Works by Yongqun He

Results: 140

A fourfold pathogen reference ontology suite.

Published in:

Journal of Biomedical Semantics, 2025, v. 16, n. 1, p. 1, doi. 10.1186/s13326-025-00333-6

By:

Beverley, John;
Babcock, Shane;
Benson, Carter;
De Colle, Giacomo;
Cohen, Sydney;
Diehl, Alexander D.;
Challa, Ram A. N. R.;
Mavrovich, Rachel A.;
Billig, Joshua;
Huffman, Anthony;
He, Yongqun

Publication type:

Article

Ontology-Based Meta-Analysis of Animal and Human Adverse Events Associated With Licensed Brucellosis Vaccines.

Published in:

Frontiers in Pharmacology, 2018, p. 1, doi. 10.3389/fphar.2018.00503

By:

Jiangan Xie;
Jessica Wang;
Zhangyong Li;
Wei Wang;
Yu Pang;
Yongqun He

Publication type:

Article

VIGET: A web portal for study of vaccine-induced host responses based on Reactome pathways and ImmPort data.

Published in:

Frontiers in Immunology, 2023, p. 1, doi. 10.3389/fimmu.2023.1141030

By:

Brunson, Timothy;
Sanati, Nasim;
Huffman, Anthony;
Maria Masci, Anna;
Jie Zheng;
Cooke, Michael F.;
Conley, Patrick;
Yongqun He;
Guanming Wu

Publication type:

Article

VIGET: A web portal for study of vaccine-induced host responses based on Reactome pathways and ImmPort data.

Published in:

Frontiers in Immunology, 2023, v. 14, p. 1, doi. 10.3389/fimmu.2023.1141030

By:

Brunson, Timothy;
Sanati, Nasim;
Huffman, Anthony;
Masci, Anna Maria;
Jie Zheng;
Cooke, Michael F.;
Conley, Patrick;
Yongqun He;
Guanming Wu

Publication type:

Article

Immunity-related genes in Ixodes scapularis--perspectives from genome information.

Published in:

Frontiers in Cellular & Infection Microbiology, 2014, p. 1, doi. 10.3389/fcimb.2014.00116

By:

Smith, Alexis A.;
Pal, Utpal;
Janakiram Seshu;
He, Yongqun "Oliver"

Publication type:

Article

Microbial modulation of host apoptosis and pyroptosis.

Published in:

Frontiers in Cellular & Infection Microbiology, 2014, v. 4, p. 1, doi. 10.3389/fcimb.2014.00083

By:

Yongqun He;
Amer, Amal O.

Publication type:

Article

Caspase-2 mediates a Brucella abortus RB51-induced hybrid cell death having features of apoptosis and pyroptosis.

Published in:

Frontiers in Cellular & Infection Microbiology, 2013, v. 3, p. 1, doi. 10.3389/fcimb.2013.00083

By:

Bronner, Denise N.;
O'Riordan, Mary X. D.;
Yongqun He

Publication type:

Article

Understanding the pneumococcus: transmission and evolution.

Published in:

Frontiers in Cellular & Infection Microbiology, 2013, v. 3, p. 1, doi. 10.3389/fcimb.2013.00007

By:

Donkor, Eric S.;
Fitzgerald, Ross;
Raoult, Didier;
He, Yongqun "Oliver"

Publication type:

Article

Linking MedDRA(®)-Coded Clinical Phenotypes to Biological Mechanisms by the Ontology of Adverse Events: A Pilot Study on Tyrosine Kinase Inhibitors.

Published in:

2016

By:

Sarntivijai, Sirarat;
Zhang, Shelley;
Jagannathan, Desikan G;
Zaman, Shadia;
Burkhart, Keith K;
Omenn, Gilbert S;
He, Yongqun;
Athey, Brian D;
Abernethy, Darrell R

Publication type:

journal article

The Ontology of Vaccine Adverse Events (OVAE) and its usage in representing and analyzing adverse events associated with US-licensed human vaccines.

Published in:

Journal of Biomedical Semantics, 2013, v. 4, n. 1, p. 2, doi. 10.1186/2041-1480-4-40

By:

Marcos, Erica;
Bin Zhao;
Yongqun He

Publication type:

Article

Network-based analysis of vaccine-related associations reveals consistent knowledge with the vaccine ontology.

