Global trends in infectious diseases of swine

K VanderWaal, J Deen - Proceedings of the National …, 2018 - National Acad Sciences
Pork accounts for more than one-third of meat produced worldwide and is an important
component of global food security, agricultural economies, and trade. Infectious diseases …

Learning from co-expression networks: possibilities and challenges

EAR Serin, H Nijveen, HWM Hilhorst… - Frontiers in plant …, 2016 - frontiersin.org
Plants are fascinating and complex organisms. A comprehensive understanding of the
organization, function and evolution of plant genes is essential to disentangle important …

[HTML][HTML] BioCreative V CDR task corpus: a resource for chemical disease relation extraction

J Li, Y Sun, RJ Johnson, D Sciaky, CH Wei… - Database, 2016 - academic.oup.com
Community-run, formal evaluations and manually annotated text corpora are critically
important for advancing biomedical text-mining research. Recently in BioCreative V, a new …

Fine-tuning large neural language models for biomedical natural language processing

R Tinn, H Cheng, Y Gu, N Usuyama, X Liu, T Naumann… - Patterns, 2023 - cell.com
Large neural language models have transformed modern natural language processing
(NLP) applications. However, fine-tuning such models for specific tasks remains challenging …

[HTML][HTML] NCBI disease corpus: a resource for disease name recognition and concept normalization

RI Doğan, R Leaman, Z Lu - Journal of biomedical informatics, 2014 - Elsevier
Abstract Information encoded in natural language in biomedical literature publications is
only useful if efficient and reliable ways of accessing and analyzing that information are …

PubTator: a web-based text mining tool for assisting biocuration

CH Wei, HY Kao, Z Lu - Nucleic acids research, 2013 - academic.oup.com
Manually curating knowledge from biomedical literature into structured databases is highly
expensive and time-consuming, making it difficult to keep pace with the rapid growth of the …

DNorm: disease name normalization with pairwise learning to rank

R Leaman, R Islamaj Doğan, Z Lu - Bioinformatics, 2013 - academic.oup.com
Motivation: Despite the central role of diseases in biomedical research, there have been
much fewer attempts to automatically determine which diseases are mentioned in a text …

tmChem: a high performance approach for chemical named entity recognition and normalization

R Leaman, CH Wei, Z Lu - Journal of cheminformatics, 2015 - Springer
Chemical compounds and drugs are an important class of entities in biomedical research
with great potential in a wide range of applications, including clinical medicine. Locating …

Community challenges in biomedical text mining over 10 years: success, failure and the future

CC Huang, Z Lu - Briefings in bioinformatics, 2016 - academic.oup.com
One effective way to improve the state of the art is through competitions. Following the
success of the Critical Assessment of protein Structure Prediction (CASP) in bioinformatics …

GNormPlus: an integrative approach for tagging genes, gene families, and protein domains

CH Wei, HY Kao, Z Lu - BioMed research international, 2015 - Wiley Online Library
The automatic recognition of gene names and their associated database identifiers from
biomedical text has been widely studied in recent years, as these tasks play an important …