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For: Vinayagam A, Stelzl U, Foulle R, Plassmann S, Zenkner M, Timm J, Assmus HE, Andrade-Navarro MA, Wanker EE. A directed protein interaction network for investigating intracellular signal transduction. Sci Signal 2011;4:rs8. [PMID: 21900206 DOI: 10.1126/scisignal.2001699] [Citation(s) in RCA: 254] [Impact Index Per Article: 18.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Number Cited by Other Article(s)
51
Interactome Mapping Provides a Network of Neurodegenerative Disease Proteins and Uncovers Widespread Protein Aggregation in Affected Brains. Cell Rep 2021;32:108050. [PMID: 32814053 DOI: 10.1016/j.celrep.2020.108050] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2019] [Revised: 02/15/2020] [Accepted: 07/28/2020] [Indexed: 12/12/2022]  Open
52
Khalid M, Paracha RZ, Nisar M, Malik S, Tariq S, Arshad I, Siddiqa A, Hussain Z, Ahmad J, Ali A. Long non-coding RNAs and their targets as potential biomarkers in breast cancer. IET Syst Biol 2021;15:137-147. [PMID: 33991433 PMCID: PMC8675856 DOI: 10.1049/syb2.12020] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Revised: 04/10/2021] [Accepted: 04/27/2021] [Indexed: 01/09/2023]  Open
53
Tsuji S, Hase T, Yachie-Kinoshita A, Nishino T, Ghosh S, Kikuchi M, Shimokawa K, Aburatani H, Kitano H, Tanaka H. Artificial intelligence-based computational framework for drug-target prioritization and inference of novel repositionable drugs for Alzheimer's disease. ALZHEIMERS RESEARCH & THERAPY 2021;13:92. [PMID: 33941241 PMCID: PMC8091739 DOI: 10.1186/s13195-021-00826-3] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Accepted: 04/12/2021] [Indexed: 11/10/2022]
54
Guo WF, Yu X, Shi QQ, Liang J, Zhang SW, Zeng T. Performance assessment of sample-specific network control methods for bulk and single-cell biological data analysis. PLoS Comput Biol 2021;17:e1008962. [PMID: 33956788 PMCID: PMC8130943 DOI: 10.1371/journal.pcbi.1008962] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Revised: 05/18/2021] [Accepted: 04/12/2021] [Indexed: 11/29/2022]  Open
55
Pham VVH, Liu L, Bracken CP, Nguyen T, Goodall GJ, Li J, Le TD. pDriver : A novel method for unravelling personalised coding and miRNA cancer drivers. Bioinformatics 2021;37:3285-3292. [PMID: 33904576 DOI: 10.1093/bioinformatics/btab262] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Revised: 03/19/2021] [Accepted: 04/22/2021] [Indexed: 02/07/2023]  Open
56
Guo WF, Zhang SW, Feng YH, Liang J, Zeng T, Chen L. Network controllability-based algorithm to target personalized driver genes for discovering combinatorial drugs of individual patients. Nucleic Acids Res 2021;49:e37. [PMID: 33434272 PMCID: PMC8053130 DOI: 10.1093/nar/gkaa1272] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Revised: 12/02/2020] [Accepted: 12/22/2020] [Indexed: 12/27/2022]  Open
57
Xiang J, Zhang J, Zheng R, Li X, Li M. NIDM: network impulsive dynamics on multiplex biological network for disease-gene prediction. Brief Bioinform 2021;22:6236070. [PMID: 33866352 DOI: 10.1093/bib/bbab080] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Revised: 02/11/2021] [Accepted: 02/21/2021] [Indexed: 12/12/2022]  Open
58
Condensing and constraining WNT by TGF-β. Nat Cell Biol 2021;23:213-214. [PMID: 33723426 DOI: 10.1038/s41556-021-00649-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
59
Li R, Lin CY, Guo WF, Akutsu T. Weighted minimum feedback vertex sets and implementation in human cancer genes detection. BMC Bioinformatics 2021;22:143. [PMID: 33752597 PMCID: PMC7986389 DOI: 10.1186/s12859-021-04062-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Accepted: 03/03/2021] [Indexed: 11/22/2022]  Open
