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For: Grechkin M, Logsdon BA, Gentles AJ, Lee SI. Identifying Network Perturbation in Cancer. PLoS Comput Biol 2016;12:e1004888. [PMID: 27145341 PMCID: PMC4856318 DOI: 10.1371/journal.pcbi.1004888] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2015] [Accepted: 03/25/2016] [Indexed: 01/08/2023]  Open
Number Cited by Other Article(s)
1
Ahn B, Chou C, Chou C, Chen J, Zug A, Baykara Y, Claus J, Hacking SM, Uzun A, Gamsiz Uzun E. The Atlas of Protein-Protein Interactions in Cancer (APPIC)-a webtool to visualize and analyze cancer subtypes. NAR Cancer 2025;7:zcae047. [PMID: 39822275 PMCID: PMC11734624 DOI: 10.1093/narcan/zcae047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2024] [Revised: 11/27/2024] [Accepted: 01/03/2025] [Indexed: 01/19/2025]  Open
2
Ferrari I, De Grossi F, Lai G, Oliveto S, Deroma G, Biffo S, Manfrini N. CancerHubs: a systematic data mining and elaboration approach for identifying novel cancer-related protein interaction hubs. Brief Bioinform 2024;26:bbae635. [PMID: 39657701 PMCID: PMC11631132 DOI: 10.1093/bib/bbae635] [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: 08/14/2024] [Revised: 10/31/2024] [Accepted: 11/22/2024] [Indexed: 12/12/2024]  Open
3
Geraghty S, Boyer JA, Fazel-Zarandi M, Arzouni N, Ryseck RP, McBride MJ, Parsons LR, Rabinowitz JD, Singh M. Integrative Computational Framework, Dyscovr, Links Mutated Driver Genes to Expression Dysregulation Across 19 Cancer Types. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.11.20.624509. [PMID: 39605479 PMCID: PMC11601522 DOI: 10.1101/2024.11.20.624509] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/29/2024]
4
Huang X, Zhang H. Detecting responsible nodes in differential Bayesian networks. Stat Med 2024;43:3294-3312. [PMID: 38831542 DOI: 10.1002/sim.10125] [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: 05/06/2023] [Revised: 03/25/2024] [Accepted: 05/18/2024] [Indexed: 06/05/2024]
5
Cheng X, Amanullah M, Liu W, Liu Y, Pan X, Zhang H, Xu H, Liu P, Lu Y. WMDS.net: a network control framework for identifying key players in transcriptome programs. Bioinformatics 2023;39:7023921. [PMID: 36727489 PMCID: PMC9925106 DOI: 10.1093/bioinformatics/btad071] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Revised: 01/16/2023] [Accepted: 02/01/2023] [Indexed: 02/03/2023]  Open
6
Ershov P, Yablokov E, Mezentsev Y, Ivanov A. Interactomics of CXXC proteins involved in epigenetic regulation of gene expression. BIOMEDITSINSKAYA KHIMIYA 2022;68:339-351. [DOI: 10.18097/pbmc20226805339] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
7
Hu CW, Xie J, Jiang J. The Emerging Roles of Protein Interactions with O-GlcNAc Cycling Enzymes in Cancer. Cancers (Basel) 2022;14:5135. [PMID: 36291918 PMCID: PMC9600386 DOI: 10.3390/cancers14205135] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Revised: 10/18/2022] [Accepted: 10/18/2022] [Indexed: 09/11/2023]  Open
8
Yue R, Dutta A. Computational systems biology in disease modeling and control, review and perspectives. NPJ Syst Biol Appl 2022;8:37. [PMID: 36192551 PMCID: PMC9528884 DOI: 10.1038/s41540-022-00247-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Accepted: 09/05/2022] [Indexed: 02/02/2023]  Open
9
Hou S, Zhang P, Yang K, Wang L, Ma C, Li Y, Li S. Decoding multilevel relationships with the human tissue-cell-molecule network. Brief Bioinform 2022;23:6585388. [PMID: 35551347 DOI: 10.1093/bib/bbac170] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Revised: 04/09/2022] [Accepted: 04/16/2022] [Indexed: 02/01/2023]  Open
