ArticleBMC bioinformatics2016
ksRepo: a generalized platform for computational drug repositioning.
Article in BMC bioinformatics, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers, 1 of them a synthesis that pooled it.
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The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
21 citing papers in PubMed, 1 synthesis or guideline pooled it, 57 citations in OpenAlex.
- A review of validation strategies for computational drug repositioning.Briefings in bioinformatics · 2018Pooled it
- Large-scale Empirical Identification of Candidate Comparators for Pharmacoepidemiological Studies.Drug safety · 2025Article
- Drug repositioning pipeline integrating community analysis in drug-drug similarity networks and automated ATC community labeling to foster molecular docking analysis.Frontiers in bioinformatics · 2025Article
- Article
- A comprehensive review of artificial intelligence and network based approaches to drug repurposing in Covid-19.Biomedicine & pharmacotherapy = Biomedecine & pharmacotherapie · 2022Review
- A chronicle review of new techniques that facilitate the understanding and development of optimal individualized therapeutic strategies for chordoma.Frontiers in oncology · 2022Review
- Reconciling multiple connectivity scores for drug repurposing.Briefings in bioinformatics · 2021Article
- Drug Discovery of Spinal Muscular Atrophy (SMA) from the Computational Perspective: A Comprehensive Review.International journal of molecular sciences · 2021Review
- Computational Drug Repositioning Identifies Potentially Active Therapies for Chordoma.Neurosurgery · 2021Article
- Bayesian Framework for Detecting Gene Expression Outliers in Individual Samples.JCO clinical cancer informatics · 2020Article
- Machine learning applications in drug development.Computational and structural biotechnology journal · 2020Review
- Pathway-Based Drug-Repurposing Schemes in Cancer: The Role of Translational Bioinformatics.Frontiers in oncology · 2020Review
- Bioengineering tools for the production of pharmaceuticals: current perspective and future outlook.Bioengineered · 2019Review
- Changing Trends in Computational Drug Repositioning.Pharmaceuticals (Basel, Switzerland) · 2018Review
- Computational repositioning and preclinical validation of mifepristone for human vestibular schwannoma.Scientific reports · 2018Article
- Leveraging Population-Based Clinical Quantitative Phenotyping for Drug Repositioning.CPT: pharmacometrics & systems pharmacology · 2018Observational
- Drug repurposing from the perspective of pharmaceutical companies.British journal of pharmacology · 2018Review
- MD-Miner: a network-based approach for personalized drug repositioning.BMC systems biology · 2017Article
- MeSHDD: Literature-based drug-drug similarity for drug repositioning.Journal of the American Medical Informatics Association : JAMIA · 2017Article
- A standard database for drug repositioning.Scientific data · 2017Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
4 authors at 2 institutions in 1 country.
Funding
Abstract
backgroundRepositioning approved drug and small molecules in novel therapeutic areas is of key interest to the pharmaceutical industry. A number of promising computational techniques have been developed to aid in repositioning, however, the majority of available methodologies require highly specific data inputs that preclude the use of many datasets and databases. There is a clear unmet need for a generalized methodology that enables the integration of multiple types of both gene expression data and database schema.
resultsksRepo eliminates the need for a single microarray platform as input and allows for the use of a variety of drug and chemical exposure databases. We tested ksRepo's performance on a set of five prostate cancer datasets using the Comparative Toxicogenomics Database (CTD) as our database of gene-compound interactions. ksRepo successfully predicted significance for five frontline prostate cancer therapies, representing a significant enrichment from over 7000 CTD compounds, and achieved specificity similar to other repositioning methods.
conclusionsWe present ksRepo, which enables investigators to use any data inputs for computational drug repositioning. ksRepo is implemented in a series of four functions in the R statistical environment under a BSD3 license. Source code is freely available at http://github.com/adam-sam-brown/ksRepo. A vignette is provided to aid users in performing ksRepo analysis.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.