Evidence map›Paper›PMID 41497538›Full record

ArticleComputational and structural biotechnology journal2026

BioLogical: a universal analysis framework for biosystem logical dynamics.

Yuxiang Yao, Dong Liu, Zheting Zhang, Chengchen Zhao, Duanqing Pei

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Computational and structural biotechnology journal, 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.

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

0 citing papers in PubMed.

No citing paper in PubMed yet.

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.

Yuxiang YaoLaboratory of Cell Fate Control, School of Life Sciences, Westlake University, Hangzhou, 310030, China.
Dong LiuLaboratory of Cell Fate Control, School of Life Sciences, Westlake University, Hangzhou, 310030, China.
Zheting ZhangLaboratory of Cell Fate Control, School of Life Sciences, Westlake University, Hangzhou, 310030, China.
Chengchen ZhaoLaboratory of Cell Fate Control, School of Life Sciences, Westlake University, Hangzhou, 310030, China.
Duanqing PeiLaboratory of Cell Fate Control, School of Life Sciences, Westlake University, Hangzhou, 310030, China.

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

Complex biosystems exhibit ordered, functional, self-organized features, yet a universal framework for exploring their logical paradigms and dynamic behaviors remains lacking. Here we present BioLogical, a user-friendly R package designed to analyze logical properties of gene regulatory systems. Through a standard workflow and multiple cases, we demonstrate its versatile capabilities in deciphering logical paradigms, computing static and dynamic biosystem indicators, simulating system evolution, and evaluating logical satisfiability. All concepts and algorithms are extended to multi-valued scenarios, and hierarchical interfaces are provided to meet diverse requirements. The open-source software is available at https://github.com/YuxiangYao/BioLogical.

Indexed as

Complex biosystemsDiscrete dynamicsGene regulatory networksLogical analysisMulti-valued logic

Identifiers

PMID41497538
PMCPMC12767838

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.