ArticlePloS one2011
Hierarchical differentiation of myeloid progenitors is encoded in the transcription factor network.
Article in PloS one, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 83 papers.
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Who cites it
83 citing papers in PubMed.
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- Molecular insights into heart field-specific cardiomyocyte differentiation - A computational study.PloS one · 2026Article
- Divergence of immune cell types in chordate blood.Current biology : CB · 2025Article
- Learning stochastic processes with intrinsic noise from cross-sectional biological data.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Emergent dynamics of cellular decision making in multi-node mutually repressive regulatory networks.Journal of the Royal Society, Interface · 2025Article
- LM-Merger: a workflow for merging logical models with an application to gene regulatory network models.BMC bioinformatics · 2025Article
- Gene2role: a role-based gene embedding method for comparative analysis of signed gene regulatory networks.BMC bioinformatics · 2025Article
- Immune cell type divergence in a basal chordate.bioRxiv : the preprint server for biology · 2025Article
- Global stabilization of Boolean networks with applications to biomolecular network control.Scientific reports · 2025Article
- CoTF-reg reveals cooperative transcription factors in oligodendrocyte gene regulation using single-cell multi-omics.Communications biology · 2025Article
- pastboon: an R package to simulate parameterized stochastic Boolean networks.Bioinformatics advances · 2025Article
- A system-level model reveals that transcriptional stochasticity is required for hematopoietic stem cell differentiation.NPJ systems biology and applications · 2024Article
- Predictive modelling of acute Promyelocytic leukaemia resistance to retinoic acid therapy.Briefings in bioinformatics · 2024Article
- Complex hierarchical structures analysis in single-cell data with Poincaré deep manifold transformation.Briefings in bioinformatics · 2024Article
- COFFEE: consensus single cell-type specific inference for gene regulatory networks.Briefings in bioinformatics · 2024Article
- Characterizing behavioural differentiation in gene regulatory networks with representation graphs.NAR genomics and bioinformatics · 2024Article
- scBoolSeq: Linking scRNA-seq statistics and Boolean dynamics.PLoS computational biology · 2024Article
- A logic-incorporated gene regulatory network deciphers principles in cell fate decisions.eLife · 2024Article
23 more citing papers are in PubMed but not listed here.
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4 authors.
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Abstract
Hematopoiesis is an ideal model system for stem cell biology with advanced experimental access. A systems view on the interactions of core transcription factors is important for understanding differentiation mechanisms and dynamics. In this manuscript, we construct a Boolean network to model myeloid differentiation, specifically from common myeloid progenitors to megakaryocytes, erythrocytes, granulocytes and monocytes. By interpreting the hematopoietic literature and translating experimental evidence into Boolean rules, we implement binary dynamics on the resulting 11-factor regulatory network. Our network contains interesting functional modules and a concatenation of mutual antagonistic pairs. The state space of our model is a hierarchical, acyclic graph, typifying the principles of myeloid differentiation. We observe excellent agreement between the steady states of our model and microarray expression profiles of two different studies. Moreover, perturbations of the network topology correctly reproduce reported knockout phenotypes in silico. We predict previously uncharacterized regulatory interactions and alterations of the differentiation process, and line out reprogramming strategies.
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