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For: Agarwal A, Zhao F, Jiang Y, Chen L. TIVAN-indel: a computational framework for annotating and predicting non-coding regulatory small insertions and deletions. Bioinformatics 2023;39:btad060. [PMID: 36707993 PMCID: PMC9900211 DOI: 10.1093/bioinformatics/btad060] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2022] [Revised: 01/20/2023] [Accepted: 01/25/2023] [Indexed: 01/29/2023]  Open
Number Cited by Other Article(s)
1
Jiang B, Quinn-Bohmann N, Diener C, Nathan VB, Han-Hallett Y, Reddivari L, Gibbons SM, Baloni P. Understanding disease-associated metabolic changes in human colon epithelial cells using i ColonEpithelium metabolic reconstruction. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.10.22.619644. [PMID: 39484551 PMCID: PMC11526933 DOI: 10.1101/2024.10.22.619644] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/03/2024]
2
Ma X, Thela SR, Zhao F, Yao B, Wen Z, Jin P, Zhao J, Chen L. Deep5hmC: predicting genome-wide 5-hydroxymethylcytosine landscape via a multimodal deep learning model. Bioinformatics 2024;40:btae528. [PMID: 39196755 PMCID: PMC11379467 DOI: 10.1093/bioinformatics/btae528] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2024] [Revised: 08/09/2024] [Accepted: 08/27/2024] [Indexed: 08/30/2024]  Open
3
Jin W, Xia Y, Thela SR, Liu Y, Chen L. In silico generation and augmentation of regulatory variants from massively parallel reporter assay using conditional variational autoencoder. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.25.600715. [PMID: 38979263 PMCID: PMC11230389 DOI: 10.1101/2024.06.25.600715] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/10/2024]
4
Jou V, Peña SM, Lehoczky JA. Regeneration-specific promoter switching facilitates Mest expression in the mouse digit tip to modulate neutrophil response. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.12.598713. [PMID: 38915675 PMCID: PMC11195169 DOI: 10.1101/2024.06.12.598713] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/26/2024]
5
Ma X, Thela SR, Zhao F, Yao B, Wen Z, Jin P, Zhao J, Chen L. Deep5hmC: Predicting genome-wide 5-Hydroxymethylcytosine landscape via a multimodal deep learning model. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.04.583444. [PMID: 38496575 PMCID: PMC10942288 DOI: 10.1101/2024.03.04.583444] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/19/2024]
6
Fu ZH, He SZ, Wu Y, Zhao GR. Design and deep learning of synthetic B-cell-specific promoters. Nucleic Acids Res 2023;51:11967-11979. [PMID: 37889080 PMCID: PMC10681721 DOI: 10.1093/nar/gkad930] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2023] [Revised: 09/20/2023] [Accepted: 10/10/2023] [Indexed: 10/28/2023]  Open
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