011 db/conf/icbo/icbo2011.html#GuttulaDWMKZS11 Jie Zheng 0001 Omar S. Harb Christian J. Stoeckert Jr. Ontology Driven Data Collection for EuPathDB. 2011 ICBO https://ceur-ws.org/Vol-833/paper13.pdf conf/icbo/2011 db/conf/icbo/icbo2011.html#ZhengHS11

James Malone Ele Holloway Tomasz Adamusiak Misha Kapushesky Jie Zheng 0001 Nikolay Kolesnikov Anna Zhukova Alvis Brazma Helen E. Parkinson Modeling sample variables with an Experimental Factor Ontology. 1112-1118 2010 26 Bioinform. 8 https://doi.org/10.1093/bioinformatics/btq099 https://www.wikidata.org/entity/Q24596875 db/journals/bioinformatics/bioinformatics26.html#MaloneHAKZKZBP10

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 0001 et al. Modeling biomedical experimental processes with OBI. S7 2010 1 J. Biomed. Semant. S-1 http://www.jbiomedsem.com/content/1/S1/S7 db/journals/biomedsem/biomedsem1S.html#BrinkmanCDFHLMPPRRSSSTZa10

Tomasz Adamusiak et al. Alexander V. Alekseyenko Beatrice Amos Sivaram Arabandi Emmanuel Arinaitwe Eliyas Asfaw Brian D. Athey Cristina Aurrecoechea James P. Balhoff Benu Bansal Matthieu Barba Laura Barisoni Ana Barreto Evelina Y. Basenko Wojciech Bazant Damayanthi Beera Daniel P. Beiting Robert Belnap Kimberly Berke Matthew Berriman Daniel C. Berrios John Beverley David L. Birtwell Ann S. Blevins Ulrike Böhme Sarah Bost Julie C. Bowker Alvis Brazma John Brestelli Ryan Remy Brinkman Mathias Brochhausen Brian P. Brunk Timothy Brunson Matthew H. Brush Gully A. P. C. BurnsGully Burns Pier Luigi Buttigieg Mark J. Caddick Jashon Cade Shon Cade Danielle Callan Nur Bengisu Çam Lahcen I. Campbell Seth Carbon Thomas E. Carey Jane M. Carlton Gabriel Carrasco-Escobar Mark Carrington Ying Cha Chuming Chen Jingfang Chen 0001Jing-Fang Chen 0001 Luonan Chen Marcus C. Chibucos Szymon Chojnacki Mikkel B. Christensen George K. Christophides Somchai Chutipongtanate Giacomo De Colle Daniel J. Cooper Michael E. Cotterell Mélanie Courtot Kathryn Crouch Jeffrey L. Curtis Mary Czelusniak Kristina Davis Jeremy D. DeBarry Dirk Derom Roshan Desai Alok Dhamanaskar Alexander D. Diehl Matthew Diller Xuetao Ding Ryan Doherty Damion M. Dooley Grant Dorsey Frederick Dowd Jinyang Du Haining Duan Yikun Duan William D. Duncan Michael Dunn Niina Eklund Helena Judge Ellis Dave Falke Mehdi Fazel-Najafabadi Irene Y. Feng Jie Feng Yipeng Feng Gabriel R. Fernandes Steve Fischer Steve Fisher Paul Flicek Jennifer Fostel Brett Fox Bindu Gajria Rachel Gallery Dionicia Gamboa Michelle G. Giglio Gloria I. Giraldo-Calderón Alejandra N. González-Beltrán Bryan Greenhouse Jinjing Guo Chaitanya Guttula Melissa A. Haendel Jens Hansen Jinghua Hao Omar S. Harb Elizabeth Harper Marcelline R. Harris Nomi L. Harris Renqing He Virginia He Yongqun He Mark Heiges Alfred O. Hero III Christiane Hertz-Fowler Mark J. Hickman Jonathan Himmelfarb Robert Hoehndorf William R. Hogan Ele Holloway Connor Howington Sufen Hu Hsin-Hui Huang Philip Huang Anthony Huffman Jay C. Humphrey Junguk Hur Regina Hurley John Iodice Ravi Iyengar Rebecca C. Jackson Jake Jaffe Sagar B. Jain San James Christianah Jemiyo Andrew R. Jones John JudkinsJohn W. Judkins Hayleigh Kahn Misha Kapushesky Sarah A. Kelly