|
~ 2024 ~
***Journal papers:
Kai Zhang, Yifang Dang, Yiming Li, Cui Tao, Junguk Hur, Yongqun He. Impact of climate change on vaccine responses and inequity. Nature Climate Change. 2024. https://doi.org/10.1038/s41558-024-02192-y.
Yuanyi Pan, Yun Han, Chuan Zhou, Jie Zheng, Lili Zhao, Xianwei Ye, Yongqun He, On Behalf of N3C Consortium (Consortium members: Farrukh M. Koraishy, Christopher G. Chute). Assessing acute kidney injury risk after COVID vaccination and infection in a large cohort study. npj Vaccines. 2024. Nov 8;9(1):213. doi: 10.1038/s41541-024-00964-3. PMID: 39516206. PMCID: PMC11549351
Hasin Rehana, Nur Bengisu Çam, Mert Basmaci, Jie Zheng, Christianah Jemiyo, Yongqun He, Arzucan Özgür, Junguk Hur. Evaluating GPT and BERT models for Protein-Protein interaction identification in biomedical text. Bioinformatics Advances. vbae133, 2024. DOI: https://doi.org/10.1093/bioadv/vbae133.
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, 14 (2024). DOI: 10.1186/s13326-024-00318-x. PMID: 39123237.
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, 12 (2024). PMID: 38890666. PMCID: PMC11186274.
Anthony Huffman*, Xumeng Zhang*, Meghana Lanka, Jie Zheng, Anna Maria Masci, Yongqun He. Ontological representation, modeling, and analysis of parasite vaccines. Journal of Biomedical Semantics. 15, 4 (2024). PMID: 38664818. PMCID: PMC11044459.
Wang Y, Ye M, Zhang F, Freeman ZH, Yu H, Ye X✉, He Y✉. Ontology-based taxonomical analysis of experimentally verified natural and laboratory human coronavirus hosts and its implication for COVID-19 virus origination and transmission. PLoS One. 2024 Jan 22;19(1):e0295541. PMID: 38252647. PMCID: PMC10802970.
Beverley J, Babcock S, Carvalho G, Cowell LG, Duesing S, He Y, Hurley R, Merrell E, Scheuermann RH, Smith B. Coordinating virus research: The Virus Infectious Disease Ontology. PLoS One. 2024 Jan 18;19(1):e0285093. PMID: 38236918. PMCID: PMC10796065.
Asfaw E*, Lin AY*, Huffman A*, Li S*, George M*, Darancou C, Kalter M, Wehbi N, Bartels D, Fleck E, Tran N, Faghihnia D, Berke K, Sutariya R, Reyal F, Tammam Y, Zhao B, Ong E, Xiang Z, He V, Song J, Seleznev AI, Guo J, Pan Y, Zheng J, He Y. CanVaxKB: a web-based cancer vaccine knowledgebase. NAR Cancer. 2024 Jan 9;6(1):zcad060. doi: 10.1093/narcan/zcad060. PMID: 38204924. PMCID: PMC10776203.
Gargano MA, Matentzoglu N, Coleman B, Addo-Lartey EB, Anagnostopoulos AV, Anderton J, Avillach P, Bagley AM, Bakštein E, Balhoff JP, Baynam G, Bello SM, Berk M, Bertram H, Bishop S, Blau H, Bodenstein DF, Botas P, Boztug K, Čady J, Callahan TJ, Cameron R, Carbon SJ, Castellanos F, Caufield JH, Chan LE, Chute CG, Cruz-Rojo J, Dahan-Oliel N, Davids JR, de Dieuleveult M, de Souza V, de Vries BBA, de Vries E, DePaulo JR, Derfalvi B, Dhombres F, Diaz-Byrd C, Dingemans AJM, Donadille B, Duyzend M, Elfeky R, Essaid S, Fabrizzi C, Fico G, Firth HV, Freudenberg-Hua Y, Fullerton JM, Gabriel DL, Gilmour K, Giordano J, Goes FS, Moses RG, Green I, Griese M, Groza T, Gu W, Guthrie J, Gyori B, Hamosh A, Hanauer M, Hanušová K, He YO, Hegde H, Helbig I, Holasová K, Hoyt CT, Huang S, Hurwitz E, Jacobsen JOB, Jiang X, Joseph L, Keramatian K, King B, Knoflach K, Koolen DA, Kraus ML, Kroll C, Kusters M, Ladewig MS, Lagorce D, Lai MC, Lapunzina P, Laraway B, Lewis-Smith D, Li X, Lucano C, Majd M, Marazita ML, Martinez-Glez V, McHenry TH, McInnis MG, McMurry JA, Mihulová M, Millett CE, Mitchell PB, Moslerová V, Narutomi K, Nematollahi S, Nevado J, Nierenberg AA, Čajbiková NN, Nurnberger JI Jr, ... ..., Mungall C, Köhler S, Haendel MA, Robinson PN. The Human Phenotype Ontology in 2024: phenotypes around the world. Nucleic Acids Res. 2024 Jan 5;52(D1):D1333-D1346. doi: 10.1093/nar/gkad1005. PMID: 37953324. PMCID: PMC10767975.
Guo C, Ge E, Yu M, Li C, Lao X, Li S, Glaser J, He Y, Almeida-Silva M, Meng S, Su WC, Zhang J, Lin S, Zhang K. Impact of heat on emergency hospital admissions related to kidney diseases in Texas: Uncovering racial disparities. Sci Total Environ. 2024 Jan 20;909:168377. doi: 10.1016/j.scitotenv.2023.168377. Epub 2023 Nov 11. PMID: 37956847.
*** Preprints:
Yichao Chen, Yuhan Zhang, Yongqun He. Enhancing Vaxign-DL for vaccine candidate prediction with added ESM-generated features. bioRxiv. Posted September 08, 2024. doi: https://doi.org/10.1101/2024.09.04.611295.
Michael Rabenberg, Carter Benson, Federico Donato, Yongqun He, Anthony Huffman, Shane Babcock, John Beverley. Grounding Realizable Entities. arRxiv. Posted April 30, 2024. doi: https://arxiv.org/abs/2405.00197.
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. arRxiv. Posted April 30, 2024. doi: https://arxiv.org/abs/2405.00186.
Yongqun Oliver He, Laura Barisoni, Avi Z Rosenberg, Peter Robinson, Alexander D. Diehl, Yichao Chen, Jimmy P. Phuong, Jens Hansen, Bruce W. Herr II, Katy Borner, Jennifer Schaub, Nikki Bonevich, Ghida Arnous, Saketh Boddapati, Jie Zheng, Fadhl Alakwaa, Pinaki Sarder, William D. Duncan, Chen Liang, M. Todd Valerius, Sanjay Jain, Ravi Iyengar, Jonathan Himmelfarb, Matthias Kretzler, Kidney Precision Medicine Project. Ontology-based modeling, integration, and analysis of heterogeneous clinical, pathological, and molecular kidney data for precision medicine. bioRxiv. Posted April 02, 2024. doi: https://doi.org/10.1101/2024.04.01.587658. PMID: 38617362. PMCID: PMC11014593.
***Book chapter:
Yongqun He, Edison Ong, Anthony Huffman. Bacterial whole-genome determination and applications (Chapter 26); in book: Molecular medical microbiology (Third Edition). Publisher: Springer, New York. Pages 511 - 525, 2024.
~ 2023 ~
***Journal papers:
Wang M, Rousseau B, Qiu K, Huang G, Zhang Y, Su H, Le Bihan-Benjamin C, Khati I, Artz O, Foote MB, Cheng YY, Lee KH, Miao MZ, Sun Y, Bousquet PJ, Hilmi M, Dumas E, Hamy AS, Reyal F, Lin L, Armistead PM, Song W, Vargason A, Arthur JC, Liu Y, Guo J, Zhou X, Nguyen J, He Y, Ting JP, Anselmo AC, Huang L. Killing tumor-associated bacteria with a liposomal antibiotic generates neoantigens that induce anti-tumor immune responses. Nat Biotechnol. 2023 Sep 25. doi: 10.1038/s41587-023-01957-8. PMID: 37749267.
Liu S, Wen A, Wang L, He H, Fu S, Miller R, Williams A, Harris D, Kavuluru R, Liu M, Abu-El-Rub N, Schutte D, Zhang R, Rouhizadeh M, Osborne JD, He Y, Topaloglu U, Hong SS, Saltz JH, Schaffter T, Pfaff E, Chute CG, Duong T, Haendel MA, Fuentes R, Szolovits P, Xu H, Liu H; National COVID Cohort Collaborative (N3C) Natural Language Processing (NLP) Subgroup, National COVID Cohort Collaborative (N3C). An Open Natural Language Processing (NLP) Framework for EHR-based Clinical Research: A Case Demonstration Using the National COVID Cohort Collaborative (N3C). J Am Med Inform Assoc. 2023 Aug 9: ocad134. PMID: 37555837.
Yoo YJ, Wilkins KJ, Alakwaa F, Liu F, Torre-Healy LA, Krichevsky S, Hong SS, Sakhuja A, Potu CK, Saltz JH, Saran R, Zhu RL, Setoguchi S, Kane-Gill SL, Mallipattu SK, He Y, Ellison DH, Byrd JB, Parikh CR, Moffitt RA, Koraishy FM; N3C and RECOVER Consortia. Geographic and Temporal Trends in COVID-Associated Acute Kidney Injury in the National COVID Cohort Collaborative. Clin J Am Soc Nephrol. 2023 Aug 1;18(8):1006-1018. PMID: 37131278.
Ling Zheng, Yehoshua Perl, Yongqun He. Big knowledge visualization of the COVID-19 CIDO ontology evolution.. BMC Med Inform Decis Mak. 2023 May 9;23(Suppl 1):88. doi: 10.1186/s12911-023-02184-6. PMID: 37161560. PMCID: PMC10169115.
Timothy Brunson*, Nasim Sanati*, Anthony Huffman*, Anna Maria Masci, Jie Zheng, Michael F Cooke, Patrick Conley, Yongqun He✉, Guanming Wu✉. VIGET: A web portal for study of vaccine-induced host responses based on Reactome pathways and ImmPort data. Frontiers in Immunology. 2023. 14:1141030. doi: 10.3389/fimmu.2023.1141030.
Yongqun He, Yongqing Li, Cao Y. Chang, Jue Liu. Editorial: Host cellular responses to viruses. Frontiers in Microbiology. 2023. 14:1110197. doi: 10.3389/fmicb.2023.1110197. PMID: 36704612. PMCID: PMC9872098.
***Peer-reviewed Conference papers:
Anthony Huffman, Edison Ong, Tim 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. Proceedings of the International Conference on Biomedical Ontologies 2023 (ICBO 2023), Brasília, Brazil, August 28 - September 1,2023. Page 1-2. https://ceur-ws.org/Vol-3603/Paper1.pdf.
***Preprint papers:
John Beverley, Yongqun He, Shane Babcock, Anthony Huffman. Grounding Realizable Entities in Applied Ontologies. OSF Preprints. December 18, 2023. Preprint. DOI: https://doi.org/10.31219/osf.io/cbqyj.
Yuhan Zhang, Anthony Huffman, Justin Johnson, Yongqun He. Vaxign-DL: A Deep Learning-based Method for Vaccine Design and its Evaluation. bioRxiv. 2023 Dec 1:2023.11.29.569096. doi: 10.1101/2023.11.29.569096. Preprint. PMID: 38076796. PMCID: PMC10705428.
Li J, Li Y, Pan Y, Guo J, Sun Z, Li F, He Y, Tao C. Mapping Vaccine Names in Clinical Trials to Vaccine Ontology using Cascaded Fine-Tuned Domain-Specific Language Models. Res Sq. 2023 Sep 27:rs.3.rs-3362256. doi: 10.21203/rs.3.rs-3362256/v1. Preprint. PMID: 37841880. PMCID: PMC10571639.
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. arXiv. 2023. Posted on March 30, 2023. doi: https://doi.org/10.48550/arXiv.2303.17728.
Yang Wang, Muhui Ye, Fengwei Zhang, Zachary Thomas Freeman, Hong Yu, Xianwei Ye, Yongqun He. Taxonomical and ontological analysis of verified natural and laboratory human coronavirus hosts. bioRxiv. 2023. Posted on February 6, 2023. doi: https://doi.org/10.1101/2023.02.05.527173.
***E-Book:
Editors: Jue Liu, Yongqun Oliver He, Cao Yong chang and Li Yongqing. Research Topic Host Cellular Responses to Viruses, by Frontiers in Microbiology. 2023. [Research Topic Website] [Download E-Book PDF] [Download E-Book EPUB]
~ 2022 ~
***Journal papers:
Hong Yu*, Li Li*, Anthony Huffman*, John Beverley*, Junguk Hur*, Eric Merrell, Hsin-Hui Huang, Yang Wang, Yingtong Liu, Edison Ong, Liang Cheng, Tao Zeng, Jingsong Zhang, Pengpai Li, Zhi-Ping Liu, Zhigang Wang, Xiangyan Zhang, Xianwei Ye, Samuel K Handelman, Jonathan Sexton, Kathryn Eaton, Gerald Arthur Higgins, Gilbert Omenn, Brian Athey, Barry Smith✉, Luonan Chen✉, Yongqun He*, ✉. A New Framework for Host-Pathogen Interaction Research. Frontiers in Immunology. 2022. 13:1066733. doi: 10.3389/fimmu.2022.1066733. PMID: 36591248. PMCID: PMC9797517.
Wenrui Zi, Qiuyue Yang, JunSu, Yongqun He, Jiangan Xie. OAE-based data mining and modeling analysis of adverse events associated with three licensed HPV vaccines. Heliyon.2022 Nov 11;8(11):e11515. PMID: 36411908. PMCID: PMC9674903.
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 Athey, Barry Smith. A Comprehensive Update on CIDO: The Community-based Coronavirus Infectious Disease Ontology. Journal of Biomedical Semantics. 13, Article number: 25 (2022). https://doi.org/10.1186/s13326-022-00279-z. PMID: 36271389. PMCID: PMC9585694.
Warren Manuel, Rashmie Abeysinghe, Yongqun He, Cui Tao, Licong Cui. Identifcation of missing hierarchical relations in the vaccine ontology using acquired term pairs. Journal of Biomedical Semantics. 2022. 13:22. PMID: 35964149. PMCID: PMC9375092.
Mali Salmon-Divon, Yongqun He, David Kornspan, Zezhang Tom Wen. Editorial: Omics approach to study the biology and virulence of microorganisms causing zoonotic diseases. Front. Microbiol. (Sec. Systems Microbiology). 2022. 13:988983. PMID: 35979481. PMCID: PMC9376672.
