The cancer omics and drug experimental response dataset (CODERData): A harmonized benchmark dataset for machine learning models of drug response prediction

J Jacobson, S Schwartz, MR Weil, N Kumar, S Gosline - Cancer Research, 2024 - AACR
Background: Determining a patient's response to a specific therapy is a vital step in
developing personalized cancer treatment. Personalized treatment relies on two key …

CREAMMIST: an integrative probabilistic database for cancer drug response prediction

H Yingtaweesittikul, J Wu, A Mongia… - Nucleic Acids …, 2023 - academic.oup.com
Extensive in vitro cancer drug screening datasets have enabled scientists to identify
biomarkers and develop machine learning models for predicting drug sensitivity. While most …

Systematic evaluation and comparison of drug response prediction models: a case study of prediction generalization across cell lines datasets

A Partin, TS Brettin, Y Zhu, J Overbeek… - Cancer …, 2023 - aacrjournals.org
Predictive modeling holds great promise for improving personalized cancer treatment and
efficiency of drug development. In recent years, deep learning (DL) has been extensively …

Computational identification of multi-omic correlates of anticancer therapeutic response

LC Stetson, T Pearl, Y Chen, JS Barnholtz-Sloan - BMC genomics, 2014 - Springer
Background A challenge in precision medicine is the transformation of genomic data into
knowledge that can be used to stratify patients into treatment groups based on predicted …

Machine learning and feature selection for drug response prediction in precision oncology applications

M Ali, T Aittokallio - Biophysical reviews, 2019 - Springer
In-depth modeling of the complex interplay among multiple omics data measured from
cancer cell lines or patient tumors is providing new opportunities toward identification of …

Abstract P2-12-02: ClinicalomicsDB-Bridging the gap between clinical omics data and machine learning

CI Moon, B Jia, B Zhang - Cancer Research, 2023 - aacrjournals.org
BACKGROUND: Clinical trials are controlled patient studies aiming to objectively assess the
effectiveness of treatment interventions. However, the average effectiveness observed at the …

Bridging the gap between clinical-omics and machine learning to improve cancer treatment

CI Moon, B Jia, B Zhang - Cancer Research, 2023 - aacrjournals.org
Background: Few omics data-based prediction models have made a clinical impact due to
lack of access to real-world, clinically relevant datasets for method development and …

A survey and systematic assessment of computational methods for drug response prediction

J Chen, L Zhang - Briefings in bioinformatics, 2021 - academic.oup.com
Drug response prediction arises from both basic and clinical research of personalized
therapy, as well as drug discovery for cancers. With gene expression profiles and other …

FORESEE: a tool for the systematic comparison of translational drug response modeling pipelines

LK Turnhoff, A Hadizadeh Esfahani, M Montazeri… - …, 2019 - academic.oup.com
Translational models that utilize omics data generated in in vitro studies to predict the drug
efficacy of anti-cancer compounds in patients are highly distinct, which complicates the …

Dr. Paso: Drug response prediction and analysis system for oncology research

F Azuaje, T Kaoma, C Jeanty, PV Nazarov, A Muller… - bioRxiv, 2017 - biorxiv.org
The prediction of anticancer drug response is crucial for achieving a more effective and
precise treatment of patients. Models based on the analysis of large cell line collections …