Zhiyong Lu

ResearcherID ORCID

Publication Activity (10 Years)

Years Active: 2017-2024
Publications (10 Years): 47

Top Topics

Systematic Review

Coronavirus Disease

Top Venues

Database : the journal of biological databases and curation

Nucleic acids research

Journal of medical Internet research

NPJ digital medicine

This page only lists publications with an associated author ORCID identifier.

Publications

Jiang Bian, Balu Bhasuran, Qiao Jin, Shubo Tian, Karim Hanna, Cindy Shavor, Lisbeth Garcia Arguello, Patrick Murray, Zhiyong Lu
Quality of Answers of Generative Large Language Models Versus Peer Users for Interpreting Laboratory Test Results for Lay Patients: Evaluation Study. Journal of medical Internet research 26 (2024)
Rezarta Islamaj, Po-Ting Lai, Chih Hsuan Wei, Ling Luo, Tiago Almeida, Richard A A Jonker, Sofia I R Conceição, Diana F Sousa, Cong-Phuoc Phan, Jung-Hsien Chiang, Jiru Li, Dinghao Pan, Wilailack Meesawad, Richard Tzong-Han Tsai, M Janina Sarol, Gibong Hong, Airat Valiev, Elena Tutubalina, Shao-Man Lee, Yi-Yu Hsu, Mingjie Li, Karin M Verspoor, Zhiyong Lu
The overview of the BioRED (Biomedical Relation Extraction Dataset) track at BioCreative VIII. Database : the journal of biological databases and curation 2024 (2024)
Jiang Bian, Balu Bhasuran, Qiao Jin, Shubo Tian, Karim Hanna, Cindy Shavor, Lisbeth Garcia Arguello, Patrick Murray, Zhiyong Lu
Quality of Answers of Generative Large Language Models Versus Peer Users for Interpreting Laboratory Test Results for Lay Patients: Evaluation Study. Journal of medical Internet research 26 (2024)
Chih Hsuan Wei, Alexis Allot, Po-Ting Lai, Robert Leaman, Shubo Tian, Ling Luo, Qiao Jin, Zhizheng Wang, Qingyu Chen, Zhiyong Lu
PubTator 3.0: an AI-powered literature resource for unlocking biomedical knowledge. Nucleic acids research 52 (W1) (2024)
Zhiyong Lu, Yifan Peng, Trevor Cohen, Marzyeh Ghassemi, Chunhua Weng, Shubo Tian
Large language models in biomedicine and health: current research landscape and future directions. Journal of the American Medical Informatics Association : JAMIA 31 (9) (2024)
Po-Ting Lai, Elisabeth Coudert, Lucila Aimo, Kristian B Axelsen, Lionel Breuza, Edouard de Castro, Marc Feuermann, Anne Morgat, Lucille Pourcel, Ivo Pedruzzi, Sylvain Poux, Nicole Redaschi, Catherine Rivoire, Anastasia Sveshnikova, Chih-Hsuan Wei, Robert Leaman, Ling Luo, Zhiyong Lu, Alan Bridge
EnzChemRED, a rich enzyme chemistry relation extraction dataset. Scientific data 11 (1) (2024)
Rezarta Islamaj, Po-Ting Lai, Chih Hsuan Wei, Ling Luo, Tiago Almeida, Richard A A Jonker, Sofia I R Conceição, Diana F Sousa, Cong-Phuoc Phan, Jung-Hsien Chiang, Jiru Li, Dinghao Pan, Wilailack Meesawad, Richard Tzong-Han Tsai, M Janina Sarol, Gibong Hong, Airat Valiev, Elena Tutubalina, Shao-Man Lee, Yi-Yu Hsu, Mingjie Li, Karin M Verspoor, Zhiyong Lu
The overview of the BioRED (Biomedical Relation Extraction Dataset) track at BioCreative VIII. Database : the journal of biological databases and curation 2024 (2024)
Jiang Bian, Balu Bhasuran, Qiao Jin, Shubo Tian, Karim Hanna, Cindy Shavor, Lisbeth Garcia Arguello, Patrick Murray, Zhiyong Lu
Quality of Answers of Generative Large Language Models Versus Peer Users for Interpreting Laboratory Test Results for Lay Patients: Evaluation Study. Journal of medical Internet research 26 (2024)
Gongbo Zhang, Qiao Jin, Yiliang Zhou, Song Wang, Betina Idnay, Yiming Luo, Elizabeth Park, Jordan Gabriela Nestor, Matthew E Spotnitz, Ali Soroush, Thomas R Campion, Zhiyong Lu, Chunhua Weng, Yifan Peng