Nor Raihan Mohammad Shabani, Che Muhammad Khairul Hisyam Ismail, Amy Amilda Anthony, Candy Chuah, Chiuan Herng Leow, 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. Computers in Biology and Medicine. 2022. 148:105900. doi: 10.1016/j.compbiomed.2022.105900. PMID: 35952542.
Wenxin Guo*, Jessica Deguise*, Yujia Tian*, Philip Chi-En Huang*, Rohit Goru*, Qiuyue Yang, Suyuan Peng, Luxia Zhang, Lili Zhao, Jiangan Xie✉, Yongqun He✉. Profiling COVID-19 vaccine adverse events by statistical and ontological analysis of VAERS case reports. Frontiers in Pharmacology. 2022. 13:870599. PMID: 35814246. PMCID: PMC9263450.
Hansen J, Sealfon R, Menon R, Eadon MT, Lake BB, Steck B, Anjani K, Parikh S, Sigdel TK, Zhang G, Velickovic D, Barwinska D, Alexandrov T, Dobi D, Rashmi P, Otto EA, Rivera M, Rose MP, Anderton CR, Shapiro JP, Pamreddy A, Winfree S, Xiong Y, He Y, de Boer IH, Hodgin JB, Barisoni L, Naik AS, Sharma K, Sarwal MM, Zhang K, Himmelfarb J, Rovin B, El-Achkar TM, Laszik Z, He JC, Dagher PC, Valerius MT, Jain S, Satlin LM, Troyanskaya OG, Kretzler M, Iyengar R, Azeloglu EU; Kidney Precision Medicine Project. A reference tissue atlas for the human kidney. Science Advances. 2022 Jun 10;8(23):eabn4965. PMID: 35675394. PMCID: PMC9176741.
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 in Bioinformatics. 2022. bbac190. doi: 10.1093/bib/bbac190. PMID:35649389.
Haihe Wang, Kaibo Zhang, Lin Wu, Qian Qin, Yongqun He. Prediction of pathogenic factors in dysbiotic gut microbiomes of colorectal cancer patients using Reverse Microbiomics. Frontiers in Oncology. 2022. 12:882874. PMID: 35574378. PMCID: PMC9091335. doi: 10.3389/fonc.2022.882874.
Jamie Ngai*, Madison Kalter*, James B. Byrd, Rebecca Racz, Yongqun He. Ontology-based classification and analysis of adverse events associated with the usage of chloroquine and hydroxychloroquine. Frontiers in Pharmacology. 2022. 13:812338. doi: 10.3389/fphar.2022.812338. PMID: 35401219. PMCID: PMC8983871.
Yang Wang, Fengwei Zhang, J. Brian Byrd, Hong Yu, Xianwei Ye✉, Yongqun He✉. Differential COVID-19 symptoms given pandemic locations, time, and comorbidities during the early pandemic. Frontiers in Medicine. 2022. 9:770031. doi: 10.3389/fmed.2022.770031. PMID: 35155491. PMCID: PMC8831795.
Meng Liu, Jialin Liu, Guitian Liu, HuiWang, XiaoliWang, Zixin Deng, Yongqun He✉, Hong-YuOu✉. ICEO, a biological ontology for representing and analyzing bacterial integrative and conjugative elements. Scientific Data. (2022) 9:11 | https://doi.org/10.1038/s41597-021-01112-5. PMID: 35058462. PMCID: PMC8776819.
Philip C. Huang*, Rohit Goru*, Anthony Huffman, Asiyah Yu Lin, Michael F. Cooke, Yongqun He. Cov19VaxKB: A Web-based Integrative COVID-19 Vaccine Knowledge Base. Vaccine: X. Volume 10, April 2022, 100139. PMID: 34981039. PMCID: PMC8716025.
*** Preprints:
Yongqun He. Ontological classification of self-replicating organic structures. OSF Preprints. Pages 1-8. October 6, 2022. doi:10.31219/osf.io/n2zkh.
Masthead, Yoo YJ, Wilkins KJ, Alakwaa F, Liu F, Torre-Healy LA, Krichevsky S, Hong SS, Sakhuja A, Potu CK, Saltz JH, Saran R, Zhu RL, Setoguchi S, Kane-Gill SL, Mallipattu SK, He Y, Ellison DH, Byrd JB, Parikh CR, Moffitt RA, Koraishy FM. COVID-19-associated AKI in hospitalized US patients: incidence, temporal trends, geographical distribution, risk factors and mortality. medRxiv. 2022 Sep 2:2022.09.02.22279398. PMID: 36093355. PMCID: PMC9460976.
*** Peer-reviewed proceeding papers:
Sam Smith , Damion Dooley, and Yongqun He. Foundational Development of an Occupation Ontology. Proceedings of the Joint Ontology Workshops 2022 (JOWO 2022), Jönköping, Sweden, August 15-19, 2022. URL: https://ceur-ws.org/Vol-3249/paper6-OSS.pdf.
***Book chapters:
Yongqun He. Development and applications of interoperable biomedical ontologies for integrative data and knowledge representation and multiscale modeling in systems medicine. In: Bai J.P., Hur J. (eds) Systems Medicine. Methods Mol Biol. 2022. 2486:233-244. doi: 10.1007/978-1-0716-2265-0_12. PMID: 35437726.
Edison Ong, Yongqun He. Vaccine Design by Reverse Vaccinology and Machine Learning. In: Bidmos F., Bossé J., Langford P. (eds) Bacterial Vaccines. Methods in Molecular Biology. 2022, vol 2414, pages 1-16. https://doi.org/10.1007/978-1-0716-1900-1_1. PMID: 34784028.
***Featured Report for He Lab Research:
Kelly Malcom. Computational methods can lead to better vaccines faster. Michigan Medicine, Unviersity of Michigan, August 12, 2022.
~ 2021 ~
***Journal papers:
Börner K, Teichmann SA, Quardokus EM, Gee JC, Brown K, Osumi-Sutherland D, Herr II BW, Bueckle A, Paul H, Haniffa M, Jardine L, Bernard A, Ding S, Miller JA, Lin S, Halushka MK, Boppana A, Longacre TA, Hickey J, Lin Y, Valerius T, He Y, Pryhuber G, Sun X, Jorgensen M, Radtke AJ, Wasserfall C, Ginty F, Ho J, Sunshine J, Beuschel RT, Brusko M, Lee S, Malhotra R, Jain S, Webe G. Anatomical structures, cell types and biomarkers of the Human Reference Atlas. Nature Cell Biology 23, 1117–1128 (2021). https://doi.org/10.1038/s41556-021-00788-6. PMID: 34750582.
Wan L, Song J, He V, Roman J, Whah G, Peng S, Zhang L, He Y. Development of the International Classification of Diseases Ontology (ICDO) and its application for COVID-19 diagnostic data analysis. BMC Bioinformatics. 22, 508 (2021). PMID: 34663204. PMCID: PMC8522253.
Zhu Y, Liu L, Gao B, Liu J, Qiao X, Lian C, He Y. TCDO: A Community-Based Ontology for Integrative Representation and Analysis of Traditional Chinese Drugs and Their Properties. Evidence-Based Complementary and Alternative Medicine, vol. 2021, Article ID 6637810, 15 pages, 2021. PMID: 34603473. PMCID: PMC8483929.
Huffman A, Masci AM, Zheng J, Sanati N, Brunson T, Wu G, He Y. CIDO ontology updates and secondary analysis of host responses to COVID-19 infection based on ImmPort reports and literature. J Biomed Semant 12, 18 (2021). DOI: 10.1186/s13326-021-00250-4. PMID: 34454610. PMCID: PMC8400831. (note: This paper was also presented in the 12th International Conference on Biomedical Ontologies - ICBO-2021 on September 16, 2021.)
Vita R, Zheng J, Jackson R, Dooley D, Overton JA, Miller MA, Berrios DC, Scheuermann RH, He Y, McGinty HK, Brochhausen M, Lin AY, Jain SB, Chibucos MC, Judkins J, Giglio MG, Feng IY, Burns G, Brush MH, Peters B, Stoeckert CJ Jr. Standardization of assay representation in the Ontology for Biomedical Investigations. Database (Oxford). 2021 Jul 9;2021:baab040. PMID: 34244718. PMCID: PMC8271124.
Zheng L, Perl Y, He Y, Ochs C, Geller J, Liu H, Keloth VK. Visual comprehension and orientation into the COVID-19 CIDO ontology. Journal of Biomedical Informatics. 2021 Jul 2:103861. PMID: 34224898. PMCID: PMC8252699.
Zhigang Wang, Yongqun He. Precision omics data integration and analysis with interoperable ontologies and their application for COVID-19 research. Briefings in Functional Genomics. 2021. elab029. Published on 22 June 2021. https://doi.org/10.1093/bfgp/elab029. PMID: 34159360. PMCID: PMC8287950 (available on 2022-06-22)
Jingsong Zhang, Yang Zhang, Jun-Yan Kang, Shuiye Chen, Yongqun He, Benhao Han, Mo-Fang Liu, Lina Lu, Li Li, Zhigang Yi & Luonan Chen. Potential transmission chains of variant B.1.1.7 and co-mutations of SARS-CoV-2. Cell Discov 2021 Jun 15;7(1):44. doi: 10.1038/s41421-021-00282-1. PMID: 34127650. PMCID: PMC8203788.
Wang Z, He Y, Huang J, Yang X. Integrative web-based analysis of omics data for study of drugs against SARS-CoV-2. Sci Rep. 11, 10763 (2021). https://doi.org/10.1038/s41598-021-89578-6. Published: 24 May 2021. PMID: 34031435. PMCID: PMC8144609.
Cheng L, Zhu Z, Wang C, Wang P, He YO, Zhang X. COVID-19 induces lower levels of IL-8, IL-10, and MCP-1 than other acute CRS-inducing diseases. Proc Natl Acad Sci U S A. May 25, 2021, 118 (21), e2102960118. https://doi.org/10.1073/pnas.2102960118. PMID: 33972411. PMCID: PMC8166110.
Ong E, Cooke MF, Huffman A, Xiang Z, Wong MU, Wang H, Seetharaman M, Valdez N, He Y. Vaxign2: the second generation of the first Web-based vaccine design program using reverse vaccinology and machine learning. Nucleic Acid Research. 2021. gkab279. PMID: 34009334. PMCID: PMC8218197
Zhu D, Patabendige HMLW, Tomlinson BR, Wang S, Hussain S, Flores D, He Y, Shaw LN, Sun X. Cwl0971, a novel peptidoglycan hydrolase, plays pleiotropic roles in Clostridioides difficile R20291. Environ Microbiol. 2021 Apr 24. doi: 10.1111/1462-2920.15529. Online ahead of print. PMID: 33893759.
Yang F, Zhang J, Wang S, Sun Z, Zhou J, Li F, Liu Y, Ding L, Liu Y, Chi W, Liu T, He Y, Xiang P, Bao Z, Olszewski MA, Zhao H, Zhang Y. Genomic population structure of Helicobacter pylori Shanghai isolates and identification of genomic features uniquely linked with pathogenicity. Virulence. 2021 Dec;12(1):1258-1270. PMID: 33904371. PMCID: PMC8081043.
Y He, J Xie, L Wan, X Yang, Y Zhu, W Zhou, Y Li, E Ong, J Wu, K Liu, H Wang, Q Liu, H Yu. Interoperable ontologies: the foundation of intelligent precision medicine (in Chinese, English abstract available). Chinese Medical Ethics. 2021. Vol 34. No. 3. Pages: 265-279. doi: 10.12026/j.issn.1001-8565.2021.03.01
Zhu Y, Zheng J, X Li, X Y, He Y. Introduction to Basic Formal Ontology and Its Chinese Version (in Chinese, English abstract available). Journal of Medical Informatics. 2021,42(1):24~28, 60. doi: 10.3969/j.issn.1673-6036.2021.01.006.
Kimberly Berke, Peter Sun, Edison Ong, Nasim Sanati, Anthony Huffman, Timothy Brunson, Fred Loney, Joseph Ostrow, Rebecca Racz, Bin Zhao, Zuoshuang Xiang, Anna Maria Masci, Jie Zheng, Guanming Wu, Yongqun He, VaximmutorDB: A web-based vaccine immune factor database and its data analysis for understanding vaccine-induced immune responses. Front. Immunol. 2021. 12:639491. PMID: 33777032. PMCID: PMC7994782.
Haihe Wang, Edison Ong, John Y Kao, Duxin Sun, Yongqun He. Reverse Microbiomics: a new reverse dysbiosis analysis strategy and its usage in prediction of autoantigens and virulent factors in dysbiotic gut microbiomes from rheumatoid arthritis patients. Front. Microbiol. 2021. 12:633732. PMID: 33717026. PMCID: PMC7947680.
de Boer IH, Alpers CE, Azeloglu EU, Balis UGJ, Barasch JM, Barisoni L, Blank KN, Bomback AS, Brown K, Dagher PC, Dighe AL, Eadon MT, El-Achkar TM, Gaut JP, Hacohen N, He Y, Hodgin JB, Jain S, Kellum JA, Kiryluk K, Knight R, Laszik ZG, Lienczewski C, Mariani LH, McClelland RL, Menez S, Moledina DG, Mooney SD, O'Toole JF, Palevsky PM, Parikh CR, Poggio ED, Rosas SE, Rosengart MR, Sarwal MM, Schaub JA, Sedor JR, Sharma K, Steck B, Toto RD, Troyanskaya OG, Tuttle KR, Vazquez MA, Waikar SS, Williams K, Wilson FP, Zhang K, Iyengar R, Kretzler M, Himmelfarb J; Kidney Precision Medicine Project. Rationale and design of the Kidney Precision Medicine Project. Kidney International (2021) 99, 498–510. PMID: 33637194. PMCID: PMC8330551.
Liu Y, Hur J, Chan WKB, Wang Z, Xie J, Sun D, Handelman S, Sexton J, Yu H, He Y. Ontological modeling and analysis of experimentally or clinically verified drugs against coronavirus infection. Sci Data 8, 16 (2021). PMID: 33441564. PMCID: PMC7806933.
Ong E, Huang X, Pearce R, Zhang Y, He Y. Computational design of SARS-CoV-2 spike glycoproteins to increase immunogenicity by T cell epitope engineering. Comput Struct Biotechnol J. 2021;19:518-529. doi: 10.1016/j.csbj.2020.12.039. Epub 2020 Dec 31. PMID: 33398234. PMCID: PMC7773544.