Published in:

Journal of Biomedical Semantics, 2013, v. 4, n. 1, p. 2, doi. 10.1186/2041-1480-4-33

By:

Yuji Zhang;
Cui Tao;
Yongqun He;
Pradip Kanjamala;
Hongfang Liu

Publication type:

Article

Ontology representation and analysis of vaccine formulation and administration and their effects on vaccine immune responses.

Published in:

Journal of Biomedical Semantics, 2012, v. 3, n. 1, p. 1, doi. 10.1186/2041-1480-3-17

By:

Yu Lin;
Yongqun He

Publication type:

Article

Identification of fever and vaccine-associated gene interaction networks using ontology-based literature mining.

Published in:

Journal of Biomedical Semantics, 2012, v. 3, n. 1, p. 1, doi. 10.1186/2041-1480-3-18

By:

Hur, Junguk;
Özgür, Arzucan;
Zuoshuang Xiang;
Yongqun He

Publication type:

Article

Ontology-based time information representation of vaccine adverse events in VAERS for temporal analysis.

Published in:

Journal of Biomedical Semantics, 2012, v. 3, n. 1, p. 13, doi. 10.1186/2041-1480-3-13

By:

Cui Tao;
Yongqun He;
Yang, Hannah;
Poland, Gregory A.;
Chute, Christopher G.

Publication type:

Article

A 2012 Workshop: Vaccine and Drug Ontology in the Study of Mechanism and Effect (VDOSME 2012).

Published in:

Journal of Biomedical Semantics, 2012, v. 3, n. 1, p. 12, doi. 10.1186/2041-1480-3-12

By:

Yongqun He;
Toldo, Luca;
Burns, Gully;
Cui Tao;
Abernethy, Darrell R.

Publication type:

Article

Mining of vaccine-associated IFN-γ gene interaction networks using the Vaccine Ontology.

Published in:

Journal of Biomedical Semantics, 2011, v. 2, n. Suppl 2, p. 1, doi. 10.1186/2041-1480-2-S2-S8

By:

Özgür, Arzucan;
Zuoshuang Xiang;
Radev, Dragomir R.;
Yongqun He

Publication type:

Article

Modeling biomedical experimental processes with OBI.

Published in:

Journal of Biomedical Semantics, 2010, v. 1, n. Suppl 1, p. 1, doi. 10.1186/2041-1480-1-S1-S7

By:

Brinkman, Ryan R.;
Courtot, Mélanie;
Derom, Dirk;
Fostel, Jennifer M.;
Yongqun He;
Lord, Phillip;
Malone, James;
Parkinson, Helen;
Peters, Bjoern;
Rocca-Serra, Philippe;
Ruttenberg, Alan;
Sansone, Susanna-Assunta;
Soldatova, Larisa N.;
Stoeckert, Jr., Christian J.;
Turner, Jessica A.;
Jie Zheng

Publication type:

Article

Precision omics data integration and analysis with interoperable ontologies and their application for COVID-19 research.

Published in:

Briefings in Functional Genomics, 2021, v. 20, n. 4, p. 235, doi. 10.1093/bfgp/elab029

By:

Wang, Zhigang;
He, Yongqun

Publication type:

Article

ICEO, a biological ontology for representing and analyzing bacterial integrative and conjugative elements.

Published in:

Scientific Data, 2022, v. 9, n. 1, p. 1, doi. 10.1038/s41597-021-01112-5

By:

Liu, Meng;
Liu, Jialin;
Liu, Guitian;
Wang, Hui;
Wang, Xiaoli;
Deng, Zixin;
He, Yongqun;
Ou, Hong-Yu

Publication type:

Article

Potential transmission chains of variant B.1.1.7 and co-mutations of SARS-CoV-2.

Published in:

Cell Discovery, 2021, v. 7, n. 1, p. 1, doi. 10.1038/s41421-021-00282-1

By:

Zhang, Jingsong;
Zhang, Yang;
Kang, Jun-Yan;
Chen, Shuiye;
He, Yongqun;
Han, Benhao;
Liu, Mo-Fang;
Lu, Lina;
Li, Li;
Yi, Zhigang;
Chen, Luonan

Publication type:

Article

Impact of climate change on vaccine responses and inequity.

