ArticleiScience2023
A quantitative evaluation of topological motifs and their coupling in gene circuit state distributions.
Article in iScience, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 4 papers.
What it found
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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.
The trial behind it
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Who cites it
4 citing papers in PubMed, 4 citations in OpenAlex.
- Network hypermotifs in biological systems: structure, dynamics, and functional implications.NPJ systems biology and applications · 2026Review
- sRACIPE 2.0: a systems biology circuit modeling toolkit for random circuit perturbation.Bioinformatics (Oxford, England) · 2026Article
- Identification of DNA motif pairs on paired sequences based on composite heterogeneous graph.Frontiers in genetics · 2024Article
- What Makes a Functional Gene Regulatory Network? A Circuit Motif Analysis.The journal of physical chemistry. B · 2022Article
Corrections and comments
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Authors and funding
2 authors at 2 institutions in 1 country.
Funding
Abstract
One of the major challenges in biology is to understand how gene interactions collaborate to determine overall functions of biological systems. Here, we present a new computational framework that enables systematic, high-throughput, and quantitative evaluation of how small transcriptional regulatory circuit motifs, and their coupling, contribute to functions of a dynamical biological system. We illustrate how this approach can be applied to identify four-node gene circuits, circuit motifs, and motif coupling responsible for various gene expression state distributions, including those derived from single-cell RNA sequencing data. We also identify seven major classes of four-node circuits from clustering analysis of state distributions. The method is applied to establish phenomenological models of gene circuits driving human neuron differentiation, revealing important biologically relevant regulatory interactions. Our study will shed light on a better understanding of gene regulatory mechanisms in creating and maintaining cellular states.
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Registered trials
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.