Köhler S, Gargano M, Matentzoglu N, Carmody LC, Lewis-Smith D, Vasilevsky NA, Danis D, Balagura G, Baynam G, Brower AM, Callahan TJ, Chute CG, Est JL, Galer PD, Ganesan S, Griese M, Haimel M, Pazmandi J, Hanauer M, Harris NL, Hartnett MJ, Hastreiter M, Hauck F, He Y, Jeske T, Kearney H, Kindle G, Klein C, Knoflach K, Krause R, Lagorce D, McMurry JA, Miller JA, Munoz-Torres MC, Peters RL, Rapp CK, Rath AM, Rind SA, Rosenberg AZ, Segal MM, Seidel MG, Smedley D, Talmy T, Thomas Y, Wiafe SA, Xian J, Yüksel Z, Helbig I, Mungall CJ, Haendel MA, Robinson PN. The Human Phenotype Ontology in 2021. Nucleic Acids Res. 2021 Jan 8;49(D1):D1207-D1217. PMID: 33264411. PMCID: PMC7778952.
El-Achkar TM, Eadon MT , R Menon MT, Lake BB, Sigdel TK, Alexandrov T, Parikh S, Zhang G, Dobib D, Dunn KW, Otto EA, Anderton CR, Carson JM, Luo J, Park C, Hamidi H, Zhou J, Hoover P, Schroeder A, Joanes M, Azeloglu EU, Sealfon R, Winfree S, Steck B, He Y, D'Agati VD, Iyengar R, Troyanskaya OG, Barisoni L, Gaut J, Zhang K, Laszik Z, Rovin B, Dagher PC, Sharma K, Sarwal M, Hodgin JB, Alpers CE, Kretzer M, Jain S, For the Kidney Precision Medicine Project. A Multimodal and Integrated Approach to Interrogate Human Kidney Biopsies with Rigor and Reproducibility: Guidelines from the Kidney Precision Medicine Project. Physiological Genomics. 2021 Jan 1;53(1):1-11. PMID: 33197228. PMCID: PMC7847045.
*** Preprints:
Jingsong Zhang, Yang Zhang, Junyan Kang, Shuiye Chen,Yongqun He, Benhao Han, Mofang Liu, Lina Lu, Li Li, Zhigang Yi, Luonan Chen. Potential transmission chains of variant B.1.1.7 and co-mutations of SARS-CoV-2. bioRxiv. 2021.04.16.440141; doi: https://doi.org/10.1101/2021.04.16.440141.
*** Peer-reviewed proceeding papers:
Yingtong Liu, Wenjun Ju, Becky Steck, Sanjay Jain, Matthias Kretzler and Yongqun He. Ontology-based modeling, representation, and analysis of biomarkers in healthy and disease kidney tissue. The 12th International Conference on Biomedical Ontologies (ICBO 2021), Virtual conference hosted in Bolzano, Italy, September 15-18, 2021. 7-page conference paper (http://ceur-ws.org/Vol-3073/paper8.pdf). Early Career presentation by Liu.
Asiyah Lin, Yuki Yamagata, William D. Duncan, Leigh Carmody, Tatsuya Kushida, Hiroshi Masuya, John Beverley, Biswanath Dutta, Michael DeBellis, Zoë May Pendlington, Paola Roncaglia and Yongqun He. A community effort for COVID-19 Ontology Harmonization. The 12th International Conference on Biomedical Ontologies (ICBO 2021), Virtual conference hosted in Bolzano, Italy, September 15-18, 2021. 6-page conference paper (http://ceur-ws.org/Vol-3073/paper17.pdf). Short oral presentation by Lin.
Easheta Shah, Roshan Desai, Yongqun He, Suyuan Peng and Luxia Zhang. Ontology modeling and analysis of COVID-19-associated Acute Kidney Injury and its underlying molecular mechanisms. The 12th International Conference on Biomedical Ontologies (ICBO 2021), Virtual conference hosted in Bolzano, Italy, September 15-18, 2021. 6-page conference paper (http://ceur-ws.org/Vol-3073/paper16.pdf). Short oral presentation by Shah.
Guirui Huang, Suyuan Peng, Luxia Zhang and Yongqun He. Identification and ontology term enrichment analysis of genes associated with COVID-19 and acute kidney disease. The 12th International Conference on Biomedical Ontologies (ICBO 2021), Virtual conference hosted in Bolzano, Italy, September 15-18, 2021. 6-page conference paper (http://ceur-ws.org/Vol-3073/paper15.pdf). Short oral presentation by Peng.
Jessica Deguise, Yongqun He. Ontology-assisted analysis of COVID-19 vaccine-associated thrombosis adverse event case reports from VAERS. The 10th International Workshop on Vaccine and Drug Ontology Studies (VDOS-2021), half-day in conjunction with The 12th International Conference on Biomedical Ontologies (ICBO 2021), September 15-18, 2021. Virtual meeting hosted in Bolzano, Italy. 8-page full length conference paper. Oral prsentation by He.
~ 2020 ~
***Journal papers:
Xie J, Zi W, Li Z, He Y. Ontology-based precision vaccinology for deep mechanism understanding and precision vaccine development. Curr Pharm Des . 2020 Nov 24. doi: 10.2174/1381612826666201125112131. PMID: 33238868.
Xie J, Zi W, Ran P, Zhang Y, Zhou W, Huang X, He Y. Feasibility analysis on the use of Ontology of Adverse Events for characterization of adverse events associated with China-licensed vaccines (in Chinese, English abstract available). Chinese Journal of Bioinformatics. 2020, 18(4): 247-253. DOI: 10.12113/201910003.
Ong E, Wang LL, Schaub J, O'Toole JF, Steck B, Rosenberg AZ, Dowd F, Hansen J, Barisoni L, Jain S, de Boer IH, Valerius MT, Waikar SS, Park C, Crawford DC, Alexandrov T, Anderton CR, Stoeckert C, Weng C, Diehl AD, Mungall CJ, Haendel M, Robinson PN, Himmelfarb J, Iyengar R, Kretzler M, Mooney S, and He Y, Kidney Precision Medicine Project. Modeling Kidney Disease Using Ontology: insights from the Kidney Precision Medicine Project. Nature Review Nephrology. 2020 Nov;16(11):686-696. doi: 10.1038/s41581-020-00335-w. PMID: 32939051. PMCID: PMC8012202.
Li F, Du J, He Y, Song HY, Madkour M, Rao G, Xiang Y, Luo Y, Chen HW, Liu S, Wang L, Liu H, Xu H, Tao C. Time event ontology (TEO): to support semantic representation and reasoning of complex temporal relations of clinical events. J Am Med Inform Assoc. 2020 Jul 6:ocaa058. doi: 10.1093/jamia/ocaa058. PMID: 32626903.
Ong E, Wong M, Huffman A, He Y. COVID-19 coronavirus vaccine design using reverse vaccinology and machine learning. Frontiers in Immunology. 11:1581. doi: 10.3389/fimmu.2020.01581. (Published: 03 July 2020.) PMID: 32719684. PMCID: PMC7350702. (Note: this paper is an extension of the bioRxiv paper with the same title as detailed below).
Tao X, Yuan G, Rao S, Li D, Liu Y, Zhang X, Yu H, He Y, Ye X. Distinct RT-PCR diagnosis profiles of father and son patients of COVID-19 using nasopharyngeal and alveolar lavage fluid samples. Inflammation and Cell Signaling. 2000; 7: e1164. doi:10.14800/ics.1164. .
He Y, Yu H, Ong E, Wang Y, Liu Y, Huffman A, Huang H, Beverley J, Hur J, Yang X, Chen L, Omenn GS, Athey B, Smith B. CIDO, a community-based ontology for coronavirus disease knowledge and data integration, sharing, and analysis. Scientific Data. (2020) 7:181. doi: 10.1038/s41597-020-0523-6. (Published: 12 June 2020) PMID: 32533075. PMCID: PMC7293349.
Zhao L, Lee S, Li R, Ong E, He Y and Freed G. (2020). Improvement in the Analysis of Vaccine Adverse Event Reporting System Database. Statistics in Biopharmaceutical Research. Accepted author version posted online on 05 May 2020. https://doi.org/10.1080/19466315.2020.1764862.
Ong E, Wang H, Wong MU, Seetharaman M, Valdez N, He Y. Vaxign-ML: supervised machine learning reverse vaccinology model for improved prediction of bacterial protective antigens. Bioinformatics. 2020 May 1;36(10):3185-3191. PMID: 32096826.
Yang X, Sheng Y, Pan H, Zhe W, Wang Z, He Y. FAIR guidelines and biomedical data standard application services (in Chinese, English abstract available). Chinese Medical Ethics. 2020. 33 (02): 153-159. DOI:10.12026/j.issn.1001-8565.2020.02.05.
Ong E, He Y, Yang Z. Epitope promiscuity and population coverage of Mycobacterium tuberculosis protein antigens in current subunit vaccines under development. Infect Genet Evol. 2020 Jan 7:104186. PMID: 31923726.
Haw R, Loney F, Ong E, He Y, Wu G. Perform Pathway Enrichment Analysis Using ReactomeFIViz. Methods Mol Biol. 2020;2074:165-179. PMID: 31583638.
*** Preprints:
Edison Ong, Xiaoqiang Huang, Robin Pearce, Yang Zhang, Yongqun He. Rational Design of SARS-CoV-2 Spike Glycoproteins To Increase Immunogenicity By T Cell Epitope Engineering. bioRxiv. Posted on August 14, 2020. URL: https://www.biorxiv.org/content/10.1101/2020.08.14.251496v1.
Jens Hansen, Rachel Sealfon, Rajasree Menon, Michael T. Eadon, Blue B. Lake, Becky Steck, Dejan Dobi, Samir Parikh, Tara K. Sidgel, Theodore Alexandrov, Andrew Schroeder, Edgar A. Otto, Christopher R. Anderton,, Daria Barwinska, Guanshi Zheng, Michael P. Rose, John P. Shapiro, Dusan Velickovic, Annapurna Pamreddy, Seth Winfree, Yongqun He, Ian H. de Boer, Jeffrey B. Hodgin, Abhijit Nair, Kumar Sharma, Minnie Sarwal, Kun Zhang, Jonathan Himmelfarb, Zoltan Laszik, Brad Rovin, Pierre C. Dagher, John Cijiang He, Tarek M. El-Achkar, Sanjay Jain, Olga G. Troyanskaya, Matthias Kretzler, Ravi Iyengar, Evren U. Azeloglu, for the Kidney Precision Medicine Project Consortium. Towards Building a Smart Kidney Atlas: Network-based integration of multimodal transcriptomic, proteomic, metabolomic and imaging data in the Kidney Precision Medicine Project. bioRxiv. posted on July 24, 2020. doi: https://doi.org/10.1101/2020.07.23.216507.
Jingsong Zhang, Junyan Kang, Mofang Liu, Benhao Han, Li Li, Yongqun He, Zhigang Yi, Luonan Chen. Multi-site co-mutations and 5'UTR CpG immunity escape drive 2 the evolution of SARS-CoV-2. bioRxiv. posted on July 21, 2020. doi: https://doi.org/10.1101/2020.07.21.213405.
Yu H, Li L, Huang H, Wang Y, Liu Y, Ong E, Huffman A, Zeng T, Zhang J, Li P, Liu Z, Zhang X, Ye X, Handelman SK, Higgins G, Omenn GS, Athey B, Hur J, Chen L, He Y. Ontology-based systematic classification and analysis of coronaviruses, hosts, and host-coronavirus interactions towards deep understanding of COVID-19. arXiv e-prints. 2020. arXiv:2006.00639. [Submitted on 31 May 2020]
Ong E, Wong M, Huffman A, He Y. COVID-19 coronavirus vaccine design using reverse vaccinology and machine learning. bioRxiv. Posted on March 23, 2020. doi: https://doi.org/10.1101/2020.03.20.000141. PMID: 32511333. PMCID: PMC7239068.
Liu Y, Chan W, Wang Z, Hur J, Xie J, Yu H, He Y. Ontological and bioinformatic analysis of anti-coronavirus drugs and their Implication for drug repurposing against COVID-19. Preprints. 2020, 2020030413 (doi: 10.20944/preprints202003.0413.v1).
*** Peer-reviewed proceeding papers:
Yongqun He, Hong Yu, Edison Ong, Yang Wang, Yingtong Liu, Anthony Huffman, Hsin-hui Huang, John Beverley, Asiyah Yu Lin, William D. Duncan, Sivaram Arabandi, Jiangan Xie, Junguk Hur, Xiaolin Yang, Luonan Chen, Gilbert S. Omenn, Brian Athey, Barry Smith. CIDO: The Community-Based Coronavirus Infectious Disease Ontology. The 11th International Conference on Biomedical Ontologies (ICBO-2020), Virtual conference hosted in Bolzano, Italy, September 17, 2020. [Slides (PDF)] CEUR proceeding article: http://ceur-ws.org/Vol-2807/paperE.pdf.
Anthony Huffman, Yongqun He. OGG-CoV: Ontology Representation and Analysis of Genes and Genomes of Coronaviruses (short paper). Early career symposium, The 11th International Conference on Biomedical Ontologies (ICBO-2020), Virtual conference hosted in Bolzano, Italy, September 17, 2020. CEUR proceeding article: . http://ceur-ws.org/Vol-2807/shortP.pdf.
Asiyah Yu Lin, Stephan Gebel, Qingliang Leon Li, Sumit Madan, Johannes Darms, Evan Bolton, Barry Smith, Martin Hofmann-Apitius, Yongqun He, Alpha Tom Kodamullil. CTO: A Community-Based Clinical Trial Ontology and Its Applications in PubChemRDF and SCAIView. The 11th International Conference on Biomedical Ontologies (ICBO-2020), Virtual conference hosted in Bolzano, Italy, September 17, 2020. CEUR proceeding article: http://ceur-ws.org/Vol-2807/paperH.pdf. Also published in PMID: 35992013, and PMCID: PMC9389640. NIHMSID: NIHMS1825680.
Ong E, Huffman A, Brunson T, Sanati N, Zheng J, Masci AM, Wu G, He Y. Ontology-based representation and analysis of vaccine immune response data in ImmPort. 8-page full length proceeding paper, the 9th International Workshop on Vaccine and Drug Ontology Studies (VDOS-2020), associated with the 11th International Conference on Biomedical Ontologies (ICBO-2020), Zoom virtual meeting, September 17, 2020.
Huffman A, Austin L, Wong MU, Ong E, He Y. Coronavirus vaccine collection, annotation, and ontology representation analysis. 8-page full length proceeding paper, the 9th International Workshop on Vaccine and Drug Ontology Studies (VDOS-2020), associated with the 11th International Conference on Biomedical Ontologies (ICBO-2020), Zoom virtual meeting, September 17, 2020.
