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Foundation model for comprehensive transcriptional regulation analysis.

作者信息

Yu Zhaowei, Zhang Yong

机构信息

State Key Laboratory of Cardiovascular Diseases and Medical Innovation Center, Institute for Regenerative Medicine, Department of Neurosurgery, Shanghai East Hospital, Shanghai Key Laboratory of Signaling and Disease Research, Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, China.

出版信息

Natl Sci Rev. 2024 Oct 14;11(11):nwae355. doi: 10.1093/nsr/nwae355. eCollection 2024 Nov.

DOI:10.1093/nsr/nwae355
PMID:39555104
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC11565239/
Abstract
摘要
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/971e/11565239/3484539ba1fb/nwae355fig1.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/971e/11565239/3484539ba1fb/nwae355fig1.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/971e/11565239/3484539ba1fb/nwae355fig1.jpg

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本文引用的文献

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Nature. 2024 Feb;626(7997):212-220. doi: 10.1038/s41586-023-06936-2. Epub 2023 Dec 12.
2
Targeted design of synthetic enhancers for selected tissues in the Drosophila embryo.针对果蝇胚胎中特定组织的合成增强子的靶向设计。
Nature. 2024 Feb;626(7997):207-211. doi: 10.1038/s41586-023-06905-9. Epub 2023 Dec 12.
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CREaTor: zero-shot cis-regulatory pattern modeling with attention mechanisms.CREaTor：基于注意力机制的零样本顺式调控模式建模。
Genome Biol. 2023 Nov 23;24(1):266. doi: 10.1186/s13059-023-03103-8.
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Multi-omics single-cell data integration and regulatory inference with graph-linked embedding.基于图链接嵌入的多组学单细胞数据整合与调控推断。
Nat Biotechnol. 2022 Oct;40(10):1458-1466. doi: 10.1038/s41587-022-01284-4. Epub 2022 May 2.
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Effective gene expression prediction from sequence by integrating long-range interactions.通过整合长程相互作用，从序列中有效预测基因表达。
Nat Methods. 2021 Oct;18(10):1196-1203. doi: 10.1038/s41592-021-01252-x. Epub 2021 Oct 4.
6
DNABERT: pre-trained Bidirectional Encoder Representations from Transformers model for DNA-language in genome.DNABERT：用于基因组中DNA语言的基于变换器的预训练双向编码器表征模型。
Bioinformatics. 2021 Aug 9;37(15):2112-2120. doi: 10.1093/bioinformatics/btab083.
7
Basset: learning the regulatory code of the accessible genome with deep convolutional neural networks.巴塞特：利用深度卷积神经网络学习可及基因组的调控密码。
Genome Res. 2016 Jul;26(7):990-9. doi: 10.1101/gr.200535.115. Epub 2016 May 3.
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Predicting effects of noncoding variants with deep learning-based sequence model.使用基于深度学习的序列模型预测非编码变异的影响。
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Nat Biotechnol. 2015 Aug;33(8):831-8. doi: 10.1038/nbt.3300. Epub 2015 Jul 27.
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Architecture of the human regulatory network derived from ENCODE data.人类调控网络的结构源自 ENCODE 数据。
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