Lu, Zhiyong

Database resources of the national center for biotechnology information

Sayers, E. W., Bolton, E. E., Brister, J. R., Canese, K., Chan, J., Comeau, D. C., Connor, R., Funk, K., Kelly, C., Kim, S., et al. (2022) · Nucleic Acids Research

Genomics and Phylogenetic StudiesGenetics, Bioinformatics, and Biomedical Research

Cited by 2,812

Opportunities and obstacles for deep learning in biology and medicine

Ching, T., Himmelstein, D. S., Beaulieu-Jones, B. K., Kalinin, A. A., Do, B. T., Way, G. P., Ferrero, E., Agapow, P.-M., Zietz, M., Hoffman, M. M., et al. (2018) · Journal of The Royal Society Interface

Machine Learning in HealthcareArtificial Intelligence in Healthcare and Education

Cited by 2,310

Transfer Learning in Biomedical Natural Language Processing: An Evaluation of BERT and ELMo on Ten Benchmarking Datasets

Peng, Y., Yan, S., & Lu, Z. (2019) · Proceedings of the 18th BioNLP Workshop and Shared Task

Topic ModelingMachine Learning in Healthcare

Cited by 899

BioWordVec, improving biomedical word embeddings with subword information and MeSH

Zhang, Y., Chen, Q., Yang, Z., Lin, H., & Lu, Z. (2019) · Scientific Data

Biomedical Text Mining and OntologiesTopic Modeling

Cited by 455

PubTator central: automated concept annotation for biomedical full text articles

Wei, C.-H., Allot, A., Leaman, R., & Lu, Z. (2019) · Nucleic Acids Research

Biomedical Text Mining and OntologiesGenomics and Phylogenetic Studies

Cited by 400

Opportunities and Challenges for ChatGPT and Large Language Models in Biomedicine and Health

Tian, S., Jin, Q., Yeganova, L., Lai, P.-T., Zhu, Q., Chen, X., Yang, Y., Chen, Q., Kim, W., Comeau, D. C., et al. (2023) · Briefings in Bioinformatics

Artificial Intelligence in Healthcare and EducationBiomedical Text Mining and Ontologies

Cited by 359

Improving large language models for clinical named entity recognition via prompt engineering

Hu, Y., Chen, Q., Du, J., Peng, X., Keloth, V. K., Zuo, X., Zhou, Y., Li, Z., Jiang, X., Lu, Z., et al. (2024) · Journal of the American Medical Informatics Association

Topic ModelingBiomedical Text Mining and Ontologies

Cited by 314

Benchmarking Retrieval-Augmented Generation for Medicine

Xiong, G., Jin, Q., Lu, Z., & Zhang, A. (2024) · arXiv

Topic ModelingInformation Retrieval and Search Behavior

Cited by 312

Benchmarking Retrieval-Augmented Generation for Medicine

Xiong, G., Jin, Q., Lu, Z., & Zhang, A. (2024) · Findings of the Association for Computational Linguistics ACL 2024

Topic ModelingInformation Retrieval and Search Behavior

Cited by 310

Keep up with the latest coronavirus research

Chen, Q., Allot, A., & Lu, Z. (2020) · Nature

Academic Publishing and Open AccessSARS-CoV-2 and COVID-19 Research

Cited by 295

Matching patients to clinical trials with large language models

Jin, Q., Wang, Z., Floudas, C. S., Chen, F., Gong, C., Bracken-Clarke, D., Xue, E., Yang, Y., Sun, J., & Lu, Z. (2024) · Nature Communications

Artificial Intelligence in Healthcare and EducationMachine Learning in Healthcare

Cited by 287

Matching Patients to Clinical Trials with Large Language Models

Jin, Q., Wang, Z., Floudas, C. S., Chen, F., Gong, C., Bracken-Clarke, D., Xue, E., Yang, Y., Sun, J., & Lu, Z. (2023) · arXiv

Artificial Intelligence in Healthcare and EducationMachine Learning in Healthcare