Hong Yu, Asiyah Yu Lin, Yongqun He. CIDO Diagnosis: COVID-19 diagnosis modeling, representation and analysis using the Coronavirus Infectious Disease Ontology. Bio-Ontologies Community of Special Interest (COSI) meeting, the 2020 virtual annual International Conference on Intelligent Systems for Molecular Biology (ISMB-2020), July 13-16, 2020. 4-page short article, Accepted.
Yang Wang, Fengwei Zhang, Hong Yu, Xianwei Ye and Yongqun He. Ontology-based collection and analysis of natural and lab animal hosts of human coronaviruses. Bio-Ontologies Community of Special Interest (COSI) meeting, the 2020 virtual annual International Conference on Intelligent Systems for Molecular Biology (ISMB-2020), July 13-16, 2020. 4-page short article, Accepted.
Ling Wan, Justin Song, Virginia He, Yongqun He. Development of the International Classification of Diseases Ontology (ICDO) and its application for COVID-19 diagnostic data analysis. The 19th International Conference on Bioinformatics (InCoB 2020), Nov 25-29, 2020, Zoom virtual meeting. Full length proceeding article, also orally presented by He Y. Note: This presentation was awarded as one of “Top 5 Best Paper Presentations”.
***Book translation:
Yan Zhu, Yongqun He (Chief translators); Jie Zheng, Xiaoying Li, Xiaolin Yang (Chief editors). 基于基本形式化本体的本体构建 (Chinese translation of "Building Ontologies with Basic Formal Ontology, Robert Arp, Barry Smith and Andrew D. Spear, The MIT Press). People's Medical Publishing House Co., Ltd. (Translation Publisher), Beijing, China.
***Report in multimedia:
10/31/2020: In This Week in Virology (TWIV) episoide 677 (title: Does antibody really know what time it is?), Dr. Rich Condit mentioned our VIOLIN vaccine database at the time of 2 hours and 33 min, and provided a positive review.
~ 2019 ~
***Journal papers:
He Y, Wang H, Zheng J, Beiting DP, Masci AM, Yu H, Liu K, Wu J, Curtis JL, Smith B, Alekseyenko AV, Obeid JS. OHMI: the ontology of host-microbiome interactions. J Biomed Semantics. 2019 Dec 30;10(1):25. PMID: 31888755. PMCID: PMC6937947.
Ong E, Sun P, Berke K, Zheng J, Wu G, He Y. VIO: ontology classification and study of vaccine responses given various experimental and analytical conditions. BMC Bioinformatics. 2019, 20(Suppl 21): 704.
PMID: 31865910. PMCID: PMC6927110.
Tiftikci M, Özgür A, He Y, Hur J. Machine learning-based identification and rule-based normalization of adverse drug reactions in drug labels. BMC Bioinformatics. 2019 20(Suppl 21):707. PMID: 31865904. PMCID:
PMC6927101.
Hur J, Tao C, He Y. A 2018 workshop: vaccine and drug ontology studies (VDOS 2018). BMC Bioinformatics. 2019 20(Suppl 21):705. PMID: 31865905. PMCID:
PMC6927102.
Yang Y, Wybrow M, Li YF, Czauderna T, He Y. OntoPlot: A Novel Visualisation for Non-hierarchical Associations in Large Ontologies. IEEE Trans Vis Comput Graph. 2019 Aug 22. [Epub ahead of print]. PMID: 31442991.
Amith M, Manion F, Liang C, Harris M, Wang D, He Y, Tao C. Architecture and usability of OntoKeeper, an ontology evaluation tool. BMC Med Inform Decis Mak. 2019 Aug 8;19(Suppl 4):152. PMID: 31391056. PMCID: PMC6686219.
Zhu D, Bullock J, He Y, Sun X.. Cwp22, a novel peptidoglycan cross-linking enzyme, plays pleiotropic roles in Clostridioides difficile.. Environ Microbiol. 2019 Jun 7. doi: 10.1111/1462-2920.14706. PMID: 31173438.
Ren JJ, Sun T, He Y, Zhang Y. A statistical analysis of vaccine-adverse event data. BMC Med Inform Decis Mak. 2019 May 28;19(1):101. PMID: 31138219.
Yu H, Nysak S, Garg N, Ong E, Ye X, Zhang X, He Y. ODAE: Ontology-based systematic representation and analysis of drug adverse events and its usage in study of adverse events given different patient age and disease conditions. BMC Bioinformatics. 2019, 20 (Suppl 7):199.
PMID: 31074377.
Sarntivijai S, He Y, Diehl AD. Cells in ExperimentaL Life Sciences (CELLS-2018): capturing the knowledge of normal and diseased cells with ontologies. BMC Bioinformatics. 2019, 20 (Suppl 5): 227–230.
PMID: 31272374.
PMCID: PMC6509796.
Y He, WD Duncan, DJ Cooper, J Hansen, R Iyengar, E Ong, K Walker, O Tibi, S Smith, LM Serra, J Zheng, S Sarntivijai, S Schürer, KS O’Shea, AD Diehl. OSCI: standardized stem cell ontology representation and use cases for stem cell investigation. BMC Bioinformatics. 2019, 20 (Suppl 5), 237.
PMID: 31272389.
PMCID: PMC6509805.
H Pan, X Bian, S Yang, Y He, X Yang, Y Liu. The cell line ontology-based representation, integration and analysis of cell lines used in China. BMC Bioinformatics. 2019, 20 (Suppl 5), 249.
PMID: 31272367. PMCID:
PMC6509802.
Sayers S, Li L, Ong E, Deng S, Fu G, Lin Y, Yang B, Zhang S, Fa Z, Zhao B, Xiang Z, Li Y, Zhao Z, Olszewski MA, Chen L, He Y. Victors: a web-based knowledge base of virulence factors in human and animal pathogens. Nucleic Acid Research. 2019 Jan 8;47(D1):D693-D700. doi: 10.1093/nar/gky999. PMID: 30365026.
PMCID: PMC6324020.
***Peer-reviewed proceeding papers:
Yang Y, Wybrow M, Li Y, Czauderna T, He Y. OntoPlot: A Novel Visualisation for Non-hierarchical Associations in Large Ontologies. Accepted at IEEE InfoVis 2019. Available at arXiv: https://arxiv.org/abs/1908.00688.
He Y, Ong E, Schaub J, Dowd F, O’Toole JF, Siapos A, Reich C, Seager S, Wan L, Yu H, Zheng J, Stoeckert C, Yang X, Yang S, Steck B, Park C, Barisoni L, Kretzler M, Himmelfarb J, Iyengar R, Mooney SD, for the Kidney Precision Medicine Project Consortium. OPMI: the Ontology of Precision Medicine and Investigation and its support for clinical data and metadata representation and analysis. The 10th International Conference on Biomedical Ontology (ICBO-2019), July 30 - August 2, 2019, Buffalo, NY, USA. 10-page full length article.
Liu M, Ou Y, He Y. ICEO: a biological ontology for representing and analyzing the bacterial integrative and conjugative element. The 10th International Conference on Biomedical Ontology (ICBO-2019), July 30 - August 2, 2019, Buffalo, NY, USA. 8-page full length article.
Wan L, Ong E, He Y. ICDO: Ontological representation of the International Classification of Diseases (ICD) and its application in English and Chinese healthy data standardization. The 10th International Conference on Biomedical Ontology (ICBO-2019), July 30 - August 2, 2019, Buffalo, NY, USA. 10-page full length article.
Kaiyong Liu, Yongqun He. Ontological Derivation of Mendeleev's Periodic Table of Chemical Elements. The 10th International Conference on Biomedical Ontology (ICBO-2019), July 30 - August 2, 2019, Buffalo, NY, USA. 1-page short paper.
Yongqun He, Jie Zheng, Anna Maria Masci, Jihad Obeid. Alignment of the Ontology of Host-Microbiome Interactions (OHMI) High Level Terms with Existing OBO Ontologies. The 10th International Conference on Biomedical Ontology (ICBO-2019), July 30 - August 2, 2019, Buffalo, NY, USA. 1-page short paper.
Hsin-Hui Huang, Meng Liu, Yongqun He. Ontological Modeling of Two-Component Regulatory Systems. The 10th International Conference on Biomedical Ontology (ICBO-2019), July 30 - August 2, 2019, Buffalo, NY, USA. 1-page short paper.
Meng Liu, Hong-Yu Ou, Yongqun He. OGG-Bac: Ontological Representation of Orthologous Bacterial Genes. The 10th International Conference on Biomedical Ontology (ICBO-2019), July 30 - August 2, 2019, Buffalo, NY, USA. 1-page short paper.
Edison Ong, Yongqun He. Ontolion: A Web-based Integrative Ontology Development Platform. The 10th International Conference on Biomedical Ontology (ICBO-2019), July 30 - August 2, 2019, Buffalo, NY, USA. 1-page short paper.
Ong E, He Y. OHPI: Ontology of Host-Pathogen Interactions and its usage in identification and analysis of virulence factors also serving the role of vaccine protective antigens. The 8th International Workshop on Vaccine and Drug Ontology Studies (VDOS-2019), in association with The 10th International Conference on Biomedical Ontology (ICBO-2019), July 30 - August 2, 2019, Buffalo, NY, USA. 6-page full length article.
*** Preprints:
El-Achkar TM, Eadon MT, Menon R, Lake BB, Sigdel TK, Alexandrov T, Parikh S, Zhang G, Dobi D, Dunn KW, Otto EA, Anderton CR, Carson CM, Luo J, Park C, Hamidi H, Zhou J, Hoover P, Schroeder A, Joanes M, Azeloglu E, Sealfon R, Winfree S, Steck B, He Y, D'Agati V, Iyengar R, Troyanskaya OG, Barisoni L, Gaut J, Zhang K, Laszik Z, Rovin B, Dagher PC, Sharma K, Sarwal M, Hodgin JB, Alpers CE, Kretzler M, Jain S. A multimodal and integrated approach to interrogate human kidney biopsies with rigor and reproducibility: The Kidney Precision Medicine Project. bioRxiv. Posted November 06, 2019. doi: https://doi.org/10.1101/828665.
~ 2018 ~
***Journal papers:
Wang Y, Wen Z, Pan X, Briles DE, He Y, Zhang JR. Novel immunoprotective proteins of Streptococcus pneumoniae identified by opsonophagocytosis killing screen. Infect Immun. 2018 Jun 11. pii: IAI.00423-18. PMID: 29891544.
Hur J, Ozgur A, He Y. Ontology-based literature mining and class effect analysis of adverse drug reactions associated with neuropathy-inducing drugs. J Biomed Semantics. 2018. 9:17.
PMID: 29880031.
PMCID: PMC5991464.
Xie J, Wang J, Li Z, Wang W, Pang Y, and He Y. Ontology-based meta-analysis of animal and human adverse events associated with licensed brucellosis vaccines. Frontiers in Pharmacology. 2018 May 15;9:503. PMID: 29867505. PMCID: PMC5962797.
Wong MU, Racz R, Ong E, He Y. Towards precision informatics of pharmacovigilance: OAE-CTCAE mapping and OAE-based representation and analysis of adverse events in patients treated with cancer drugs. AMIA Annu Symp Proc. 2018 Apr 16;2017:1793-1801. PMID: 29854250, PMCID: PMC5977606.
Du J, Cai Y, Chen Y, He Y, Tao C. Analysis of individual differences in vaccine pharmacovigilance using VAERS data and MedDRA system organ classes: A use case study with trivalent influenza vaccine. Biomed Inform Insights. 2017 Apr 11;9:1-8. PMID: 28469434. PMCID: PMC5391193.
He Y, Yu H, Yang X, Shao C, Zhou W, Zhu Y, Wang H, Liu Q, Xie J, Zheng J, Zhu W. Ontology: Foundation of biomedical big data and precision medicine research (in Chinese, English abstract available). Chinese Journal of Bioinformatics. 2018, 16(1): 7-14.
doi:10.3969/j.issn.1672-5565.201710006.
He Y, Xiang Z, Zheng J, Lin Y, Overton JA, Ong E. The eXtensible ontology development (XOD) principles and tool implementation to support ontology interoperability. J Biomed Semantics. 2018 Jan 12;9(1):3. PMID: 29329592. PMCID: PMC5765662.
***Peer-reviewed proceeding papers:
He Y, Steck B, Ong E, Mariani L, Lienczewski C, Balis U, Kretzler M, Himmelfarb J, Bertram JF, Azeloglu E, Iyengar R, Hoshizaki D, Mooney SD, for the KPMP Consortium. KTAO: A kidney tissue atlas ontology to support community-based kidney knowledge base development and data integration (http://ceur-ws.org/Vol-2285/ICBO_2018_paper_28.pdf). International Conference on Biomedical Ontology 2018 (ICBO-2018), August 7-10, 2018, Corvallis, Oregon, USA. Full length paper. Pages 1-6.
Ong E, He Y, Zheng J. eXtensible ontology development (XOD) using web-based Ontoanimal tools (http://ceur-ws.org/Vol-2285/ICBO_2018_paper_24.pdf). International Conference on Biomedical Ontology 2018 (ICBO-2018), August 7-10, 2018, Corvallis, Oregon, USA. Software demo. Pages 1-2.
Otte JN, Stansbury C, Vajda J, Manion F, Umberfield E, He Y, Harris M, Obeid J, Brochhausen M, Duncan W, Tao C. Coordinated evolution of Ontologies of Informed Consent (http://ceur-ws.org/Vol-2285/ICBO_2018_paper_59.pdf). International Conference on Biomedical Ontology 2018 (ICBO-2018), August 7-10, 2018, Corvallis, Oregon, USA. Pages 1-2.
He Y, Duncan WD, Cooper DJ, Hansen J, Iyengar R, Ong E, Walker K, Tibi O, Smith S, Serra L, Zheng J, Sarntivijai S, Schurer S, O’shea KS, Diehl AD. OSCI: Standardized stem cell ontology representation and use cases for stem cell investigation. The 2nd International Workshop on Cells in ExperimentaL Life Science (CELLS-2018), August 7, 2018, in conjunction with International Conference on Biomedical Ontology 2018 (ICBO-2018), August 7-10, 2018, Corvallis, Oregon, USA. Full length paper. Pages 1-8.
Pan H, Bian X, Yang S, He Y, Liu Y, Yang X. The Cell Line Ontology-based Representation, Integration and Analysis of Cell Lines Used in China. The 2nd International Workshop on Cells in ExperimentaL Life Science (CELLS-2018), August 7, 2018, in conjunction with International Conference on Biomedical Ontology 2018 (ICBO-2018), August 7-10, 2018, Corvallis, Oregon, USA. Full length paper. Pages 1-8.
