Evidence map›Paper›PMID 41093751›Full record

ArticleBioinformatics (Oxford, England)2025

BIWT: a bioinformatics walkthrough for embedding spatial multiomics in agent-based models for virtual cells.

Daniel R Bergman, Jeanette A I Johnson, Marwa Naji, Max Booth, Heber Lima da Rocha, Atul Deshpande, Dimitrios N Sidiropoulos, Tamara Lopez-Vidal, Randy Heiland, Luciane T Kagohara and 6 more

Abstract read
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In one paragraph

Article in Bioinformatics (Oxford, England), 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 1 paper.

0numbers the graph read from it
0cells of the map it votes in
1citing 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

1 citing paper in PubMed.

  1. Article
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

16 authors.

Daniel R BergmanDepartment of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD, 21218, United States.ORCID 0000-0002-2166-6616
Jeanette A I JohnsonDepartment of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD, 21218, United States.
Marwa NajiDepartment of Biology, Johns Hopkins University, Baltimore, MD, 21218, United States.
Max BoothDepartment of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD, 21218, United States.
Heber Lima da RochaDepartment of Intelligent Systems Engineering, Indiana University, Bloomington, IN, 47408, United States.
Atul DeshpandeDepartment of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD, 21218, United States.
Dimitrios N SidiropoulosDepartment of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD, 21218, United States.
Tamara Lopez-VidalDepartment of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD, 21218, United States.
Randy HeilandDepartment of Intelligent Systems Engineering, Indiana University, Bloomington, IN, 47408, United States.
Luciane T KagoharaDepartment of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD, 21218, United States.
Robert A AndersDepartment of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD, 21218, United States.
Lei ZhengDepartment of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD, 21218, United States.
Elizabeth M JaffeeDepartment of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD, 21218, United States.
Genevieve Stein-O'BrienDepartment of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD, 21218, United States.
Paul MacklinDepartment of Intelligent Systems Engineering, Indiana University, Bloomington, IN, 47408, United States.
Elana J FertigDepartment of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD, 21218, United States.

Funding

Transforming Human Pancreatic Cancer Into An Immunologic DiseaseP01CA247886 · NCI · JOHNS HOPKINS UNIVERSITY · PI ANDERS, ROBERT A. · 2021 to 2025
$12.7M
Tumor Microenvironment Crosstalk Drives Early Lesions in Pancreatic CancerU54CA274371 · NCI · UNIVERSITY OF TX MD ANDERSON CAN CTR · PI Elana Fertig · 2022 to 2026
$9.5M
Mapping the single cell state basis of metastasis in space and timeU01CA284090 · NCI · JOHNS HOPKINS UNIVERSITY · PI Andrew Josef Ewald · 2023 to 2026
$2.7M
Informing mechanistic rules of agent-based models with single-cell multi-omicsU24CA284156 · NCI · TRUSTEES OF INDIANA UNIVERSITY · PI Elana Fertig, Paul T Macklin · 2024 to 2026
$2.3M
Single-cell and imaging data integration software to spatially resolve the tumor microenvironmentU01CA253403 · NCI · JOHNS HOPKINS UNIVERSITY · PI FERTIG, ELANA · 2020 to 2022
$1.2M
Resolving Spatiotemporal Determinants of Cell Specification in Corticogenesis with Latent Space MethodsR00NS122085 · NINDS · JOHNS HOPKINS UNIVERSITY · PI STEIN-O'BRIEN, GENEVIEVE LAUREN · 2023 to 2025
$697k
National Cancer Institute - Cancer Center SupportNCI NIH HHS P01 CA247886NCI NIH HHS U01 CA253403NCI NIH HHS U01 CA284090NCI NIH HHS U24 CA284156NCI NIH HHS U54 CA274371NINDS NIH HHS R00 NS122085
6 · The paper itself

Abstract

summaryWhereas transcriptomic and spatial profiling offer static snapshots of tissue structure, mechanistic models use biological rules to predict how tissues evolve. We present the BioInformatics WalkThrough (BIWT) software to directly initialize spatial agent-based models from single-cell and spatial molecular data. We demonstrate how initialization strategies affect tumor-immune dynamics and spatial clustering, positioning BIWT as a software suite to generate data-driven virtual cells representing both experimental and clinical contexts. AVAILABILITY AND IMPLEMENTATION: The BIWT software is available at https://github.com/PhysiCell-Tools/PhysiCell-Studio. The sample dataset for running the BIWT is available at https://zenodo.org/records/16365625. The code and instructions for reproducing the use case example is available at https://github.com/drbergman/BIWT-Paper.

Indexed as

Computational BiologyModels, BiologicalSoftwareHumansMultiomicsNeoplasmsSingle-Cell Analysis

Identifiers

PMID41093751
PMCPMC12597895

What OpenQuestion holds

Textmetadata
LicenceCC BY
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 OpenQuestion graph.