Graph representation learning in bioinformatics: trends, methods and applications

HC Yi, ZH You, DS Huang… - Briefings in …, 2022 - academic.oup.com
Graph is a natural data structure for describing complex systems, which contains a set of
objects and relationships. Ubiquitous real-life biomedical problems can be modeled as …

Machine learning approaches and databases for prediction of drug–target interaction: a survey paper

M Bagherian, E Sabeti, K Wang… - Briefings in …, 2021 - academic.oup.com
The task of predicting the interactions between drugs and targets plays a key role in the
process of drug discovery. There is a need to develop novel and efficient prediction …

Comparative toxicogenomics database (CTD): update 2021

AP Davis, CJ Grondin, RJ Johnson… - Nucleic acids …, 2021 - academic.oup.com
Abstract The public Comparative Toxicogenomics Database (CTD; http://ctdbase. org/) is an
innovative digital ecosystem that relates toxicological information for chemicals, genes …

Comparative toxicogenomics database (CTD): update 2023

AP Davis, TC Wiegers, RJ Johnson… - Nucleic acids …, 2023 - academic.oup.com
Abstract The Comparative Toxicogenomics Database (CTD; http://ctdbase. org/) harmonizes
cross-species heterogeneous data for chemical exposures and their biological …

The comparative toxicogenomics database: update 2019

AP Davis, CJ Grondin, RJ Johnson… - Nucleic acids …, 2019 - academic.oup.com
Abstract The Comparative Toxicogenomics Database (CTD; http://ctdbase. org/) is a premier
public resource for literature-based, manually curated associations between chemicals …

The harmonizome: a collection of processed datasets gathered to serve and mine knowledge about genes and proteins

AD Rouillard, GW Gundersen, NF Fernandez… - Database, 2016 - academic.oup.com
Genomics, epigenomics, transcriptomics, proteomics and metabolomics efforts rapidly
generate a plethora of data on the activity and levels of biomolecules within mammalian …

An attention-based BiLSTM-CRF approach to document-level chemical named entity recognition

L Luo, Z Yang, P Yang, Y Zhang, L Wang, H Lin… - …, 2018 - academic.oup.com
Motivation In biomedical research, chemical is an important class of entities, and chemical
named entity recognition (NER) is an important task in the field of biomedical information …

[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 …

The comparative toxicogenomics database: update 2017

AP Davis, CJ Grondin, RJ Johnson… - Nucleic acids …, 2017 - academic.oup.com
Abstract The Comparative Toxicogenomics Database (CTD; http://ctdbase. org/) provides
information about interactions between chemicals and gene products, and their …

Epigenetic inheritance and the missing heritability

M Trerotola, V Relli, P Simeone, S Alberti - Human genomics, 2015 - Springer
Genome-wide association studies of complex physiological traits and diseases consistently
found that associated genetic factors, such as allelic polymorphisms or DNA mutations, only …