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RESEARCH PAPER · Nature Communications · 2022

Knowledge integration and decision support for accelerated discovery of antibiotic resistance genes

Jason Youn, Navneet Rai, Ilias Tagkopoulos

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29 direct citing papers in this saved network. Explore the next layer with second-order citations.

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42 direct citing works

Knowledge integration and decision support for accelerated discovery of antibiotic resistance genesOriginalKGLM: Integrating Knowledge Graph Structure in Language Models for Link Prediction29NAFLDkb: A Knowledge Base and Platform for Drug Development against Nonalcoholic Fatty Liver Disease9From Data to Wisdom: Biomedical Knowledge Graphs for Real-World Data Insights21Navigating Healthcare Insights: A Bird’s Eye View of Explainability with Knowledge Graphs6Deep learning tools to accelerate antibiotic discovery70Fast, lightweight, and accurate metagenomic functional profiling using FracMinHash sketches6Tackling the Antimicrobial Resistance “Pandemic” with Machine Learning Tools: A Summary of Available Evidence22Distance-decay equations of antibiotic resistance genes across freshwater reservoirs2Mitigation potential of antibiotic resistance genes in water and soil by clay-based adsorbents25Artificial intelligence applications in the diagnosis and treatment of bacterial infections65Data-Driven Insights into the Contamination of Polycyclic Aromatic Hydrocarbons in Marine Bays4InteractOA: Showcasing the representation of knowledge from scientific literature in Wikidata1Artificial intelligence in food and nutrition evidence: The challenges and opportunities27Artificial intelligence in drug development498Molecular insights fast-tracked: AI in biosynthetic pathway research32ENQUIRE automatically reconstructs, expands, and drives enrichment analysis of gene and Mesh co-occurrence networks from context-specific biomedical literature2RETRACTED: AI-driven Design of Drug Delivery Systems: Strategies and Challenges in Overcoming Biological Barriers7Carbapenem Resistance in Acinetobacter baumannii: Mechanisms, Therapeutics, and Innovations42From oxidative stress to metabolic revival: Pyrite-based constructed wetlands harness S-Fe-N synergy to combat nanoplastics toxicity6A review on knowledge graphs for healthcare: Resources, applications, and promises51Proteomic and metabolomic responses of priority bacterial pathogens to subinhibitory concentration of antibiotics5Advancing AI in Agriculture through Large-Scale Collaborative Research3Knowledge graph embedding for predicting and analyzing microbial interactions1A New Era of Artificial Intelligence (AI): Transforming Drug Discovery and Development21Genome-wide screening of antibiotic survival genes in Escherichia coli MG16550Antibiotic resistance genes against “last-resort” antibiotics within the One Health framework: Dissemination, mechanisms, and AI-driven opportunities7BRIDGE – Biological Antimicrobial Resistance Inference via Domain-Knowledge Graph Embeddings0Computational paradigms for antimicrobial resistance prediction: integrating multi-omics, structural modeling, and foundation artificial intelligence systems4AResKGLM: a graph-grounded language-model framework for interpretable multi-hop antimicrobial resistance reasoning0

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29 direct citing papers saved.

  1. KGLM: Integrating Knowledge Graph Structure in Language Models for Link Prediction

    Joint Conference on Lexical and Computational Semantics · 2023-01-01

    Jason Youn, Ilias Tagkopoulos

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  2. NAFLDkb: A Knowledge Base and Platform for Drug Development against Nonalcoholic Fatty Liver Disease

    Journal of Chemical Information and Modeling · 2023-05-11

    Tingjun Xu, Wenxing Gao, Lixin Zhu, Wanning Chen, Chaoqun Niu, Wenjing Yin, Liangxiao Ma, Xinyue Zhu, Yunchao Ling, Sheng Gao, Lei Liu, Na Jiao, Wei‐Ming Chen, Guoqing Zhang, Ruixin Zhu, Dingfeng Wu

    Read original paper ↗ ·

  3. From Data to Wisdom: Biomedical Knowledge Graphs for Real-World Data Insights

    Journal of Medical Systems · 2023-05-17

    Katrin Hänsel, Sarah Nixon Dudgeon, Kei‐Hoi Cheung, Thomas J S Durant, Wade L. Schulz

