ArticlePLoS computational biology2018
iDREM: Interactive visualization of dynamic regulatory networks.
Article in PLoS computational biology, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 30 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
30 citing papers in PubMed.
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- A deep generative model for deciphering cellular dynamics and in silico drug discovery in complex diseases.Nature biomedical engineering · 2025Article
- DENetwork unveils non-differentially expressed genes with functional relevance across conditions through information flow perturbation.Nucleic acids research · 2025Article
- Dynamic Ca2+-Dependent Transcription Links Metabolic Stress to Impaired β-Cell Identity.Diabetes · 2025Article
- Harnessing agent-based frameworks in CellAgentChat to unravel cell-cell interactions from single-cell and spatial transcriptomics.Genome research · 2025Article
- Cell-Type Specific miRNA Regulatory Network Responses to ABA Stress Revealed by Time Series Transcriptional Atlases in Arabidopsis.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2025Article
- Perspective on recent developments and challenges in regulatory and systems genomics.Bioinformatics advances · 2025Review
- Temporal Expression Analysis to Unravel Gene Regulatory Dynamics by microRNAs.Methods in molecular biology (Clifton, N.J.) · 2025Article
- Single-cell multi-omics identify novel regulators required for osteoclastogenesis during aging.iScience · 2024Article
- Time-course swRNA-seq uncovers a hierarchical gene regulatory network in controlling the response-repair-remodeling after wounding.Communications biology · 2024Article
- Multiomics analysis identifies novel facilitators of human dopaminergic neuron differentiation.EMBO reports · 2024Article
- A review of artificial intelligence-assisted omics techniques in plant defense: current trends and future directions.Frontiers in plant science · 2024Review
- Mechanically induced localisation of SECONDARY WALL INTERACTING bZIP is associated with thigmomorphogenic and secondary cell wall gene expression.Quantitative plant biology · 2024Article
- An Integrative Multiomics Framework for Identification of Therapeutic Targets in Pulmonary Fibrosis.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2023Article
- Network Biology Analyses and Dynamic Modeling of Gene Regulatory Networks under Drought Stress Reveal Major Transcriptional Regulators inInternational journal of molecular sciences · 2023Article
- Computational approaches to understand transcription regulation in development.Biochemical Society transactions · 2023Review
- TCDD alters essential transcriptional regulators of osteogenic differentiation in multipotent mesenchymal stem cells.Toxicological sciences : an official journal of the Society of Toxicology · 2023Article
- Temporal modelling using single-cell transcriptomics.Nature reviews. Genetics · 2022Review
- To the proteome and beyond: advances in single-cell omics profiling for plant systems.Plant physiology · 2022Article
- BrainDevo: Spatio-Temporal Gene Regulation Repository of Brain Development.Frontiers in molecular neuroscience · 2022Article
Corrections and comments
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Authors and funding
5 authors.
Funding
Abstract
The Dynamic Regulatory Events Miner (DREM) software reconstructs dynamic regulatory networks by integrating static protein-DNA interaction data with time series gene expression data. In recent years, several additional types of high-throughput time series data have been profiled when studying biological processes including time series miRNA expression, proteomics, epigenomics and single cell RNA-Seq. Combining all available time series and static datasets in a unified model remains an important challenge and goal. To address this challenge we have developed a new version of DREM termed interactive DREM (iDREM). iDREM provides support for all data types mentioned above and combines them with existing interaction data to reconstruct networks that can lead to novel hypotheses on the function and timing of regulators. Users can interactively visualize and query the resulting model. We showcase the functionality of the new tool by applying it to microglia developmental data from multiple labs.
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What OpenQuestion holds
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.