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For: Chen C, Jiang L, Fu G, Wang M, Wang Y, Shen B, Liu Z, Wang Z, Hou W, Berceli SA, Wu R. An omnidirectional visualization model of personalized gene regulatory networks. NPJ Syst Biol Appl 2019;5:38. [PMID: 31632690 PMCID: PMC6789114 DOI: 10.1038/s41540-019-0116-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2019] [Accepted: 09/18/2019] [Indexed: 01/09/2023]  Open
Number Cited by Other Article(s)
1
Che J, Wang Y, Feng L, Gragnoli C, Griffin C, Wu R. High-order interaction modeling of tumor-microenvironment crosstalk for tumor growth. Phys Life Rev 2025;54:11-23. [PMID: 40412053 DOI: 10.1016/j.plrev.2025.05.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2025] [Accepted: 05/16/2025] [Indexed: 05/27/2025]
2
Wu S, Pan W, Dong A. idopNetwork Analysis of Salt-Responsive Transcriptomes Reveals Hub Regulatory Modules and Genes in Populus euphratica. Int J Mol Sci 2025;26:4091. [PMID: 40362331 PMCID: PMC12071587 DOI: 10.3390/ijms26094091] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2025] [Revised: 04/18/2025] [Accepted: 04/22/2025] [Indexed: 05/15/2025]  Open
3
Cui X, Song J, Li Q, Ren J. Identification of biomarkers and target drugs for melanoma: a topological and deep learning approach. Front Genet 2025;16:1471037. [PMID: 40098976 PMCID: PMC11911340 DOI: 10.3389/fgene.2025.1471037] [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: 07/26/2024] [Accepted: 02/04/2025] [Indexed: 03/19/2025]  Open
4
Cui Y. GLMY Homology Theory Meets idopNetwork: Dissecting Soil Microbiota Resilience Under Forest Thinning and Climate Change: Comment on "Topological change of soil microbiota networks for forest resilience under global warming" by Gong et al. Phys Life Rev 2025;52:44-45. [PMID: 39616896 DOI: 10.1016/j.plrev.2024.11.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2024] [Accepted: 11/27/2024] [Indexed: 03/01/2025]
5
Sun Z, Ye J, Sun W, Jiang L, Shan B, Zhang M, Xu J, Li W, Liu J, Jing H, Zhang T, Hou M, Xie C, Wu R, Pan H, Yuan J. Cooperation of TRADD- and RIPK1-dependent cell death pathways in maintaining intestinal homeostasis. Nat Commun 2025;16:1890. [PMID: 39987261 PMCID: PMC11846980 DOI: 10.1038/s41467-025-57211-z] [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: 09/11/2024] [Accepted: 02/12/2025] [Indexed: 02/24/2025]  Open
6
Che J, Jin Y, Gragnoli C, Yau ST, Wu R. IdopNetwork as a genomic predictor of drug response. Drug Discov Today 2025;30:104252. [PMID: 39603519 DOI: 10.1016/j.drudis.2024.104252] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2024] [Revised: 11/13/2024] [Accepted: 11/21/2024] [Indexed: 11/29/2024]
7
Berg A. Causal inference from high-dimensional static data in soil microbiota networks: Comment on "Topological change of soil microbiota networks for forest resilience under global warming" by Gong et al. Phys Life Rev 2024;51:281-282. [PMID: 39476548 DOI: 10.1016/j.plrev.2024.10.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2024] [Accepted: 10/23/2024] [Indexed: 12/06/2024]
8
Hsiao YC, Dutta A. Network Modeling and Control of Dynamic Disease Pathways, Review and Perspectives. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2024;21:1211-1230. [PMID: 38498762 DOI: 10.1109/tcbb.2024.3378155] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/20/2024]
9
Gong H, Wang H, Wang Y, Zhang S, Liu X, Che J, Wu S, Wu J, Sun X, Zhang S, Yau ST, Wu R. Topological change of soil microbiota networks for forest resilience under global warming. Phys Life Rev 2024;50:228-251. [PMID: 39178631 DOI: 10.1016/j.plrev.2024.08.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2024] [Revised: 07/31/2024] [Accepted: 08/02/2024] [Indexed: 08/26/2024]
10
Ding Y, Bajpai AK, Wu F, Lu W, Xu L, Mao J, Li Q, Pan Q, Lu L, Wang X. 5-methylcytosine RNA modification regulators-based patterns and features of immune microenvironment in acute myeloid leukemia. Aging (Albany NY) 2024;16:2340-2361. [PMID: 38277218 PMCID: PMC10911375 DOI: 10.18632/aging.205484] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Accepted: 12/26/2023] [Indexed: 01/27/2024]