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  4. Navigating Healthcare Insights: A Bird’s Eye View of Explainability with Knowledge Graphs

    IEEE International Conference on Artificial Intelligence and Knowledge Engineering (AIKE) · 2023-09-25

    Satvik Garg, Shivam B. Parikh, Somya Garg

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  5. Deep learning tools to accelerate antibiotic discovery

    Expert Opinion on Drug Discovery · 2023-10-04

    Angela Cesaro, Mojtaba Bagheri, Marcelo D. T. Torres, Fang Wan, César de la Fuente‐Núñez

    Read original paper ↗ ·

  6. Fast, lightweight, and accurate metagenomic functional profiling using FracMinHash sketches

    bioRxiv (Cold Spring Harbor Laboratory) · 2023-11-06

    Mahmudur Rahman Hera, Shaopeng Liu, Wei Wei, Judith S. Rodriguez, Chunyu Ma, David Koslicki

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  7. Tackling the Antimicrobial Resistance “Pandemic” with Machine Learning Tools: A Summary of Available Evidence

    Microorganisms · 2024-04-23

    Doris Rušić, Marko Kumrić, Ana Šešelja Perišin, Dario Leskur, Josipa Bukić, Darko Modun, Marino Vilović, Josip Vrdoljak, Dinko Martinović, Marko Grahovac, Joško Božić

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  8. Distance-decay equations of antibiotic resistance genes across freshwater reservoirs

    Water Research · 2024-05-23

    Zhao‐Feng Guo, Kiranmoy Das, Wiebke J. Boeing, Yaoyang Xu, Edoardo Borgomeo, Dong Zhang, Sicheng Ao, Xiao‐Ru Yang

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  9. Mitigation potential of antibiotic resistance genes in water and soil by clay-based adsorbents

    npj Materials Sustainability · 2024-07-25

    Raj Mukhopadhyay, Barbara Drigo, Binoy Sarkar

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  10. Artificial intelligence applications in the diagnosis and treatment of bacterial infections

    Frontiers in Microbiology · 2024-08-06

    Xiaoyu Zhang, Xiaoyu Zhang, Deng Zhang, Xin Zhang, Xifan Zhang, Xin Zhang, Xin Zhang

    Read original paper ↗ ·

  11. Data-Driven Insights into the Contamination of Polycyclic Aromatic Hydrocarbons in Marine Bays

    Environmental Science & Technology · 2024-08-13

    Dong Liu, Yan Luo, Wei-Hong Bao, Muhammad Junaid, Zhao‐Feng Guo, Yaoyang Xu

    Read original paper ↗ ·

  12. InteractOA: Showcasing the representation of knowledge from scientific literature in Wikidata

    Semantic Web · 2024-08-19

    Muhammad Elhossary, Konrad U. Förstner

    Read original paper ↗ ·

  13. Artificial intelligence in food and nutrition evidence: The challenges and opportunities

    PNAS Nexus · 2024-10-15

    Regan Lucas Bailey, Amanda J MacFarlane, Martha S. Field, Ilias Tagkopoulos, Sergio E. Baranzini, Kristen M. Edwards, Christopher James Rose, Nicholas J. Schork, Akshat Singhal, Byron Wallace, Kelly R. Fisher, Konstantinos Markakis, Patrick J. Stover

    Read original paper ↗ ·

  14. Artificial intelligence in drug development

    Nature Medicine · 2025-01-01

    Kang Zhang, Xin Yang, Yifei Wang, Yunfang Yu, Niu Huang, Gen Lin Li, Xiaokun Li, Joseph C. Wu, Shengyong Yang

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  15. Molecular insights fast-tracked: AI in biosynthetic pathway research

    Natural Product Reports · 2025-01-01

    Lijuan Liao, Mengjun Xie, Xiaoshan Zheng, Zhao Zhou, Zixin Deng, Jiangtao Gao

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  16. ENQUIRE automatically reconstructs, expands, and drives enrichment analysis of gene and Mesh co-occurrence networks from context-specific biomedical literature

