Evidence map›Paper›PMID 41691282›Full record

ArticleGenome biology2026

Modeling nascent transcription from chromatin landscape and structure with CLASTER.

Marc Pielies Avellí, Arnór Ingi Sigurdsson, Joaquim Ollé López, Takeo Narita, Nils Krietenstein, Chunaram Choudhary, Simon Rasmussen

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Genome biology, 2026. 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

7 authors.

Marc Pielies AvellíNovo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, 2200, Denmark.ORCID http://orcid.org/0009-0007-4801-008X
Arnór Ingi SigurdssonNovo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, 2200, Denmark.ORCID http://orcid.org/0000-0002-3880-9505
Joaquim Ollé LópezCenter for Epigenetic Cell Memory, Danish Cancer Society, Copenhagen, 2100, Denmark.ORCID http://orcid.org/0000-0003-1150-3896
Takeo NaritaNovo Nordisk Foundation Center for Protein Research, Department of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen, 2200, Denmark.ORCID http://orcid.org/0000-0002-2705-7838
Nils KrietensteinCenter for Epigenetic Cell Memory, Danish Cancer Society, Copenhagen, 2100, Denmark.ORCID http://orcid.org/0000-0003-2519-6305
Chunaram ChoudharyNovo Nordisk Foundation Center for Protein Research, Department of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen, 2200, Denmark.ORCID http://orcid.org/0000-0002-9863-433X
Simon RasmussenNovo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, 2200, Denmark. srasmuss@sund.ku.dk.ORCID http://orcid.org/0000-0001-6323-9041

Funding

Danmarks Grundforskningsfond DNRF195European Research Council ACT-SIGNAL, 101142708Novo Nordisk Fonden NNF14CC0001
6 · The paper itself

Abstract

We present the Chromatin Landscape and Structure to Expression Regressor (CLASTER), an epigenetic-based deep neural network that can integrate different data modalities describing the chromatin landscape and its 3D structure. CLASTER effectively translates them into nascent transcription levels measured at a kilobasepair resolution. The model provides a platform to understand the epigenetic drivers and learned rules of nascent transcription, and to predict the impact of in silico epigenetic perturbations. We conclude that the predominant locality of current machine learning approaches emerges as a signature of genomic organization, having broad implications for future modeling approaches.

Indexed as

ChromatinModels, GeneticNeural Networks, ComputerTranscription, GeneticEpigenesis, GeneticHumansChromatinChromatin landscapeChromatin structureDeep neural networksEU-seqNascent transcription

Identifiers

PMID41691282
PMCPMC13011747

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.