The DOI matches its Crossref record; 38 of the 38 references it cites were found in a registry or an index.
ChIP-Atlas 2021 update: a data-mining suite for exploring epigenomic landscapes by fully integrating ChIP-seq, ATAC-seq and Bisulfite-seq data
Open accessAbstract
ChIP-Atlas (https://chip-atlas.org) is a web service providing both GUI- and API-based data-mining tools to reveal the architecture of the transcription regulatory landscape. ChIP-Atlas is powered by comprehensively integrating all data sets from high-throughput ChIP-seq and DNase-seq, a method for profiling chromatin regions accessible to DNase. In this update, we further collected all the ATAC-seq and whole-genome bisulfite-seq data for six model organisms (human, mouse, rat, fruit fly, nematode, and budding yeast) with the latest genome assemblies. These together with ChIP-seq data can be visualized with the Peak Browser tool and a genome browser to explore the epigenomic landscape of a query genomic locus, such as its chromatin accessibility, DNA methylation status, and protein–genome interactions. This epigenomic landscape can also be characterized for multiple genes and genomic loci by querying with the Enrichment Analysis tool, which, for example, revealed that inflammatory bowel disease-associated SNPs are the most significantly hypo-methylated in neutrophils. Therefore, ChIP-Atlas provides a panoramic view of the whole epigenomic landscape. All datasets are free to download via either a simple button on the web page or an API.
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Cites
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Comprehensive Mapping of Long-Range Interactions Reveals Folding Principles of the Human Genome
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Cited by
scGPT: Towards Building a Foundation Model for Single-Cell Multi-omics Using Generative AI
Cui, H., Wang, C., Maan, H., Pang, K., Luo, F., & Wang, B. (2023) · doi:10.1101/2023.04.30.538439 · Cited by 1,694
“We validated scGPT’s attention-based most influenced gene selection method in the ChIP994 Atlas database [56] which contains experiment-validated gene targets for known transcription fac995 tors.”
BackgroundMethodTopological structures and syntenic conservation in sea anemone genomes
Zimmermann, B., Montenegro, J. D., Robb, S. M. C., Fropf, W. J., Weilguny, L., He, S., Chen, S., Lovegrove-Walsh, J., Hill, E. M., Chen, C.-Y., et al. (2023) · Nature Communications · doi:10.1038/s41467-023-44080-7 · Cited by 106
A large-scale benchmark for network inference from single-cell perturbation data
Chevalley, M., Roohani, Y. H., Mehrjou, A., Leskovec, J., & Schwab, P. (2025) · Communications Biology · doi:10.1038/s42003-025-07764-y · Cited by 26
Click-code-seq reveals strand biases of DNA oxidation and depurination in human genome
Takhaveev, V., Püllen, N. J. L., Singh, N. K., Lefevre, L., Aghajani, E. A., Huber, S. M., Schauer, S., Gahlon, H. L., Poetsch, A. R., & Sturla, S. J. (2026) · Nature Chemical Biology · doi:10.1038/s41589-025-02052-6 · Cited by 10
Arimura, Y., Konishi, H. A., & Funabiki, H. (2025) · eLife · doi:10.7554/elife.103486.3 · Cited by 4
Metadata
- Authors
- Zou, Z., Ohta, T., Miura, F., & Oki, S.
- Venue
- Nucleic Acids Research
- Publisher
- Oxford University Press (OUP)
- Published
- 2022-03-24
- Volume
- 50
- Issue
- W1
- Pages
- W175-W182
- ISSN
- 0305-1048 (ISSN-L)
- 1362-4962
- OpenAlex
- W4221102522
- Cited by
- 357
- References
- 38
- FWCI
- 22.86
- Type
- journal article
- Language
- en
- Open access
- gold
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- Zou, Z., Ohta, T., Miura, F., & Oki, S. (2022). ChIP-Atlas 2021 update: a data-mining suite for exploring epigenomic landscapes by fully integrating ChIP-seq, ATAC-seq and Bisulfite-seq data. Nucleic Acids Research. https://doi.org/10.1093/nar/gkac199
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