ArticlePatterns (New York, N.Y.)2022
Machine learning and network medicine approaches for drug repositioning for COVID-19.
Article in Patterns (New York, N.Y.), 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 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
23 citing papers in PubMed, 1 synthesis or guideline pooled it, 61 citations in OpenAlex.
- Combating COVID-19 Crisis using Artificial Intelligence (AI) Based Approach: Systematic Review.Current topics in medicinal chemistry · 2024Pooled it
- Safety and efficacy of sirolimus in hospitalised patients with COVID-19 pneumonia.Respiratory investigation · 2024Trial
- Antiviral Efficacy, Cytotoxicity, Transcriptomics, and Discriminatory Function of 3D8 scFv Against Dengue and Zika Viruses.International journal of molecular sciences · 2026Article
- Host centric drug repurposing for viral diseases.PLoS computational biology · 2025Article
- Improving drug repositioning accuracy using non-negative matrix tri-factorization.Scientific reports · 2025Article
- Comparing gene-gene co-expression network approaches for the analysis of cell differentiation and specification on scRNAseq data.Computational and structural biotechnology journal · 2025Article
- sChemNET: a deep learning framework for predicting small molecules targeting microRNA function.Nature communications · 2024Article
- Staying Ahead of the Game: How SARS-CoV-2 has Accelerated the Application of Machine Learning in Pandemic Management.BioDrugs : clinical immunotherapeutics, biopharmaceuticals and gene therapy · 2023Review
- The use of alpha 1 thymosin as an immunomodulator of the response against SARS-Cov2.Immunity & ageing : I & A · 2023Article
- Development of complemented comprehensive networks for rapid screening of repurposable drugs applicable to new emerging disease outbreaks.Journal of translational medicine · 2023Article
- A machine learning method for the identification and characterization of novel COVID-19 drug targets.Scientific reports · 2023Article
- A network medicine approach for identifying diagnostic and prognostic biomarkers and exploring drug repurposing in human cancer.Computational and structural biotechnology journal · 2023Article
- Article
- Machine learning prediction of side effects for drugs in clinical trials.Cell reports methods · 2022Article
- Systematic comparison of differential expression networks in MTB mono-, HIV mono- and MTB/HIV co-infections for drug repurposing.PLoS computational biology · 2022Article
- Are Nutraceuticals Effective in COVID-19 and Post-COVID Prevention and Treatment?Foods (Basel, Switzerland) · 2022Review
- A comprehensive review of artificial intelligence and network based approaches to drug repurposing in Covid-19.Biomedicine & pharmacotherapy = Biomedecine & pharmacotherapie · 2022Review
- Article
- Navigating an early career in genomics and data science, written from the perspective of a current PhD student.Patterns (New York, N.Y.) · 2022Article
- Looking at COVID-19 from a Systems Biology Perspective.Biomolecules · 2022Review
Corrections and comments
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Authors and funding
6 authors at 3 institutions in 3 countries.
Funding
Abstract
We present two machine learning approaches for drug repurposing. While we have developed them for COVID-19, they are disease-agnostic. The two methodologies are complementary, targeting SARS-CoV-2 and host factors, respectively. Our first approach consists of a matrix factorization algorithm to rank broad-spectrum antivirals. Our second approach, based on network medicine, uses graph kernels to rank drugs according to the perturbation they induce on a subnetwork of the human interactome that is crucial for SARS-CoV-2 infection/replication. Our experiments show that our top predicted broad-spectrum antivirals include drugs indicated for compassionate use in COVID-19 patients; and that the ranking obtained by our kernel-based approach aligns with experimental data. Finally, we present the COVID-19 repositioning explorer (CoREx), an interactive online tool to explore the interplay between drugs and SARS-CoV-2 host proteins in the context of biological networks, protein function, drug clinical use, and Connectivity Map. CoREx is freely available at: https://paccanarolab.org/corex/.
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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.