[HTML][HTML] pRRophetic: an R package for prediction of clinical chemotherapeutic response from tumor gene expression levels

P Geeleher, N Cox, RS Huang - PloS one, 2014 - journals.plos.org
We recently described a methodology that reliably predicted chemotherapeutic response in
multiple independent clinical trials. The method worked by building statistical models from …

Computational models for predicting drug responses in cancer research

F Azuaje - Briefings in bioinformatics, 2017 - academic.oup.com
The computational prediction of drug responses based on the analysis of multiple types of
genome-wide molecular data is vital for accomplishing the promise of precision medicine in …

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 …

oncoPredict: an R package for predicting in vivo or cancer patient drug response and biomarkers from cell line screening data

D Maeser, RF Gruener, RS Huang - Briefings in bioinformatics, 2021 - academic.oup.com
Cell line drug screening datasets can be utilized for a range of different drug discovery
applications from drug biomarker discovery to building translational models of drug …

Predicting in vitro drug sensitivity using Random Forests

G Riddick, H Song, S Ahn, J Walling… - …, 2011 - academic.oup.com
Motivation: Panels of cell lines such as the NCI-60 have long been used to test drug
candidates for their ability to inhibit proliferation. Predictive models of in vitro drug sensitivity …

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

F Xia, 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 …

Drug sensitivity prediction from cell line-based pharmacogenomics data: guidelines for developing machine learning models

H Sharifi-Noghabi… - Briefings in …, 2021 - academic.oup.com
The goal of precision oncology is to tailor treatment for patients individually using the
genomic profile of their tumors. Pharmacogenomics datasets such as cancer cell lines are …

[HTML][HTML] Clinical drug response can be predicted using baseline gene expression levels and in vitrodrug sensitivity in cell lines

P Geeleher, NJ Cox, RS Huang - Genome biology, 2014 - Springer
We demonstrate a method for the prediction of chemotherapeutic response in patients using
only before-treatment baseline tumor gene expression data. First, we fitted models for whole …

[HTML][HTML] An ensemble based top performing approach for NCI-DREAM drug sensitivity prediction challenge

Q Wan, R Pal - PloS one, 2014 - journals.plos.org
We consider the problem of predicting sensitivity of cancer cell lines to new drugs based on
supervised learning on genomic profiles. The genetic and epigenetic characterization of a …

TANDEM: a two-stage approach to maximize interpretability of drug response models based on multiple molecular data types

N Aben, DJ Vis, M Michaut, LF Wessels - Bioinformatics, 2016 - academic.oup.com
Motivation Clinical response to anti-cancer drugs varies between patients. A large portion of
this variation can be explained by differences in molecular features, such as mutation status …