10
Tan YT, Ou-Yang L, Jiang X, Yan H, Zhang XF. Identifying Gene Network Rewiring Based on Partial Correlation. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2022;19:513-521. [PMID: 32750866 DOI: 10.1109/tcbb.2020.3002906] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
11
Liu C, Cai D, Zeng W, Huang Y. Inferring Differential Networks by Integrating Gene Expression Data With Additional Knowledge. Front Genet 2021;12:760155. [PMID: 34858477 PMCID: PMC8632038 DOI: 10.3389/fgene.2021.760155] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Accepted: 10/13/2021] [Indexed: 11/23/2022]  Open
12
Network-based protein-protein interaction prediction method maps perturbations of cancer interactome. PLoS Genet 2021;17:e1009869. [PMID: 34727106 PMCID: PMC8610286 DOI: 10.1371/journal.pgen.1009869] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Revised: 11/23/2021] [Accepted: 10/09/2021] [Indexed: 01/09/2023]  Open
13
Tu JJ, Ou-Yang L, Zhu Y, Yan H, Qin H, Zhang XF. Differential network analysis by simultaneously considering changes in gene interactions and gene expression. Bioinformatics 2021;37:4414-4423. [PMID: 34245246 DOI: 10.1093/bioinformatics/btab502] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Revised: 06/13/2021] [Accepted: 07/05/2021] [Indexed: 11/14/2022]  Open
14
Xu T, Ou-Yang L, Yan H, Zhang XF. Time-Varying Differential Network Analysis for Revealing Network Rewiring over Cancer Progression. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2021;18:1632-1642. [PMID: 31647444 DOI: 10.1109/tcbb.2019.2949039] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
15
Xie J, Yang F, Wang J, Karikomi M, Yin Y, Sun J, Wen T, Nie Q. DNF: A differential network flow method to identify rewiring drivers for gene regulatory networks. Neurocomputing 2020;410:202-210. [PMID: 34025035 PMCID: PMC8139126 DOI: 10.1016/j.neucom.2020.05.028] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
16
Rangaswamy U, Dharshini SAP, Yesudhas D, Gromiha MM. VEPAD - Predicting the effect of variants associated with Alzheimer's disease using machine learning. Comput Biol Med 2020;124:103933. [PMID: 32828070 DOI: 10.1016/j.compbiomed.2020.103933] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Revised: 07/25/2020] [Accepted: 07/25/2020] [Indexed: 12/26/2022]
17
Amin V, Ağaç D, Barnes SD, Çobanoğlu MC. Accurate differential analysis of transcription factor activity from gene expression. Bioinformatics 2020;35:5018-5029. [PMID: 31099391 DOI: 10.1093/bioinformatics/btz398] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2018] [Revised: 04/02/2019] [Accepted: 05/08/2019] [Indexed: 12/17/2022]  Open
18
Liu E, Zhang ZZ, Cheng X, Liu X, Cheng L. SCNrank: spectral clustering for network-based ranking to reveal potential drug targets and its application in pancreatic ductal adenocarcinoma. BMC Med Genomics 2020;13:50. [PMID: 32241274 PMCID: PMC7119297 DOI: 10.1186/s12920-020-0681-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]  Open
19
Yuan R, Ou-Yang L, Hu X, Zhang XF. Identifying Gene Network Rewiring Using Robust Differential Graphical Model with Multivariate t-Distribution. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2020;17:712-718. [PMID: 30802872 DOI: 10.1109/tcbb.2019.2901473] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
20
