Evidence map›Paper›PMID 40923360›Full record

ArticleActa crystallographica. Section D, Structural biology2025

How many (distinguishable) classes can we identify in single-particle analysis?

O Lauzirika, M Pernica, D Herreros, E Ramírez-Aportela, J Krieger, M Gragera, M Iceta, P Conesa, Y Fonseca, J Jiménez and 3 more

Abstract read
In one paragraph

Article in Acta crystallographica. Section D, Structural biology, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 2 papers.

0numbers the graph read from it
0cells of the map it votes in
2citing 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

2 citing papers in PubMed.

  1. Article
  2. 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

13 authors.

O LauzirikaCentro Nacional de Biotecnologia-CSIC, Calle Darwin 3, 28049 Cantoblanco, Madrid, Spain.
M PernicaFaculty of Informatics, Masaryk University, Brno, Czech Republic.
D HerrerosCentro Nacional de Biotecnologia-CSIC, Calle Darwin 3, 28049 Cantoblanco, Madrid, Spain.ORCID 0000-0003-1509-1649
E Ramírez-AportelaCentro Nacional de Biotecnologia-CSIC, Calle Darwin 3, 28049 Cantoblanco, Madrid, Spain.
J KriegerCentro Nacional de Biotecnologia-CSIC, Calle Darwin 3, 28049 Cantoblanco, Madrid, Spain.
M GrageraCentro Nacional de Biotecnologia-CSIC, Calle Darwin 3, 28049 Cantoblanco, Madrid, Spain.ORCID 0000-0002-3097-1743
M IcetaCentro Nacional de Biotecnologia-CSIC, Calle Darwin 3, 28049 Cantoblanco, Madrid, Spain.
P ConesaCentro Nacional de Biotecnologia-CSIC, Calle Darwin 3, 28049 Cantoblanco, Madrid, Spain.
Y FonsecaCentro Nacional de Biotecnologia-CSIC, Calle Darwin 3, 28049 Cantoblanco, Madrid, Spain.
J JiménezCentro Nacional de Biotecnologia-CSIC, Calle Darwin 3, 28049 Cantoblanco, Madrid, Spain.
J FilipovicInstitute of Computer Science, Masaryk University, Brno, Czech Republic.
J M CarazoCentro Nacional de Biotecnologia-CSIC, Calle Darwin 3, 28049 Cantoblanco, Madrid, Spain.
C O S SorzanoCentro Nacional de Biotecnologia-CSIC, Calle Darwin 3, 28049 Cantoblanco, Madrid, Spain.

Funding

Agencia Estatal de Investigación CEX2023-001386-SAgencia Estatal de Investigación PID2022-136594NB-I00Comunidad de Madrid S2022/BMD-7232Fundacion la Caixa LCF/BQ/DR24/1208003HORIZON EUROPE Framework Programme 101024130HORIZON EUROPE Framework Programme 101094131HORIZON EUROPE Framework Programme 101131875HORIZON EUROPE Framework Programme 101163317Ministerio de Ciencia, Innovación y Universidades 716450
6 · The paper itself

Abstract

Heterogeneity in cryoEM is essential for capturing the structural variability of macromolecules, reflecting their functional states and biological significance. However, estimating heterogeneity remains challenging due to particle misclassification and algorithmic biases, which can lead to reconstructions that blend distinct conformations or fail to resolve subtle differences. Furthermore, the low signal-to-noise ratio inherent in cryo-EM data makes it nearly impossible to detect minute structural changes, as noise often obscures subtle variations in macromolecular projections. In this paper, we investigate the use of p-values associated with the null hypothesis that the observed classification differs from a random partition of the input data set, thereby providing a statistical framework for determining the number of distinguishable classes present in a given data set.

Indexed as

Cryoelectron MicroscopyMacromolecular SubstancesSingle Molecule ImagingAlgorithmsSignal-To-Noise RatioMacromolecular Substances3D classificationcryo-electron microscopyreproducibility analysisstatistical significancestructural heterogeneity

Identifiers

PMID40923360
PMCPMC12485487

What OpenQuestion holds

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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 OpenQuestion graph.