Big data in chemical toxicity research: the use of high-throughput screening assays to identify potential toxicants

H Zhu, J Zhang, MT Kim, A Boison… - Chemical research in …, 2014 - ACS Publications
High-throughput screening (HTS) assays that measure the in vitro toxicity of environmental
compounds have been widely applied as an alternative to in vivo animal tests of chemical …

[HTML][HTML] Metabolomics and systems pharmacology: why and how to model the human metabolic network for drug discovery

DB Kell, R Goodacre - Drug Discovery Today, 2014 - Elsevier
Highlights•We now have metabolic network models; the metabolome is represented by their
nodes.•Metabolite levels are sensitive to changes in enzyme activities.•Drugs hitchhike on …

ChemProt-3.0: a global chemical biology diseases mapping

J Kringelum, SK Kjaerulff, S Brunak, O Lund… - Database, 2016 - academic.oup.com
ChemProt is a publicly available compilation of chemical-protein-disease annotation
resources that enables the study of systems pharmacology for a small molecule across …

Assessing drug target association using semantic linked data

B Chen, Y Ding, DJ Wild - PLoS computational biology, 2012 - journals.plos.org
The rapidly increasing amount of public data in chemistry and biology provides new
opportunities for large-scale data mining for drug discovery. Systematic integration of these …

Predicting drug target interactions using meta-path-based semantic network analysis

G Fu, Y Ding, A Seal, B Chen, Y Sun, E Bolton - BMC bioinformatics, 2016 - Springer
Background In the context of drug discovery, drug target interactions (DTIs) can be predicted
based on observed topological features of a semantic network across the chemical and …

The promiscuous binding of pharmaceutical drugs and their transporter-mediated uptake into cells: what we (need to) know and how we can do so

DB Kell, PD Dobson, E Bilsland, SG Oliver - Drug discovery today, 2013 - Elsevier
A recent paper in this journal sought to counter evidence for the role of transport proteins in
effecting drug uptake into cells, and questions that transporters can recognize drug …

PubChemRDF: towards the semantic annotation of PubChem compound and substance databases

G Fu, C Batchelor, M Dumontier, J Hastings… - Journal of …, 2015 - Springer
Background PubChem is an open repository for chemical structures, biological activities and
biomedical annotations. Semantic Web technologies are emerging as an increasingly …

Modern bioinformatics meets traditional Chinese medicine

P Gu, H Chen - Briefings in Bioinformatics, 2014 - academic.oup.com
Abstract Motivation: Traditional Chinese medicine (TCM) is gaining increasing attention with
the emergence of integrative medicine and personalized medicine, characterized by pattern …

Optimizing drug–target interaction prediction based on random walk on heterogeneous networks

A Seal, YY Ahn, DJ Wild - Journal of cheminformatics, 2015 - Springer
Background Predicting novel drug–target associations is important not only for developing
new drugs, but also for furthering biological knowledge by understanding how drugs work …

One hundred thousand mouse clicks down the road: selected online resources supporting drug discovery collected over a decade

BO Villoutreix, D Lagorce, CM Labbe, O Sperandio… - Drug Discovery …, 2013 - Elsevier
Highlights•There are many in silico resources and databases that can assist drug discovery;
yet it is almost impossible to track all these new services.•We provide a comprehensive list of …