High‐throughput molecular assays for inclusion in personalised oncology trials–State‐of‐the‐art and beyond

A Edsjö, HG Russnes, J Lehtiö… - Journal of internal …, 2024 - Wiley Online Library
In the last decades, the development of high‐throughput molecular assays has
revolutionised cancer diagnostics, paving the way for the concept of personalised cancer …

A phenocopy signature of TP53 loss predicts response to chemotherapy

H Bakhtiar, MN Sharifi, KT Helzer, Y Shi… - NPJ Precision …, 2024 - nature.com
In preclinical studies, p53 loss of function impacts chemotherapy response, but this has not
been consistently validated clinically. We trained a TP53-loss phenocopy gene expression …

Best holdout assessment is sufficient for cancer transcriptomic model selection

J Crawford, M Chikina, CS Greene - Patterns, 2024 - cell.com
Guidelines in statistical modeling for genomics hold that simpler models have advantages
over more complex ones. Potential advantages include cost, interpretability, and improved …

Machine learning enabled prediction of digital biomarkers from whole slide histopathology images

ZR McCaw, A Shcherbina, Y Shah, D Huang, S Elliott… - medRxiv, 2024 - medrxiv.org
Current predictive biomarkers generally leverage technologies such as immunohis-
tochemistry or genetic analysis, which may require specialized equipment, be time-intensive …

Bayesian inference for multivariate probit model with latent envelope

K Lee, Y Park - Biometrics, 2024 - academic.oup.com
The response envelope model proposed by Cook et al. is an efficient method to estimate the
regression coefficient under the context of the multivariate linear regression model. It …

Optimizer's dilemma: optimization strongly influences model selection in transcriptomic prediction

J Crawford, M Chikina, CS Greene - Bioinformatics Advances, 2024 - academic.oup.com
Motivation Most models can be fit to data using various optimization approaches. While
model choice is frequently reported in machine-learning-based research, optimizers are not …

Methods of generating phenocopy signatures and uses thereof

S Zhao, H Bakhtiar - US Patent App. 18/522,977, 2024 - Google Patents
Methods of generating phenocopy signatures and uses thereof. The methods of generating
phenocopy signatures can include determining gene expression signatures that predict the …