lu

Zhiyong Lu, PhD

Earl Stadtman Investigator
Biomedical Text Mining Group
NCBI, NLM, NIH

We're always interested in possible postdocs or research assistants. If interested, email me for more information.

Short Biography

Dr. Lu is a Stadtman investigator at the National Institutes of Health, where he joined after earning a PhD in Bioinformatics at the University of Colorado School of Medicine. His research laboratory is developing computational methods and software tools for text mining research (analyzing and making sense of natural language data in biomedical literature and clincial text). Some of his recent research has been successfully integrated and widely used in PubMed and other NCBI databases for improving information access and accelerating scientific 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 data curatoin)
  • 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/conferences in BioNLP, Bioinformatics, and Health Informatics.

Recent Publications (see all...)

Tools and Downloads (see all...)

  • 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
  • PubMed query corpus: 10,000 queries annotated with UMLS concepts
  • Related Journals: mined based on PubMed user logs
Quick Links:
tmChem
DNorm
PubTator
tmVar
SR4GN
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:
Ritu Khare
Robert Leaman
Yuqing Mao
Chih-Hsuan Wei
 
Group Alumni:
Rezarta Dogan
Aurelie Neveol
Jiao Li
Bethany Harris
Minlie Huang
 
Contact Information:
MSC3825 NCBI/NLM/NIH
Bldg 38A, Rm 1003A
8600 Rockville Pike
Bethesda, MD, 20894
Tel: 301-594-7089
Fax: 301-480-2288
zhiyong.lu@nih.gov