Published in:

Nature Climate Change, 2024, v. 14, n. 12, p. 1216, doi. 10.1038/s41558-024-02192-y

By:

Zhang, Kai;
Dang, Yifang;
Li, Yiming;
Tao, Cui;
Hur, Junguk;
He, Yongqun

Publication type:

Article

IL-17A promotes intracellular growth of Mycobacterium by inhibiting apoptosis of infected macrophages.

Published in:

Frontiers in Immunology, 2015, p. 1, doi. 10.3389/fimmu.2015.00498

By:

Cruz, Andrea;
Ludovico, Paula;
Torrado, Egidio;
Gama, José Bernardo;
Sousa, Jeremy;
Gaifem, Joana;
Appelberg, Rui;
Rodrigues, Fernando;
Cooper, Andrea M.;
Pedrosa, Jorge;
Saraiva, Margarida;
Castro, Antonio G.;
Yongqun He;
Strobl, Birgit

Publication type:

Article

Protegen: a web-based protective antigen database and analysis system.

Published in:

Nucleic Acids Research, 2011, v. 39, n. suppl_1, p. D1073, doi. 10.1093/nar/gkq944

By:

Yang, Brian;
Sayers, Samantha;
Xiang, Zuoshuang;
He, Yongqun

Publication type:

Article

VIOLIN: vaccine investigation and online information network.

Published in:

Nucleic Acids Research, 2008, v. 36, p. D923

By:

Xiang, Zuoshuang;
Todd, Thomas;
Ku, Kim P.;
Kovacic, Bethany L.;
Larson, Charles B.;
Chen, Fang;
Hodges, Andrew P.;
Tian, Yuying;
Olenzek, Elizabeth A.;
Zhao, Boyang;
Colby, Lesley A.;
Rush, Howard G.;
Gilsdorf, Janet R.;
Jourdian, George W.;
He, Yongqun

Publication type:

Article

OntoFox: web-based support for ontology reuse.

Published in:

BMC Research Notes, 2010, v. 3, p. 175, doi. 10.1186/1756-0500-3-175

By:

Zuoshuang Xiang;
Courtot, Mélanie;
Brinkman, Ryan R.;
Ruttenberg, Alan;
Yongqun He

Publication type:

Article

Development of the International Classification of Diseases Ontology (ICDO) and its application for COVID‑19 diagnostic data analysis.

Published in:

BMC Bioinformatics, 2021, v. 22, n. 1, p. 1, doi. 10.1186/s12859-021-04402-2

By:

Ling Wan;
Song, Justin;
He, Virginia;
Roman, Jennifer;
Whah, Grace;
Suyuan Peng;
Luxia Zhang;
Yongqun He

Publication type:

Article

miniTUBA: medical inference by network integration of temporal data using Bayesian analysis.

Published in:

Bioinformatics, 2007, v. 23, n. 18, p. 2423, doi. 10.1093/bioinformatics/btm372

By:

Zuoshuang Xiang;
Rebecca M. Minter;
Xiaoming Bi;
Peter J. Woolf;
Yongqun He

Publication type:

Article

CRCView: a web server for analyzing and visualizing microarray gene expression data using model-based clustering.

Published in:

Bioinformatics, 2007, v. 23, n. 14, p. 1843, doi. 10.1093/bioinformatics/btm238

By:

Zuoshuang Xiang;
Zhaohui S. Qin;
Yongqun He

Publication type:

Article

PIML: the Pathogen Information Markup Language.

Published in:

Bioinformatics, 2005, v. 21, n. 1, p. 116

By:

Yongqun He

Publication type:

Article

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.

Published in:

Frontiers in Microbiology, 2021, v. 11, p. N.PAG, doi. 10.3389/fmicb.2021.633732

By:

Wang, Haihe;
Ong, Edison;
Kao, John Y.;
Sun, Duxin;
He, Yongqun

Publication type:

Article

Cwl0971, a novel peptidoglycan hydrolase, plays pleiotropic roles in Clostridioides difficile R20291.

