A mechanistic pan-cancer pathway model informed by multi-omics data interprets stochastic cell fate responses to drugs and mitogens

M Bouhaddou, AM Barrette, AD Stern… - PLoS computational …, 2018 - journals.plos.org
Most cancer cells harbor multiple drivers whose epistasis and interactions with expression
context clouds drug and drug combination sensitivity prediction. We constructed a …

Cell signaling heterogeneity is modulated by both cell-intrinsic and-extrinsic mechanisms: An integrated approach to understanding targeted therapy

E Kim, JY Kim, MA Smith, EB Haura… - PLoS biology, 2018 - journals.plos.org
During the last decade, our understanding of cancer cell signaling networks has significantly
improved, leading to the development of various targeted therapies that have elicited …

Perturbation biology links temporal protein changes to drug responses in a melanoma cell line

E Nyman, RR Stein, X Jing, W Wang… - PLoS computational …, 2020 - journals.plos.org
Cancer cells have genetic alterations that often directly affect intracellular protein signaling
processes allowing them to bypass control mechanisms for cell death, growth and division …

A scalable, open-source implementation of a large-scale mechanistic model for single cell proliferation and death signaling

C Erdem, A Mutsuddy, EM Bensman, WB Dodd… - Nature …, 2022 - nature.com
Mechanistic models of how single cells respond to different perturbations can help integrate
disparate big data sets or predict response to varied drug combinations. However, the …

[HTML][HTML] Sequential application of anticancer drugs enhances cell death by rewiring apoptotic signaling networks

MJ Lee, SY Albert, AK Gardino, AM Heijink, PK Sorger… - Cell, 2012 - cell.com
Crosstalk and complexity within signaling pathways and their perturbation by oncogenes
limit component-by-component approaches to understanding human disease. Network …

[HTML][HTML] Integration of transcriptomics data into agent-based models of solid tumor metastasis

J Retzlaff, X Lai, C Berking, J Vera - Computational and structural …, 2023 - Elsevier
Recent progress in our understanding of cancer mostly relies on the systematic profiling of
patient samples with high-throughput techniques like transcriptomics. With this approach …

Navigating multi-scale cancer systems biology towards model-driven clinical oncology and its applications in personalized therapeutics

MN Gondal, SU Chaudhary - Frontiers in Oncology, 2021 - frontiersin.org
Rapid advancements in high-throughput omics technologies and experimental protocols
have led to the generation of vast amounts of scale-specific biomolecular data on cancer …

[HTML][HTML] A text-based computational framework for patient-specific modeling for classification of cancers

H Imoto, S Yamashiro, M Okada - Iscience, 2022 - cell.com
Patient heterogeneity precludes cancer treatment and drug development; hence,
development of methods for finding prognostic markers for individual treatment is urgently …

Efficient parameter estimation enables the prediction of drug response using a mechanistic pan-cancer pathway model

F Fröhlich, T Kessler, D Weindl, A Shadrin… - Cell systems, 2018 - cell.com
Mechanistic models are essential to deepen the understanding of complex diseases at the
molecular level. Nowadays, high-throughput molecular and phenotypic characterizations …

Integrating transcriptomic data with mechanistic systems pharmacology models for virtual drug combination trials

AM Barrette, M Bouhaddou… - ACS chemical …, 2018 - ACS Publications
Monotherapy clinical trials with mutation-targeted kinase inhibitors, despite some success in
other cancers, have yet to impact glioblastoma (GBM). Besides insufficient blood–brain …