    PLoS Computational Biology · 2025-02-11

    Luca Musella, Alejandro Afonso Castro, Xin Lai, Max Widmann, Julio Vera

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  17. RETRACTED: AI-driven Design of Drug Delivery Systems: Strategies and Challenges in Overcoming Biological Barriers

    Acta Pharmaceutica Sinica B · 2025-06-01

    Jiong Wu, Dilei Yan, Xiaoyan Du, Chen Wu, Xuan Lin, Bohui Xu, Ying Cao Xu, Jun Ye, Yan Shen

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  18. Carbapenem Resistance in Acinetobacter baumannii: Mechanisms, Therapeutics, and Innovations

    Microorganisms · 2025-06-27

    Joyce de Souza, Helena Regina Salomé D’Espindula, Isabel de Farias Ribeiro, Geiziane Aparecida Gonçalves, Marcelo Pillonetto, Helisson Faoro

    Read original paper ↗ ·

  19. From oxidative stress to metabolic revival: Pyrite-based constructed wetlands harness S-Fe-N synergy to combat nanoplastics toxicity

    Chemical Engineering Journal · 2025-07-04

    Mengran Guo, Xiangwei Meng, Tuoshi Zhang, Yunan Wang, Yutong Wang, Ning Hou, Xinyue Zhao

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  20. A review on knowledge graphs for healthcare: Resources, applications, and promises

    Journal of Biomedical Informatics · 2025-07-23

    Hejie Cui, Jiaying Lu, Ran Xu, Shi-Yu Wang, Wenjing Ma, Yue Yu, Shaojun Yu, Xuan Kan, Chen Ling, Liang Zhao, Zhaohui Steve Qin, Joyce C. Ho, Tianfan Fu, Jing Ma, Mengdi Huai, Fei Wang, Carl Yang

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  21. Proteomic and metabolomic responses of priority bacterial pathogens to subinhibitory concentration of antibiotics

    npj Antimicrobials and Resistance · 2025-09-16

    Monika Subanovic, Dean Frawley, Ciara Tierney, Trinidad Velasco‐Torrijos, Fiona Walsh

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  22. Advancing AI in Agriculture through Large-Scale Collaborative Research

    Communications of the ACM · 2025-11-19

    Vikram Adve, Steve Brown, Alan Fern, Baskar Ganapathysubramanian, Ananth Kalyanaraman, Shashi Shekhar, Ilias Tagkopoulos, Jessica Wedow

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  23. Knowledge graph embedding for predicting and analyzing microbial interactions

    Scientific Reports · 2025-11-21

    Mohammed Khatbane, Cécile Mangavel, Frédéric Borges, Sabeur Aridhi, Yannick Toussaint

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  24. A New Era of Artificial Intelligence (AI): Transforming Drug Discovery and Development

    Journal of Medicinal Chemistry · 2025-11-27

    Saghir Ali, Xiaochen Tian, Haiying Chen, Jia Zhou

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  25. Genome-wide screening of antibiotic survival genes in Escherichia coli MG1655

    BMC Microbiology · 2026-01-28

    Xinyu Li, Qinglei Gan, Chenguang Fan

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  26. Antibiotic resistance genes against “last-resort” antibiotics within the One Health framework: Dissemination, mechanisms, and AI-driven opportunities

    Journal of Hazardous Materials · 2026-01-29

    Yining Wu, Lin Zhu, Na Li, Chuze Lu, Chengdong Zhang, Meizhen Wang

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  27. BRIDGE – Biological Antimicrobial Resistance Inference via Domain-Knowledge Graph Embeddings

    bioRxiv (Cold Spring Harbor Laboratory) · 2026-02-11

    Aravind Iyer, Yusuff Kazeem, Somayeh Kafaie, Enayat Rajabi

    Read original paper ↗ ·

  28. Computational paradigms for antimicrobial resistance prediction: integrating multi-omics, structural modeling, and foundation artificial intelligence systems

    Briefings in Bioinformatics · 2026-04-21

    Elias Hossain, Niloofar Yousefi

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  29. AResKGLM: a graph-grounded language-model framework for interpretable multi-hop antimicrobial resistance reasoning

    Briefings in Bioinformatics · 2026-08-07

    Jie Ren, Ziyi Yang, Wei Liu, Man Tat Alexander Ng

    Read original paper ↗ ·
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