60
Pham VVH, Liu L, Bracken C, Goodall G, Li J, Le TD. Computational methods for cancer driver discovery: A survey. Am J Cancer Res 2021;11:5553-5568. [PMID: 33859763 PMCID: PMC8039954 DOI: 10.7150/thno.52670] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Accepted: 01/20/2021] [Indexed: 12/21/2022]  Open
61
Ruiz C, Zitnik M, Leskovec J. Identification of disease treatment mechanisms through the multiscale interactome. Nat Commun 2021;12:1796. [PMID: 33741907 PMCID: PMC7979814 DOI: 10.1038/s41467-021-21770-8] [Citation(s) in RCA: 91] [Impact Index Per Article: 22.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Accepted: 02/04/2021] [Indexed: 12/12/2022]  Open
62
Sowa AS, Popova TG, Harmuth T, Weber JJ, Pereira Sena P, Schmidt J, Hübener-Schmid J, Schmidt T. Neurodegenerative phosphoprotein signaling landscape in models of SCA3. Mol Brain 2021;14:57. [PMID: 33741019 PMCID: PMC7980345 DOI: 10.1186/s13041-020-00723-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Accepted: 12/28/2020] [Indexed: 01/01/2023]  Open
63
Guo Z, Fu Y, Huang C, Zheng C, Wu Z, Chen X, Gao S, Ma Y, Shahen M, Li Y, Tu P, Zhu J, Wang Z, Xiao W, Wang Y. NOGEA: A Network-oriented Gene Entropy Approach for Dissecting Disease Comorbidity and Drug Repositioning. GENOMICS, PROTEOMICS & BIOINFORMATICS 2021;19:549-564. [PMID: 33744433 PMCID: PMC9040018 DOI: 10.1016/j.gpb.2020.06.023] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/03/2019] [Revised: 04/04/2020] [Accepted: 09/24/2020] [Indexed: 10/31/2022]
64
Pham VVH, Liu L, Bracken CP, Goodall GJ, Li J, Le TD. DriverGroup: a novel method for identifying driver gene groups. Bioinformatics 2021;36:i583-i591. [PMID: 33381812 DOI: 10.1093/bioinformatics/btaa797] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]  Open
65
Chaudhary MS, Pham VVH, Le TD. NIBNA: A network-based node importance approach for identifying breast cancer drivers. Bioinformatics 2021;37:2521-2528. [PMID: 33677485 DOI: 10.1093/bioinformatics/btab145] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Revised: 01/21/2021] [Accepted: 02/28/2021] [Indexed: 12/11/2022]  Open
66
Esposito M, Fang C, Cook KC, Park N, Wei Y, Spadazzi C, Bracha D, Gunaratna RT, Laevsky G, DeCoste CJ, Slabodkin H, Brangwynne CP, Cristea IM, Kang Y. TGF-β-induced DACT1 biomolecular condensates repress Wnt signalling to promote bone metastasis. Nat Cell Biol 2021;23:257-267. [PMID: 33723425 PMCID: PMC7970447 DOI: 10.1038/s41556-021-00641-w] [Citation(s) in RCA: 80] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Accepted: 01/26/2021] [Indexed: 02/07/2023]
67
Paci P, Fiscon G, Conte F, Wang RS, Farina L, Loscalzo J. Gene co-expression in the interactome: moving from correlation toward causation via an integrated approach to disease module discovery. NPJ Syst Biol Appl 2021;7:3. [PMID: 33479222 PMCID: PMC7819998 DOI: 10.1038/s41540-020-00168-0] [Citation(s) in RCA: 60] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Accepted: 10/19/2020] [Indexed: 01/29/2023]  Open
68
Li R, Zhang W, Yan Z, Liu W, Fan J, Feng Y, Zeng Z, Cao D, Haydon RC, Luu HH, Deng ZL, He TC, Zou Y. Long non-coding RNA (LncRNA) HOTAIR regulates BMP9-induced osteogenic differentiation by targeting the proliferation of mesenchymal stem cells (MSCs). Aging (Albany NY) 2021;13:4199-4214. [PMID: 33461171 PMCID: PMC7906180 DOI: 10.18632/aging.202384] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Accepted: 11/17/2020] [Indexed: 12/29/2022]
69
Banerjee S, Velásquez-Zapata V, Fuerst G, Elmore JM, Wise RP. NGPINT: a next-generation protein-protein interaction software. Brief Bioinform 2020;22:6046042. [PMID: 33367498 DOI: 10.1093/bib/bbaa351] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Revised: 10/23/2020] [Accepted: 11/02/2020] [Indexed: 12/27/2022]  Open
