ArticlePLoS computational biology2018
Topological and statistical analyses of gene regulatory networks reveal unifying yet quantitatively different emergent properties.
Article in PLoS computational biology, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 31 papers, 1 of them a synthesis that pooled it.
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Who cites it
31 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Lightweight Software Architecture Evaluation for Industry: A Comprehensive Review.Sensors (Basel, Switzerland) · 2022Pooled it
- Data-driven discovery of digital twins in biomedical research.Briefings in bioinformatics · 2026Review
- Topology-based metrics for finding the optimal sparsity in gene regulatory network inference.Bioinformatics (Oxford, England) · 2025Article
- Evolutionary trajectory of transcription factors and selection of targets for metabolic engineering.Philosophical transactions of the Royal Society of London. Series B, Biological sciences · 2024Review
- Topological benchmarking of algorithms to infer gene regulatory networks from single-cell RNA-seq data.Bioinformatics (Oxford, England) · 2024Article
- Breaking reflection symmetry: evolving long dynamical cycles in Boolean systems.New journal of physics · 2024Article
- The cluster D-trace loss for differential network analysis.Journal of applied statistics · 2024Article
- From qualitative to quantitative: the state of the art and challenges for plant synthetic biology.Quantitative biology (Beijing, China) · 2023Review
- Inferring gene regulatory network from single-cell transcriptomes with graph autoencoder model.PLoS genetics · 2023Article
- GRaNIE and GRaNPA: inference and evaluation of enhancer-mediated gene regulatory networks.Molecular systems biology · 2023Article
- Building High-Confidence Gene Regulatory Networks by Integrating Validated TF-Target Gene Interactions Using ConnecTF.Methods in molecular biology (Clifton, N.J.) · 2023Article
- Global Landscape of Native Protein Complexes in Synechocystis sp. PCC 6803.Genomics, proteomics & bioinformatics · 2022Article
- Benchmarking imputation methods for network inference using a novel method of synthetic scRNA-seq data generation.BMC bioinformatics · 2022Article
- Comparative Network Biology Discovers Protein Complexes That Underline Cellular Differentiation in Anabaena sp.Molecular & cellular proteomics : MCP · 2022Article
- Cis-regulatory sequences in plants: Their importance, discovery, and future challenges.The Plant cell · 2022Review
- Network approach to understand biological systems: From single to multilayer networks.Journal of biosciences · 2022Article
- Three topological features of regulatory networks control life-essential and specialized subsystems.Scientific reports · 2021Article
- Complex small-world regulatory networks emerge from the 3D organisation of the human genome.Nature communications · 2021Article
- Detection of Genes inGenes · 2021Article
- Convergent and distributed effects of the 3q29 deletion on the human neural transcriptome.Translational psychiatry · 2021Article
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3 authors.
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No grant is acknowledged in the PubMed record.
Abstract
Understanding complexity in physical, biological, social and information systems is predicated on describing interactions amongst different components. Advances in genomics are facilitating the high-throughput identification of molecular interactions, and graphs are emerging as indispensable tools in explaining how the connections in the network drive organismal phenotypic plasticity. Here, we describe the architectural organization and associated emergent topological properties of gene regulatory networks (GRNs) that describe protein-DNA interactions (PDIs) in several model eukaryotes. By analyzing GRN connectivity, our results show that the anticipated scale-free network architectures are characterized by organism-specific power law scaling exponents. These exponents are independent of the fraction of the GRN experimentally sampled, enabling prediction of properties of the complete GRN for an organism. We further demonstrate that the exponents describe inequalities in transcription factor (TF)-target gene recognition across GRNs. These observations have the important biological implication that they predict the existence of an intrinsic organism-specific trans and/or cis regulatory landscape that constrains GRN topologies. Consequently, architectural GRN organization drives not only phenotypic plasticity within a species, but is also likely implicated in species-specific phenotype.
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