Published in:

Environmental Microbiology, 2021, v. 23, n. 9, p. 5222, doi. 10.1111/1462-2920.15529

By:

Zhu, Duolong;
Patabendige, Hiran Malinda Lamabadu Warnakulasuriya;
Tomlinson, Brooke Rene;
Wang, Shaohui;
Hussain, Syed;
Flores, Domenica;
He, Yongqun;
Shaw, Lindsey N.;
Sun, Xingmin

Publication type:

Article

Cwp22, a novel peptidoglycan cross‐linking enzyme, plays pleiotropic roles in Clostridioides difficile.

Published in:

Environmental Microbiology, 2019, v. 21, n. 8, p. 3076, doi. 10.1111/1462-2920.14706

By:

Zhu, Duolong;
Bullock, Jessica;
He, Yongqun;
Sun, Xingmin

Publication type:

Article

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.

Published in:

PLoS ONE, 2016, v. 11, n. 10, p. 1, doi. 10.1371/journal.pone.0164792

By:

Xie, Jiangan;
Codd, Christopher;
Mo, Kevin;
He, Yongqun

Publication type:

Article

The Ontology for Biomedical Investigations.

Published in:

PLoS ONE, 2016, v. 11, n. 4, p. 1, doi. 10.1371/journal.pone.0154556

By:

Bandrowski, Anita;
Brinkman, Ryan;
Brochhausen, Mathias;
Brush, Matthew H.;
Bug, Bill;
Chibucos, Marcus C.;
Clancy, Kevin;
Courtot, Mélanie;
Derom, Dirk;
Dumontier, Michel;
Fan, Liju;
Fostel, Jennifer;
Fragoso, Gilberto;
Gibson, Frank;
Gonzalez-Beltran, Alejandra;
Haendel, Melissa A.;
He, Yongqun;
Heiskanen, Mervi;
Hernandez-Boussard, Tina;
Jensen, Mark

Publication type:

Article

Antibiotic Resistance Determinant-Focused Acinetobacter baumannii Vaccine Designed Using Reverse Vaccinology.

Published in:

International Journal of Molecular Sciences, 2017, v. 18, n. 2, p. 458, doi. 10.3390/ijms18020458

By:

Zhaohui Ni;
Yan Chen;
Edison Ong;
Yongqun He

Publication type:

Article

Machine learning-based identification and rule-based normalization of adverse drug reactions in drug labels.

Published in:

BMC Bioinformatics, 2019, v. 20, n. 1, p. 1, doi. 10.1186/s12859-019-3195-5

By:

Tiftikci, Mert;
Özgür, Arzucan;
He, Yongqun;
Hur, Junguk

Publication type:

Article

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

Published in:

BMC Bioinformatics, 2019, v. 20, n. 1, p. 1, doi. 10.1186/s12859-019-3194-6

By:

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

Publication type:

Article

A 2018 workshop: vaccine and drug ontology studies (VDOS 2018).

Published in:

2019

By:

Hur, Junguk;
Tao, Cui;
He, Yongqun

Publication type:

Editorial

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.

Published in:

BMC Bioinformatics, 2019, v. 20, n. 7, p. 1, doi. 10.1186/s12859-019-2729-1

By:

Yu, Hong;
Nysak, Solomiya;
Garg, Noemi;
Ong, Edison;
Ye, Xianwei;
Zhang, Xiangyan;
He, Yongqun

Publication type:

Article

The cell line ontology-based representation, integration and analysis of cell lines used in China.

Published in:

BMC Bioinformatics, 2019, v. 20, n. 1, p. 249, doi. 10.1186/s12859-019-2724-6

By:

Pan, Hongjie;
Bian, Xiaocui;
Yang, Sheng;
He, Yongqun;
Yang, Xiaolin;
Liu, Yuqin

Publication type:

Article

OSCI: standardized stem cell ontology representation and use cases for stem cell investigation.

Published in:

BMC Bioinformatics, 2019, v. 20, n. 1, p. 237, doi. 10.1186/s12859-019-2723-7

By:

He, Yongqun;
Duncan, William D.;
Cooper, Daniel J.;
Hansen, Jens;
Iyengar, Ravi;
Ong, Edison;
Walker, Kendal;
Tibi, Omar;
Smith, Sam;
Serra, Lucas M.;
Zheng, Jie;
Sarntivijai, Sirarat;
Schürer, Stephan;
O'Shea, K. Sue;
Diehl, Alexander D.

