Evidence map›Paper›PMID 41394716›Full record

ArticlebioRxiv : the preprint server for biology2025

Accurate and robust 3D genome feature discovery from multiplexed DNA FISH.

Hongyu Yu, Lingbo Zhou, Liangqi Xie, Caterina Strambio-De-Castillia, Ming Hu, Yun Li

Abstract readPreprint
PubMed Full text at PMC Publisher
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

6 authors.

Hongyu YuDepartment of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
Lingbo ZhouDepartment of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
Liangqi XieDepartment of Infection Biology, Lerner Research Institute, Cleveland Clinic Foundation, Cleveland, OH, USA.
Caterina Strambio-De-CastilliaProgram in Molecular Medicine, UMass Chan Medical School, Worcester, MA, USA.
Ming HuDepartment of Quantitative Biology, Lerner Research Institute, Cleveland Clinic Foundation, Cleveland, OH, USA.
Yun LiDepartment of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.

Funding

Preclinical CoreP50HD103573 · NICHD · UNIV OF NORTH CAROLINA CHAPEL HILL · PI GABRIEL S DICHTER · 2020 to 2026
$9.7M
Center for Integrated Multi-modal and Multi-scale Nucleome ResearchUM1HG011585 · NHGRI · UNIVERSITY OF CALIFORNIA, SAN DIEGO · PI DULAC, CATHERINE, LEIN, ED · 2020 to 2024
$6.7M
Study of Selective Cell and System Vulnerability in Alzheimer's DiseaseR01AG079291 · NIA · UNIV OF NORTH CAROLINA CHAPEL HILL · PI Li Gan, Yun Li · 2023 to 2026
$5.4M
Model-based methods for single cell chromatin interactomic dataR35HG011922 · NHGRI · CLEVELAND CLINIC LERNER COM-CWRU · PI HU, MING · 2021 to 2025
$2.4M
NHGRI NIH HHS R35 HG011922NHGRI NIH HHS UM1 HG011585NIA NIH HHS R01 AG079291NICHD NIH HHS P50 HD103573
6 · The paper itself

Abstract

Multiplexed DNA FISH (also known as FISH Omics) is a powerful imaging technology to map three-dimensional (3D) genome organization in thousands of single cells at kilobase resolution. However, existing computational approaches to identify 3D genome features, such as A/B compartments, topologically associating domains (TADs) and chromatin loops, have been mainly adapted from Hi-C and do not account for the distinct measurement errors across the three XYZ physical axes. Here we present ArcFISH (

Identifiers

PMID41394716
PMCPMC12697545

What Socratic holds

Textmetadata
LicenceCC BY
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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.