Evidence map›Paper›PMID 40631300›Full record

ArticlebioRxiv : the preprint server for biology2025

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

Thomas Veith, Richard Beck, Vural Tagal, Tao Li, Saeed Alahmari, Jackson Cole, Daniel Hannaby, John Kyei, Xiaoqing Yu, Konstantin Maksin and 7 more

Abstract readPreprint
In one paragraph

Article in bioRxiv : the preprint server for biology, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.

0numbers the graph read from it
0cells of the map it votes in
0citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

0 citing papers in PubMed.

No citing paper in PubMed yet.

4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

17 authors.

Thomas VeithDepartment of Integrated Mathematical Oncology, H Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA.ORCID 0000-0001-8411-9911
Richard BeckDepartment of Integrated Mathematical Oncology, H Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA.ORCID 0000-0002-6983-8835
Vural TagalDepartment of Integrated Mathematical Oncology, H Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA.ORCID 0000-0002-0489-9725
Tao LiDepartment of Integrated Mathematical Oncology, H Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA.ORCID 0000-0002-9595-5218
Saeed AlahmariDepartment of Computer Science, Najran University, Najran 66462, Saudi Arabia.ORCID 0000-0001-7344-9448
Jackson ColeDepartment of Integrated Mathematical Oncology, H Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA.ORCID 0009-0006-3416-6641
Daniel HannabyDepartment of Computer Science, Najran University, Najran 66462, Saudi Arabia.
John KyeiDepartment of Integrated Mathematical Oncology, H Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA.
Xiaoqing YuDepartment of Biostatistics and Bioinformatics, H Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA.ORCID 0000-0003-4585-9372
Konstantin MaksinThe University of Commerce and Services, Medical Department (WSHIU), Poznan, Poland.ORCID 0000-0001-6190-217X
Andrew SchultzDepartment of Integrated Mathematical Oncology, H Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA.ORCID 0009-0002-1783-6931
HoJoon LeeDepartment of Medicine, Stanford University, CA, USA.ORCID 0000-0002-0973-9544
Issam ElNaqaDepartment of Machine Learning, H Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA.ORCID 0000-0001-6023-1132
Steven EschrichDepartment of Biostatistics and Bioinformatics, H Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA.ORCID 0000-0002-9833-2788
Hanlee P JiDepartment of Medicine, Stanford University, CA, USA.ORCID 0000-0003-3772-3424
Aaron DiazDepartment of Epidemiology & Biostatistics, University of California San Francisco, CA, USA.ORCID 0000-0001-9059-9501
Noemi AndorDepartment of Integrated Mathematical Oncology, H Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA.ORCID 0000-0002-2469-5180

Funding

Characterizing cytotoxic therapy induced shifts in the cost-to-benefit ratio of high ploidyR37CA266727 · NCI · H. LEE MOFFITT CANCER CTR & RES INST · PI Noemi Andor · 2022 to 2026
$2.6M
Integrating cancer genomics and spatial architecture of tumor infiltrating lymphocytesR01CA280089 · NCI · STANFORD UNIVERSITY · PI Hanlee P Ji · 2023 to 2026
$1.9M
Multimodal iterative sequencing of cancer genomes and single tumor cellsR33CA247700 · NCI · STANFORD UNIVERSITY · PI JI, HANLEE P · 2021 to 2023
$1.1M
IMAT-ITCR Collaboration: Engineering model-based systems to monitor and steer subclonal dynamicsR21CA269415 · NCI · H. LEE MOFFITT CANCER CTR & RES INST · PI ANDOR, NOEMI · 2023 to 2024
$499k
A framework to integrate live-cell imaging with single-cell sequencing and learn how cells adapt to new environmentsR03CA259873 · NCI · H. LEE MOFFITT CANCER CTR & RES INST · PI ANDOR, NOEMI, HEISER, LAURA MADELINE · 2022 to 2023
$179k
NCI NIH HHS R01 CA280089NCI NIH HHS R03 CA259873NCI NIH HHS R21 CA269415NCI NIH HHS R33 CA247700NCI NIH HHS R37 CA266727
6 · The paper itself

Abstract

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.

Identifiers

PMID40631300
PMCPMC12236826

What Socratic holds

Textmetadata
LicenceCC BY-NC
Read underepoch 390

Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the Socratic graph.