Translating clinical genomics and health informatics into precision oncology

HT Yang, DC Crawford, ME Abazeed - Frontiers in Genetics, 2022 - frontiersin.org
Some cancers are driven by targetable genomic alterations that dysregulate key pathways
influencing cell growth and survival. These tumors lend themselves to significant, although …

Systematic identification of combinatorial drivers and targets in cancer cell lines

A Tabchy, N Eltonsy, DE Housman, GB Mills - PloS one, 2013 - journals.plos.org
There is an urgent need to elicit and validate highly efficacious targets for combinatorial
intervention from large scale ongoing molecular characterization efforts of tumors. We …

A mesoscopic simulator to uncover heterogeneity and evolutionary dynamics in tumors

JS Juan, MR Álvaro, P Anton, PB Julián, A Youness… - bioRxiv, 2020 - biorxiv.org
Increasingly complex in-silico modeling approaches offer a way to simultaneously access
cancerous processes at different spatio-temporal scales. High-level models, such as those …

Phenotypic maps for precision medicine: a promising systems biology tool for assessing therapy response and resistance at a personalized level

S Bhattacharyya, SF Ehsan… - Frontiers in Network …, 2023 - frontiersin.org
In this perspective we discuss how tumor heterogeneity and therapy resistance necessitate
a focus on more personalized approaches, prompting a shift toward precision medicine. At …

Patient-Derived In Vitro and In Vivo Models of Cancer

SE Claridge, JA Cavallo, BD Hopkins - Computational Methods for …, 2022 - Springer
Over the last two decades, cancer researchers have taken the promise offered by the
Human Genome Project and have expanded its capacity to use sequencing to identify the …

Tumor biology gets smart

R Zearfoss - Cell, 2022 - cell.com
It's what we've all searched for at one time or another. That seemingly magical effect when
two plus two appears to add up to more than four. We search for it in datasets. We try to …

Multiscale network modeling reveals the gene regulatory landscape driving cancer prognosis in 32 cancer types

P Xu, B Zhang - Genome Research, 2023 - genome.cshlp.org
Cancer is a complex disease with diverse molecular mechanisms that affect patient
prognosis. Network-based approaches are effective in revealing a holistic picture of cancer …

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 …

AI meets exascale computing: Advancing cancer research with large-scale high performance computing

T Bhattacharya, T Brettin, JH Doroshow… - Frontiers in …, 2019 - frontiersin.org
The application of data science in cancer research has been boosted by major advances in
three primary areas:(1) Data: diversity, amount, and availability of biomedical data;(2) …

[HTML][HTML] CELLector: genomics-guided selection of cancer in vitro models

H Najgebauer, M Yang, HE Francies, C Pacini… - Cell systems, 2020 - cell.com
Selecting appropriate cancer models is a key prerequisite for maximizing translational
potential and clinical relevance of in vitro oncology studies. We developed CELLector: an R …