Ong E, Zheng J, Wu G, He Y. VIO: Ontology classification and analysis of vaccine responses given different experimental conditions. The 7th International Workshop on Vaccine and Drug Ontology Studies (VDOS-2018), August 10, 2018, in conjunction with International Conference on Biomedical Ontology 2018 (ICBO-2018), August 7-10, 2018, Corvallis, Oregon, USA. Full length paper. Pages 1-6.
***Report introducing Oliver He's sabbatical in China in 2017:
University of Michigan Medical School Global Reach report. Ode to Ontologies: Helping Chinese collaborators share big data. February 2018 report.
~ 2017 ~
***Journal papers:
Ong E, Xie J, Ni Z, Liu Q, Sarntivijai S, Lin Y, Cooper D, Terryn R, Stathias V, Chung C, Schürer S, He Y. Ontological representation, integration, and analysis of LINCS cell line cells and their cellular responses. BMC Bioinformatics. 2017 Dec 21;18(Suppl 17):556. PMID: 29322930. PMCID: PMC5763302.
Sarntivijai S, Diehl AD, He Y. Cells in experimental life sciences - challenges and solution to the rapid evolution of knowledge. BMC Bioinformatics. 2017 Dec 21;18(Suppl 17):560. PMID: 29322916. PMCID: PMC5763506.
Ong E, Sarntivijai S, Jupp S, Parkinson H, He Y. Comparison, alignment, and synchronization of cell line information between CLO and EFO. BMC Bioinformatics. 2017 Dec 21;18(Suppl 17):557. PMID: 29322915. PMCID: PMC5763470.
Liu Q, Wang J, Zhu Y, He Y. Ontology-based systematic representation and analysis of traditional Chinese drugs against rheumatism. BMC Systems Biology. 2017 Dec 21;11(Suppl 7):130.
PMID: 29322929 PMCID: PMC5763303.
Zheng J, Li H, Liu Q, He Y. The Ontology of Biological and Clinical Statistics (OBCS)-based statistical method standardization and meta-analysis of host responses to yellow fever vaccines. Quantitative Biology.
2017. 5(4):291-301. PMID: 30034908. PMCID: PMC6054478.
Ong E, Wong MU, He Y. Identification of new features from known bacterial protective vaccine antigens enhances rational vaccine design. Frontiers in Immunology. 2017 Oct 26;8:1382.
PMID: 29123525.
Wang L, Li M, Xie J, Cao Y, Liu H, He Y. Ontology-based systematical representation and drug class effect analysis of package insert-reported adverse events associated with cardiovascular drugs used in China. Sci Rep. 2017 Oct 23;7(1):13819. doi: 10.1038/s41598-017-12580-4. PMID: 29061976.
PMCID: PMC5653862.
Perez-Martinez AP, Ong E, Zhang L, Marrs CF, He Y, Yang Z. Conservation in
gene encoding Mycobacterium tuberculosis antigen Rv2660 and a high predicted
population coverage of H56 multistage vaccine in South Africa. Infection, Genetics and Evolution. 2017 Sep 21;55:244-250. PMID: 28941991.
Du J, Cai Y, Chen Y, He Y, Tao C. Analysis of individual differences in vaccine pharmacovigilance using VAERS data and MedDRA system organ classes: A use case study with trivalent Influenza vaccine. Biomedical Informatics Insights. 2017. Volume 9: 1-8. PMID: 28469434, PMCID: PMC5391193.
Hur J, Ozgur A, He Y. Ontology-based literature mining of E. coli vaccine-associated gene interaction networks. J Biomed Semantics. 2017:12. DOI: 10.1186/s13326-017-0122-4. PMID: 28288685. PMCID: PMC5348867.
The Knowledge Base workgroup of the Observational Health Data Sciences and Informatics (OHDSI) collaborative. Large-scale adverse effects related to treatment evidence standardization (LAERTES): an open scalable system for linking pharmacovigilance evidence sources with clinical data. J Biomed Semantics. 2017 Mar 7;8(1):11. PMID: 28270198. PMCID: PMC5341176.
Ni Z, Chen Y, Ong E, He Y. Antibiotic resistance determinants-focused Acinetobacter baumannii vaccine design using reverse vaccinology. International Journal of Molecular Sciences. 2017, 18(2), 458. PMID: 28230771. PMCID: PMC5343991.
Lopera-Madrid J, Osorio JE, He Y, Xiang Z, Adams LG, Laughlin RC, Mwangi W, Subramanya S, Neilan J, Brake D, Burrage TG, Brown WC, Clavijo A, Bounpheng MA. Safety and immunogenicity of mammalian cell derived and modified-vaccinia Ankara vectored African swine fever subunit antigens in swine. Veterinary Immunology and Immunopathology. 2017. DOI: 10.1016/j.vetimm.2017.01.004. PMID: 28241999.
Li J, Tai C, Deng Z, Zhong W, He Y, Ou H. VRprofile: gene-cluster-detection-based profiling of virulence and antibiotic resistance traits encoded within genome sequences of pathogenic bacteria. Briefings in Bioinformatics. 2017, 1-9. PMID: 28077405.
Ong E, Xiang Z, Zhao B, Liu Y, Lin Y, Zheng J, Mungall C, Courtot M, Ruttenberg A, He Y. Ontobee: A linked ontology data server to support ontology term
dereferencing, linkage, query, and integration. Nucleic Acid Research. 2017 Jan 4;45(D1):D347-D352. PMID: 27733503. PMCID: PMC5210626.
***Book chapters:
Xie J, He Y. Ontology-based vaccine adverse event representation and analysis. Adv Exp Med Biol. 2017;1028:89-103. PMID: 29058218.
***Peer-reviewed proceeding papers:
Ong E， He Y. OLOBO: A new ontology for linking and integrating open biological and biomedical ontologies. International Conference on Biomedical Ontology 2017 (ICBO-2017), September 13-15, 2017, Newcastle upon Tyne, UK. Pages 1-2.
Liu Q, Wang J, Zhu Y, He Y. Ontology-based systematic representation and analysis of traditional Chinese drugs against rheumatism. The 16th International Conference on Bioinformatics (InCoB 2017), Shenzhen, Guangdong, China.
Wong, M, Racz R, Ong E, He Y. Towards precision informatics of pharmacovigilance: OAE-CTCAE mapping and OAE-based representation and analysis of adverse events in patients treated with cancer drugs. AMIA (American Medical Informatics Association) 2017 Annual Symposium, Washington Hilton, Washington DC, USA, November 8, 2017. (Full length paper publication, oral presentation).
***Report introducing Oliver He
生物医学本体基础培训会议在京召开 ( in Chinese, translation: "Biomedical Ontology Basics Training in Beijing"), reported by HC3i 中国数字医疗网/尹聪颖. Reported on July 27, 2017.
何勇群：生物医学本体在大数据与精准医学的运用 (in Chinese, translation: "Yonggun He: Applications of Biomedical Ontologies in Big data and Precision medicine"), reported by HC3i 中国数字医疗网/刘中正. Report on June 27, 2017.
~ 2016 ~
***Journal papers:
Hur J, Özgür A, He Y. The Interaction Network Ontology-supported modeling and mining of complex interactions represented with multiple keywords in biomedical literature. BioData Mining. 2016 Dec 19;9:41. PMID: 28031747. PMCID: PMC5168857.
Huang J, Eilbeck K, Smith B, Blake JA, Dou D, Huang W, Natale DA, Ruttenberg A, Huan J, Zimmermann MT, Jiang G, Lin Y, Wu B, Strachan HJ, de Silva N, Kasukurthi MV, Jha VK, He Y, Zhang S, Wang X, Liu Z, Borchert GM, Tan M. The development of non-coding RNA ontology. Int J Data Min Bioinform. 2016; 15(3):214-232. PMID: 27990175. PMCID: PMC5156483.
Xie J, Codd C, Mo K, He Y. Differential adverse event profiles associated with BCG as a preventive tuberculosis vaccine or therapeutic bladder cancer vaccine identified by comparative ontology-based VAERS and literature meta-analysis. PLoS ONE. 2016 Oct 17;11(10):e0164792. PMID: 27749923. PMCID: PMC5066964.
Malachowski AN, Yosri M, Park G, Bahn YS, He Y, Olszewski MA. Systemic approach to virulence gene network analysis for gaining new insight into cryptococcal virulence. Frontiers in Microbiology. 2016. 7:1652. PMID: 27833589. PMCID: PMC5081415.
Xie J, Zhao L, Zhou S, He Y. Statistical and ontological analysis of adverse events associated with monovalent and combination vaccines against hepatitis A and B diseases. Scientific Reports. 2016. 6:3418. PMID: 27694888. PMCID: PMC5046117.
Zheng J, Harris MR, Masci AM, Lin Y, Hero A, Smith B, He Y. The Ontology of Biological and Clinical Statistics (OBCS) for Standardized and Reproducible Statistical Analysis. J Biomed Semantics. 2016. Sep 14;7(1):53. PMID: 27627881. PMCID:
PMC5024438.
Ong E, He Y. Community-based ontology development, annotation and discussion with MediaWiki extension Ontokiwi and Ontokiwi-based Ontobedia. AMIA Jt Summits Transl Sci Proc. 2016 Jul 20;2016:65-74. eCollection 2016. PMID: 27570653. PMCID: PMC5001762.
Diehl AD, Meehan TF, Bradford YM, Brush MH, Dahdul WM, Dougall DS, He Y, Osumi-Sutherland D, Ruttenberg A, Sarntivijai S, Van Slyke CE, Vasilevsky NA, Haendel MA, Blake JA, Mungall CJ. The Cell Ontology 2016: enhanced content, modularization, and ontology interoperability. J Biomed Semantics. 2016 Jul 4;7(1):44. PMID: 27377652. PMCID: PMC4932724.
He Y, Ong E, Xie J. Integrative representations and analyses of vaccine-induced intended protective immunity and unintended adverse events using ontology-based and theory-guided approaches. Global Vaccines and Immunology. 2016. 1 (2): 37-39. DOI: 10.15761/GVI.1000110. [PDF] PMID: 27868103. PMCID: PMC5111632.
Guo A*, Racz R*, Hur J, Lin Y, Xiang Z, Zhao L, Rinder J, Jiang G, Zhu Q, He Y. Ontology-based collection, representation and analysis of drug-associated neuropathy adverse events. Journal of Biomedical Semantics. 2016. 7:29. PMID: 27213033. PMCID: PMC4875649.
Bandrowski A, Brinkman R, Brochhausen M, Brush MH, Bug B, Chibucos MC, Clancy K, Courtot M, Derom D, Dumontier M, Fan L, Fostel J, Fragoso G, Gibson F, Gonzalez-Beltran A, Haendel MA, He Y, Heiskanen M, Hernandez-Boussard T, Jensen M, Lin Y, Lister AL, Lord P, Malone J, Manduchi E, McGee M, Morrison N, Overton JA, Parkinson H, Peters B, Rocca-Serra P, Ruttenberg A, Sansone S, Scheuermann RH, Schober D, Smith B, Soldatova LN, Stoeckert Jr. CJ, Taylor CF, Torniai C, Turner JA, Vita R, Whetzel PL, Zheng J. The Ontology for Biomedical Investigations. PLoS ONE. 11(4): e0154556. PMID: 27128319. PMCID: PMC4851331.
Huang J, Eilbeck K, Smith B, Blake JA, Dou, D, Huang W, Natale DA, Ruttenberg A, Huan J, Zimmermann MT, Jiang G, Lin Y, Wu B, Strachan HJ, He Y, Zhang S, Wang X, Liu Z, Borchert G, Tan M. The Non-Coding RNA Ontology (NCRO): A comprehensive resource for the unification of non-coding RNA biology. Journal of Biomedical Semantics. 2016. 7:24. DOI: 10.1186/s13326-016-0066-0. PMID: 27152146. PMCID: PMC4857245.
Lin Y, Zheng J, He Y. VICO: Ontology-based representation and integrative analysis of vaccination informed consent forms. J Biomed Semantics. 2016 Apr 19;7:20. doi: 10.1186/s13326-016-0062-4. PMID: 27099700. PMCID: PMC4837519.
Racz R, He Y. The web-based DNA vaccine database DNAVaxDB and Its usage for rational DNA vaccine design. Methods Mol Biol. 2016;1404:741-52. doi: 10.1007/978-1-4939-3389-1_48. PMID: 27076334.
Sarntivijai S, Zhang S, Jagannathan DG, Zaman S, Burkhart KK, Omenn GS, He Y, Athey BD, Abernethy DR. Linking MedDRA-coded clinical phenotypes to biological mechanisms by the Ontology of Adverse Events: A pilot study on Tyrosine Kinase Inhibitors (TKIs). Drug Safety. 2016. pp 1-11. First online: 22 March 2016. DOI: 10.1007/s40264-016-0414-0. PMID: 27003817. PMCID: PMC4933310 [Available on 2017-07-01]
He Y. Ontology-based vaccine and drug adverse event representation and theory-guided systematic causal network analysis toward integrative pharmacovigilance research. Current Pharmacology Reports. 2016, Volume 2, Issue 3, pp 113-128. DOI: 10.1007/s40495-016-0055-0. PMID: 27458549. PMCID: PMC4957564.
Todd T*, Dunn N*, Xiang Z, He Y. Vaxar: A web-based database of laboratory animal responses to vaccinations and its application in the meta-analysis of different animal responses to tuberculosis vaccinations. Comparative Medicine. 2016. 66(2):119-28. PMID: 27053566. PMCID: PMC4825961.
Tao C, He Y, Arabandi S. Vaccine and Drug Ontology Studies (VDOS 2014). Journal of Biomedical Semantics..2016, 7:6.
DOI: 10.1186/s13326-015-0039-8. PMID: 26918107. PMCID: PMC4766598.
***Peer-reviewed proceeding papers:
Edison Ong, Jiangan Xie, Zhaohui Ni, Qingping Liu, Yu Lin, Vasileios Stathias, Caty Chung, Stephan Schurer, Yongqun He. The Cell Line Ontology Integration and Analysis of the Knowledge of LINCS Cell Lines. International Conference on Biomedical Ontologies (ICBO-2016), August 1-4, 2016, Oregon State University, Corvallis, OR, USA. 2-page proceeding paper.
He Y, Zheng J, Qin Z. EGO: a biomedical ontology for integrative epigenome representation and analysis. International Conference on Biomedical Ontologies (ICBO-2016), August 1-4, 2016, Oregon State University, Corvallis, OR, USA. 2-page proceeding paper.
Ozgur A, Hur J, Xiang Z, Ong E, Radev D, He Y. Ignet: A centrality and INO-based web system for analyzing and visualizing literature-mined networks. August 1-2, 2016, joint session ICBO+BioCreative, at the International Conference on Biomedical Ontologies (ICBO-2016) and BioCreative 2016, August 1-4, 2016, Oregon State University, Corvallis, OR, USA. 2-page proceeding paper.
