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Publication search results
found 142 matches
- 2024
- Anthony Huffman, Xumeng Zhang, Meghana Lanka, Jie Zheng, Anna Maria Masci, Yongqun He:
Ontological representation, modeling, and analysis of parasite vaccines. J. Biomed. Semant. 15(1): 4 (2024) - Jianfu Li, Yiming Li, Yuanyi Pan, Jinjing Guo, Zenan Sun, Fang Li, Yongqun He, Cui Tao:
Mapping vaccine names in clinical trials to vaccine ontology using cascaded fine-tuned domain-specific language models. J. Biomed. Semant. 15(1): 14 (2024) - 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:
Empowering standardization of cancer vaccines through ontology: enhanced modeling and data analysis. J. Biomed. Semant. 15(1): 12 (2024) - Hasin Rehana, Benu Bansal, Nur Bengisu Çam, Jie Zheng, Yongqun He, Arzucan Özgür, Junguk Hur:
Nested Named Entity Recognition using Multilayer BERT-based Model. CLEF (Working Notes) 2024: 197-206 - John Beverley, Robin McGill, Sam Smith, Jie Zheng, Giacomo De Colle, Finn Wilson, Matthew Diller, William D. Duncan, William R. Hogan, Yongqun He:
Credentials in the Occupation Ontology. CoRR abs/2405.00186 (2024) - Michael Rabenberg, Carter Benson, Federico Donato, Yongqun He, Anthony Huffman, Shane Babcock, John Beverley:
Grounding Realizable Entities. CoRR abs/2405.00197 (2024) - 2023
- Sijia Liu, Andrew Wen, Liwei Wang, Huan He, Sunyang Fu, Robert T. Miller, Andrew E. Williams, Daniel R. Harris, Ramakanth Kavuluru, Mei Liu, Noor Abu-El-Rub, Dalton Schutte, Rui Zhang, Masoud Rouhizadeh, John D. Osborne, Yongqun He, Umit Topaloglu, Stephanie S. Hong, Joel H. Saltz, Thomas Schaffter, Emily R. Pfaff, Christopher G. Chute, Tim Duong, Melissa A. Haendel, Rafael Fuentes, Peter Szolovits, Hua Xu, Hongfang Liu:
An open natural language processing (NLP) framework for EHR-based clinical research: a case demonstration using the National COVID Cohort Collaborative (N3C). J. Am. Medical Informatics Assoc. 30(12): 2036-2040 (2023) - Ling Zheng, Yehoshua Perl, Yongqun He:
Big knowledge visualization of the COVID-19 CIDO ontology evolution. BMC Medical Informatics Decis. Mak. 23(1): 88 (2023) - Anthony Huffman, Edison Ong, Timothy Brunson, Nasim Sanati, Jie Zheng, Anna Maria Masci, Guanming Wu, Yongqun He:
Ontology-based Representation and Analysis of Conditional Vaccine Immune Responses Using Omics Data. ICBO 2023: 1-12 - John Beverley, Sam Smith, Matthew Diller, William D. Duncan, Jie Zheng, John W. Judkins, William R. Hogan, Robin McGill, Damion M. Dooley, Yongqun He:
The Occupation Ontology (OccO): Building a Bridge between Global Occupational Standards. JOWO 2023 - Hasin Rehana, Nur Bengisu Çam, Mert Basmaci, Yongqun He, Arzucan Özgür, Junguk Hur:
Evaluation of GPT and BERT-based models on identifying protein-protein interactions in biomedical text. CoRR abs/2303.17728 (2023) - 2022
- Anthony Huffman, Edison Ong, Junguk Hur, Adonis D'mello, Hervé Tettelin, Yongqun He:
COVID-19 vaccine design using reverse and structural vaccinology, ontology-based literature mining and machine learning. Briefings Bioinform. 23(4) (2022) - 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:
A comprehensive update on CIDO: the community-based coronavirus infectious disease ontology. J. Biomed. Semant. 13(1): 25 (2022) - Warren Manuel, Rashmie Abeysinghe, Yongqun He, Cui Tao, Licong Cui:
Identification of missing hierarchical relations in the vaccine ontology using acquired term pairs. J. Biomed. Semant. 13(1): 22 (2022) - Nor Raihan Mohammad Shabani, Che Muhammad Khairul Hisyam Ismail, Amy Amilda Anthony, Chiuan Herng Leow, Candy Chuah, Abu Bakar Abdul Majeed, Norazmi Mohd Nor, Yongqun He, Kirnpal Kaur Banga Singh, Chiuan Yee Leow:
Mass spectrometry-based immunopeptidomics and computational vaccinology strategies for the identification of universal Shigella immunogenic candidates. Comput. Biol. Medicine 148: 105900 (2022) - Yongqun He, Samuel Smith, Damion M. Dooley:
Foundational Development of an Occupation Ontology. JOWO 2022 - 2021
- 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.:
Standardization of assay representation in the Ontology for Biomedical Investigations. Database J. Biol. Databases Curation 2021 (2021) - Anthony Huffman, Anna Maria Masci, Jie Zheng, 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. J. Biomed. Semant. 12(1): 18 (2021) - Ling Wan, Justin Song, Virginia He, Jennifer Roman, Grace Whah, Suyuan Peng, Luxia Zhang, Yongqun He:
Development of the International Classification of Diseases Ontology (ICDO) and its application for COVID-19 diagnostic data analysis. BMC Bioinform. 22-S(6): 508 (2021) - Ling Zheng, Yehoshua Perl, Yongqun He, Christopher Ochs, James Geller, Hao Liu, Vipina Kuttichi Keloth:
Visual comprehension and orientation into the COVID-19 CIDO ontology. J. Biomed. Informatics 120: 103861 (2021) - Sebastian Köhler, Michael A. Gargano, Nicolas Matentzoglu, Leigh Carmody, David Lewis-Smith, Nicole A. Vasilevsky, Daniel Danis, Ganna Balagura, Gareth Baynam, Amy M. Brower, Tiffany J. Callahan, Christopher G. Chute, Johanna L. Est, Peter D. Galer, Shiva Ganesan, Matthias Griese, Matthias Haimel, Julia Pazmandi, Marc Hanauer, Nomi L. Harris, Michael Hartnett, Maximilian Hastreiter, Fabian Hauck, Yongqun He, Tim Jeske, Hugh Kearney, Gerhard Kindle, Christoph Klein, Katrin Knoflach, Roland Krause, David Lagorce, Julie A. McMurry, Jillian A. Miller, Monica C. Munoz-Torres, Rebecca L. Peters, Christina K. Rapp, Ana Rath, Shahmir A. Rind, Avi Z. Rosenberg, Michael M. Segal, Markus G. Seidel, Damian Smedley, Tomer Talmy, Yarlalu Thomas, Samuel A. Wiafe, Julie Xian, Zafer Yüksel, Ingo Helbig, Christopher J. Mungall, Melissa A. Haendel, Peter N. Robinson:
The Human Phenotype Ontology in 2021. Nucleic Acids Res. 49(Database-Issue): D1207-D1217 (2021) - Edison Ong, Michael F. Cooke, Anthony Huffman, Zuoshuang Xiang, Mei U. Wong, Haihe Wang, Meenakshi Seetharaman, Ninotchka Valdez, Yongqun He:
Vaxign2: the second generation of the first Web-based vaccine design program using reverse vaccinology and machine learning. Nucleic Acids Res. 49(Webserver-Issue): 671-678 (2021) - Guirui Huang, Suyuan Peng, Luxia Zhang, Yongqun He:
Identification and Ontology Term Enrichment Analysis of Genes Associated with COVID-19 and Acute Kidney Disease. ICBO 2021: 110-115 - Asiyah Yu Lin, Yuki Yamagata, William D. Duncan, Leigh C. Carmody, Tatsuya Kushida, Hiroshi Masuya, John Beverley, Biswanath Dutta, Michael DeBellis, Zoë May Pendlington, Paola Roncaglia, Yongqun He:
A Community Effort for COVID-19 Ontology Harmonization. ICBO 2021: 122-127 - Yingtong Liu, Wenjun Ju, Becky Steck, Sanjay Jain, Matthias Kretzler, Yongqun He:
Ontology-based Modeling, Representation, and Analysis of Biomarkers in Healthy and Disease Kidney Tissue. ICBO 2021: 70-76 - Easheta Shah, Roshan Desai, Suyuan Peng, Luxia Zhang, Yongqun He:
Ontology Modeling and Analysis of COVID-19-associated Acute Kidney Injury and Its Underlying Molecular Mechanisms. ICBO 2021: 116-121 - Sijia Liu, Andrew Wen, Liwei Wang, Huan He, Sunyang Fu, Robert T. Miller, Andrew E. Williams, Daniel R. Harris, Ramakanth Kavuluru, Mei Liu, Noor Abu-El-Rub, Rui Zhang, John D. Osborne, Masoud Rouhizadeh, Yongqun He, Emily R. Pfaff, Christopher G. Chute, Tim Duong, Melissa A. Haendel, Rafael Fuentes, Peter Szolovits, Hua Xu, Hongfang Liu:
An Open Natural Language Processing Development Framework for EHR-based Clinical Research: A case demonstration using the National COVID Cohort Collaborative (N3C). CoRR abs/2110.10780 (2021) - 2020
- Edison Ong, Haihe Wang, Mei U. Wong, Meenakshi Seetharaman, Ninotchka Valdez, Yongqun He:
Vaxign-ML: supervised machine learning reverse vaccinology model for improved prediction of bacterial protective antigens. Bioinform. 36(10): 3185-3191 (2020) - Fang Li, Jingcheng Du, Yongqun He, Hsing-yi Song, Mohcine Madkour, Guozheng Rao, Yang Xiang, Yi Luo, Henry W. Chen, Sijia Liu, Liwei Wang, Hongfang Liu, Hua Xu, Cui Tao:
Time event ontology (TEO): to support semantic representation and reasoning of complex temporal relations of clinical events. J. Am. Medical Informatics Assoc. 27(7): 1046-1056 (2020) - Ying Yang, Michael Wybrow, Yuan-Fang Li, Tobias Czauderna, Yongqun He:
OntoPlot: A Novel Visualisation for Non-hierarchical Associations in Large Ontologies. IEEE Trans. Vis. Comput. Graph. 26(1): 1140-1150 (2020)
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