ArticleCell systems2017
Dynamic Gene Regulatory Networks of Human Myeloid Differentiation.
Article in Cell systems, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 70 papers.
What it found
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Who cites it
70 citing papers in PubMed, 129 citations in OpenAlex.
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- Impact of Fluorophore and Epitope Position on Destabilized Reporter Performance inbioRxiv : the preprint server for biology · 2026Article
- Multiomic Profiling Reveals the Regulation of Many Immune-Related Genes by PU.1 in Porcine Alveolar Macrophages.Animals : an open access journal from MDPI · 2026Article
- Shaping neutrophil morphology and function: the importance of a segmented nucleus.Nature reviews. Immunology · 2026Review
- Directing stem cell differentiation by chromatin state approximation.Nucleic acids research · 2026Article
- An integrated multi-omics and network analysis of neutrophil differentiation from initial- to late-stage.Genome biology · 2026Article
- Interactions between Innate Immune Memory and the Central Nervous System.Neuroimmunomodulation · 2026Review
- Hypoxia-induced EGR1 remodels neutrophils to suppress antitumor immunity.Science immunology · 2025Article
- Multiomic analyses on the contribution of transposable elements to the cis-regulatory landscape of different types of immune cells.BMC genomics · 2025Article
- Haplotype rather than single causal variants effects contribute to regulatory gene expression associations in human myeloid cells.bioRxiv : the preprint server for biology · 2025Article
- A multiomics approach reveals RNA dynamics promote cellular sensitivity to DNA hypomethylation.Scientific reports · 2024Article
- Protein arginine methyltransferase 2 controls inflammatory signaling in acute myeloid leukemia.Communications biology · 2024Article
- Comparative transcriptomics coupled to developmental grading via transgenic zebrafish reporter strains identifies conserved features in neutrophil maturation.Nature communications · 2024Article
- Neutrophil nucleus: shaping the past and the future.Journal of leukocyte biology · 2023Article
- Gene regulatory network inference in the era of single-cell multi-omics.Nature reviews. Genetics · 2023Review
- Whole-genome screens reveal regulators of differentiation state and context-dependent migration in human neutrophils.Nature communications · 2023Article
- Dictys: dynamic gene regulatory network dissects developmental continuum with single-cell multiomics.Nature methods · 2023Article
- From time-series transcriptomics to gene regulatory networks: A review on inference methods.PLoS computational biology · 2023Review
- Liver X Receptor-Inducible Host E3 Ligase IDOL Targets a Human Cytomegalovirus Reactivation Determinant.Journal of virology · 2023Article
10 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
6 authors at 2 institutions in 2 countries.
Funding
Abstract
The reconstruction of gene regulatory networks underlying cell differentiation from high-throughput gene expression and chromatin data remains a challenge. Here, we derive dynamic gene regulatory networks for human myeloid differentiation using a 5-day time series of RNA-seq and ATAC-seq data. We profile HL-60 promyelocytes differentiating into macrophages, neutrophils, monocytes, and monocyte-derived macrophages. We find a rapid response in the expression of key transcription factors and lineage markers that only regulate a subset of their targets at a given time, which is followed by chromatin accessibility changes that occur later along with further gene expression changes. We observe differences between promyelocyte- and monocyte-derived macrophages at both the transcriptional and chromatin landscape level, despite using the same differentiation stimulus, which suggest that the path taken by cells in the differentiation landscape defines their end cell state. More generally, our approach of combining neighboring time points and replicates to achieve greater sequencing depth can efficiently infer footprint-based regulatory networks from long series data.
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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.