Drug repurposing: progress, challenges and recommendations

S Pushpakom, F Iorio, PA Eyers, KJ Escott… - Nature reviews Drug …, 2019 - nature.com
Given the high attrition rates, substantial costs and slow pace of new drug discovery and
development, repurposing of'old'drugs to treat both common and rare diseases is …

[HTML][HTML] Next-generation machine learning for biological networks

DM Camacho, KM Collins, RK Powers, JC Costello… - Cell, 2018 - cell.com
Machine learning, a collection of data-analytical techniques aimed at building predictive
models from multi-dimensional datasets, is becoming integral to modern biological research …

The STRING database in 2023: protein–protein association networks and functional enrichment analyses for any sequenced genome of interest

D Szklarczyk, R Kirsch, M Koutrouli… - Nucleic acids …, 2023 - academic.oup.com
Much of the complexity within cells arises from functional and regulatory interactions among
proteins. The core of these interactions is increasingly known, but novel interactions …

The STRING database in 2021: customizable protein–protein networks, and functional characterization of user-uploaded gene/measurement sets

D Szklarczyk, AL Gable, KC Nastou, D Lyon… - Nucleic acids …, 2021 - academic.oup.com
Cellular life depends on a complex web of functional associations between biomolecules.
Among these associations, protein–protein interactions are particularly important due to their …

Systems biology in cardiovascular disease: a multiomics approach

A Joshi, M Rienks, K Theofilatos, M Mayr - Nature Reviews Cardiology, 2021 - nature.com
Omics techniques generate large, multidimensional data that are amenable to analysis by
new informatics approaches alongside conventional statistical methods. Systems theories …

Machine learning for integrating data in biology and medicine: Principles, practice, and opportunities

M Zitnik, F Nguyen, B Wang, J Leskovec… - Information …, 2019 - Elsevier
New technologies have enabled the investigation of biology and human health at an
unprecedented scale and in multiple dimensions. These dimensions include a myriad of …

Gene co-expression analysis for functional classification and gene–disease predictions

S Van Dam, U Vosa, A van der Graaf… - Briefings in …, 2018 - academic.oup.com
Gene co-expression networks can be used to associate genes of unknown function with
biological processes, to prioritize candidate disease genes or to discern transcriptional …

Predicting multicellular function through multi-layer tissue networks

M Zitnik, J Leskovec - Bioinformatics, 2017 - academic.oup.com
Motivation Understanding functions of proteins in specific human tissues is essential for
insights into disease diagnostics and therapeutics, yet prediction of tissue-specific cellular …

The BioGRID interaction database: 2017 update

A Chatr-Aryamontri, R Oughtred, L Boucher… - Nucleic acids …, 2017 - academic.oup.com
Abstract The Biological General Repository for Interaction Datasets (BioGRID:
https://thebiogrid. org) is an open access database dedicated to the annotation and archival …

Toxicity testing in the 21st century: progress in the past decade and future perspectives

D Krewski, ME Andersen, MG Tyshenko… - Archives of …, 2020 - Springer
Advances in the biological sciences have led to an ongoing paradigm shift in toxicity testing
based on expanded application of high-throughput in vitro screening and in silico methods …