ArticleJournal of the American Statistical Association2014
Sparse Additive Ordinary Differential Equations for Dynamic Gene Regulatory Network Modeling.
Article in Journal of the American Statistical Association, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 31 papers.
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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
31 citing papers in PubMed.
- mmVelo: a deep generative model for estimating cell state-dependent dynamics across multiple modalities.Bioinformatics (Oxford, England) · 2026Article
- Measuring Regulatory Network Inheritance in Dividing Yeast Cells Using Ordinary Differential Equations.bioRxiv : the preprint server for biology · 2025Article
- The WRKY46-MYC2 module plays a critical role in E-2-hexenal-induced anti-herbivore responses by promoting flavonoid accumulation.Plant communications · 2024Article
- A Network-Based Approach for Improving Annotation of Transcription Factor Functions and Binding Sites inGenes · 2023Article
- Competition-cooperation mechanism betweenFrontiers in microbiology · 2023Article
- A statistical framework for recovering pseudo-dynamic networks from static data.Bioinformatics (Oxford, England) · 2022Article
- Granger Causality: A Review and Recent Advances.Annual review of statistics and its application · 2022Article
- A nonlinear sparse neural ordinary differential equation model for multiple functional processes.The Canadian journal of statistics = Revue canadienne de statistique · 2022Article
- Kernel Ordinary Differential Equations.Journal of the American Statistical Association · 2022Article
- Vaginal microbiota networks as a mechanistic predictor of aerobic vaginitis.Frontiers in microbiology · 2022Article
- A Joint estimation approach to sparse additive ordinary differential equations.Statistics and computing · 2022Article
- Reverse engineering gene regulatory network based on complex-valued ordinary differential equation model.BMC bioinformatics · 2021Article
- Article
- Gene Regulatory Network Inference: Connecting Plant Biology and Mathematical Modeling.Frontiers in genetics · 2020Review
- SEGN: Inferring real-time gene networks mediating phenotypic plasticity.Computational and structural biotechnology journal · 2020Article
- Boolean gene regulatory network model of centromere function in Saccharomyces cerevisiae.Journal of biological physics · 2019Article
- Restructured GEO: restructuring Gene Expression Omnibus metadata for genome dynamics analysis.Database : the journal of biological databases and curation · 2019Article
- Parameter Estimation and Variable Selection for Big Systems of Linear Ordinary Differential Equations: A Matrix-Based Approach.Journal of the American Statistical Association · 2019Article
- An omnidirectional visualization model of personalized gene regulatory networks.NPJ systems biology and applications · 2019Article
- Co-emergence and Collapse: The Mesoscopic Approach for Conceptualizing and Investigating the Functional Integration of Organisms.Frontiers in physiology · 2019Article
Corrections and comments
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Authors and funding
4 authors.
Funding
Abstract
The gene regulation network (GRN) is a high-dimensional complex system, which can be represented by various mathematical or statistical models. The ordinary differential equation (ODE) model is one of the popular dynamic GRN models. High-dimensional linear ODE models have been proposed to identify GRNs, but with a limitation of the linear regulation effect assumption. In this article, we propose a sparse additive ODE (SA-ODE) model, coupled with ODE estimation methods and adaptive group LASSO techniques, to model dynamic GRNs that could flexibly deal with nonlinear regulation effects. The asymptotic properties of the proposed method are established and simulation studies are performed to validate the proposed approach. An application example for identifying the nonlinear dynamic GRN of T-cell activation is used to illustrate the usefulness of the proposed method.
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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.