Zhiyong Lu, PhD

Senior Investigator


Short Biography

Dr. Lu is a Senior Investigator at the National Center for Biotechnology Information (NCBI), National Library of Medicine (NLM), National Institutes of Health (NIH), where he joined in 2007 and was the first Earl Stadtman Investigator in Computational Biology. At NCBI/NLM, Dr. Lu directs Text Mining Research and is also the head of PubMed/Literature Search. He and his team are developing computational methods and software tools for analyzing and making sense of unstructured text data in biomedical literature and clincial notes towards accelerated discovery. His many recent publications and invited talks generally have a focus on the following topics:

  • BioNLP & Text Mining (e.g. biomedical literature analysis and retrieval)
  • eCuration (e.g. computer-assisted biomedical digital curation)
  • Health Informatics (e.g. web access to consumer health information)
  • Translational Bioinformatics (e.g. computational drug repurposing)

Dr. Lu is an Associate Editor for BMC Bioinformatics and serves on the Editorial Borad for the journal Database. He is a member of the BioCreative Organizing Committee and has been invovled in organzing a number of international meetings and workshops in his research field (e.g. recent PSB sessions on drug repurposing/crowdsourcing; 2013 IEEE Conference on Healthcare Informatics). He has also participated in both US (NSF/NIH) and international (MRC/NSERC) grant reviews and served as ad-hoc editor/reviewers for major journals/confeences in BioNLP, Bioinformatics, and Health Informatics. He has authored or co-authored over 120 scientific publications.

Recent Publications (see all...)

Tools and Downloads (see all...)

  • tmChem: an open source tool for chemical and drug name normalization
  • DNorm: an open source tool for disease name normalization
  • PubTator: a Web-based tool for computer-assisted annotation
  • tmVar: an open source tool for extracting sequence variants in biomedical text
  • SR4GN: a species recogntion software tool for gene normalization
  • NCBI disease corpus: 793 PubMed abstracts with disease annotations
Quick Links:
NCBI Disease Corpus
BioCreative IV - GO task
ICHI 2013
PSB 2015 - Crowdsourcing and Learning
PSB 2014 - Drug Repurposing
Recent Projects:
PubMed query log analysis
Document keywords analysis
Biomedical entity recognition
Research Group:
Don Comeau
Rezarta Dogan
Nicolas Fiorini
Edwin Huang
Alan Hsu
Sun Kim
Won Kim
Robert Leaman
Xiaoxia Liu
Wanli Liu
Yifan Peng
Ayush Singhal
Chih-Hsuan Wei
Natalie Xie
Lana Yeganova
Group Alumni:
Yuqing Mao
Ritu Khare
Rezarta Dogan
Aurelie Neveol
Jiao Li
Bethany Harris
Minlie Huang
Contact Information:
Bldg 38A, Rm 1003A
8600 Rockville Pike
Bethesda, MD, 20894
Tel: 301-594-7089
Fax: 301-480-2288