70
Farrall AL, Lienhard M, Grimm C, Kuhl H, Sluka SHM, Caparros M, Forejt J, Timmermann B, Herwig R, Herrmann BG, Morkel M. PWD/Ph-Encoded Genetic Variants Modulate the Cellular Wnt/β-Catenin Response to Suppress Apc Min-Triggered Intestinal Tumor Formation. Cancer Res 2020;81:38-49. [PMID: 33154092 DOI: 10.1158/0008-5472.can-20-1480] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Revised: 08/26/2020] [Accepted: 10/15/2020] [Indexed: 11/16/2022]
71
Zeng L, Fan X, Wang X, Deng H, Zhang X, Zhang K, He S, Li N, Han Q, Liu Z. Involvement of NEK2 and its interaction with NDC80 and CEP250 in hepatocellular carcinoma. BMC Med Genomics 2020;13:158. [PMID: 33109182 PMCID: PMC7590453 DOI: 10.1186/s12920-020-00812-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2019] [Accepted: 06/25/2020] [Indexed: 12/16/2022]  Open
72
Hook SC, Chadt A, Heesom KJ, Kishida S, Al-Hasani H, Tavaré JM, Thomas EC. TBC1D1 interacting proteins, VPS13A and VPS13C, regulate GLUT4 homeostasis in C2C12 myotubes. Sci Rep 2020;10:17953. [PMID: 33087848 PMCID: PMC7578007 DOI: 10.1038/s41598-020-74661-1] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Accepted: 09/07/2020] [Indexed: 01/01/2023]  Open
73
Ackerman EE, Shoemaker JE. Network Controllability-Based Prioritization of Candidates for SARS-CoV-2 Drug Repositioning. Viruses 2020;12:v12101087. [PMID: 32993136 PMCID: PMC7650805 DOI: 10.3390/v12101087] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Revised: 09/22/2020] [Accepted: 09/23/2020] [Indexed: 12/12/2022]  Open
74
Peng J, Guan J, Hui W, Shang X. A novel subnetwork representation learning method for uncovering disease-disease relationships. Methods 2020;192:77-84. [PMID: 32946974 DOI: 10.1016/j.ymeth.2020.09.002] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Revised: 08/20/2020] [Accepted: 09/07/2020] [Indexed: 12/12/2022]  Open
75
Hao Shi, Yan KK, Ding L, Qian C, Chi H, Yu J. Network Approaches for Dissecting the Immune System. iScience 2020;23:101354. [PMID: 32717640 PMCID: PMC7390880 DOI: 10.1016/j.isci.2020.101354] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2020] [Revised: 06/21/2020] [Accepted: 07/08/2020] [Indexed: 02/06/2023]  Open
76
Goto K, Nishitsuji H, Sugiyama M, Nishida N, Mizokami M, Shimotohno K. Orchestration of Intracellular Circuits by G Protein-Coupled Receptor 39 for Hepatitis B Virus Proliferation. Int J Mol Sci 2020;21:ijms21165661. [PMID: 32784555 PMCID: PMC7460832 DOI: 10.3390/ijms21165661] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Revised: 08/04/2020] [Accepted: 08/05/2020] [Indexed: 12/14/2022]  Open
77
Kim KJ, Moon SJ, Park KS, Tagkopoulos I. Network-based modeling of drug effects on disease module in systemic sclerosis. Sci Rep 2020;10:13393. [PMID: 32770109 PMCID: PMC7414841 DOI: 10.1038/s41598-020-70280-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2020] [Accepted: 07/10/2020] [Indexed: 01/13/2023]  Open
78
Song E, Wang R, Leopold JA, Loscalzo J. Network determinants of cardiovascular calcification and repositioned drug treatments. FASEB J 2020;34:11087-11100. [PMID: 32638415 PMCID: PMC7497212 DOI: 10.1096/fj.202001062r] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Revised: 06/03/2020] [Accepted: 06/15/2020] [Indexed: 01/31/2023]
79
Pan X, Zeng T, Zhang YH, Chen L, Feng K, Huang T, Cai YD. Investigation and Prediction of Human Interactome Based on Quantitative Features. Front Bioeng Biotechnol 2020;8:730. [PMID: 32766217 PMCID: PMC7379396 DOI: 10.3389/fbioe.2020.00730] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2020] [Accepted: 06/09/2020] [Indexed: 01/27/2023]  Open
80
