ArticleBioinformatics (Oxford, England)2017
NetLand: quantitative modeling and visualization of Waddington's epigenetic landscape using probabilistic potential.
Article in Bioinformatics (Oxford, England), 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 9 papers.
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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
9 citing papers in PubMed, 27 citations in OpenAlex.
- Modeling combinatorial regulation from single-cell multi-omics provides regulatory units underpinning cell type landscape using cRegulon.Genome biology · 2025Article
- CanSeer: a translational methodology for developing personalized cancer models and therapeutics.Scientific reports · 2025Article
- Inferring gene regulatory networks using transcriptional profiles as dynamical attractors.PLoS computational biology · 2023Article
- Statistical mechanics meets single-cell biology.Nature reviews. Genetics · 2021Review
- Computational Analysis ofCancer informatics · 2020Article
- The developmental-genetics of canalization.Seminars in cell & developmental biology · 2019Review
- Towards a Quantitative Understanding of Cell Identity.Trends in cell biology · 2018Review
- Transition state characteristics during cell differentiation.PLoS computational biology · 2018Article
- HopLand: single-cell pseudotime recovery using continuous Hopfield network-based modeling of Waddington's epigenetic landscape.Bioinformatics (Oxford, England) · 2017Article
Corrections and comments
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Authors and funding
5 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
summaryWaddington's epigenetic landscape is a powerful metaphor for cellular dynamics driven by gene regulatory networks (GRNs). Its quantitative modeling and visualization, however, remains a challenge, especially when there are more than two genes in the network. A software tool for Waddington's landscape has not been available in the literature. We present NetLand, an open-source software tool for modeling and simulating the kinetic dynamics of GRNs, and visualizing the corresponding Waddington's epigenetic landscape in three dimensions without restriction on the number of genes in a GRN. With an interactive and graphical user interface, NetLand can facilitate the knowledge discovery and experimental design in the study of cell fate regulation (e.g. stem cell differentiation and reprogramming). AVAILABILITY AND IMPLEMENTATION: NetLand can run under operating systems including Windows, Linux and OS X. The executive files and source code of NetLand as well as a user manual, example models etc. can be downloaded from http://netland-ntu.github.io/NetLand/ . CONTACT: zhengjie@ntu.edu.sg. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
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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.