Evidence map›Paper›PMID 37506571›Full record

ReviewCurrent opinion in cell biology2023

Techniques for and challenges in reconstructing 3D genome structures from 2D chromosome conformation capture data.

Zilong Li, Stephanie Portillo-Ledesma, Tamar Schlick

Abstract readReview
PubMed Full text at PMC Publisher
In one paragraph

Review in Current opinion in cell biology, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 7 papers.

0numbers the graph read from it
0cells of the map it votes in
7citing 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

7 citing papers in PubMed.

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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

3 authors.

Zilong LiDepartment of Chemistry, New York University, 100 Washington Square East, Silver Building, New York, 10003, NY, USA; Simons Center for Computational Physical Chemistry, New York University, 24 Waverly Place, Silver Building, New York, NY, 10003, USA.
Stephanie Portillo-LedesmaDepartment of Chemistry, New York University, 100 Washington Square East, Silver Building, New York, 10003, NY, USA; Simons Center for Computational Physical Chemistry, New York University, 24 Waverly Place, Silver Building, New York, NY, 10003, USA.
Tamar SchlickDepartment of Chemistry, New York University, 100 Washington Square East, Silver Building, New York, 10003, NY, USA; Courant Institute of Mathematical Sciences, New York University, 251 Mercer St., New York, 10012, NY, USA; New York University-East China Normal University Center for Computational Chemistry, New York University Shanghai, Room 340, Geography Building, 3663 North Zhongshan Road, Shanghai, 200122, China; Simons Center for Computational Physical Chemistry, New York University, 24 Waverly Place, Silver Building, New York, NY, 10003, USA. Electronic address: schlick@nyu.edu.

Funding

Bridging Disparate Structural/Functional Scales: Multiscale Modeling of the Chromatin Fiber and RNA Tertiary StructuresR35GM122562 · NIGMS · NEW YORK UNIVERSITY · PI Tamar Schlick · 2017 to 2026
$4.6M
NIGMS NIH HHS R35 GM122562
6 · The paper itself

Abstract

Chromosome conformation capture technologies that provide frequency information for contacts between genomic regions have been crucial for increasing our understanding of genome folding and regulation. However, such data do not provide direct evidence of the spatial 3D organization of chromatin. In this opinion article, we discuss the development and application of computational methods to reconstruct chromatin 3D structures from experimental 2D contact data, highlighting how such modeling provides biological insights and can suggest mechanisms anchored to experimental data. By applying different reconstruction methods to the same contact data, we illustrate some state-of-the-art of these techniques and discuss our gene resolution approach based on Brownian dynamics and Monte Carlo sampling.

Indexed as

ChromatinChromosomesGenomeGenomicsMolecular ConformationChromatin

Identifiers

PMID37506571
PMCPMC10529954

What OpenQuestion holds

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Registered trials

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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.