Sean Kindya Jessica C. Kissinger Nikolay Kolesnikov Michal Kouril Matthias Kretzler Dae Kun Kwon Kristopher Lamoureux Meghana Lanka Cris Lawrence Daniel Lawson Suzanna LewisSuzanna E. Lewis Donghui Li Huan Li Rui Li 0087 Wei Li 0031 Xingxian Li Zixuan Li Yile Liang Hongsen Liao Kallie Lies Aisyah Yu Lin Asiyah Yu Lin Yu Lin Hongfang Liu Junmin Liu Kaiyong Liu Qingzhi Liu Yingtong Liu Yue Liu Disha Lodha Flora J. Logan-Klumpler Jamie Long Phillip LordPhillip W. Lord Christos Louis Haocheng Luo Avi Ma'ayan Robert M. MacCallum Michael J. MacCoss Paula Maguina-Mercedes James Malone Elisabetta Manduchi Anna Maria Masci Gareth Maslen Hiroshi Masuya Nicolas Matentzoglu Andrea Matlock Rachel A. Mavrovich Shannon McCall Mary Ann McDowell Robin McGill Hande McGintyHande Küçük-McGinty Brett A. McGregor Mario Medvedovic Terrence F. Meehan Jaroslaw MellerJarek Meller Eric Merrell John A. Miller 0001 Mark A. Miller Sean D. Mooney Jeremy Muhlich Chris MungallChristopher J. Mungall Jarek NabrzyskiJaroslaw Nabrzyski Yukio Nakamura Darren A. Natale Wen Niu Jihad S. Obeid Francislon S. Oliveira Gilbert S. Omenn Edison Ong K. Sue O'Shea David Osumi-Sutherland John F. O'Toole Fatima Oudeif James A. Overton Arzucan Özgür Jize Pan Yuanyi Pan Zi-Xiao PanZixiao Pan Chao Pang Priti Parikh Christopher Park Helen E. Parkinson Jacob Parnell Zoë May Pendlington Su-Yuan PengSuyuan Peng Yehoshua Perl Björn PetersBjoern Peters Marcin Pilarczyk Ajay Pillai Deborah F. Pinney Anna V. Protasio Jane A. Pulman Zhaohui S. Qin Alessandro Racioppi Hasin Rehana Christian G. Reich Hollen N. Reischer Hao Ren Philippe Rocca-Serra Paola Roncaglia David S. Roos Karen E. RossKaren Ross Samuel S. C. Rund Alan Ruttenberg Satya Sanket Sahoo Kaoru Saijo Nasim Sanati Susanna-Assunta Sansone Sirarat Sarntivijai Jennifer Schaub Richard H. Scheuermann Lynn M. Schriml Stephanie wever Schulman Stephan C. Schürer Sarah Seager Andrey I. Seleznev Lucas M. Serra Easheta Shah Zalan Shah Behrouz Shamsaei Achchuthan Shanmugasundram Amit P. Sheth Anastasios Siapos Kaisa Silander Fatima Silva-Franco Vasily Sitnik Chenqi Situ Fatima Zohra Smaili Barry Smith 0001 Sam Smith Larisa N. Soldatova Justin Song Drew Spruill David Starns David J. States Becky Steck Sascha Steinbiss Christian J. Stoeckert Jr. Julia Stoyanovich Steven Sullivan Peter Sun Yang Sun Zhizhao Sun Terue Takatsuki Yi-Wei Tang Yujia Tian Omar Tibi Sheena Shah Tomko Pantelis Topalis Emily Tran Long Tran Jessica A. Turner John Turner Nicole A. Vasilevsky Uma VempatiUma D. Vempati Dusica Vidovic Clarissa Savluchinske Feio Vieira Joseph Vinetz Randi Vita Kendal Walker Ramona L. Walls Haihe Wang Haiming Wang Jingjing WangJing-jing Wang Li Wang Ling Wang 0001 Liwei Wang 0010 Rui Wang Shengyao Wang Xing Wang 0015 Yang Wang Zhigang Wang Susanne Warrenfeltz Robert Wieck Paul A. Wilkinson Heather Williams Finn D. Wilson Cathy H. WuCathy Wu 0001 Guanming Wu Jianmin Wu Yuting Wu Zuoshuang Xiang Jiangan Xie Ke Xing Lin Xu Yuxiang Xu Sheng Yang Xiaolin Yang Xianwei Ye Leo Yeh Feifan Yin Hong Yu 0014 Yang Yu 0005 Luxia Zhang Xumeng Zhang Bin Zhao Jiuxia Zhao Ling Zheng Yueqiang Zheng Qingte Zhou Xinying Zhuang Anna Zhukova