Edison Ong, Zuoshuang Xiang, Jie Zheng, Barry Smith, Yongqun He. Ontobull and BFOConvert: Web-based Programs to Support Automatic Ontology Conversion. August 1-2, 2016, joint session ICBO+BioCreative, at the International Conference on Biomedical Ontologies (ICBO-2016) and BioCreative 2016, August 1-4, 2016, Oregon State University, Corvallis, OR, USA. 2-page proceeding paper (SOftware Demo).
Hur J, Ozgur A, Ong E, He Y. Ontology-based literature mining of E. coli vaccine-associated gene interaction networks. Vaccines and Drug Ontology Studies workshop (VDOS-2016), August 1, 2016, in connection with International Conference on Biomedical Ontologies (ICBO-2016), August 1-4, 2016, Oregon State University, Corvallis, OR, USA. 6-page full-length proceeding paper.
Boyce RD, Voss E, Huser V, Evans L, Reich C, Duke J, Tatonetti N, Dumontier M, Hauben M, Wallberg M, Peng L, Dempster S, He Y, Sena A, Ryan P. LAERTES : An open scalable architecture for linking pharmacovigilance evidence sources with clinical data. Vaccines and Drug Ontology Studies workshop (VDOS-2016), August 1, 2016, in connection with International Conference on Biomedical Ontologies (ICBO-2016), August 1-4, 2016, Oregon State University, Corvallis, OR, USA. 6-page full-length proceeding paper.
Ong E, He Y. Community-based Ontology Development, Annotation and Discussion with MediaWiki extension Ontokiwi and Ontokiwi-based Ontobedia. 2016 Joint Summits on Translational Science, American Medical Informatics Association (AMIA), March 21-24, San Francisco, CA, USA. Full-length 10-page paper, accepted for oral presentation (Conference presentation link).
***Book chapters:
Bhattacharyya A, He Y. Genome Sequence Databases: Annotation. Reference Module in Biomedical Sciences. Elsevier. 11-Jan-2016. doi: 10.1016/B978-0-12-801238-3.98823-8.
~ 2015 ~
***Journal papers:
Karadeniz İ, Hur J*, He Y*, Ozgur A*. Literature mining and ontology based analysis of host-Brucella gene-gene interaction network. Front. Microbiol. 2015 Dec 9; 6:1386. PMID: 26696993. PMCID: PMC4673313.
Lin Y, Xiang Z, and He Y. Ontology-based representation and analysis of host-Brucella interactions. J Biomed Semantics. 2015, 6:37. DOI: 10.1186/s13326-015-0036-y. PMID: 26445639. PMCID: PMC4594885.
Nemzek JA, Hodges AP, He Y. Bayesian network analysis of multi-compartmentalized immune responses in a murine model of sepsis and direct lung injury. BMC Research Notes. 2015 Sep 30;8(1):516. PMID: 26423575. PMCID: PMC4589912.
Deng S, Martin C, Patil R, Zhu F, Zhao B, Xiang Z, He Y. Vaxvec: The first web-based recombinant vaccine vector database and its data analysis. Vaccine. 2015 Nov 27;33(48):6938-6946. Epub 2015 Sep 25. PMID: 26403370. PMCID: PMC4679550 [Available on 2016-11-27]
Bronner DN, Abuaita BH, Chen X, Fitzgerald KA, Nunez G, He Y, Yin XM, O’Riordan MXD. ER stress activates the inflammasome via NLRP3-caspase-2 driven mitochondrial damage. Immunity. 2015 Sep 15;43(3):451-62. PMID: 26341399. PMCID: PMC4582788.
Liu W, Dong H, Li J, Ou Q, Lv Y, Wang X, Xiang Z, He Y*, Wu Q*. RNA-seq reveals the critical role of OtpR in regulating Brucella melitensis metabolism and virulence under acidic stress. Scientific Reports. 2015 Aug 5;5:10864. doi: 10.1038/srep10864. PMID: 26242322. PMCID: PMC4542472.
Zhang B, Xiao R, Ronan EA, He Y, Hsu AL, Liu J, Xu XZ. Environmental temperature differentially modulates C. elegans longevity through a thermosensitive TRP channel. Cell Rep. 2015 Jun 9;11(9):1414-24. doi: 10.1016/j.celrep.2015.04.066. PMID: 26027928. PMCID: PMC4758836.
Xiang Z, Zheng J, Lin Y, He Y. Ontorat: Automatic generation of new ontology terms, annotations, and axioms based on ontology design patterns. Journal of Biomedical Semantics. 2015, 6:4 doi:10.1186/2041-1480-6-4. PMID: 25785185. PMCID: PMC4362828.
Hur J, Özgür A, Xiang Z, He Y. Development and application of an Interaction Network Ontology for literature mining of vaccine-associated gene-gene interactions. Journal of Biomedical Semantics. 2015, 6:2. doi:10.1186/2041-1480-6-2. PMID: 25785184. PMCID: PMC4362819.
Dean AR, Lewis SE, Huala E, Anzaldo SS, Ashburner M, Balhoff JP, Blackburn DC, Blake JA, Burleigh JG, Chanet B, Cooper LD, Courtot M, Csõsz S, Cui H, Dahdul W, Das S, Dececchi TA, Dettai A, Diogo R, Druzinsky RE, Dumontier M, Franz NM, Friedrich F, Gkoutos GV, Haendle M, Harmon LJ, Hayamizu TF, He Y, Hines HM, Ibrahim N, Jackson LM, Jaiswal P, James-Zorn C, Köhler S, Lapp H, Lawrence CJ, Le Novère N, Lecointre G, Lundberg JG, Macklin J, Mast AR, Midford PE, Mikó I, Mungall CJ, Oellrich A, Osumi-Sutherland D, Parkinson H, Ramírez MJ, Richter S, Robinson PN, Ruttenberg A, Schulz KS, Segerdell E, Seltmann KC, Sharkey MJ, Smith AD, Smith B, Specht CD, Squires RB, Thacker RW, Thessen A, Fernandez-Triana J, Vihinen M, Vize PD, Voget L, Wall CE, Walls RL, Westerfield M, Wharton RA, Wirkner CS, Wooley JB, Yoder MJ, Zorn AM, Mabee PM. Finding our way through phenotypes. PLOS Biology. 13(1): e1002033. PMID: 25562316. PMCID: PMC4285398.
***Peer-reviewed proceeding papers:
Jingshan Huang, Karen Eilbeck, Judith Blake, Dejing Dou, Darren Natale, Alan Ruttenberg, Barry Smith, Michael Zimmermann, Guoqian Jiang, Yu Lin, Bin Wu, Yongqun He, Shaojie Zhang, Xiaowei Wang, He Zhang, David Schmitt, and Ming Tan. Non-Coding RNA Ontology: A comprehensive resource for unification of non-coding RNA biology. The 2015 IEEE International Conference on Bioinformatics and Biomedicine (BIBM'15), Washington D.C., Nov 9-12, 2015. 4-page short paper accepted.
Ozgur A, Hur J, He Y. Extension of the Interaction Network Ontology for literature mining of gene-gene interaction networks from sentences with multiple interaction keywords. The 2015 International Workshop on Biomedical Data Mining, Modeling, and Semantic Integration (BDM2I 2015) workshop, The International Semantic Web Conference (ISWC 2015), October 11-15, 2015, Bethlehem, PA, USA. 12 pages full-length proceeding paper. Full time oral presentation.
Guo A, Racz R, Hur J, Lin Y, Xiang Z, Zhao L, Jiang G, Zhu Q, Bai J, He Y. Ontology-based collection, representation and analysis of drug-associated neuropathy adverse events. Vaccines and Drug Ontology Studies workshop (VDOS-2015), in connection with International Conference on Biomedical Ontologies (ICBO 2015), Lisbon, Portugal, July 27-30, 2015. Full-length proceeding paper. Full time oral presentation.
Lin Y, Zheng J, He Y. Ontology-based representation and analysis of vaccination informed consent. Vaccines and Drug Ontology Studies workshop (VDOS-2015), in connection with International Conference on Biomedical Ontologies (ICBO), Lisbon, Portugal, July 27-30, 2015. Full-length proceeding paper. Full time oral presentation.
He Y, Zheng J, Lin Y. Onto-animal tools for reusing ontologies, generating and editing ontology terms, and dereferencing ontology terms.International Conference on Biomedical Ontologies (ICBO-2015). Lisbon, Portugal, July 27-30, 2015. 2-page short paper for poster presentation and flask talk. URL: http://ceur-ws.org/Vol-1515/poster3.pdf.
He Y, Jiang G. Bridging Vaccine Ontology and NCIt vaccine domain for cancer vaccine data integration and analysis. International Conference on Biomedical Ontologies (ICBO-2015). Lisbon, Portugal, July 27-30, 2015. 2-page short paper for poster presentation and flask talk. URL: http://ceur-ws.org/Vol-1515/poster4.pdf.
Ong E, He Y. GOfox: Semantics-based simplified hierarchical classification and interactive visualization to support GO enrichment analysis. International Conference on Biomedical Ontologies (ICBO-2015). Lisbon, Portugal, July 27-30, 2015. 2-page short paper for software demonstration. URL: http://ceur-ws.org/Vol-1515/demo1.pdf.
He Y, Zheng J, Lin Y. Ontorat: Automatic generation and editing of ontology terms. International Conference on Biomedical Ontologies (ICBO-2015). Lisbon, Portugal, July 27-30, 2015. 2-page short paper for software demonstration. URL: http://ceur-ws.org/Vol-1515/demo2.pdf.
***Book chapter:
Racz R, He Y. The web-based DNA vaccine database DNAVaxDB and its usage for rational DNA vaccine design. In book: Vaccine Design, Methods in Molecular Biology Series. Editor: Sunil Thomas. Springer. 2015. ISBN 978-1-4939-3387-7.
He Y. Bacterial whole genome determination and applications (Chapter 20). 2015. Volume 1. In book: Molecular Medical Microbiology, Second Edition, Editors: Yi-Wei Tang, Max Sussman, Dongyou Liu, Ian R. Poxton, and Joseph D. Schwartzman. Elsevier Ltd. Volume 1, 2015. Pages 357-368. ISBN: 9780123971692. [Elsevier link] [Amazon link] [Google Books]. https://doi.org/10.1016/B978-0-12-397169-2.00020-2.
~ 2014 ~
***Journal papers:
Sarntivijai S, Lin Y, Xiang Z, Meehan TF, Diehl AD, Vempati UD, Schürer TC, Pang C, Malone J, Parkinson H, Liu Y, Takatsuki T, Saijo K, Masuya H, Nakamura Y, Brush MH, Haendel MA, Zheng J, Stoeckert CJ, Peters B, Mungall CJ, Carey TE, States DJ, Athey BD, He Y. CLO: The Cell Line Ontology. Journal of Biomedical Semantics. 2014, 5:37. doi:10.1186/2041-1480-5-37. PMID: 25852852. PMCID: PMC4387853.
Yongqun He Y, Sirarat Sarntivijai, Yu Lin, Zuoshuang Xiang, Abra Guo, Shelley Zhang, Desikan Jagannathan, Luca Toldo, Cui Tao and Barry Smith. OAE: The Ontology of Adverse Events. Journal of Biomedical Semantics. 2014, 5:29 doi:10.1186/2041-1480-5-29. PMID: 25093068.PMCID: PMC4120740.
He Y, Amer AO. Microbial modulation of host apoptosis and pyroptosis. Front. Cell. Infect. Microbiol. doi: 10.3389/fcimb.2014.00083. Accepted on June 3, 2014. PMID: 24995165. PMCID: PMC4062964.
He Y. Ontology-supported research on vaccine efficacy, safety, and integrative biological networks. Expert Reviews in Vaccines. 2014 Jul;13(7):825-41. doi: 10.1586/14760584.2014.923762. Epub 2014 Jun 7. PMID: 24909153. PMCID: PMC4815432. (Note: In this paper, the “One Network (OneNet) Theory of Life” was introduced for the first time.)
Lin Y, He Y. The Ontology of Genetic Susceptibility Factors (OGSF) and its application in modeling genetic susceptibility to vaccine adverse events. Journal of Biomedical Semantics. 2014, 5:19. doi:10.1186/2041-1480-5-19. PMID: 24963371. PMCID: PMC4068904.
Tao C, He Y, Arabandi S. A 2013 Workshop: Vaccine and Drug Ontology Studies (VDOS 2013). Journal of Biomedical Semantics. 2014 Mar 20;5(1):16. doi: 10.1186/2041-1480-5-16. PMID: 24650607. PMCID: PMC3994568.
Racz R, Li X, Patel M, Xiang Z, and He Y. DNAVaxDB: the first web-based DNA vaccine database and its data analysis. BMC Bioinformatics. 2014, 15(Suppl 4):S2. PMID: 25104313.
De Groot AS, De Groot P, He Y. ICoVax 2013: The 3rd ISV Pre-conference Computational Vaccinology Workshop. BMC Bioinformatics. 2014, 15(Suppl 4):I1. PMID: 25104130. PMCID: PMC4094997.
He Y. Vaccine adjuvant informatics: from data integration and analysis to rational vaccine adjuvant design. Front. Immunol. 2014. doi: 10.3389/fimmu.2014.00032. PMID: 24550916. PMCID: PMC3909948.
Zheng J, Xiang Z, Stoeckert Jr. CJ, He Y. Ontodog: a web-based ontology community view generation tool. Bioinformatics. 2014, 30(9):1340-2. doi: 10.1093/bioinformatics/btu008. [PDF] PMID: 24413522. PMCID: PMC3998133.
He Y, Racz R, Sayers S, Lin Y, Todd T, Hur J, Li X, Patel M, Zhao B, Chung M, Ostrow J, Sylora A, Dungarani P, Ulysse G, Kochhar K, Vidri B, Strait K, Jourdian GW, Xiang Z. Updates on the web-based VIOLIN vaccine database and analysis system. Nucleic Acids Research. 2014. 42 (D1): D1124-D1132. doi: 10.1093/nar/gkt1133. First published online: November 19, 2013. [PDF]. PMID: 24259431. PMCID: PMC3964998.
