Evidence map›Paper›PMID 34876518›Full record

ArticleProceedings of the National Academy of Sciences of the United States of America2021

Entropy-regularized deconvolution of cellular cryotransmission electron tomograms.

Matthew Croxford, Michael Elbaum, Muthuvel Arigovindan, Zvi Kam, David Agard, Elizabeth Villa, John Sedat

Open access · hybridAbstract read
In one paragraph

Article in Proceedings of the National Academy of Sciences of the United States of America, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.

0numbers the graph read from it
0cells of the map it votes in
16citing papers in PubMed
3.6field-weighted citation impact, top 6% of its field
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

16 citing papers in PubMed, 25 citations in OpenAlex.

  1. The molecular architecture of tunneling nanotubes.bioRxiv : the preprint server for biology · 2026
    Article
  2. Article
  3. Review
  4. Article
  5. Article
  6. Deconvolution to restore cryo-EM maps with anisotropic resolution.bioRxiv : the preprint server for biology · 2025
    Article
  7. Helical coiled nucleosome chromosome architectures during cell cycle progression.Proceedings of the National Academy of Sciences of the United States of America · 2024
    Article
  8. Review
  9. Review
  10. Review
  11. Article
  12. Computational methods forFrontiers in cellular and infection microbiology · 2023
    Review
  13. Article
  14. A proposed unified interphase nucleus chromosome structure: Preliminary preponderance of evidence.Proceedings of the National Academy of Sciences of the United States of America · 2022
    Article
  15. A proposed unified mitotic chromosome architecture.Proceedings of the National Academy of Sciences of the United States of America · 2022
    Article
  16. 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 at 4 institutions in 3 countries.

Matthew CroxfordSection of Molecular Biology, Division of Biological Sciences, University of California San Diego, La Jolla, CA 92093.ORCID 0000-0002-9908-1466
Michael ElbaumDepartment of Chemical and Biological Physics, Weizmann Institute of Science, Rehovot 760001, Israel.ORCID 0000-0001-7915-5512
Muthuvel ArigovindanDepartment of Electrical Engineering, Indian Institute of Science, Bengaluru 560012, India.
Zvi KamDepartment of Molecular Cell Biology, Weizmann Institute of Science, Rehovot 760001, Israel.
David AgardDepartment of Biochemistry and Biophysics, University of California, San Francisco, CA 94158.ORCID 0000-0003-3512-695X
Elizabeth VillaSection of Molecular Biology, Division of Biological Sciences, University of California San Diego, La Jolla, CA 92093; evilla@ucsd.edu sedat@msg.ucsf.edu.ORCID 0000-0003-4677-9809
John SedatDepartment of Biochemistry and Biophysics, University of California, San Francisco, CA 94158; evilla@ucsd.edu sedat@msg.ucsf.edu.
University of California San Diego · USUniversity of California, San Francisco · USWeizmann Institute of Science · ILIndian Institute of Science Bangalore · IN

Funding

Structure & Mechanism: microtubule nucleation, centrosomes, phage cytoskeletonR35GM118099 · NIGMS · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI AGARD, DAVID A. · 2016 to 2022
$3.6M
Opening Windows into the Cell: Revealing the Molecular Architecture of the Nuclear PeripheryDP2GM123494 · NIGMS · UNIVERSITY OF CALIFORNIA, SAN DIEGO · PI VILLA, ELIZABETH · 2016 to 2019
$2.5M
NIGMS NIH HHS DP2 GM123494NIGMS NIH HHS R35 GM118099
6 · The paper itself

Abstract

Cryo-electron tomography (cryo-ET) allows for the high-resolution visualization of biological macromolecules. However, the technique is limited by a low signal-to-noise ratio (SNR) and variance in contrast at different frequencies, as well as reduced Z resolution. Here, we applied entropy-regularized deconvolution (ER-DC) to cryo-ET data generated from transmission electron microscopy (TEM) and reconstructed using weighted back projection (WBP). We applied deconvolution to several in situ cryo-ET datasets and assessed the results by Fourier analysis and subtomogram analysis (STA).

Indexed as

EntropyComputer SimulationCryoelectron MicroscopyHEK293 CellsHumansSaccharomyces cerevisiaeTomography, X-Ray Computedcryo-electron tomographydeconvolutionmissing wedgestructural biologysubtomogram analysis

Identifiers

PMID34876518
PMCPMC8685678
OpenAlexW4226205603

What OpenQuestion holds

Textmetadata
LicenceCC BY-NC-ND
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.