Closing the gap between open source and commercial large language models for medical evidence summarization. NPJ digital medicine 7 (1) (2024)
Qiao Jin, Yifan Yang, Qingyu Chen, Zhiyong Lu
GeneGPT: augmenting large language models with domain tools for improved access to biomedical information. Bioinformatics (Oxford, England) 40 (2) (2024)
Qiao Jin, Fangyuan Chen, Yiliang Zhou, Ziyang Xu, Justin M Cheung, Robert Chen, Ronald M Summers, Justin F Rousseau, Peiyun Ni, Marc J Landsman, Sally L Baxter, Subhi J Al'Aref, Yijia Li, Alexander Chen, Josef A Brejt, Michael F Chiang, Yifan Peng, Zhiyong Lu
Hidden flaws behind expert-level accuracy of multimodal GPT-4 vision in medicine. NPJ digital medicine 7 (1) (2024)
Qiao Jin, Fangyuan Chen, Yiliang Zhou, Ziyang Xu, Justin M Cheung, Robert Chen, Ronald M Summers, Justin F Rousseau, Peiyun Ni, Marc J Landsman, Sally L Baxter, Subhi J Al'Aref, Yijia Li, Alexander Chen, Josef A Brejt, Michael F Chiang, Yifan Peng, Zhiyong Lu
Hidden flaws behind expert-level accuracy of multimodal GPT-4 vision in medicine. NPJ digital medicine 7 (1) (2024)
Jiang Bian, Balu Bhasuran, Qiao Jin, Shubo Tian, Karim Hanna, Cindy Shavor, Lisbeth Garcia Arguello, Patrick Murray, Zhiyong Lu
Quality of Answers of Generative Large Language Models Versus Peer Users for Interpreting Laboratory Test Results for Lay Patients: Evaluation Study. Journal of medical Internet research 26 (2024)
Yifan Yang, Xiaoyu Liu, Qiao Jin, Furong Huang, Zhiyong Lu
Unmasking and quantifying racial bias of large language models in medical report generation. Communications medicine 4 (1) (2024)
Zhiyong Lu, Yifan Peng, Trevor Cohen, Marzyeh Ghassemi, Chunhua Weng, Shubo Tian
Large language models in biomedicine and health: current research landscape and future directions. Journal of the American Medical Informatics Association : JAMIA 31 (9) (2024)
Chih Hsuan Wei, Alexis Allot, Po-Ting Lai, Robert Leaman, Shubo Tian, Ling Luo, Qiao Jin, Zhizheng Wang, Qingyu Chen, Zhiyong Lu
PubTator 3.0: an AI-powered literature resource for unlocking biomedical knowledge. Nucleic acids research (2024)
Jiang Bian, Balu Bhasuran, Qiao Jin, Shubo Tian, Karim Hanna, Cindy Shavor, Lisbeth Garcia Arguello, Patrick Murray, Zhiyong Lu
Quality of Answers of Generative Large Language Models Versus Peer Users for Interpreting Laboratory Test Results for Lay Patients: Evaluation Study. Journal of medical Internet research 26 (2024)
Zhiyong Lu, Yifan Peng, Trevor Cohen, Marzyeh Ghassemi, Chunhua Weng, Shubo Tian
Large language models in biomedicine and health: current research landscape and future directions. Journal of the American Medical Informatics Association : JAMIA 31 (9) (2024)
Jiang Bian, Balu Bhasuran, Qiao Jin, Shubo Tian, Karim Hanna, Cindy Shavor, Lisbeth Garcia Arguello, Patrick Murray, Zhiyong Lu
Quality of Answers of Generative Large Language Models Versus Peer Users for Interpreting Laboratory Test Results for Lay Patients: Evaluation Study. Journal of medical Internet research 26 (2024)
Qiao Jin, Fangyuan Chen, Yiliang Zhou, Ziyang Xu, Justin M Cheung, Robert Chen, Ronald M Summers, Justin F Rousseau, Peiyun Ni, Marc J Landsman, Sally L Baxter, Subhi J Al'Aref, Yijia Li, Alexander Chen, Josef A Brejt, Michael F Chiang, Yifan Peng, Zhiyong Lu
Hidden flaws behind expert-level accuracy of multimodal GPT-4 vision in medicine. NPJ digital medicine 7 (1) (2024)