11
Wang Y, Sang M, Feng L, Gragnoli C, Griffin C, Wu R. A pleiotropic-epistatic entangelement model of drug response. Drug Discov Today 2023;28:103790. [PMID: 37758020 DOI: 10.1016/j.drudis.2023.103790] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2023] [Revised: 09/10/2023] [Accepted: 09/20/2023] [Indexed: 10/03/2023]
12
Wu S, Liu X, Dong A, Gragnoli C, Griffin C, Wu J, Yau ST, Wu R. The metabolomic physics of complex diseases. Proc Natl Acad Sci U S A 2023;120:e2308496120. [PMID: 37812720 PMCID: PMC10589719 DOI: 10.1073/pnas.2308496120] [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: 05/21/2023] [Accepted: 08/15/2023] [Indexed: 10/11/2023]  Open
13
Chen C, Shen B, Zhang L, Yu T, Wang M, Wu R. A Cartographic Tool to Predict Disease Risk-associated Pseudo-Dynamic Networks from Tissue-specific Gene Expression. Bio Protoc 2023;13:e4583. [PMID: 36789091 PMCID: PMC9901473 DOI: 10.21769/bioprotoc.4583] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2022] [Revised: 09/05/2022] [Accepted: 12/13/2022] [Indexed: 01/06/2023]  Open
14
Wang Q, Dong A, Zhao J, Wang C, Griffin C, Gragnoli C, Xue F, Wu R. Vaginal microbiota networks as a mechanistic predictor of aerobic vaginitis. Front Microbiol 2022;13:998813. [PMID: 36338093 PMCID: PMC9631484 DOI: 10.3389/fmicb.2022.998813] [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: 07/20/2022] [Accepted: 09/09/2022] [Indexed: 09/07/2024]  Open
15
Chen C, Shen B, Ma T, Wang M, Wu R. A statistical framework for recovering pseudo-dynamic networks from static data. Bioinformatics 2022;38:2481-2487. [PMID: 35218338 PMCID: PMC9991900 DOI: 10.1093/bioinformatics/btac038] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Revised: 12/06/2021] [Indexed: 11/13/2022]  Open
16
A graph model of combination therapies. Drug Discov Today 2022;27:1210-1217. [PMID: 35143962 DOI: 10.1016/j.drudis.2022.02.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Revised: 12/31/2021] [Accepted: 02/02/2022] [Indexed: 11/24/2022]
17
A Single-Cell Omics Network Model of Cell Crosstalk during the Formation of Primordial Follicles. Cells 2022;11:cells11030332. [PMID: 35159142 PMCID: PMC8834074 DOI: 10.3390/cells11030332] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Revised: 01/04/2022] [Accepted: 01/11/2022] [Indexed: 12/27/2022]  Open
18
Cao X, Dong A, Kang G, Wang X, Duan L, Hou H, Zhao T, Wu S, Liu X, Huang H, Wu R. Modeling spatial interaction networks of the gut microbiota. Gut Microbes 2022;14:2106103. [PMID: 35921525 PMCID: PMC9351588 DOI: 10.1080/19490976.2022.2106103] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Revised: 06/03/2022] [Accepted: 07/21/2022] [Indexed: 02/04/2023]  Open
19
The Genomic Physics of COVID-19 Pathogenesis and Spread. Cells 2021;11:cells11010080. [PMID: 35011641 PMCID: PMC8750765 DOI: 10.3390/cells11010080] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Revised: 12/19/2021] [Accepted: 12/23/2021] [Indexed: 12/11/2022]  Open
20
Feng L, Jiang P, Li C, Zhao J, Dong A, Yang D, Wu R. Genetic dissection of growth trajectories in forest trees: From FunMap to FunGraph. FORESTRY RESEARCH 2021;1:19. [PMID: 39524511 PMCID: PMC11524299 DOI: 10.48130/fr-2021-0019] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Accepted: 10/14/2021] [Indexed: 11/16/2024]
21
Wang H, Ye M, Fu Y, Dong A, Zhang M, Feng L, Zhu X, Bo W, Jiang L, Griffin CH, Liang D, Wu R. Modeling genome-wide by environment interactions through omnigenic interactome networks. Cell Rep 2021;35:109114. [PMID: 33979624 DOI: 10.1016/j.celrep.2021.109114] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Revised: 03/11/2021] [Accepted: 04/21/2021] [Indexed: 10/21/2022]  Open
22
Sun L, Jiang L, Grant CN, Wang HG, Gragnoli C, Liu Z, Wu R. Computational Identification of Gene Networks as a Biomarker of Neuroblastoma Risk. Cancers (Basel) 2020;12:cancers12082086. [PMID: 32731407 PMCID: PMC7465094 DOI: 10.3390/cancers12082086] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2020] [Revised: 07/24/2020] [Accepted: 07/25/2020] [Indexed: 01/03/2023]  Open
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