Salviato E, Djordjilović V, Chiogna M, Romualdi C. SourceSet: A graphical model approach to identify primary genes in perturbed biological pathways. PLoS Comput Biol 2019;15:e1007357. [PMID: 31652275 PMCID: PMC6834292 DOI: 10.1371/journal.pcbi.1007357] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2018] [Revised: 11/06/2019] [Accepted: 08/23/2019] [Indexed: 11/24/2022]  Open
21
Mukherjee S, Perumal TM, Daily K, Sieberts SK, Omberg L, Preuss C, Carter GW, Mangravite LM, Logsdon BA. Identifying and ranking potential driver genes of Alzheimer's disease using multiview evidence aggregation. Bioinformatics 2019;35:i568-i576. [PMID: 31510680 PMCID: PMC6612835 DOI: 10.1093/bioinformatics/btz365] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]  Open
22
Xu T, Ou-Yang L, Hu X, Zhang XF. Identifying Gene Network Rewiring by Integrating Gene Expression and Gene Network Data. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2018;15:2079-2085. [PMID: 29994068 DOI: 10.1109/tcbb.2018.2809603] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
23
McGillivray P, Clarke D, Meyerson W, Zhang J, Lee D, Gu M, Kumar S, Zhou H, Gerstein M. Network Analysis as a Grand Unifier in Biomedical Data Science. Annu Rev Biomed Data Sci 2018. [DOI: 10.1146/annurev-biodatasci-080917-013444] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
24
Mukherjee S, Carignano A, Seelig G, Lee SI. Identifying progressive gene network perturbation from single-cell RNA-seq data. ANNUAL INTERNATIONAL CONFERENCE OF THE IEEE ENGINEERING IN MEDICINE AND BIOLOGY SOCIETY. IEEE ENGINEERING IN MEDICINE AND BIOLOGY SOCIETY. ANNUAL INTERNATIONAL CONFERENCE 2018;2018:5034-5040. [PMID: 30441472 DOI: 10.1109/embc.2018.8513444] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
25
Dramatic dysbalancing of the Wnt pathway in breast cancers. Sci Rep 2018;8:7329. [PMID: 29743726 PMCID: PMC5943245 DOI: 10.1038/s41598-018-25672-6] [Citation(s) in RCA: 56] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2018] [Accepted: 04/26/2018] [Indexed: 12/15/2022]  Open
26
Tu JJ, Ou-Yang L, Hu X, Zhang XF. Identifying gene network rewiring by combining gene expression and gene mutation data. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2018;16:1042-1048. [PMID: 29993891 DOI: 10.1109/tcbb.2018.2834529] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
27
Singh AJ, Ramsey SA, Filtz TM, Kioussi C. Differential gene regulatory networks in development and disease. Cell Mol Life Sci 2018;75:1013-1025. [PMID: 29018868 PMCID: PMC11105524 DOI: 10.1007/s00018-017-2679-6] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2017] [Revised: 09/19/2017] [Accepted: 10/04/2017] [Indexed: 02/02/2023]
28
Wang J, Li Z, Lei M, Fu Y, Zhao J, Ao M, Xu L. Integrated DNA methylome and transcriptome analysis reveals the ethylene-induced flowering pathway genes in pineapple. Sci Rep 2017;7:17167. [PMID: 29215068 PMCID: PMC5719354 DOI: 10.1038/s41598-017-17460-5] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2017] [Accepted: 11/27/2017] [Indexed: 01/09/2023]  Open
29
Zhang XF, Ou-Yang L, Yan H. Node-based differential network analysis in genomics. Comput Biol Chem 2017;69:194-201. [DOI: 10.1016/j.compbiolchem.2017.03.010] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2017] [Accepted: 03/27/2017] [Indexed: 12/26/2022]
30
Zhang XF, Ou-Yang L, Yan H. Incorporating prior information into differential network analysis using non-paranormal graphical models. Bioinformatics 2017;33:2436-2445. [DOI: 10.1093/bioinformatics/btx208] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2016] [Accepted: 04/05/2017] [Indexed: 02/02/2023]  Open
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