Cited by 287

Understanding PubMed(R) user search behavior through log analysis

Islamaj Dogan, R., Murray, G. C., Neveol, A., & Lu, Z. (2009) · Database

Information Retrieval and Search BehaviorLibrary Science and Information Literacy

Cited by 265

LitCovid: an open database of COVID-19 literature

Chen, Q., Allot, A., & Lu, Z. (2021) · Nucleic Acids Research

Academic Publishing and Open AccessBiomedical Text Mining and Ontologies

Cited by 253

Benchmarking large language models for biomedical natural language processing applications and recommendations

Chen, Q., Hu, Y., Peng, X., Xie, Q., Jin, Q., Gilson, A., Singer, M. B., Ai, X., Lai, P.-T., Wang, Z., et al. (2025) · Nature Communications

Biomedical Text Mining and OntologiesTopic Modeling

Cited by 219

Assessing the state of the art in biomedical relation extraction: overview of the BioCreative V chemical-disease relation (CDR) task

Wei, C.-H., Peng, Y., Leaman, R., Davis, A. P., Mattingly, C. J., Li, J., Wiegers, T. C., & Lu, Z. (2016) · Database

Biomedical Text Mining and OntologiesAdvanced Text Analysis Techniques

Cited by 198

GeneGPT: Augmenting Large Language Models with Domain Tools for Improved Access to Biomedical Information

Jin, Q., Yang, Y., Chen, Q., & Lu, Z. (2024) · Bioinformatics

Biomedical Text Mining and OntologiesArtificial Intelligence in Healthcare and Education

Cited by 176

Best Match: New relevance search for PubMed

Fiorini, N., Canese, K., Starchenko, G., Kireev, E., Kim, W., Miller, V., Osipov, M., Kholodov, M., Ismagilov, R., Mohan, S., et al. (2018) · PLOS Biology

Information Retrieval and Search BehaviorRecommender Systems and Techniques

Cited by 175

MedCPT: Contrastive Pre-trained Transformers with large-scale PubMed search logs for zero-shot biomedical information retrieval

Jin, Q., Kim, W., Chen, Q., Comeau, D. C., Yeganova, L., Wilbur, W. J., & Lu, Z. (2023) · Bioinformatics

Information Retrieval and Search BehaviorBiomedical Text Mining and Ontologies

Cited by 175

NegBio: a high-performance tool for negation and uncertainty detection in radiology reports

Peng, Y., Wang, X., Lu, L., Bagheri, M., Summers, R., & Lu, Z. (2017) · arXiv

Biomedical Text Mining and OntologiesMachine Learning in Healthcare

Cited by 175

Hidden flaws behind expert-level accuracy of multimodal GPT-4 vision in medicine

Jin, Q., Chen, F., Zhou, Y., Xu, Z., Cheung, J. M., Chen, R., Summers, R. M., Rousseau, J. F., Ni, P., Landsman, M. J., et al. (2024) · npj Digital Medicine

Artificial Intelligence in Healthcare and EducationMultimodal Machine Learning Applications

Cited by 146

On expert curation and scalability: UniProtKB/Swiss-Prot as a case study

Poux, S., Arighi, C. N., Magrane, M., Bateman, A., Wei, C.-H., Lu, Z., Boutet, E., Bye-A-Jee, H., Famiglietti, M. L., Roechert, B., et al. (2017) · Bioinformatics

Biomedical Text Mining and OntologiesBioinformatics and Genomic Networks

Cited by 135

Recent advances in biomedical literature mining

Zhao, S., Su, C., Lu, Z., & Wang, F. (2021) · Briefings in Bioinformatics

Biomedical Text Mining and OntologiesAdvanced Text Analysis Techniques

Cited by 134

Advancing entity recognition in biomedicine via instruction tuning of large language models

Keloth, V. K., Hu, Y., Xie, Q., Peng, X., Wang, Y., Zheng, A., Selek, M., Raja, K., Wei, C. H., Jin, Q., et al. (2024) · Bioinformatics

Biomedical Text Mining and OntologiesTopic Modeling

Cited by 104