Publication type:

Article

Cells in ExperimentaL Life Sciences (CELLS-2018): capturing the knowledge of normal and diseased cells with ontologies.

Published in:

BMC Bioinformatics, 2019, v. 20, n. 1, p. 227, doi. 10.1186/s12859-019-2721-9

By:

Sarntivijai, Sirarat;
He, Yongqun;
Diehl, Alexander D.

Publication type:

Article

COVID-19 vaccine design using reverse and structural vaccinology, ontology-based literature mining and machine learning.

Published in:

Briefings in Bioinformatics, 2022, v. 23, n. 4, p. 1, doi. 10.1093/bib/bbac190

By:

Huffman, Anthony;
Ong, Edison;
Hur, Junguk;
D'Mello, Adonis;
Tettelin, Hervé;
He, Yongqun

Publication type:

Article

VRprofile: gene-cluster-detection-based profiling of virulence and antibiotic resistance traits encoded within genome sequences of pathogenic bacteria.

Published in:

Briefings in Bioinformatics, 2018, v. 19, n. 4, p. 566, doi. 10.1093/bib/bbw141

By:

Li, Jun;
Tai, Cui;
Deng, Zixin;
Zhong, Weihong;
He, Yongqun;
Ou, Hong-Yu

Publication type:

Article

Genomic population structure of Helicobacter pylori Shanghai isolates and identification of genomic features uniquely linked with pathogenicity.

Published in:

Virulence, 2021, v. 12, n. 1, p. 1258, doi. 10.1080/21505594.2021.1920762

By:

Yang, Feng;
Zhang, Jinghao;
Wang, Su;
Sun, Zhaoyang;
Zhou, Jun;
Li, Feng;
Liu, Yue;
Ding, Li;
Liu, Yixin;
Chi, Wenjing;
Liu, Tao;
He, Yongqun;
Xiang, Ping;
Bao, Zhijun;
Olszewski, Michal A.;
Zhao, Hu;
Zhang, Yanmei

Publication type:

Article

Genomic population structure of Helicobacter pylori Shanghai isolates and identification of genomic features uniquely linked with pathogenicity.

Published in:

Virulence, 2021, v. 12, n. 1, p. 1258, doi. 10.1080/21505594.2021.1920762

By:

Feng Yang;
Jinghao Zhang;
Su Wang;
Zhaoyang Sun;
Jun Zhou;
Feng Li;
Yue Liu;
Li Ding;
Yixin Liu;
Wenjing Chi;
Tao Liu;
Yongqun He;
Ping Xiang;
Zhijun Bao;
Olszewski, Michal A.;
Hu Zhao;
Yanmei Zhang

Publication type:

Article

BN+1 Bayesian network expansion for identifying molecular pathway elements.

Published in:

Communicative & Integrative Biology, 2010, v. 3, n. 6, p. 549, doi. 10.4161/cib.3.6.12845

By:

Hodges, Andrew P.;
Woolf, Peter;
He, Yongqun

Publication type:

Article

Ontology-supported research on vaccine efficacy, safety and integrative biological networks.

Published in:

Expert Review of Vaccines, 2014, v. 13, n. 7, p. 825, doi. 10.1586/14760584.2014.923762

By:

He, Yongqun

Publication type:

Article

Ontological representation, integration, and analysis of LINCS cell line cells and their cellular responses.

Published in:

BMC Bioinformatics, 2017, v. 18, p. 1, doi. 10.1186/s12859-017-1981-5

By:

Ong, Edison;
Jiangan Xie;
Zhaohui Ni;
Qingping Liu;
Sarntivijai, Sirarat;
Yu Lin;
Cooper, Daniel;
Terryn, Raymond;
Stathias, Vasileios;
Chung, Caty;
Schürer, Stephan;
Yongqun He

Publication type:

Article

Comparison, alignment, and synchronization of cell line information between CLO and EFO.

Published in:

BMC Bioinformatics, 2017, v. 18, p. 1, doi. 10.1186/s12859-017-1979-z

By:

Ong, Edison;
Sarntivijai, Sirarat;
Jupp, Simon;
Parkinson, Helen;
Yongqun He

Publication type:

Article