Evidence map›Paper›PMID 40739342›Full record

ArticleNature2025

Design of highly functional genome editors by modelling CRISPR-Cas sequences.

Jeffrey A Ruffolo, Stephen Nayfach, Joseph Gallagher, Aadyot Bhatnagar, Joel Beazer, Riffat Hussain, Jordan Russ, Jennifer Yip, Emily Hill, Martin Pacesa and 3 more

Abstract read
In one paragraph

Article in Nature, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 81 papers.

0numbers the graph read from it
0cells of the map it votes in
81citing 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

81 citing papers in PubMed.

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  19. Harnessing artificial intelligence in plant breeding: innovations in digital phenotyping and breeding methodologies.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2026
    Review
  20. Review

21 more citing papers are in PubMed but not listed here.

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.

Jeffrey A Ruffolo *Profluent Bio, Berkeley, CA, USA.ORCID 0000-0002-3385-9191
Stephen Nayfach *Profluent Bio, Berkeley, CA, USA.
Joseph Gallagher *Profluent Bio, Berkeley, CA, USA.
Aadyot Bhatnagar *Profluent Bio, Berkeley, CA, USA.
Joel BeazerProfluent Bio, Berkeley, CA, USA.
Riffat HussainProfluent Bio, Berkeley, CA, USA.
Jordan RussProfluent Bio, Berkeley, CA, USA.
Jennifer YipProfluent Bio, Berkeley, CA, USA.
Emily HillProfluent Bio, Berkeley, CA, USA.
Martin PacesaProfluent Bio, Berkeley, CA, USA.
Alexander J MeeskeProfluent Bio, Berkeley, CA, USA.ORCID 0000-0003-3878-531X
Peter CameronProfluent Bio, Berkeley, CA, USA.
Ali MadaniProfluent Bio, Berkeley, CA, USA. ali@profluent.bio.ORCID 0000-0002-3092-1295

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

Gene editing has the potential to solve fundamental challenges in agriculture, biotechnology and human health. CRISPR-based gene editors derived from microorganisms, although powerful, often show notable functional tradeoffs when ported into non-native environments, such as human cells

Indexed as

Artificial IntelligenceCRISPR-Cas SystemsGene EditingGenome, HumanModels, GeneticCRISPR-Associated Protein 9CRISPR-Associated ProteinsHumansMetagenomeOperonRNA, Guide, CRISPR-Cas SystemsCRISPR-Associated Protein 9CRISPR-Associated ProteinsRNA, Guide, CRISPR-Cas Systems

Identifiers

PMID40739342
PMCPMC12422970

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.