ArticleProceedings of the National Academy of Sciences of the United States of America2003
Reverse engineering gene networks: integrating genetic perturbations with dynamical modeling.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2003. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 125 papers.
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Who cites it
125 citing papers in PubMed, 447 citations in OpenAlex.
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- Identifying Qingkailing ingredients-dependent mesenchymal-epithelial transition factor-axiation "π" structuring module with angiogenesis and neurogenesis effects.Journal of traditional Chinese medicine = Chung i tsa chih ying wen pan · 2024Article
- Gene regulatory network reconstruction: harnessing the power of single-cell multi-omic data.NPJ systems biology and applications · 2023Review
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- Reproducibility and FAIR principles: the case of a segment polarity network model.Frontiers in cell and developmental biology · 2023Article
- DAGBagM: learning directed acyclic graphs of mixed variables with an application to identify protein biomarkers for treatment response in ovarian cancer.BMC bioinformatics · 2022Article
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- Predicting synchronized gene coexpression patterns from fibration symmetries in gene regulatory networks in bacteria.BMC bioinformatics · 2021Article
- Identifiability and experimental design in perturbation studies.Bioinformatics (Oxford, England) · 2020Article
- Bayesian differential analysis of gene regulatory networks exploiting genetic perturbations.BMC bioinformatics · 2020Article
- Inference of differential gene regulatory networks based on gene expression and genetic perturbation data.Bioinformatics (Oxford, England) · 2020Article
- Massive computational acceleration by using neural networks to emulate mechanism-based biological models.Nature communications · 2019Article
- Single Cell RNA-Sequencing for the Study of Atherosclerosis.Journal of lipid and atherosclerosis · 2019Review
- Efficient proximal gradient algorithm for inference of differential gene networks.BMC bioinformatics · 2019Article
- Cell-machine interfaces for characterizing gene regulatory network dynamics.Current opinion in systems biology · 2019Article
- Automated transition analysis of activated gene regulation during diauxic nutrient shift in Escherichia coli and adipocyte differentiation in mouse cells.BMC bioinformatics · 2018Article
- Inferring a nonlinear biochemical network model from a heterogeneous single-cell time course data.Scientific reports · 2018Article
65 more citing papers are in PubMed but not listed here.
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Authors and funding
4 authors at 1 institution in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
While the fundamental building blocks of biology are being tabulated by the various genome projects, microarray technology is setting the stage for the task of deducing the connectivity of large-scale gene networks. We show how the perturbation of carefully chosen genes in a microarray experiment can be used in conjunction with a reverse engineering algorithm to reveal the architecture of an underlying gene regulatory network. Our iterative scheme identifies the network topology by analyzing the steady-state changes in gene expression resulting from the systematic perturbation of a particular node in the network. We highlight the validity of our reverse engineering approach through the successful deduction of the topology of a linear in numero gene network and a recently reported model for the segmentation polarity network in Drosophila melanogaster. Our method may prove useful in identifying and validating specific drug targets and in deconvolving the effects of chemical compounds.
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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.