Advances in natural language processing

J Hirschberg, CD Manning - Science, 2015 - science.org
Natural language processing employs computational techniques for the purpose of learning,
understanding, and producing human language content. Early computational approaches to …

A survey on clinical natural language processing in the United Kingdom from 2007 to 2022

H Wu, M Wang, J Wu, F Francis, YH Chang… - NPJ digital …, 2022 - nature.com
Much of the knowledge and information needed for enabling high-quality clinical research is
stored in free-text format. Natural language processing (NLP) has been used to extract …

The STRING database in 2021: customizable protein–protein networks, and functional characterization of user-uploaded gene/measurement sets

D Szklarczyk, AL Gable, KC Nastou, D Lyon… - Nucleic acids …, 2021 - academic.oup.com
Cellular life depends on a complex web of functional associations between biomolecules.
Among these associations, protein–protein interactions are particularly important due to their …

COVID-19 literature knowledge graph construction and drug repurposing report generation

Q Wang, M Li, X Wang, N Parulian, G Han, J Ma… - arxiv preprint arxiv …, 2020 - arxiv.org
To combat COVID-19, both clinicians and scientists need to digest vast amounts of relevant
biomedical knowledge in scientific literature to understand the disease mechanism and …

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 …

Gene duplicability of core genes is highly consistent across all angiosperms

Z Li, J Defoort, S Tasdighian, S Maere… - The Plant …, 2016 - academic.oup.com
Gene duplication is an important mechanism for adding to genomic novelty. Hence, which
genes undergo duplication and are preserved following duplication is an important question …

Landscape and flux theory of non-equilibrium dynamical systems with application to biology

J Wang - Advances in Physics, 2015 - Taylor & Francis
We present a review of the recently developed landscape and flux theory for non-equilibrium
dynamical systems. We point out that the global natures of the associated dynamics for non …

Automated assembly of molecular mechanisms at scale from text mining and curated databases

JA Bachman, BM Gyori, PK Sorger - Molecular Systems Biology, 2023 - embopress.org
The analysis of omic data depends on machine‐readable information about protein
interactions, modifications, and activities as found in protein interaction networks, databases …

What is stress? Dose-response effects in commonly used in vitro stress assays

H Claeys, S Van Landeghem, M Dubois… - Plant …, 2014 - academic.oup.com
In vitro stress assays are commonly used to study the responses of plants to abiotic stress
and to assess stress tolerance. A literature review reveals that most studies use very high …