ArticleNPJ systems biology and applications2019
An omnidirectional visualization model of personalized gene regulatory networks.
Article in NPJ systems biology and applications, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
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Who cites it
17 citing papers in PubMed.
- Omnidirectional Interaction Networks Modulating Phenotypic Plasticity in the Gut Microbiota Towards Ulcerative Colitis.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Statistical learning of stochastic complex systems via the Yau-Yau nonlinear filter.Innovation (Cambridge (Mass.)) · 2026Article
- An omnigenic interactome model to chart the genetic architecture of individual plants.Horticulture research · 2026Article
- A Statistical Mechanics Model to Decode Tissue Crosstalk During Graft Formation.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- idopNetwork Analysis of Salt-Responsive Transcriptomes Reveals Hub Regulatory Modules and Genes inInternational journal of molecular sciences · 2025Article
- Cooperation of TRADD- and RIPK1-dependent cell death pathways in maintaining intestinal homeostasis.Nature communications · 2025Article
- Identification of biomarkers and target drugs for melanoma: a topological and deep learning approach.Frontiers in genetics · 2025Article
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- The metabolomic physics of complex diseases.Proceedings of the National Academy of Sciences of the United States of America · 2023Article
- A Cartographic Tool to Predict Disease Risk-associated Pseudo-Dynamic Networks from Tissue-specific Gene Expression.Bio-protocol · 2023Article
- A statistical framework for recovering pseudo-dynamic networks from static data.Bioinformatics (Oxford, England) · 2022Article
- A Single-Cell Omics Network Model of Cell Crosstalk during the Formation of Primordial Follicles.Cells · 2022Article
- Vaginal microbiota networks as a mechanistic predictor of aerobic vaginitis.Frontiers in microbiology · 2022Article
- Review
- Genetic dissection of growth trajectories in forest trees: From FunMap to FunGraph.Forestry research · 2021Review
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- Article
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Authors and funding
11 authors.
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Abstract
Gene regulatory networks (GRNs) have been widely used as a fundamental tool to reveal the genomic mechanisms that underlie the individual's response to environmental and developmental cues. Standard approaches infer GRNs as holistic graphs of gene co-expression, but such graphs cannot quantify how gene-gene interactions vary among individuals and how they alter structurally across spatiotemporal gradients. Here, we develop a general framework for inferring informative, dynamic, omnidirectional, and personalized networks (idopNetworks) from routine transcriptional experiments. This framework is constructed by a system of quasi-dynamic ordinary differential equations (qdODEs) derived from the combination of ecological and evolutionary theories. We reconstruct idopNetworks using genomic data from a surgical experiment and illustrate how network structure is associated with surgical response to infrainguinal vein bypass grafting and the outcome of grafting. idopNetworks may shed light on genotype-phenotype relationships and provide valuable information for personalized medicine.
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Registered trials
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