Qiao Jin, Fangyuan Chen, Yiliang Zhou, Ziyang Xu, Justin M Cheung, Robert Chen, Ronald M Summers, Justin F Rousseau, Peiyun Ni, Marc J Landsman, Sally L Baxter, Subhi J Al'Aref, Yijia Li, Alexander Chen, Josef A Brejt, Michael F Chiang, Yifan Peng, Zhiyong Lu
Hidden flaws behind expert-level accuracy of multimodal GPT-4 vision in medicine. NPJ digital medicine 7 (1) (2024)
Chih Hsuan Wei, Alexis Allot, Po-Ting Lai, Robert Leaman, Shubo Tian, Ling Luo, Qiao Jin, Zhizheng Wang, Qingyu Chen, Zhiyong Lu
PubTator 3.0: an AI-powered literature resource for unlocking biomedical knowledge. Nucleic acids research (2024)
Jiang Bian, Balu Bhasuran, Qiao Jin, Shubo Tian, Karim Hanna, Cindy Shavor, Lisbeth Garcia Arguello, Patrick Murray, Zhiyong Lu
Quality of Answers of Generative Large Language Models Versus Peer Users for Interpreting Laboratory Test Results for Lay Patients: Evaluation Study. Journal of medical Internet research 26 (2024)
Vipina K Keloth, Yan Hu, Qianqian Xie, Xueqing Peng, Yan Wang, Andrew Zheng, Melih Selek, Kalpana Raja, Chih Hsuan Wei, Qiao Jin, Zhiyong Lu, Qingyu Chen, Hua Xu
Advancing entity recognition in biomedicine via instruction tuning of large language models. Bioinformatics (Oxford, England) 40 (4) (2024)
Chih Hsuan Wei, Alexis Allot, Po-Ting Lai, Robert Leaman, Shubo Tian, Ling Luo, Qiao Jin, Zhizheng Wang, Qingyu Chen, Zhiyong Lu
PubTator 3.0: an AI-powered literature resource for unlocking biomedical knowledge. Nucleic acids research 52 (W1) (2024)
Qiao Jin, Won Kim, Qingyu Chen, Donald C Comeau, Lana Yeganova, W John Wilbur, Zhiyong Lu
MedCPT: Contrastive Pre-trained Transformers with large-scale PubMed search logs for zero-shot biomedical information retrieval. Bioinformatics (Oxford, England) 39 (11) (2023)
Eric W Sayers, Jeff Beck, Evan E Bolton, J Rodney Brister, Jessica Chan, Donald C Comeau, Ryan Connor, Michael DiCuccio, Catherine M Farrell, Michael Feldgarden, Anna M Fine, Kathryn Funk, Eneida Hatcher, Marilu Hoeppner, Megan Kane, Sivakumar Kannan, Kenneth S Katz, Christopher Kelly, William Klimke, Sunghwan Kim, Avi Kimchi, Melissa Landrum, Stacy Lathrop, Zhiyong Lu, Adriana Malheiro, Aron Marchler-Bauer, Terence D Murphy, Lon Phan, Arjun B Prasad, Shashikant Pujar, Amanda Sawyer, Erin Schmieder, Valerie A Schneider, Conrad L Schoch, Shobha Sharma, Françoise Thibaud-Nissen, Barton W Trawick, Thilakam Venkatapathi, Jiyao Wang, Kim D Pruitt, Stephen T Sherry
Database resources of the National Center for Biotechnology Information. Nucleic acids research (2023)
Alexis Allot, Chih-Hsuan Wei, Lon Phan, Timothy Hefferon, Melissa Landrum, Michael J Bamshad, Zhiyong Lu
Tracking genetic variants in the biomedical literature using LitVar 2.0. Nature genetics (2023)
Robert Leaman, Rezarta Islamaj, Virginia Adams, Mohammed A Alliheedi, João Rafael Almeida, Rui Antunes, Robert Bevan, Yung-Chun Chang, Arslan Erdengasileng, Matthew Hodgskiss, Ryuki Ida, Hyunjae Kim, Keqiao Li, Robert E Mercer, Lukrécia Mertová, Ghadeer Mobasher, Hoo-Chang Shin, Mujeen Sung, Tomoki Tsujimura, Wen-Chao Yeh, Zhiyong Lu
Chemical identification and indexing in full-text articles: an overview of the NLM-Chem track at BioCreative VII. Database : the journal of biological databases and curation 2023 (2023)
Robert Leaman, Rezarta Islamaj, Virginia Adams, Mohammed A Alliheedi, João Rafael Almeida, Rui Antunes, Robert Bevan, Yung-Chun Chang, Arslan Erdengasileng, Matthew Hodgskiss, Ryuki Ida, Hyunjae Kim, Keqiao Li, Robert E Mercer, Lukrécia Mertová, Ghadeer Mobasher, Hoo-Chang Shin, Mujeen Sung, Tomoki Tsujimura, Wen-Chao Yeh, Zhiyong Lu
