TISON: a next-generation multi-scale modeling theatre for in silico systems oncology

MN Gondal, MU Sultan, A Arif, A Rehman, HA Awan… - BioRxiv, 2021 - biorxiv.org
Multi-scale models integrating biomolecular data from genetic, transcriptional, and
translational levels, coupled with extracellular microenvironments can assist in decoding the …

Navigating Multi-scale Cancer Systems Biology towards Model-driven Personalized Therapeutics

MN Gondal, SU Chaudhary - bioRxiv, 2021 - biorxiv.org
Rapid advancements in high-throughput omics technologies and experimental protocols
have led to the generation of vast amounts of biomolecular data on cancer that now …

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 …

Artificial Intelligence (AI) Optimized Systems Modeling for the Deeper Understanding of Human Cancers

Z Ji, S Tao, B Wang - Frontiers in Bioengineering and Biotechnology, 2021 - frontiersin.org
Cancer research in the field of Computational Systems Biology attempts to address
questions that will advance current knowledge in the mechanisms of cancer progression or …

Integration of Clinical Trial Spatial Multi-omics Analysis and Virtual Clinical Trials Enables Immunotherapy Response Prediction and Biomarker Discovery

S Zhang, A Deshpande, BK Verma, H Wang, H Mi… - Cancer Research, 2024 - AACR
Computational methods that simulate tumors mathematically to describe cellular and
molecular interactions are emerging as promising tools to simulate the impact of therapy …

Article commentary: Predictive modeling of drug treatment in the area of personalized medicine

LA Ogilvie, C Wierling, T Kessler… - Cancer …, 2015 - journals.sagepub.com
Despite a growing body of knowledge on the mechanisms underlying the onset and
progression of cancer, treatment success rates in oncology are at best modest. Current …

In silico signaling modeling to understand cancer pathways and treatment responses

M Kunz, J Jeromin, M Fuchs, J Christoph… - Briefings in …, 2020 - academic.oup.com
Precision medicine has changed thinking in cancer therapy, highlighting a better
understanding of the individual clinical interventions. But what role do the drivers and …

[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 …

Constructing predictive cancer systems biology models

JA Rohrs, SZ Makaryan, SD Finley - bioRxiv, 2018 - biorxiv.org
Abstract Systems biology combines computational modeling with quantitative experimental
measurements to study complex biological processes. Here, we outline an approach for …

High-throughput cancer hypothesis testing with an integrated PhysiCell-EMEWS workflow

J Ozik, N Collier, JM Wozniak, C Macal, C Cockrell… - BMC …, 2018 - Springer
Background Cancer is a complex, multiscale dynamical system, with interactions between
tumor cells and non-cancerous host systems. Therapies act on this combined cancer-host …