Yao H, Wu C, Chen Y, Guo L, Chen W, Pan Y, Fu X, Wang G, Ding Y. Spectrum of gene mutations identified by targeted next-generation sequencing in Chinese leukemia patients. Mol Genet Genomic Med 2020;8:e1369. [PMID: 32638549 PMCID: PMC7507579 DOI: 10.1002/mgg3.1369] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Revised: 05/23/2020] [Accepted: 05/28/2020] [Indexed: 12/13/2022]  Open
81
Xiang J, Zhang NR, Zhang JS, Lv XY, Li M. PrGeFNE: Predicting disease-related genes by fast network embedding. Methods 2020;192:3-12. [PMID: 32610158 DOI: 10.1016/j.ymeth.2020.06.015] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Revised: 06/13/2020] [Accepted: 06/22/2020] [Indexed: 12/14/2022]  Open
82
MELK mediates the stability of EZH2 through site-specific phosphorylation in extranodal natural killer/T-cell lymphoma. Blood 2020;134:2046-2058. [PMID: 31434700 DOI: 10.1182/blood.2019000381] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Accepted: 08/09/2019] [Indexed: 02/07/2023]  Open
83
van der Wal T, Lambooij JP, van Amerongen R. TMEM98 is a negative regulator of FRAT mediated Wnt/ß-catenin signalling. PLoS One 2020;15:e0227435. [PMID: 31961879 PMCID: PMC6974163 DOI: 10.1371/journal.pone.0227435] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2019] [Accepted: 12/18/2019] [Indexed: 12/19/2022]  Open
84
Su Y, Zhu H, Zhang L, Zhang X. Identifying Disease Modules Based on Connectivity and Semantic Similarities. COMMUNICATIONS IN COMPUTER AND INFORMATION SCIENCE 2020:26-40. [DOI: 10.1007/978-981-15-3415-7_3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/03/2025]
85
Browaeys R, Saelens W, Saeys Y. NicheNet: modeling intercellular communication by linking ligands to target genes. Nat Methods 2019;17:159-162. [DOI: 10.1038/s41592-019-0667-5] [Citation(s) in RCA: 1055] [Impact Index Per Article: 175.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Accepted: 10/29/2019] [Indexed: 12/15/2022]
86
Pham VVH, Liu L, Bracken CP, Goodall GJ, Long Q, Li J, Le TD. CBNA: A control theory based method for identifying coding and non-coding cancer drivers. PLoS Comput Biol 2019;15:e1007538. [PMID: 31790386 PMCID: PMC6907873 DOI: 10.1371/journal.pcbi.1007538] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2019] [Revised: 12/12/2019] [Accepted: 11/12/2019] [Indexed: 02/06/2023]  Open
87
Ramos PIP, Arge LWP, Lima NCB, Fukutani KF, de Queiroz ATL. Leveraging User-Friendly Network Approaches to Extract Knowledge From High-Throughput Omics Datasets. Front Genet 2019;10:1120. [PMID: 31798629 PMCID: PMC6863976 DOI: 10.3389/fgene.2019.01120] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2019] [Accepted: 10/16/2019] [Indexed: 11/13/2022]  Open
88
Li X, Xiang J, Hu X, Wu FX, Li M. DualRank: multiplex network-based dual ranking for heterogeneous complex disease analysis. 2019 IEEE INTERNATIONAL CONFERENCE ON BIOINFORMATICS AND BIOMEDICINE (BIBM) 2019:812-817. [DOI: 10.1109/bibm47256.2019.8983050] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/03/2025]
89
Genetic mapping of distal femoral, stifle, and tibial radiographic morphology in dogs with cranial cruciate ligament disease. PLoS One 2019;14:e0223094. [PMID: 31622367 PMCID: PMC6797204 DOI: 10.1371/journal.pone.0223094] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2018] [Accepted: 09/14/2019] [Indexed: 11/19/2022]  Open
90
Mostafavi A, Fozi MA, Koshkooieh AE, Mohammadabadi M, Babenko OI, Klopenko NI. Effect of LCORL gene polymorphism on body size traits in horse populations. ACTA SCIENTIARUM: ANIMAL SCIENCES 2019. [DOI: 10.4025/actascianimsci.v42i1.47483] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]  Open
91
