Revealing transcriptomic responses in

Yuan Yuan, Ying Hefner, Richard Szubin, Jaemin Sung, Bernhard O Palsson

Abstract read

In one paragraph

Article in mSystems, 2026. 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.

Exosomes delivering a high-throughput-screened RNA polymerase inhibitor for highly effective therapy of multidrug-resistant bacterial infected pneumonia.Bioactive materials · 2026
Article
Sequence of Antibiotic Administration for the Treatment ofAntibiotics (Basel, Switzerland) · 2026
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

5 authors.

Yuan YuanShu Chien-Gene Lay Department of Bioengineering, University of California San Diego, La Jolla, California, USA.ORCID 0000-0002-9509-9167

Ying HefnerShu Chien-Gene Lay Department of Bioengineering, University of California San Diego, La Jolla, California, USA.

Richard SzubinShu Chien-Gene Lay Department of Bioengineering, University of California San Diego, La Jolla, California, USA.

Jaemin SungShu Chien-Gene Lay Department of Bioengineering, University of California San Diego, La Jolla, California, USA.

Bernhard O PalssonShu Chien-Gene Lay Department of Bioengineering, University of California San Diego, La Jolla, California, USA.ORCID 0000-0003-2357-6785

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

The earliest responses of pathogenic bacteria to antibiotics can affect the outcome of an infection. While long-term adaptations have been extensively studied, the immediate transcriptional changes that unfold immediately following antibiotic exposure remain poorly understood. Here, we applied iModulon analysis to time-resolved transcriptomic data from

Indexed as

Anti-Bacterial AgentsEscherichia coliGene Expression Regulation, BacterialTranscriptomeAmpicillinCiprofloxacinGene Expression ProfilingStress, PhysiologicalAmpicillinAnti-Bacterial AgentsCiprofloxacinantibiotic resistancecomputational biologygene regulationRNA-Seqsystems biology

Identifiers

PMID41805196

DOI10.1128/msystems.01584-25

PMCPMC13098195

What Socratic holds

Textmetadata

LicenceCC BY

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 Socratic graph.