Evidence map›Paper›PMID 39702707›Full record

ReviewMethods in molecular biology (Clifton, N.J.)2025

Modeling ncRNA-Mediated Circuits in Cell Fate Decision: From Systems Biology to Synthetic Biology.

Xiao-Jun Tian, Rong Zhang, Manuela Vanegas Ferro, Hanah Goetz

Abstract readReview
PubMed Publisher
In one paragraph

Review in Methods in molecular biology (Clifton, N.J.), 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 1 paper.

0numbers the graph read from it
0cells of the map it votes in
1citing 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

1 citing paper in PubMed.

  1. Exploring the CeRNA landscape in plants: advances, methods, and challenges.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2026
    Review
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

4 authors.

Xiao-Jun TianSchool of Biological and Health Systems Engineering, Arizona State University, Tempe, AZ, USA. xiaojun.tian@asu.edu.
Rong ZhangSchool of Biological and Health Systems Engineering, Arizona State University, Tempe, AZ, USA.
Manuela Vanegas FerroSchool of Biological and Health Systems Engineering, Arizona State University, Tempe, AZ, USA.
Hanah GoetzSchool of Biological and Health Systems Engineering, Arizona State University, Tempe, AZ, USA.

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

Noncoding RNAs (ncRNAs) play critical roles in essential cell fate decisions. However, the exact molecular mechanisms underlying ncRNA-mediated bistable switches remain elusive and controversial. In recent years, systematic mathematical and quantitative experimental analyses have made significant contributions to elucidating the molecular mechanisms of controlling ncRNA-mediated cell fate decision processes. In this chapter, we review and summarize the general framework of mathematical modeling of ncRNA in a pedagogical way and the application of this general framework to real biological processes. We discuss the emerging properties resulting from the reciprocal regulation between mRNA, miRNA, and competing endogenous mRNA (ceRNA). We also explore the efforts within the synthetic biology approach to understand the fundamental design principles underlying cell fate decisions. Both the positive feedback loops between ncRNAs and transcription factors and the emerging properties from the miRNA-mRNA reciprocal regulation enable bistable switches to direct cell fate decisions.

Indexed as

Cell DifferentiationGene Regulatory NetworksRNA, UntranslatedSynthetic BiologySystems BiologyAnimalsCell LineageGene Expression RegulationHumansMicroRNAsRNA, MessengerMicroRNAsRNA, MessengerRNA, UntranslatedBistabilityCell fate decisionCompeting endogenous mRNAMathematical modelingPost-transcriptionalUltrasensitivity

Identifiers

PMID39702707

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.