Bag AK, Mandloi S, Jarmalavicius S, Mondal S, Kumar K, Mandal C, Walden P, Chakrabarti S, Mandal C. Connecting signaling and metabolic pathways in EGF receptor-mediated oncogenesis of glioblastoma. PLoS Comput Biol 2019;15:e1007090. [PMID: 31386654 PMCID: PMC6684045 DOI: 10.1371/journal.pcbi.1007090] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2018] [Accepted: 05/13/2019] [Indexed: 12/21/2022]  Open
92
Hu Y, Vinayagam A, Nand A, Comjean A, Chung V, Hao T, Mohr SE, Perrimon N. Molecular Interaction Search Tool (MIST): an integrated resource for mining gene and protein interaction data. Nucleic Acids Res 2019;46:D567-D574. [PMID: 29155944 PMCID: PMC5753374 DOI: 10.1093/nar/gkx1116] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2017] [Accepted: 10/25/2017] [Indexed: 12/16/2022]  Open
93
Béganton B, Solassol I, Mangé A, Solassol J. Protein interactions study through proximity-labeling. Expert Rev Proteomics 2019;16:717-726. [PMID: 31269821 DOI: 10.1080/14789450.2019.1638769] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
94
Silverbush D, Sharan R. A systematic approach to orient the human protein-protein interaction network. Nat Commun 2019;10:3015. [PMID: 31289271 PMCID: PMC6617457 DOI: 10.1038/s41467-019-10887-6] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2018] [Accepted: 06/06/2019] [Indexed: 11/16/2022]  Open
95
Guo WF, Zhang SW, Liu LL, Liu F, Shi QQ, Zhang L, Tang Y, Zeng T, Chen L. Discovering personalized driver mutation profiles of single samples in cancer by network control strategy. Bioinformatics 2019;34:1893-1903. [PMID: 29329368 DOI: 10.1093/bioinformatics/bty006] [Citation(s) in RCA: 70] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2017] [Accepted: 01/09/2018] [Indexed: 12/17/2022]  Open
96
Wiatr K, Piasecki P, Marczak Ł, Wojciechowski P, Kurkowiak M, Płoski R, Rydzanicz M, Handschuh L, Jungverdorben J, Brüstle O, Figlerowicz M, Figiel M. Altered Levels of Proteins and Phosphoproteins, in the Absence of Early Causative Transcriptional Changes, Shape the Molecular Pathogenesis in the Brain of Young Presymptomatic Ki91 SCA3/MJD Mouse. Mol Neurobiol 2019;56:8168-8202. [PMID: 31201651 PMCID: PMC6834541 DOI: 10.1007/s12035-019-01643-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2019] [Accepted: 05/10/2019] [Indexed: 12/19/2022]
97
Zeng Q, Lei F, Chang Y, Gao Z, Wang Y, Gao Q, Niu P, Li Q. An oncogenic gene, SNRPA1, regulates PIK3R1, VEGFC, MKI67, CDK1 and other genes in colorectal cancer. Biomed Pharmacother 2019;117:109076. [PMID: 31203132 DOI: 10.1016/j.biopha.2019.109076] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2019] [Revised: 05/26/2019] [Accepted: 06/02/2019] [Indexed: 02/07/2023]  Open
98
Gundogdu R, Hergovich A. MOB (Mps one Binder) Proteins in the Hippo Pathway and Cancer. Cells 2019;8:cells8060569. [PMID: 31185650 PMCID: PMC6627106 DOI: 10.3390/cells8060569] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2019] [Revised: 06/03/2019] [Accepted: 06/04/2019] [Indexed: 12/22/2022]  Open
99
Ackerman EE, Alcorn JF, Hase T, Shoemaker JE. A dual controllability analysis of influenza virus-host protein-protein interaction networks for antiviral drug target discovery. BMC Bioinformatics 2019;20:297. [PMID: 31159726 PMCID: PMC6545738 DOI: 10.1186/s12859-019-2917-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2019] [Accepted: 05/28/2019] [Indexed: 01/25/2023]  Open
100
Gong H, An J, Dong Q, Li J, Yang W, Sun W, Su Z, Zhang S. Discovery of SCY45, a Natural Small-Molecule MDM2-p53 Interaction Inhibitor. Chem Biodivers 2019;16:e1900081. [PMID: 30989812 DOI: 10.1002/cbdv.201900081] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2019] [Accepted: 04/15/2019] [Indexed: 01/09/2023]
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