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July 3rd, 2025
Version: 2
H. Lee Moffitt Cancer Center
bioinformatics
biorxiv

CLONEID: A Framework for Longitudinal Integration of Phenotypic and Genotypic Data to Monitor and Steer Subclonal Dynamics

Veith, T.Open in Google Scholar•Beck, R. J.Open in Google Scholar•Tagal, V.Open in Google Scholar•Li, T.Open in Google Scholar•Alahmari, S.Open in Google Scholar•Cole, J.Open in Google Scholar•Hannaby, D.Open in Google Scholar•Kyei, J.Open in Google Scholar•Yu, X.Open in Google Scholar•Maksin, K.Open in Google Scholaret al.

Understanding how genetic and phenotypic diversity emerges and evolves within cancer cell populations is a fundamental challenge in cancer biology. CLONEID is a novel framework designed to organize and analyze clone-specific measures as structured time-series data. By integrating and monitoring genotypic and phenotypic experimental data over time, CLONEID facilitates hypothesis-driven and hypothesis-generating research in cancer biology. This article outlines the development, utility, and applications of CLONEID, emphasizing its role in overcoming challenges in data reproducibility, mathematical modeling, and multi-modal data integration. A webportal to the CLONEID database is available at dev.cloneid.org.

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