ArticleComputational and structural biotechnology journal2023
A novel Boolean network inference strategy to model early hematopoiesis aging.
Article in Computational and structural biotechnology journal, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
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14 citing papers in PubMed, 27 citations in OpenAlex.
- AstroLogics: a simulation-based framework for the analysis of boolean model ensembles.Bioinformatics (Oxford, England) · 2026Article
- A velocity-informed framework for resolving functional stratification in rare human stem cells.Leukemia · 2026Article
- Data driven network inference and longitudinal transcriptomics unveil dynamic regulation in Chronic Lymphocytic Leukaemia models.NPJ systems biology and applications · 2026Article
- Data-driven inference of Boolean networks from transcriptomes to predict cellular differentiation and reprogramming.NPJ systems biology and applications · 2025Article
- Differentiation, ageing and leukaemia alter the metabolic profile of human bone marrow haematopoietic stem and progenitor cells.Nature cell biology · 2025Article
- LM-Merger: a workflow for merging logical models with an application to gene regulatory network models.BMC bioinformatics · 2025Article
- Refining Boolean models with the partial most permissive scheme.Bioinformatics (Oxford, England) · 2025Article
- Predictive modelling of acute Promyelocytic leukaemia resistance to retinoic acid therapy.Briefings in bioinformatics · 2024Article
- scBoolSeq: Linking scRNA-seq statistics and Boolean dynamics.PLoS computational biology · 2024Article
- Data-driven modeling of core gene regulatory network underlying leukemogenesis in IDH mutant AML.NPJ systems biology and applications · 2024Article
- Current and future directions in network biology.Bioinformatics advances · 2024Article
- Identification and validation of aging-related genes in neuropathic pain using bioinformatics.Frontiers in genetics · 2024Article
- Quantifying cancer cell plasticity with gene regulatory networks and single-cell dynamics.Frontiers in network physiology · 2023Review
- Single Cell Transcriptomics to Understand HSC Heterogeneity and Its Evolution upon Aging.Cells · 2022Review
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4 authors at 1 institution in 1 country.
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Abstract
Hematopoietic stem cell (HSC) aging is a multifactorial event leading to changes in HSC properties and functions, which are intrinsically coordinated and affect the early hematopoiesis. To better understand the mechanisms and factors controlling these changes, we developed an original strategy to construct a Boolean model of HSC differentiation. Based on our previous scRNA-seq data, we exhaustively characterized active transcription modules or regulons along the differentiation trajectory and constructed an influence graph between 15 selected components involved in the dynamics of the process. Then we defined dynamical constraints between observed cellular states along the trajectory and using answer set programming with in silico perturbation analysis, we obtained a Boolean model explaining the early priming of HSCs. Finally, perturbations of the model based on age-related changes revealed important deregulations, such as the overactivation of Egr1 and Junb or the loss of Cebpa activation by Gata2. These new regulatory mechanisms were found to be relevant for the myeloid bias of aged HSC and explain the decreased transcriptional priming of HSCs to all mature cell types except megakaryocytes.
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