Chemical identification and indexing in full-text articles: an overview of the NLM-Chem track at BioCreative VII. Database : the journal of biological databases and curation 2023 (2023)
Robert Leaman, Rezarta Islamaj, Virginia Adams, Mohammed A Alliheedi, João Rafael Almeida, Rui Antunes, Robert Bevan, Yung-Chun Chang, Arslan Erdengasileng, Matthew Hodgskiss, Ryuki Ida, Hyunjae Kim, Keqiao Li, Robert E Mercer, Lukrécia Mertová, Ghadeer Mobasher, Hoo-Chang Shin, Mujeen Sung, Tomoki Tsujimura, Wen-Chao Yeh, Zhiyong Lu
Chemical identification and indexing in full-text articles: an overview of the NLM-Chem track at BioCreative VII. Database : the journal of biological databases and curation 2023 (2023)
Qingyu Chen, Alexis Allot, Robert Leaman, Chih-Hsuan Wei, Elaheh Aghaarabi, John J Guerrerio, Lilly Xu, Zhiyong Lu
LitCovid in 2022: an information resource for the COVID-19 literature. Nucleic acids research (2022)
Ling Luo, Po-Ting Lai, Chih-Hsuan Wei, Zhiyong Lu
A sequence labeling framework for extracting drug-protein relations from biomedical literature. Database : the journal of biological databases and curation 2022 (2022)
Eric W Sayers, Evan E Bolton, J Rodney Brister, Kathi Canese, Jessica Chan, Donald C Comeau, Catherine M Farrell, Michael Feldgarden, Anna M Fine, Kathryn Funk, Eneida Hatcher, Sivakumar Kannan, Christopher Kelly, Sunghwan Kim, William Klimke, Melissa J Landrum, Stacy Lathrop, Zhiyong Lu, Thomas L Madden, Adriana Malheiro, Aron Marchler-Bauer, Terence D Murphy, Lon Phan, Shashikant Pujar, Sanjida H Rangwala, Valerie A Schneider, Tony Tse, Jiyao Wang, Jian Ye, Barton W Trawick, Kim D Pruitt, Stephen T Sherry
Database resources of the National Center for Biotechnology Information in 2023. Nucleic acids research (2022)
Rezarta Islamaj, Robert Leaman, David Cissel, Cathleen Coss, Joseph Denicola, Carol Fisher, Rob Guzman, Preeti Gokal Kochar, Nicholas Miliaras, Zoe Punske, Keiko Sekiya, Dorothy Trinh, Deborah Whitman, Susan Schmidt, Zhiyong Lu
NLM-Chem-BC7: manually annotated full-text resources for chemical entity annotation and indexing in biomedical articles. Database : the journal of biological databases and curation 2022 (2022)
Chih Hsuan Wei, Alexis Allot, Kevin Riehle, Aleksandar Milosavljevic, Zhiyong Lu
tmVar 3.0: an improved variant concept recognition and normalization tool. Bioinformatics (Oxford, England) 38 (18) (2022)
Qingyu Chen, Alexis Allot, Robert Leaman, Rezarta Islamaj, Jingcheng Du, Li Fang, Kai Wang, Shuo Xu, Yuefu Zhang, Parsa Bagherzadeh, Sabine Bergler, Aakash Bhatnagar, Nidhir Bhavsar, Yung-Chun Chang, Sheng-Jie Lin, Wentai Tang, Hongtong Zhang, Ilija Tavchioski, Senja Pollak, Shubo Tian, Jinfeng Zhang, Yulia Otmakhova, Antonio Jimeno Yepes, Hang Dong, Honghan Wu, Richard Dufour, Yanis Labrak, Niladri Chatterjee, Kushagri Tandon, Fréjus A A Laleye, Loïc Rakotoson, Emmanuele Chersoni, Jinghang Gu, Annemarie Friedrich, Subhash Chandra Pujari, Mariia Chizhikova, Naveen Sivadasan, Saipradeep Vg, Zhiyong Lu
Multi-label classification for biomedical literature: an overview of the BioCreative VII LitCovid Track for COVID-19 literature topic annotations. Database : the journal of biological databases and curation 2022 (2022)
