Evidence map›Paper›PMID 34400556›Full record

ReviewCold Spring Harbor perspectives in biology2022

Uncovering the Principles of Genome Folding by 3D Chromatin Modeling.

Asli Yildirim, Lorenzo Boninsegna, Yuxiang Zhan, Frank Alber

Abstract readReview
PubMed Full text at PMC Publisher
In one paragraph

Review in Cold Spring Harbor perspectives in biology, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.

0numbers the graph read from it
0cells of the map it votes in
15citing 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

15 citing papers in PubMed.

  1. Article
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  14. Integrative approaches in genome structure analysis.Structure (London, England : 1993) · 2022
    Review
  15. Review
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

4 authors.

Asli YildirimInstitute for Quantitative and Computational Biosciences, Department of Microbiology, Immunology and Molecular Genetics, University of California Los Angeles, Los Angeles, California 90095, USA.
Lorenzo BoninsegnaInstitute for Quantitative and Computational Biosciences, Department of Microbiology, Immunology and Molecular Genetics, University of California Los Angeles, Los Angeles, California 90095, USA.
Yuxiang ZhanInstitute for Quantitative and Computational Biosciences, Department of Microbiology, Immunology and Molecular Genetics, University of California Los Angeles, Los Angeles, California 90095, USA.
Frank AlberInstitute for Quantitative and Computational Biosciences, Department of Microbiology, Immunology and Molecular Genetics, University of California Los Angeles, Los Angeles, California 90095, USA.

Funding

Multiscale Analyses of 4D Nucleome Structure and Function by Comprehensive Multimodal Data IntegrationUM1HG011593 · NHGRI · CARNEGIE-MELLON UNIVERSITY · PI ALBER, FRANK, BELMONT, ANDREW STEVEN · 2020 to 2024
$10.4M
Mapping the 3D Genome LandscapeU54DK107981 · NIDDK · UNIVERSITY OF SOUTHERN CALIFORNIA · PI CHEN, LIN · 2015 to 2019
$4.2M
NHGRI NIH HHS UM1 HG011593NIDDK NIH HHS U54 DK107981
6 · The paper itself

Abstract

Our understanding of how genomic DNA is tightly packed inside the nucleus, yet is still accessible for vital cellular processes, has grown dramatically over recent years with advances in microscopy and genomics technologies. Computational methods have played a pivotal role in the structural interpretation of experimental data, which helped unravel some organizational principles of genome folding. Here, we give an overview of current computational efforts in mechanistic and data-driven 3D chromatin structure modeling. We discuss strengths and limitations of different methods and evaluate the added value and benefits of computational approaches to infer the 3D structural and dynamic properties of the genome and its underlying mechanisms at different scales and resolution, ranging from the dynamic formation of chromatin loops and topological associated domains to nuclear compartmentalization of chromatin and nuclear bodies.

Indexed as

ChromatinChromatin Assembly and DisassemblyCell NucleusChromosomesGenomeChromatin

Identifiers

PMID34400556
PMCPMC9248826

What OpenQuestion holds

Textmetadata
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.