***Peer-reviewed proceeding papers:
He Y, Liu Y, Zhao B. OGG: a biological ontology for representing genes and genomes in specific organisms. Proceedings of the 5th International Conference on Biomedical Ontologies (ICBO), Houston, Texas, USA. October 8-9, 2014. Pages 13-20. [http://ceur-ws.org/Vol-1327/icbo2014_paper_23.pdf, or: http://www.hegroup.org/docs/OGG-ICBO2014.pdf, whcih has correctly formatted Figure 3]
Zheng J, Harris MR, Masci AM, Lin Y, Hero A, Smith B, He Y. OBCS: The Ontology of Biological and Clinical Statistics.Proceedings of the 5th International Conference on Biomedical Ontologies (ICBO), Houston, Texas, USA. October 8-9, 2014. Page 65. [http://ceur-ws.org/Vol-1327/icbo2014_paper_21.pdf]
Lin Y, Harris MR, Manion FJ, Eisenhauer E, Zhao B, Shi W, Karnovsky, He Y. Development of a BFO-based Informed Consent Ontology (ICO). Proceedings of the 5th International Conference on Biomedical Ontologies (ICBO), Houston, Texas, USA. October 8-9, 2014. Page 84-86. [http://ceur-ws.org/Vol-1327/icbo2014_paper_54.pdf]
Xiang Z, Lin Y, He Y. Ontobat: An Ontology-based semantic web approach for linked data processing and analysis. Proceedings of the 5th International Conference on Biomedical Ontologies (ICBO), Houston, Texas, USA. October 8-9, 2014. Page 93-95. [http://ceur-ws.org/Vol-1327/icbo2014_paper_58.pdf]
Hur J, Özgür A, Xiang Z, He Y. Development and application of an Interaction Network Ontology (INO) for literature mining of vaccine-associated gene-gene interactions. Vaccines and Drug Ontology Studies workshop (VDOS-2014), in connection with International Conference on Biomedical Ontologies (ICBO), Houston, Texas, USA. October 7, 2014. Full-length proceeding paper (Note: this paper was later extended and published in 2015 in the Journal of Biomedical Semantics. 2015, 6:4 doi:10.1186/2041-1480-6-2. See above.)
***E-Book:
Editors: He Y, Amer AO. Microbial modulation of host apoptosis and pyroptosis, by Front. Cell. Infect. Microbiol. 2014. [Research Topic Website] [Download E-Book PDF] [Download E-Book EPUB].
~ 2013 ~
***Journal papers:
Bronner DN, O'Riordan MXD, He Y. Caspase-2 mediates a Brucella abortus RB51-induced hybrid cell death having features of apoptosis and pyroptosis. Frontiers in Cellular and Infection Microbiology. 2013. 3:83. PMID: 24350060. PMCID: PMC3842122.
Marcos E , Zhao B, He Y. The ontology of vaccine adverse events (OVAE) and its usage in representing and analyzing adverse events associated with US-licensed human vaccines. Journal of Biomedical Semantics. 2013 Nov 26;4(1):40. PMID: 24279920.
Y Zhang, C Tao, Y He, P Kanjamala, H Liu. Network-based analysis of vaccine-related associations reveals consistent knowledge with the vaccine ontology. Journal of Biomedical Semantics 2013, 4:33 doi:10.1186/2041-1480-4-33. PMID: 24209834.
Xiang Z, Qin T, Qin Z, He Y. A genome-wide MeSH-based literature mining system predicts implicit gene-to-gene relationships and networks. BMC Systems Biology. 2013, 7(Suppl 3):S9. doi:10.1186/1752-0509-7-S3-S9. (note: this paper was also presented in InCoB2013 and collected in F1000Posters; see the presentation slides) PMID: 24555475. PMCID: PMC3852244.
Ma J, He Y, Hu B, Luo Z. Genome sequence of an environmental isolate of the bacterial pathogen Legionella pneumophila. Genome Announcement. 2013 vol. 1 no. 3 e00320-13. PMID: 23792742. PMCID: PMC3675512.
Todd TE, Tibi O, Lin Y, Sayers S, Bronner DN, Xiang Z, He Y. Meta-analysis of variables affecting mouse protection efficacy of whole organism Brucella vaccines and vaccine candidates. BMC Bioinformatics. 2013, 14(Suppl 6):S3. PMID: 23735014. PMCID: PMC3633026.
He Y, Xiang Z. Databases and in silico tools for vaccine design. Methods Mol Biol. 2013;993:115-27. doi: 10.1007/978-1-62703-342-8_8. PMID: 23568467. [Note: this is Chapter 8 in book: In Silico Models for Drug Discovery, Editor: Sandhya Kortagere.]
Xiang Z, He Y. Genome-wide prediction of vaccine targets for human herpes simplex viruses using Vaxign reverse vaccinology. BMC Bioinformatics. 2013, 14(Suppl 4):S2 (8 March 2013). PMID: 23514126; PMCID: PMC3599071.
He Y, Cao Z, De Groot AS, Brusic V, Schönbach C, Petrovsky N. Computational vaccinology and the ICoVax 2012 workshop. BMC Bioinformatics. 2013, 14(Suppl 4):I1 (8 March 2013). PMID: 23514034; PMCID: PMC3599086.
Racz R, Chung M, Xiang Z, and He Y. Systematic annotation and analysis of “virmugens” - virulence factors whose mutants can be used as live attenuated vaccines. Vaccine. 2013 Jan 21;31(5):797-805. Epub Dec. DOI: 10.1016/j.vaccine.2012.11.066. PMID: 23219434. PMCID: PMC3556277.
***Peer-reviewed proceeding papers:
Racz R, Li X, Patel M, Xiang Z, and He Y. DNAVaxDB: the first web-based DNA vaccine database and its data analysis. The 3rd Pre-ISV Computational Vaccinology workshop (ICoVax 2013), October 26 , 2013, Sitges, Barcelona, Spain. Full length article.
Marcos E , He Y. The Ontology of Vaccine Adverse Events (OVAE) and its usage in representing and analyzing vaccine adverse events. Workshop “Vaccine and Drug Ontology Studies (VDOS 2013)". International Conference on Biomedical Ontologies (ICBO), Montreal, Qc, Canada. July 7, 2013 . Full-length proceeding paper. [http://ceur-ws.org/Vol-1061/Paper9_vdos2013.pdf]
Lin Y, He Y. Ontology modeling of genetic susceptibility to adverse events following vaccination. Workshop “Vaccine and Drug Ontology Studies (VDOS 2013)". International Conference on Biomedical Ontologies (ICBO), Montreal, Qc, Canada. July 7, 2013 . Full-length proceeding paper. [http://ceur-ws.org/Vol-1061/Paper3_vdos2013.pdf]
Zhang Y, Tao C, He Y, Kanjamala P, Liu H. Analysis of Vaccine-related Networks using Semantic MEDLINE and the Vaccine Ontology. Workshop “Vaccine and Drug Ontology Studies (VDOS 2013)". International Conference on Biomedical Ontologies (ICBO), Montreal, Qc, Canada. July 7, 2013 . Full-length proceeding paper. [http://ceur-ws.org/Vol-1061/Paper6_vdos2013.pdf]
***Book chapter:
He Y. Genome-based computational vaccine discovery by reverse vaccinology (Chapter 5); in book: Immunomic Discovery of Adjuvants and Candidate Subunit Vaccines, edited by Darren R. Flower, Yvonne Perrie. Publisher: Springer, New York, 2013. ISBN-13: 978-1461450696. ISBN 978-1-4614-5070-2 (eBook). Links in: Google eBook, and Amazon book.
***Electronic preprint full-length paper:
He Y, Xiang Z. HINO: a BFO-aligned ontology representing human molecular interactions and pathways. arXiv. 2013. arXiv:1311.3355.
***Special Feature Report on Dr. He and He group by International Innovation:
Yongqun He: 'Analysing multidisciplinary vaccine mechanisms'. In research topic: The Mechanics of Health, International Innovation, July 2013, (Research Media, pp 41-43) ISSN 2041-4552.
(Note: International Innovation is the leading global dissemination resource for the wider scientific, technology and research communities, dedicated to disseminating the latest science, research and technological innovations on a global level. More information and a complimentary subscription offer to the publication can be found at: www.researchmedia.eu).
~ 2012 ~
***Journal papers:
Lin Y, He Y. Ontology representation and analysis of vaccine formulation and administration and their effects on vaccine immune responses. Journal of Biomedical Semantics. 2012, 3:17. PMID: 23256535. PMCID: PMC3639077.
Hur J, Özgür A, Xiang Z, He Y. Identification of fever and vaccine-associated gene interaction networks using ontology-based literature mining. Journal of Biomedical Semantics. 2012, 3:18. PMID: 23256563. PMCID: PMC3599673.
Tao C, He Y, Yang H, Gregory PA, Chute CG. Ontology-based time information representation of vaccine adverse events in VAERS for temporal analysis. Journal of Biomedical Semantics. 2012, 3:13. PMID: 23256916. PMCID: PMC3554604.
He Y, Toldo L, Burns G, Tao C, Abernethy DR. A 2012 Workshop: Vaccine and Drug Ontology in the Study of Mechanism and Effect (VDOSME 2012). Journal of Biomedical Semantics 2012, 3:12. PMID: 23249650. PMCID: PMC3554582.
Sarntivijai S, Xiang Z, Shedden KA, Markel H, Omenn GS, Athey BD, and He Y. Ontology-based combinatorial comparative analysis of adverse events associated with killed and live influenza vaccines. PLoS ONE. 2012, 7(11): e49941. doi:10.1371/journal.pone.0049941. PMID: 23209624. PMCID: PMC3509157.
Liu W, Jing Z, Ou Q, Cui B, He Y*, Wu Q*. Complete genome sequence of Brucella melitensis biovar 3 strain NI, isolated from an aborted bovine fetus. Journal of Bacteriology. 2012, 194(22):6321. PMID: 23105063. PMCID: PMC3486367.
Li X, He Y. Caspase-2-dependent dendritic cell death, maturation, and priming of T cells in response to Brucella abortus infection. PLoS ONE, 2012, 7(8): e43512. doi:10.1371/journal.pone.0043512. PMID: 22927979. PMCID: PMC3425542.
Lin Y, He Y. New era of developing and using ontologies for microbiology research and diagnosis. Journal of Microbiology and Diagnosis. 2012. 1:e107. doi:10.4172/2161- 0703.1000e107.
Banai M, He Y. Systems biology and bioinformatics help decipher Brucella antigens involved in clinical manifestation of the disease. Frontiers in Cellular and Infection Microbiology. 2012. 2:34. Epub 2012 Mar 21. PMID: 22919626. PMCID: PMC3417652.
Akhtar R, He Y, Larson CB, Chaudhary ZI, ud-Din Ahmad M. Differential stimulatory activities of smooth and rough Brucella abortus lipopolysaccharide in murine macrophages. Pak Vet J. 2012. 32(3): 339-344.
He Y. Analyses of Brucella pathogenesis, host immunity, and vaccine targets using systems biology and bioinformatics. Frontiers in Cellular and Infection Microbiology. 2012. 2:2. doi: 10.3389/fcimb.2012.00002. PMID: 22919594. PMCID: PMC3417401.
Sayers S, Ulysse G, Xiang Z, and He Y. Vaxjo: a web-based vaccine adjuvant database and its application for analysis of vaccine adjuvants and their uses in vaccine development. Journal of Biomedicine and Biotechnology. 2012;2012:831486. Epub 2012 Mar 13. PMID: 22505817. PMCID: PMC3312338.
***Peer-reviewed proceeding papers:
He Y, Xiang Z. Bioinformatics analysis of bacterial protective antigens in manually curated Protegen database. Procedia in Vaccinology. 2012. Volume 6. Pages 3 – 9.
Lin Y, He Y. Ontology representation and analysis of vaccine formulation and administration and their effects on vaccine immune responses. Workshop “Vaccine and Drug Ontology in the Study of Mechanism and Effect (VDOSME-2012)”, International Conference on Biomedical Ontologies (ICBO), University of Graz, Austria, July 2012. URL: http://kr-med.org/icbofois2012/vdosme/index.htm. Full-length proceeding paper.
Hur J, Özgür A, Xiang Z, He Y. Identification of fever and vaccine-associated gene interaction networks using ontology-based literature mining. Workshop “Vaccine and Drug Ontology in the Study of Mechanism and Effect (VDOSME-2012)”, International Conference on Biomedical Ontologies (ICBO), University of Graz, Austria, July 2012. Full-length proceeding paper.
Tao C, He Y, Poland G, Chute C. Time Modeling of Vaccine Adverse Events in VAERS for Temporal Analysis. Workshop “Vaccine and Drug Ontology in the Study of Mechanism and Effect (VDOSME-2012)”, International Conference on Biomedical Ontologies (ICBO), University of Graz, Austria, July 2012. Full-length proceeding paper.
***Book chapter:
He Y. Omics-based systems vaccinology for vaccine target identification. Drug Development Research. In: Special Issue: Impact of Omics on Drug Discovery and Development. Part II. Volume 73, Issue 8, pages 559–568, December 2012. DOI: 10.1002/ddr.21049.
***Interviewd for peer-reviewed article:
Jones D. Reverse vaccinology on the cusp. Nature Reviews Drug Discovery. 2012 Feb 10;11(3):175-6. PMID: 22322255. doi: 10.1038/nrd3679.
~ 2011 ~
***Journal papers:
Zhu J*, Larson CB*, Ramaker MA, Quandt K, Wendte J, Ku K, Chen F, Jourdian G, Vemulapalli R, Schurig GG, He Y. Characterization of recombinant B. abortus strain RB51SOD towards understanding the uncorrelated innate and adaptive immune responses induced by RB51SOD compared to its parent vaccine strain RB51. Front. Cell. Inf. Microbio. 1:10. doi: 10.3389/fcimb.2011.00010. (*: co-first authors). PMID: 22919576. PMCID: PMC3417361.
Lin Y, Xiang Z, He Y. Brucellosis Ontology (IDOBRU) as an extension of the Infectious Disease Ontology. Journal of Biomedical Semantics. 2011 Oct 31;2(1):9. [Epub ahead of print] PMID: 22041276. PMCID: PMC3217896.
Hur J, Xiang Z, Feldman EL, He Y. Ontology-based Brucella vaccine literature indexing and systematic analysis of gene-vaccine association network. BMC Immunology. 12(1):49 2011 Aug 26. PMID: 21871085. PMCID: PMC3180695.
Akhtar R, Chaudhary ZI, He Y, Ahmad MU, Younus M. (2011). Murine macrophages are more brucellicidal than bovine macrophages. Pakistan Journal of Zoology. In press.
He Y, Rappuoli R, De Groot A, Chen RT. Vaccine informatics. Journal of Biomedicine and Biotechnology. 2010;2010:765762. Epub 2011 Jun 22. PMID: 21772788. PMCID: PMC3134834.
He Y, Rappuoli R, De Groot A, Chen RT. Emerging vaccine informatics. Journal of Biomedicine and Biotechnology. 2010 (2010), Article ID 218590, 26 pages. 2010;2010:218590. Epub 2011 Jun 15. (Note: This is a comprehensive 26-page review article in the Special Issue on Vaccine Informatics.) PMID: 21772787. PMCID: PMC3134832.
