ArticleAdvanced science (Weinheim, Baden-Wurttemberg, Germany)2021
A Dimension Reduction Approach for Energy Landscape: Identifying Intermediate States in Metabolism-EMT Network.
Article in Advanced science (Weinheim, Baden-Wurttemberg, Germany), 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 28 papers.
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Who cites it
28 citing papers in PubMed, 45 citations in OpenAlex.
- Cell dynamics on energy landscape: Comparing attractor detection in Boolean network and diffusion-based models under in silico gene perturbations.Quantitative biology (Beijing, China) · 2026Article
- Learning stochastic dynamics and cell-fate landscapes from single-cell snapshots via optimal transport.Science advances · 2026Article
- Multiscale learning of gene network-driven phenotypic dynamics of single cells.Molecular systems biology · 2026Article
- A Mechanistic Model of the HIF-1/HIF-2 Switch Regulating Hypoxia-Induced Cancer Stemness.International journal of molecular sciences · 2026Article
- Inferring stochastic dynamics by biophysical Neural ODE using single-cell transcriptomics.Nature communications · 2026Article
- Design principles for robust multistability in coupled feedforward-feedback regulatory circuits.NPJ systems biology and applications · 2026Article
- Incoherent feedforward loop dominates the robustness and tunability of necroptosis biphasic, emergent, and coexistent dynamics.Fundamental research · 2026Article
- Modulation of Network Plasticity Opens Novel Therapeutic Possibilities in Cancer, Diabetes, and Neurodegeneration.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Review
- Reconstructing gene network structure and dynamics from single cell data.Bioinformatics (Oxford, England) · 2025Article
- Reconstructing noisy gene regulation dynamics using extrinsic-noise-driven neural stochastic differential equations.PLoS computational biology · 2025Article
- Energy Landscape Reveals the Underlying Mechanism of Cancer-Adipose Conversion in Gene Network Models.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2024Article
- EPR-Net: constructing a non-equilibrium potential landscape via a variational force projection formulation.National science review · 2024Article
- Transcriptome free energy can serve as a dynamic patient-specific biomarker in acute myeloid leukemia.NPJ systems biology and applications · 2024Article
- Data-driven energy landscape reveals critical genes in cancer progression.NPJ systems biology and applications · 2024Article
- Landscape quantifies the intermediate state and transition dynamics in ecological networks.PLoS computational biology · 2024Article
- Perspectives on computational modeling of biological systems and the significance of the SysMod community.Bioinformatics advances · 2024Article
- Controlling brain dynamics: Landscape and transition path for working memory.PLoS computational biology · 2023Article
- Quantifying cancer cell plasticity with gene regulatory networks and single-cell dynamics.Frontiers in network physiology · 2023Review
- circCAPRIN1 interacts with STAT2 to promote tumor progression and lipid synthesis via upregulating ACC1 expression in colorectal cancer.Cancer communications (London, England) · 2023Article
- Quantitative landscapes reveal trajectories of cell-state transitions associated with drug resistance in melanoma.iScience · 2022Article
Corrections and comments
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Authors and funding
2 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Dimension reduction is a challenging problem in complex dynamical systems. Here, a dimension reduction approach of landscape (DRL) for complex dynamical systems is proposed, by mapping a high-dimensional system on a low-dimensional energy landscape. The DRL approach is applied to three biological networks, which validates that new reduced dimensions preserve the major information of stability and transition of original high-dimensional systems. The consistency of barrier heights calculated from the low-dimensional landscape and transition actions calculated from the high-dimensional system further shows that the landscape after dimension reduction can quantify the global stability of the system. The epithelial-mesenchymal transition (EMT) and abnormal metabolism are two hallmarks of cancer. With the DRL approach, a quadrastable landscape for metabolism-EMT network is identified, including epithelial (E), abnormal metabolic (A), hybrid E/M (H), and mesenchymal (M) cell states. The quantified energy landscape and kinetic transition paths suggest that for the EMT process, the cells at E state need to first change their metabolism, then enter the M state. The work proposes a general framework for the dimension reduction of a stochastic dynamical system, and advances the mechanistic understanding of the underlying relationship between EMT and cellular metabolism.
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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.