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For: Signorini LF, Almozlino T, Sharan R. ANAT 3.0: a framework for elucidating functional protein subnetworks using graph-theoretic and machine learning approaches. BMC Bioinformatics 2021;22:526. [PMID: 34706638 PMCID: PMC8555137 DOI: 10.1186/s12859-021-04449-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Accepted: 10/13/2021] [Indexed: 12/29/2022]  Open
Number Cited by Other Article(s)
1
Sheinin R, Sharan R, Madi A. scNET: learning context-specific gene and cell embeddings by integrating single-cell gene expression data with protein-protein interactions. Nat Methods 2025;22:708-716. [PMID: 40097811 PMCID: PMC11978505 DOI: 10.1038/s41592-025-02627-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2024] [Accepted: 02/07/2025] [Indexed: 03/19/2025]
2
Kupershmidt Y, Kasif S, Sharan R. SPIDER: constructing cell-type-specific protein-protein interaction networks. BIOINFORMATICS ADVANCES 2024;4:vbae130. [PMID: 39346952 PMCID: PMC11438548 DOI: 10.1093/bioadv/vbae130] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/04/2024] [Revised: 08/11/2024] [Accepted: 08/28/2024] [Indexed: 10/01/2024]
3
Pirak D, Sharan R. D'or: deep orienter of protein-protein interaction networks. Bioinformatics 2024;40:btae355. [PMID: 38862241 PMCID: PMC11254290 DOI: 10.1093/bioinformatics/btae355] [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: 05/07/2023] [Revised: 04/19/2024] [Accepted: 06/06/2024] [Indexed: 06/13/2024]  Open
4
Zadok N, Ast G, Sharan R. A network-based method for associating genes with autism spectrum disorder. FRONTIERS IN BIOINFORMATICS 2024;4:1295600. [PMID: 38525240 PMCID: PMC10960359 DOI: 10.3389/fbinf.2024.1295600] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2023] [Accepted: 02/26/2024] [Indexed: 03/26/2024]  Open
5
Kałuzińska-Kołat Ż, Kołat D, Kośla K, Płuciennik E, Bednarek AK. Molecular landscapes of glioblastoma cell lines revealed a group of patients that do not benefit from WWOX tumor suppressor expression. Front Neurosci 2023;17:1260409. [PMID: 37781246 PMCID: PMC10540236 DOI: 10.3389/fnins.2023.1260409] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Accepted: 08/28/2023] [Indexed: 10/03/2023]  Open
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