A cross-study analysis of drug response prediction in cancer cell lines

F **a, J Allen, P Balaprakash, T Brettin… - Briefings in …, 2022 - academic.oup.com
To enable personalized cancer treatment, machine learning models have been developed
to predict drug response as a function of tumor and drug features. However, most algorithm …

SynergyFinder plus: toward better interpretation and annotation of drug combination screening datasets

S Zheng, W Wang, J Aldahdooh… - Genomics …, 2022 - academic.oup.com
Combinatorial therapies have been recently proposed to improve the efficacy of anticancer
treatment. The SynergyFinder R package is a software used to analyze pre-clinical drug …

Advancing targeted protein degradation via multiomics profiling and artificial intelligence

M Duran-Frigola, M Cigler… - Journal of the American …, 2023 - ACS Publications
Only around 20% of the human proteome is considered to be druggable with small-molecule
antagonists. This leaves some of the most compelling therapeutic targets outside the reach …

Deep representation learning of chemical-induced transcriptional profile for phenotype-based drug discovery

X Tong, N Qu, X Kong, S Ni, J Zhou, K Wang… - Nature …, 2024 - nature.com
Artificial intelligence transforms drug discovery, with phenotype-based approaches
emerging as a promising alternative to target-based methods, overcoming limitations like …

DrugComb update: a more comprehensive drug sensitivity data repository and analysis portal

S Zheng, J Aldahdooh, T Shadbahr… - Nucleic acids …, 2021 - academic.oup.com
Combinatorial therapies that target multiple pathways have shown great promises for
treating complex diseases. DrugComb (https://drugcomb. org/) is a web-based portal for the …

Integrating and formatting biomedical data as pre-calculated knowledge graph embeddings in the Bioteque

A Fernández-Torras, M Duran-Frigola, M Bertoni… - Nature …, 2022 - nature.com
Biomedical data is accumulating at a fast pace and integrating it into a unified framework is a
major challenge, so that multiple views of a given biological event can be considered …

Cancer mutations converge on a collection of protein assemblies to predict resistance to replication stress

X Zhao, A Singhal, S Park, JH Kong, R Bachelder… - Cancer …, 2024 - aacrjournals.org
Rapid proliferation is a hallmark of cancer associated with sensitivity to therapeutics that
cause DNA replication stress (RS). Many tumors exhibit drug resistance, however, via …

A Transcriptome-Based Precision Oncology Platform for Patient–Therapy Alignment in a Diverse Set of Treatment-Resistant Malignancies

PS Mundi, FS Dela Cruz, A Grunn, D Diolaiti… - Cancer …, 2023 - aacrjournals.org
Predicting in vivo response to antineoplastics remains an elusive challenge. We performed
a first-of-kind evaluation of two transcriptome-based precision cancer medicine …

A complete graph-based approach with multi-task learning for predicting synergistic drug combinations

X Wang, H Zhu, D Chen, Y Yu, Q Liu, Q Liu - Bioinformatics, 2023 - academic.oup.com
Motivation Drug combination therapy shows significant advantages over monotherapy in
cancer treatment. Since the combinational space is difficult to be traversed experimentally …

Systematic elucidation and pharmacological targeting of tumor-infiltrating regulatory T cell master regulators

A Obradovic, C Ager, M Turunen, T Nirschl… - Cancer Cell, 2023 - cell.com
Due to their immunosuppressive role, tumor-infiltrating regulatory T cells (TI-Tregs)
represent attractive immuno-oncology targets. Analysis of TI vs. peripheral Tregs (P-Tregs) …