ArticleProceedings of the National Academy of Sciences of the United States of America2013
Reconstructing dynamic microRNA-regulated interaction networks.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 42 papers.
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Who cites it
42 citing papers in PubMed.
- Longitudinal omics data analysis: approaches and applications.Computational and structural biotechnology journal · 2026Review
- NPI-HetGNN: A Prediction Model of ncRNA-Protein Interactions Based on Heterogeneous Graph Neural Networks.Interdisciplinary sciences, computational life sciences · 2025Article
- MicroRNAs in long COVID: roles, diagnostic biomarker potential and detection.Human genomics · 2025Review
- Temporal Expression Analysis to Unravel Gene Regulatory Dynamics by microRNAs.Methods in molecular biology (Clifton, N.J.) · 2025Article
- Constructing the dynamic transcriptional regulatory networks to identify phenotype-specific transcription regulators.Briefings in bioinformatics · 2024Article
- TRIOBP modulates β-catenin signaling by regulation of miR-29b in idiopathic pulmonary fibrosis.Cellular and molecular life sciences : CMLS · 2023Article
- ncRPI-LGAT: Prediction of ncRNA-protein interactions with line graph attention network framework.Computational and structural biotechnology journal · 2023Article
- Article
- miR-338-3p blocks TGFβ-induced myofibroblast differentiation through the induction of PTEN.American journal of physiology. Lung cellular and molecular physiology · 2022Article
- BrainDevo: Spatio-Temporal Gene Regulation Repository of Brain Development.Frontiers in molecular neuroscience · 2022Article
- Deep learning of gene relationships from single cell time-course expression data.Briefings in bioinformatics · 2021Article
- A shift from glycolytic and fatty acid derivatives toward one-carbon metabolites in the developing lung during transitions of the early postnatal period.American journal of physiology. Lung cellular and molecular physiology · 2021Article
- MicroRNA 219-5p inhibits alveolarization by reducing platelet derived growth factor receptor-alpha.Respiratory research · 2021Article
- Circulating microRNA trafficking and regulation: computational principles and practice.Briefings in bioinformatics · 2020Review
- Inferring TF activation order in time series scRNA-Seq studies.PLoS computational biology · 2020Article
- Integrating multiomics longitudinal data to reconstruct networks underlying lung development.American journal of physiology. Lung cellular and molecular physiology · 2019Article
- Large-scale inference of competing endogenous RNA networks with sparse partial correlation.Bioinformatics (Oxford, England) · 2019Article
- MicroRNA-30a as a candidate underlying sex-specific differences in neonatal hyperoxic lung injury: implications for BPD.American journal of physiology. Lung cellular and molecular physiology · 2019Article
- An HDAC9-MALAT1-BRG1 complex mediates smooth muscle dysfunction in thoracic aortic aneurysm.Nature communications · 2018Article
- iDREM: Interactive visualization of dynamic regulatory networks.PLoS computational biology · 2018Article
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6 authors.
Funding
Abstract
The regulation of gene expression in cells, including by microRNAs (miRNAs), is a dynamic process. Current methods for identifying miRNA targets by combining sequence and miRNA and mRNA expression data do not adequately use the temporal information and thus miss important miRNAs and their targets. We developed the MIRna Dynamic Regulatory Events Miner (mirDREM), a probabilistic modeling method that uses input-output hidden Markov models to reconstruct dynamic regulatory networks that explain how temporal gene expression is jointly regulated by miRNAs and transcription factors. We measured miRNA and mRNA expression for postnatal lung development in mice and used mirDREM to study the regulation of this process. The reconstructed dynamic network correctly identified known miRNAs and transcription factors. The method has also provided predictions about additional miRNAs regulating this process and the specific developmental phases they regulate, several of which were experimentally validated. Our analysis uncovered links between miRNAs involved in lung development and differentially expressed miRNAs in idiopathic pulmonary fibrosis patients, some of which we have experimentally validated using proliferation assays. These results indicate that some disease progression pathways in idiopathic pulmonary fibrosis may represent partial reversal of lung differentiation.
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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.