ArticleProceedings of the National Academy of Sciences of the United States of America2012
Predictive computation of genomic logic processing functions in embryonic development.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 86 papers.
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Who cites it
86 citing papers in PubMed.
- Multiscale Modeling of Embryonic Morphogenesis from Fertilization to Organogenesis.NPJ systems biology and applications · 2026Review
- Discontinuous genomic coding and paradigm shifts in molecular biology and immunology: revolutions via "normal science".Natural sciences (Weinheim, Germany) · 2026Article
- Transcriptional network dynamics in early T cell development.The Journal of experimental medicine · 2024Review
- Combinatorial regulatory states define cell fate diversity during embryogenesis.Nature communications · 2024Article
- Inferring Gene Regulatory Networks and Predicting the Effect of Gene Perturbations via IQCELL.Methods in molecular biology (Clifton, N.J.) · 2024Article
- A digital twin reproducing gene regulatory network dynamics of early Ciona embryos indicates robust buffers in the network.PLoS genetics · 2023Article
- Self-Organization and Genomic Causality in Models of Morphogenesis.Entropy (Basel, Switzerland) · 2023Review
- Speed and navigation control of thymocyte development by the fetal T-cell gene regulatory network.Immunological reviews · 2023Review
- Article
- CELLoGeNe - An energy landscape framework for logical networks controlling cell decisions.iScience · 2022Article
- Single-cell network biology characterizes cell type gene regulation for drug repurposing and phenotype prediction in Alzheimer's disease.PLoS computational biology · 2022Article
- IQCELL: A platform for predicting the effect of gene perturbations on developmental trajectories using single-cell RNA-seq data.PLoS computational biology · 2022Article
- Tempos and modes of collectivity in the history of life.Theory in biosciences = Theorie in den Biowissenschaften · 2021Review
- The complex landscape of haematopoietic lineage commitments is encoded in the coarse-grained endogenous network.Royal Society open science · 2021Article
- Neural tube patterning: from a minimal model for rostrocaudal patterning toward an integrated 3D model.iScience · 2021Article
- The gene regulatory system for specifying germ layers in early embryos of the simple chordate.Science advances · 2021Article
- Using linkage logic theory to control dynamics of a gene regulatory network of a chordate embryo.Scientific reports · 2021Article
- Dynamic Modeling of Transcriptional Gene Regulatory Networks.Methods in molecular biology (Clifton, N.J.) · 2021Article
- Systematic comparison of sea urchin and sea star developmental gene regulatory networks explains how novelty is incorporated in early development.Nature communications · 2020Article
- Genetics in Light of Transcriptional Adaptation.Trends in genetics : TIG · 2020Review
26 more citing papers are in PubMed but not listed here.
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3 authors.
Funding
Abstract
Gene regulatory networks (GRNs) control the dynamic spatial patterns of regulatory gene expression in development. Thus, in principle, GRN models may provide system-level, causal explanations of developmental process. To test this assertion, we have transformed a relatively well-established GRN model into a predictive, dynamic Boolean computational model. This Boolean model computes spatial and temporal gene expression according to the regulatory logic and gene interactions specified in a GRN model for embryonic development in the sea urchin. Additional information input into the model included the progressive embryonic geometry and gene expression kinetics. The resulting model predicted gene expression patterns for a large number of individual regulatory genes each hour up to gastrulation (30 h) in four different spatial domains of the embryo. Direct comparison with experimental observations showed that the model predictively computed these patterns with remarkable spatial and temporal accuracy. In addition, we used this model to carry out in silico perturbations of regulatory functions and of embryonic spatial organization. The model computationally reproduced the altered developmental functions observed experimentally. Two major conclusions are that the starting GRN model contains sufficiently complete regulatory information to permit explanation of a complex developmental process of gene expression solely in terms of genomic regulatory code, and that the Boolean model provides a tool with which to test in silico regulatory circuitry and developmental perturbations.
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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.