iDrug: Integration of drug repositioning and drug-target prediction via cross-network embedding

PLoS Computational Biology
Huiyuan ChenJing Li

Abstract

Computational drug repositioning and drug-target prediction have become essential tasks in the early stage of drug discovery. In previous studies, these two tasks have often been considered separately. However, the entities studied in these two tasks (i.e., drugs, targets, and diseases) are inherently related. On one hand, drugs interact with targets in cells to modulate target activities, which in turn alter biological pathways to promote healthy functions and to treat diseases. On the other hand, both drug repositioning and drug-target prediction involve the same drug feature space, which naturally connects these two problems and the two domains (diseases and targets). By using the wisdom of the crowds, it is possible to transfer knowledge from one of the domains to the other. The existence of relationships among drug-target-disease motivates us to jointly consider drug repositioning and drug-target prediction in drug discovery. In this paper, we present a novel approach called iDrug, which seamlessly integrates drug repositioning and drug-target prediction into one coherent model via cross-network embedding. In particular, we provide a principled way to transfer knowledge from these two domains and to enhance prediction perf...Continue Reading

References

Mar 26, 2003·Journal of Chemical Information and Computer Sciences·Christoph SteinbeckEgon Willighagen
Aug 3, 2004·Nature Reviews. Drug Discovery·Ted T Ashburn, Karl B Thor
Oct 9, 2007·Nature Biotechnology·Muhammed A YildirimMarc Vidal
Jul 17, 2009·Bioinformatics·Kevin Bleakley, Yoshihiro Yamanishi
Dec 18, 2010·Nature Reviews. Genetics·Albert-László BarabásiJoseph Loscalzo
Jun 10, 2011·Molecular Systems Biology·Assaf GottliebRoded Sharan
Sep 7, 2011·Bioinformatics·Twan van LaarhovenElena Marchiori
Apr 28, 2012·Molecular BioSystems·Xing ChenGui-Ying Yan
Mar 20, 2013·Nature Chemical Biology·Monica SchenonePaul A Clemons
Jan 2, 2014·Pharmacological Reviews·Gregory SliwoskiEdward W Lowe
Feb 26, 2014·BMC Systems Biology·Chao WuAnil G Jegga
Apr 12, 2014·Briefings in Bioinformatics·Tapio PahikkalaTero Aittokallio
May 3, 2014·Molecular Cancer Therapeutics·Luiz Fernando ZerbiniTowia A Libermann
Apr 3, 2015·Briefings in Bioinformatics·Jiao LiZhiyong Lu
May 15, 2015·Computational and Mathematical Methods in Medicine·Hailin ChenWenliang Tang
Aug 19, 2015·Briefings in Bioinformatics·Xing ChenYongdong Zhang
Jan 24, 2016·BMC Bioinformatics·André C A NascimentoIvan G Costa
Feb 19, 2016·IEEE/ACM Transactions on Computational Biology and Bioinformatics·Ali EzzatChee-Keong Kwoh
May 4, 2016·Perspectives in Clinical Research·Ajay Francis ChristopherParveen Bansal
Jul 16, 2016·PLoS Computational Biology·Xing ChenGuiying Yan
Jul 31, 2016·Molecular Systems Biology·Christof AngermuellerOliver Stegle
Sep 25, 2017·ELife·Daniel Scott HimmelsteinSergio E Baranzini
Jan 18, 2019·Molecular Therapy. Nucleic Acids·Jia QuJian-Qiang Li
Mar 15, 2019·Nature Communications·Feixiong ChengAlbert-László Barabási
May 23, 2019·Bioinformatics·Xiangxiang ZengFeixiong Cheng

❮ Previous
Next ❯

Citations

Feb 6, 2021·Expert Opinion on Drug Discovery·Ziaurrehman TanoliTero Aittokallio
Feb 22, 2021·Interdisciplinary Sciences, Computational Life Sciences·Xin ChenJiawei Luo
May 8, 2021·Expert Opinion on Drug Discovery·Mateus Sá Magalhães SerafimKathia Maria Honorio
Jun 3, 2021·BMC Bioinformatics·Hai-Cheng YiTong-Hai Jiang
Aug 10, 2021·Frontiers in Oncology·Binsheng HeXiangzuo Xiao

❮ Previous
Next ❯

Software Mentioned

TL
AUROC
ProbS
MBiRW
AUPR
GRMF
iDrug
HGBI
HeatS

Related Concepts

Trending Feeds

COVID-19

Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.

Blastomycosis

Blastomycosis fungal infections spread through inhaling Blastomyces dermatitidis spores. Discover the latest research on blastomycosis fungal infections here.

Nuclear Pore Complex in ALS/FTD

Alterations in nucleocytoplasmic transport, controlled by the nuclear pore complex, may be involved in the pathomechanism underlying multiple neurodegenerative diseases including Amyotrophic Lateral Sclerosis and Frontotemporal Dementia. Here is the latest research on the nuclear pore complex in ALS and FTD.

Applications of Molecular Barcoding

The concept of molecular barcoding is that each original DNA or RNA molecule is attached to a unique sequence barcode. Sequence reads having different barcodes represent different original molecules, while sequence reads having the same barcode are results of PCR duplication from one original molecule. Discover the latest research on molecular barcoding here.

Chronic Fatigue Syndrome

Chronic fatigue syndrome is a disease characterized by unexplained disabling fatigue; the pathology of which is incompletely understood. Discover the latest research on chronic fatigue syndrome here.

Evolution of Pluripotency

Pluripotency refers to the ability of a cell to develop into three primary germ cell layers of the embryo. This feed focuses on the mechanisms that underlie the evolution of pluripotency. Here is the latest research.

Position Effect Variegation

Position Effect Variagation occurs when a gene is inactivated due to its positioning near heterochromatic regions within a chromosome. Discover the latest research on Position Effect Variagation here.

STING Receptor Agonists

Stimulator of IFN genes (STING) are a group of transmembrane proteins that are involved in the induction of type I interferon that is important in the innate immune response. The stimulation of STING has been an active area of research in the treatment of cancer and infectious diseases. Here is the latest research on STING receptor agonists.

Microbicide

Microbicides are products that can be applied to vaginal or rectal mucosal surfaces with the goal of preventing, or at least significantly reducing, the transmission of sexually transmitted infections. Here is the latest research on microbicides.

© 2021 Meta ULC. All rights reserved