Simon J van Heeringen
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Explore the profile of Simon J van Heeringen including associated specialties, affiliations and a list of published articles.
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51
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2871
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Recent Articles
1.
Wu H, Yang A, Stelloo S, Roos F, Te Morsche R, Verkerk A, et al.
Dis Model Mech
. 2025 Jan;
18(1).
PMID: 39878507
Hepatic organoid cultures are a powerful model to study liver development and diseases in vitro. However, hepatocyte-like cells differentiated from these organoids remain immature compared to primary human hepatocytes (PHHs),...
2.
Smits J, Qu J, Pardow F, van den Brink N, Rodijk-Olthuis D, van Vlijmen-Willems I, et al.
J Invest Dermatol
. 2024 Feb;
144(9):2013-2028.e2.
PMID: 38401701
The aryl hydrocarbon receptor (AHR) is an evolutionary conserved environmental sensor identified as an indispensable regulator of epithelial homeostasis and barrier organ function. Molecular signaling cascade and target genes upon...
3.
Smits J, Arts J, Frolich S, Snabel R, Heuts B, Martens J, et al.
F1000Res
. 2023 Dec;
12:243.
PMID: 38116584
The recent development of single-cell techniques is essential to unravel complex biological systems. By measuring the transcriptome and the accessible genome on a single-cell level, cellular heterogeneity in a biological...
4.
van der Sande M, Frolich S, Schafers T, Smits J, Snabel R, Rinzema S, et al.
PeerJ
. 2023 Nov;
11:e16380.
PMID: 38025697
Sequencing databases contain enormous amounts of functional genomics data, making them an extensive resource for genome-scale analysis. Reanalyzing publicly available data, and integrating it with new, project-specific data sets, can...
5.
Identification of the regulatory circuit governing corneal epithelial fate determination and disease
Smits J, Lima Cunha D, Amini M, Bertolin M, Laberthonniere C, Qu J, et al.
PLoS Biol
. 2023 Oct;
21(10):e3002336.
PMID: 37856539
The transparent corneal epithelium in the eye is maintained through the homeostasis regulated by limbal stem cells (LSCs), while the nontransparent epidermis relies on epidermal keratinocytes for renewal. Despite their...
6.
Smits J, Qu J, Pardow F, van den Brink N, Rodijk-Olthuis D, van Vlijmen-Willems I, et al.
bioRxiv
. 2023 Jun;
PMID: 37333234
The aryl hydrocarbon receptor (AHR) is an evolutionary conserved environmental sensor identified as indispensable regulator of epithelial homeostasis and barrier organ function. Molecular signaling cascade and target genes upon AHR...
7.
Neikes H, Kliza K, Grawe C, Wester R, Jansen P, Lamers L, et al.
Nat Biotechnol
. 2023 Mar;
41(12):1801-1809.
PMID: 36973556
Transcription factor binding across the genome is regulated by DNA sequence and chromatin features. However, it is not yet possible to quantify the impact of chromatin context on transcription factor...
8.
Frolich S, van der Sande M, Schafers T, van Heeringen S
Bioinformatics
. 2023 Mar;
39(3).
PMID: 36882164
Motivation: Analyzing a functional genomics experiment, such as ATAC-, ChIP-, or RNA-sequencing, requires genomic resources such as a reference genome assembly and gene annotation. These data can generally be retrieved...
9.
van der Sande M, Frolich S, van Heeringen S
Biochem Soc Trans
. 2023 Jan;
51(1):1-12.
PMID: 36695505
Gene regulatory networks (GRNs) serve as useful abstractions to understand transcriptional dynamics in developmental systems. Computational prediction of GRNs has been successfully applied to genome-wide gene expression measurements with the...
10.
Luna Velez M, Neikes H, Snabel R, Quint Y, Qian C, Martens A, et al.
Nucleic Acids Res
. 2023 Jan;
51(3):1277-1296.
PMID: 36625255
Microfold (M) cells reside in the intestinal epithelium of Peyer's patches (PP). Their unique ability to take up and transport antigens from the intestinal lumen to the underlying lymphoid tissue...