Valérie de Crécy-Lagard, Rocio Amorin de Hegedus, Cecilia Noemi Arighi, Jill Babor, Alex Bateman, Ian K Blaby, Crysten Blaby-Haas, Alan J Bridge, Stephen K Burley, Stacey Cleveland, Lucy J Colwell, Ana Conesa, Christian Dallago, Antoine Danchin, Anita de Waard, Adam Deutschbauer, Raquel Dias, Yousong Ding, Gang Fang, Iddo Friedberg, John Gerlt, Joshua Goldford, Mark Gorelik, Benjamin M Gyori, Christopher Henry, Geoffrey Hutinet, Marshall Jaroch, Peter D Karp, Liudmyla Kondratova, Zhiyong Lu, Aron Marchler-Bauer, Maria-Jesus Martin, Claire McWhite, Gaurav D Moghe, Paul Monaghan, Anne Morgat, Christopher John Mungall, Darren A Natale, William C Nelson, Seán O'Donoghue, Christine Orengo, Katherine H O'Toole, Predrag Radivojac, Colbie Reed, Richard J Roberts, Dmitri Rodionov, Irina A Rodionova, Jeffrey D Rudolf, Lana Saleh, Gloria M Sheynkman, Francoise Thibaud-Nissen, Paul D Thomas, Peter Uetz, David Vallenet, Erica Watson Carter, Peter R Weigele, Valerie Wood, Elisha M Wood-Charlson, Jin Xu
A roadmap for the functional annotation of protein families: a community perspective. Database : the journal of biological databases and curation 2022 (2022)
Ling Luo, Chih Hsuan Wei, Po-Ting Lai, Qingyu Chen, Rezarta Islamaj, Zhiyong Lu
Assigning species information to corresponding genes by a sequence labeling framework. Database : the journal of biological databases and curation 2022 (2022)
Eric W Sayers, Evan E Bolton, J Rodney Brister, Kathi Canese, Jessica Chan, Donald C Comeau, Ryan Connor, Kathryn Funk, Chris Kelly, Sunghwan Kim, Tom Madej, Aron Marchler-Bauer, Christopher Lanczycki, Stacy Lathrop, Zhiyong Lu, Francoise Thibaud-Nissen, Terence D Murphy, Lon Phan, Yuri Skripchenko, Tony Tse, Jiyao Wang, Rebecca Williams, Barton W Trawick, Kim D Pruitt, Stephen T Sherry
Database resources of the national center for biotechnology information. Nucleic acids research (2021)
Qingyu Chen, Alex Rankine, Yifan Peng, Elaheh Aghaarabi, Zhiyong Lu
Benchmarking Effectiveness and Efficiency of Deep Learning Models for Semantic Textual Similarity in the Clinical Domain: Validation Study. JMIR medical informatics 9 (12) (2021)
Alexis Allot, Myunggyo Lee, Qingyu Chen, Ling Luo, Zhiyong Lu
LitSuggest: a web-based system for literature recommendation and curation using machine learning. Nucleic acids research 49 (W1) (2021)
Qingyu Chen, Myunggyo Lee, Shankai Yan, Sun Kim, Chih-Hsuan Wei, Zhiyong Lu
BioConceptVec: Creating and evaluating literature-based biomedical concept embeddings on a large scale. PLoS computational biology 16 (4) (2020)
Robert Leaman, Chih Hsuan Wei, Alexis Allot, Zhiyong Lu
Ten tips for a text-mining-ready article: How to improve automated discoverability and interpretability. PLoS biology 18 (6) (2020)
Travers Ching, Daniel Scott Himmelstein, Brett K Beaulieu-Jones, Alexandr A Kalinin, Brian T Do, Gregory P Way, Enrico Ferrero, Paul-Michael Agapow, Michael Zietz, Michael M Hoffman, Wei Xie, Gail L Rosen, Benjamin J Lengerich, Johnny Israeli, Jack Lanchantin, Stephen Woloszynek, Anne E Carpenter, Avanti Shrikumar, Jinbo Xu, Evan M Cofer, Christopher A Lavender, Srinivas C Turaga, Amr M Alexandari, Zhiyong Lu, David J Harris, Dave DeCaprio, Yanjun Qi, Anshul Kundaje, Yifan Peng, Laura K Wiley, Marwin H S Segler, Simina M Boca, S Joshua Swamidass, Austin Huang, Anthony Gitter, Casey S Greene
Opportunities and obstacles for deep learning in biology and medicine. Journal of the Royal Society, Interface 15 (141) (2019)
Myunggyo Lee, Maria Livia Famiglietti, Aoife C McMahon, Chih-Hsuan Wei, Jacqueline Ann Langdon MacArthur, Sylvain Poux, Lionel Breuza, Alan J Bridge, Fiona Cunningham, Ioannis Xenarios, Zhiyong Lu
Scaling up data curation using deep learning: An application to literature triage in genomic variation resources. PLoS computational biology 14 (8) (2018)
Nicolas Fiorini, David J Lipman, Zhiyong Lu
Towards PubMed 2.0. eLife 6 (2017)