Ozgur A, Xiang Z, Radev D, He Y. Mining of vaccine-associated IFN-γ gene interaction networks using the Vaccine Ontology. Journal of Biomedical Semantics. 2011, 2(Suppl 2):S8. PMID: 21624163. PMCID: PMC3102897.
Vigil1 PD, Stapleton AE, Johnson JR, Hooton TM, Hodges AP, He Y, Mobley HLT. Putative Repeat-in-Toxin (RTX) gene tosA of Escherichia coli predicts successful colonization of the urinary tract. MBio. 2011 May 3;2(3). pii: e00066-11. doi: 10.1128/mBio.00066-11. PMID: 21540363. PMCID: PMC3088117.
Chen F, Ding X, Ding Y, Xiang Z, Li X, Ghosh D, Schurig GG, Sriranganathan N, Boyle SM, He Y. Proinflammatory caspase-2 mediated macrophage cell death induced by rough attenuated Brucella suis. Infection and Immunity. 2011 Jun;79(6):2460-9. PMID: 21464087. PMCID: PMC3125819.
Yang B*, Sayers S*, Xiang Z, He Y. Protegen: a web-based protective antigen database and analysis system. Nucleic Acids Research. 2011 Jan;39(Database issue):D1073-8. Epub 2010 Oct 19. PMID: 20959289. PMCID: PMC3013795. (*: co-first authors)
Shayman JA, Kelly R, Kollmeyer J, He Y, Abe A. Group XV phospholipase A2, a lysosomal phospholipase A2. Prog Lipid Res. 2011 Jan;50(1):1-13. Epub 2010 Nov 11. PMID: 21074554. PMCID: PMC3039127.
***Peer-reviewed proceeding papers:
He Y, Xiang Z, Sarntivijai S, Toldo L, Ceusters W. AEO: a realism-based biomedical ontology for the representation of adverse events. Adverse Event Representation Workshop, International Conference on Biomedical Ontologies (ICBO), University at Buffalo, NY, July 26-30, 2011. Full length paper. Pages 309 - 315. [http://ceur-ws.org/Vol-833/paper59.pdf]
Sarntivijai S, Xiang Z, Meehan TF, Diehl AD,Vempati U, Schurer S, Pang C, Malone J, Parkinson H, Athey BD, He Y. Cell Line Ontology: Redesigning Cell Line Knowledgebase to Aid Integrative Translational Informatics. Proceedings of the 2nd International Conference on Biomedical Ontologies (ICBO-2011), Buffalo, NY, USA, July 28-30, 2011. Pages 25 - 32. [http://ceur-ws.org/Vol-833/paper4.pdf]
Lin Y, Xiang Z, He Y. Towards a Semantic Web application: Ontology-driven ortholog clustering analysis. Proceedings of the 2nd International Conference on Biomedical Ontologies (ICBO-2011), Buffalo, NY, USA, July 28-30, 2011. Page 33 - 40. [http://ceur-ws.org/Vol-833/paper5.pdf]
Xiang Z, Mungall C, Ruttenberg A, He Y. Ontobee: A Linked Data Server and Browser for Ontology Terms. Proceedings of the 2nd International Conference on Biomedical Ontologies (ICBO), Buffalo, NY, USA, July 28-30, 2011. Pages 279-281. [http://ceur-ws.org/Vol-833/paper48.pdf]
***Book chapter:
Hodges AP, Woolf P, He Y. Prediction of novel pathway elements and interactions using Bayesian networks. A chapter in book: "Bioinformatics - Experimental Biology Systems". ISBN 978-953-307-280-7. Editor: Ning-Sun Yang. InTech - Open Access Publisher. Page 185-204.
~ 2010 ~
***Journal papers:
Akhtar R, Chaudhary ZI, He Y. Modified method for isolation of peripheral blood neutrophils from bovines and humans. International Journal of Agro Veterinary Medicine. 2010. 4: 8-14.
He Y, Xiang Z. Bioinformatics analysis of Brucella vaccines and vaccine targets using VIOLIN. Immunome Research. 2010 Sep 27;6 Suppl 1:S5. PMID: 20875156.
PMCID: PMC2946783.
Hodges AP, Woolf P, He Y. BN+1 Bayesian network expansion for identifying molecular pathway elements. Communicative & Integrative Biology. 2010. Volume 3, Issue 6, Page 1-6. PMID: 21331236. PMCID: PMC3038060. (NOTE: this is an invited Addendum Article to our recent PloS ONE paper with PMID: 20209085)
Xiang Z, Courtot M, Brinkman RR, Ruttenberg A, He Y. OntoFox: web-based support for ontology reuse. BMC Research Notes. 2010, 3:175. PMID: 20569493. PMCID: PMC2911465.
He Y, Xiang Z, Mobley HLT. Vaxign: the first web-based vaccine design program for reverse vaccinology and an application for vaccine development. Journal of Biomedicine and Biotechnology. Volume 2010 (2010), Article ID 297505, 15 pages. [PMID: 20671958]. PMCID: PMC2910479.
Ozgur A, Xiang Z, Radev D, He Y. Literature-based discovery of IFN-γ and vaccine-mediated gene interaction networks. Journal of Biomedicine and Biotechnology. Volume 2010 (2010), Article ID 426479, 13 pages. PMID: 20625487. PMCID: PMC2896678.
Brinkman RR, Courtot M, Derom D, Fostel JM, He Y, Lord P, Malone J, Parkinson H, Peters B, Rocca-Serra P, Ruttenberg A, Sansone S, Soldatova LN, Stoeckert Jr. CJ, Turner J, Zheng J, the OBI consortium. Modeling biomedical experimental processes with OBI. Journal of Biomedical Semantics. 2010, 1(Suppl 1):S7. PMID: 20626927. PMCID: PMC2903726.
McNamara L, He Y, Yang Z. Using epitope predictions to evaluate efficacy and population coverage of the Mtb72f vaccine for tuberculosis. BMC Immunology. 2010 Mar 30;11(1):18. PMID: 20353587. PMCID: PMC2862017.
Hodges AP, Dai D, Xiang Z, Woolf P, Xi C, He Y. Bayesian network expansion identifies new ROS and biofilm regulators. PLoS ONE. 2010 Mar 3;5(3):e9513. PMID: 20209085. PMCID: PMC2831072.
Sloat BR, Sandoval MA, Hau AM, He Y, Cui Z. Strong antibody responses induced by protein antigens conjugated onto the surface of lecithin-based nanoparticles. J Control Release. 2010 Jan 4;141(1):93-100. PMID: 19729045. PMCID: PMC2789915.
***Peer-reviewed proceeding papers:
Ozgur A, Xiang Z, Radev D, He Y. Mining of vaccine-associated IFN-γ gene interaction networks using the Vaccine Ontology. Proceeding of Bio-Ontologies 2010: Semantic Applications in Life Sciences, ISMB, July 9-10, 2010. Boston, MA, USA. Full length paper.
He Y, Xiang Z, Todd T, Courtot M, Brinkman R, Zheng J, Stoeckert CJ, Malone J, Rocca-Serra P, Sansone S, Fostel J, Soldatova LN, Peters B, Rutternberg A. Ontology representation and ANOVA analysis of vaccine protection investigation. Proceeding of Bio-Ontologies 2010: Semantic Applications in Life Sciences, ISMB, July 9-10, 2010. Boston, MA, USA. Full length paper.
***Book chapter:
He Y, Xiang Z. miniTUBA: a web-based dynamic Bayesian network analysis system and an application in host-pathogen interaction analysis. Bayesian Network, Ahmed Rebai (Ed.), ISBN: 978-953-307-124-4, Sciyo, Available from: http://www.intechopen.com/articles/show/title/minituba-a-web-based-dynamic-bayesian-network-analysis-system-.
~ 2009 ~
***Journal paper:
Chen F, He Y. Caspase-2 mediated apoptotic and necrotic murine macrophage cell death induced by rough Brucella abortus. PLoS ONE. 2009 Aug 28;4(8):e6830. PMID: 19714247. PMCID: PMC2729395.
***peer-reviewed proceeding papers:
In alphabetic order: Brinkman RR, Courtot M, Derom D, Foste JM, He Y, Lord P, Malone J, Parkinson H, Peters B, Rocca-Serra P, Ruttenberg A, Sansone S, Soldatova LN, Stoeckert Jr. CJ, Jessica Turner J, Zheng J, and the OBI consortium. 2009. The modeling of biomedical experimental processes with OBI. Bio-Ontolgies Workshop (at ISMB 2009). Full length paper.
Xiang Z, He Y. Vaxign: a web-based vaccine target design program for reverse vaccinology. Procedia in Vaccinology. 2009. Volume 1, Issue 1, Pages 23-29.
***Book chapter:
Boyle SM, He Y, Tsolis RM. 2009. Genome mapping and microarray contributions to understanding Brucella pathobiology and host responses to Brucella infections (Brucella subchapter 9). In: V. Nene, and C. Cole, editors. Genome Mapping and Genomics in Animal-Associated Microbes (ISBN: 978-3-540-74040-7). Springer, New York, NY. p. 44-50.
~ 2008 ~
Xiang Z, Todd T, Ku KP, Kovacic BL, Larson CB, Chen F, Hodges AP, Tian Y, Olenzek EA, Zhao B, Colby LA, Rush HG, Gilsdorf JR, Jourdian GW, He Y. VIOLIN: Vaccine Investigation and Online Information Network. Nucleic Acids Research. 2008, Vol. 36, Database issue D923-D928. [NAR link] [PMID: 18025042]. PMCID: PMC2238972.
~ 2007 ~
Xiang Z, Minter RM, Bi X, Woolf PJ, He Y. miniTUBA: medical inference by network integration of temporal data using Bayesian analysis. Bioinformatics. 2007 Sep 15;23(18):2423-32. PMID: 17644819.
Xiang Z, Tian Y, He Y. PHIDIAS: a pathogen-host interaction data integration and analysis system. Genome Biology. 2007 Jul 30;8(7):R150. PMID: 17663773. PMCID: PMC2323235.
Xiang Z, Qin ZS, He Y. CRCView: A web server for analyzing and visualizing microarray gene expression data using model-based clustering. Bioinformatics. 2007 Jul 15;23(14):1843-5. PMID: 17485426.
He Y, Rush HG, Liepman RS, Xiang Z, Colby LA. Pathobiology and management of laboratory rodents administered CDC Category A agents. Comparative Medicine. 2007. Feb;57(1):18-32. PMID: 17348288.
~ 2006 ~
He Y, Reichow S, Ramamoorthy S, Ding X, Lathigra R, Craig JC, Sobral BW, Schurig GG, Sriranganathan N, Boyle SM. Brucella melitensis triggers time-dependent modulation of apoptosis and down-regulation of mitochondria-associated gene expression in mouse macrophages. Infection and Immunity. 2006 Sep;74(9):5035-46. PMID: 16926395. PMCID: PMC1594834.
Xiang Z, Zheng W, He Y. BBP: Brucella genome annotation with literature mining and curation. BMC Bioinformatics. 2006 Jul 16;7(1):347. (Highly accessed). PMID: 16842628. PMCID: PMC1539029.
Ratushna VG, Sturgill DM, Ramamoorthy S, Reichow SA, He Y, Lathigra R, Sriranganathan N, Halling SM, Boyle SM, Gibas CJ. Molecular targets for rapid identification of Brucella spp. BMC Microbiol. 2006 Feb 22;6:13. PMID: 16504063. PMCID: PMC1413539.
~ 2005 ~
He Y, Vines RR, Wattam AR, Abramochkin GV, Dickerman AW, Eckart JD, Sobral BW. PIML: The Pathogen Information Markup Language. Bioinformatics. 2005;21(1):116-21. PMID: 15297293.
***Book chapter:
Lathigra R, He Y, Vines RR, Nordberg EK, Sobral BWS. 2005. A biologist's view of systems integration for system biology - the Pathogen Portal Project (Chapter 13). In: J. Perry Gustafson, Randy Shoemaker and John W. Snape, editors. Genome Exploitation: Data Mining the Genome (ISBN: 0-387-24123-X). Springer, New York, NY. p 183-196.
~ 2002 ~
Vemulapalli R, He Y, Sriranganathan N, Boyle SM, Schurig GG. Brucella abortus RB51: Enhancing vaccine efficacy and developing multivalent vaccines. Veterinary Microbiology, 2002, 2406: 1-12. PMID: 12414168.
He Y, Vemulapalli R, Schurig GG. Recombinant Ochrobactrum anthropi expressing Brucella Cu/Zn-superoxide dismutase protects mice against B. abortus infection only after switching immune responses to Th1 type. Infection and Immunity, 2002, 70(5): 2535-2543. PMID: 11953393. PMCID: PMC127893.
~ 2001 ~
He Y, Vemulapalli R, Zeytun A, Schurig GG. Induction of specific cytotoxic lymphocytes in mice vaccinated with Brucella abortus RB51. Infection and Immunity. 2001, 69(9): 5502-5508. PMID: 11500423. PMCID: PMC98663.
~ 2000 ~
Vemulapalli R, He Y, Buccolo LS, Boyle SM, Sriranganathan N, Schurig GG. Complementation of Brucella abortus RB51 with a functional wboA gene results in O-antigen synthesis and enhanced vaccine efficacy but no change in its rough phenotype and attenuation. Infection and Immunity. 2000. 68(7): 3927-3932. PMID: 10858205. PMCID: PMC101669.
Vemulapalli R, He Y, Boyle SM, Sriranganathan N, Schurig GG. Brucella abortus RB51 as a vector for heterologous protein expression and induction of specific Th-1 type immune responses in mice. Infection and Immunity. 2000. 68(6): 3290-3296. PMID: 10816476. PMCID: PMC97584.
Vemulapalli R, He Y, Cravero S, Sriranganathan N, Boyle SM, Schurig GG. Overexpression of protective antigen as a novel approach to enhance vaccine efficacy of Brucella abortus strain RB51. Infection and Immunity. 2000. 68(6): 3286-3289. PMID: 10816475. PMCID: PMC97582.
~ Before 2000 ~
Yongqun He, Zhongzhi Zhang, Hanchun Yang. A serological survey of the reticuloendotheliosis virus infection in Beijing chicken flocks. Chinese Journal of Animal and Veterinary Sciences (i.e., Acta Veterinaria et Zootechnica Sinica). 1998. 29 (1): 71-78.
Haiquan Gui, Jianming Zhang, Yongqun He, Shuling Xie. A diagnosis report of a duck NewCastle Disease. Contemporary Animal Husbandry. 1993. 1: 23-24.
Note: See more about Yongqun He (Oliver)'s and He group's publications from other repositories, you can check:
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