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EpiCompare: an online tool to define and explore genomic regions with tissue or cell type-specific epigenomic features.
Bioinformatics. 2017 Oct 15;33(20):3268-3275. doi: 10.1093/bioinformatics/btx371.
2
methylC Track: visual integration of single-base resolution DNA methylation data on the WashU EpiGenome Browser.
Bioinformatics. 2014 Aug 1;30(15):2206-7. doi: 10.1093/bioinformatics/btu191. Epub 2014 Apr 10.
3
Haystack: systematic analysis of the variation of epigenetic states and cell-type specific regulatory elements.
Bioinformatics. 2018 Jun 1;34(11):1930-1933. doi: 10.1093/bioinformatics/bty031.
4
AIKYATAN: mapping distal regulatory elements using convolutional learning on GPU.
BMC Bioinformatics. 2019 Oct 7;20(1):488. doi: 10.1186/s12859-019-3049-1.
5
WashU Epigenome Browser update 2022.
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6
Epigenome overlap measure (EPOM) for comparing tissue/cell types based on chromatin states.
BMC Genomics. 2016 Jan 11;17 Suppl 1(Suppl 1):10. doi: 10.1186/s12864-015-2303-9.
7
GREGOR: evaluating global enrichment of trait-associated variants in epigenomic features using a systematic, data-driven approach.
Bioinformatics. 2015 Aug 15;31(16):2601-6. doi: 10.1093/bioinformatics/btv201. Epub 2015 Apr 16.
8
Identifying co-opted transposable elements using comparative epigenomics.
Dev Growth Differ. 2018 Jan;60(1):53-62. doi: 10.1111/dgd.12423. Epub 2018 Jan 24.
9
Comparing genomic and epigenomic features across species using the WashU Comparative Epigenome Browser.
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引用本文的文献

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Epilogos: information-theoretic navigation of multi-tissue functional genomic annotations.
bioRxiv. 2025 Jun 23:2025.06.18.660301. doi: 10.1101/2025.06.18.660301.
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Robust chromatin state annotation.
Genome Res. 2024 Apr 25;34(3):469-483. doi: 10.1101/gr.278343.123.
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A framework for group-wise summarization and comparison of chromatin state annotations.
Bioinformatics. 2023 Jan 1;39(1). doi: 10.1093/bioinformatics/btac722.
4
Computational methods to explore chromatin state dynamics.
Brief Bioinform. 2022 Nov 19;23(6). doi: 10.1093/bib/bbac439.
5
Epigenomic analysis of Parkinson's disease neurons identifies Tet2 loss as neuroprotective.
Nat Neurosci. 2020 Oct;23(10):1203-1214. doi: 10.1038/s41593-020-0690-y. Epub 2020 Aug 17.
7
The NIH Common Fund/Roadmap Epigenomics Program: Successes of a comprehensive consortium.
Sci Adv. 2019 Jul 10;5(7):eaaw6507. doi: 10.1126/sciadv.aaw6507. eCollection 2019 Jul.
9
EpiAlign: an alignment-based bioinformatic tool for comparing chromatin state sequences.
Nucleic Acids Res. 2019 Jul 26;47(13):e77. doi: 10.1093/nar/gkz287.

本文引用的文献

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Hepatocyte nuclear factor 1 coordinates multiple processes in a model of intestinal epithelial cell function.
Biochim Biophys Acta. 2016 Apr;1859(4):591-8. doi: 10.1016/j.bbagrm.2016.02.005. Epub 2016 Feb 6.
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Enhancer divergence and cis-regulatory evolution in the human and chimp neural crest.
Cell. 2015 Sep 24;163(1):68-83. doi: 10.1016/j.cell.2015.08.036. Epub 2015 Sep 10.
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FTO Obesity Variant Circuitry and Adipocyte Browning in Humans.
N Engl J Med. 2015 Sep 3;373(10):895-907. doi: 10.1056/NEJMoa1502214. Epub 2015 Aug 19.
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FOXA2 regulates a network of genes involved in critical functions of human intestinal epithelial cells.
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Spectacle: fast chromatin state annotation using spectral learning.
Genome Biol. 2015 Feb 12;16(1):33. doi: 10.1186/s13059-015-0598-0.
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hiHMM: Bayesian non-parametric joint inference of chromatin state maps.
Bioinformatics. 2015 Jul 1;31(13):2066-74. doi: 10.1093/bioinformatics/btv117. Epub 2015 Feb 27.
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Integrative analysis of 111 reference human epigenomes.
Nature. 2015 Feb 19;518(7539):317-30. doi: 10.1038/nature14248.
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Epigenomic annotation of genetic variants using the Roadmap Epigenome Browser.
Nat Biotechnol. 2015 Apr;33(4):345-6. doi: 10.1038/nbt.3158.

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