ReviewAnnual review of plant biology2021
Time-Based Systems Biology Approaches to Capture and Model Dynamic Gene Regulatory Networks.
Review in Annual review of plant biology, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
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.
The trial behind it
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.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
21 citing papers in PubMed.
- A Biomarker-Driven Ovary-Endometrium Organ-on-a-Chip Mimicking 3D Multicellular Complexity and Menstrual Cyclicity for Predicting Reproductive Toxicity.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- A tissue-resolved, network-based transcriptomic framework for abiotic stress responses in sorghum.The Plant journal : for cell and molecular biology · 2026Article
- Chromatin state architecture governs transcription factor accessibility across plant genomes.PLoS genetics · 2026Article
- Grafting enhances growth vigor and photosynthetic capacity in the progeny of critically endangered Abies beshanzuensis.BMC plant biology · 2025Article
- OsNRT1.1B-OsCNGC14/16-CaAdvanced science (Weinheim, Baden-Wurttemberg, Germany) · 2025Article
- Molecular Insights into ABA-Mediated Regulation of Stress Tolerance and Development in Plants.International journal of molecular sciences · 2025Review
- Unlocking gene regulatory networks for crop resilience and sustainable agriculture.Nature biotechnology · 2025Review
- Model-to-crop conserved NUE Regulons enhance machine learning predictions of nitrogen use efficiency.The Plant cell · 2025Article
- A space for time. Exploring temporal regulation of plant development across spatial scales.The Plant journal : for cell and molecular biology · 2025Review
- A network-enabled pipeline for gene discovery and validation in non-model plant species.Cell reports methods · 2025Article
- Time-series transcriptome analysis reveals the cascade mechanism of biological processes following the perturbation of the MVA pathway in Salvia miltiorrhiza.Plant molecular biology · 2025Article
- Dynamics of ER stress-induced gene regulation in plants.Nature reviews. Genetics · 2024Review
- Differential leaf flooding resilience in Arabidopsis thaliana is controlled by ethylene signaling-activated and age-dependent phosphorylation of ORESARA1.Plant communications · 2024Article
- Nitrogen sensing and regulatory networks: it's about time and space.The Plant cell · 2024Review
- A K homology (KH) domain protein identified by a forward genetic screen affects bundle sheath anatomy inPlant direct · 2024Article
- Network Biology Analyses and Dynamic Modeling of Gene Regulatory Networks under Drought Stress Reveal Major Transcriptional Regulators inInternational journal of molecular sciences · 2023Article
- Article
- Integrative omics approaches for biosynthetic pathway discovery in plants.Natural product reports · 2022Review
- The biology of time: dynamic responses of cell types to developmental, circadian and environmental cues.The Plant journal : for cell and molecular biology · 2022Review
- Role of long non-coding RNAs in rice reproductive development.Frontiers in plant science · 2022Review
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
4 authors.
Funding
Abstract
All aspects of transcription and its regulation involve dynamic events. However, capturing these dynamic events in gene regulatory networks (GRNs) offers both a promise and a challenge. The promise is that capturing and modeling the dynamic changes in GRNs will allow us to understand how organisms adapt to a changing environment. The ability to mount a rapid transcriptional response to environmental changes is especially important in nonmotile organisms such as plants. The challenge is to capture these dynamic, genome-wide events and model them in GRNs. In this review, we cover recent progress in capturing dynamic interactions of transcription factors with their targets-at both the local and genome-wide levels-and how they are used to learn how GRNs operate as a function of time. We also discuss recent advances that employ time-based machine learning approaches to forecast gene expression at future time points, a key goal of systems biology.
Indexed as
Identifiers
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.