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For: Franceschini A, Lin J, von Mering C, Jensen LJ. SVD-phy: improved prediction of protein functional associations through singular value decomposition of phylogenetic profiles. Bioinformatics 2015;32:1085-7. [PMID: 26614125 PMCID: PMC4896368 DOI: 10.1093/bioinformatics/btv696] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2015] [Accepted: 11/24/2015] [Indexed: 11/15/2022]  Open
Number Cited by Other Article(s)
51
Li Q, Xie Y, Xu G, Lebrilla CB. Identification of potential sialic acid binding proteins on cell membranes by proximity chemical labeling. Chem Sci 2019;10:6199-6209. [PMID: 31360427 PMCID: PMC6585875 DOI: 10.1039/c9sc01360a] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2019] [Accepted: 05/14/2019] [Indexed: 01/28/2023]  Open
52
Long non-coding RNA SNHG6 is upregulated in prostate cancer and predicts poor prognosis. Mol Biol Rep 2019;46:2771-2778. [PMID: 30911973 DOI: 10.1007/s11033-019-04723-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2018] [Accepted: 02/27/2019] [Indexed: 10/27/2022]
53
Huminiecki L. Magic roundabout is an endothelial-specific ohnolog of ROBO1 which neo-functionalized to an essential new role in angiogenesis. PLoS One 2019;14:e0208952. [PMID: 30802244 PMCID: PMC6389290 DOI: 10.1371/journal.pone.0208952] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2018] [Accepted: 11/26/2018] [Indexed: 12/25/2022]  Open
54
Chen Y, Bi F, An Y, Yang Q. Coexpression network analysis identified Krüppel-like factor 6 (KLF6) association with chemosensitivity in ovarian cancer. J Cell Biochem 2019;120:2607-2615. [PMID: 30206992 DOI: 10.1002/jcb.27567] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2018] [Accepted: 08/06/2018] [Indexed: 02/06/2023]
55
Neves HHR, Vargas G, Brito LF, Schenkel FS, Albuquerque LG, Carvalheiro R. Genetic and genomic analyses of testicular hypoplasia in Nellore cattle. PLoS One 2019;14:e0211159. [PMID: 30677076 PMCID: PMC6345487 DOI: 10.1371/journal.pone.0211159] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2018] [Accepted: 01/08/2019] [Indexed: 12/11/2022]  Open
56
Zhu R, Li G, Liu JX, Dai LY, Guo Y. ACCBN: ant-Colony-clustering-based bipartite network method for predicting long non-coding RNA-protein interactions. BMC Bioinformatics 2019;20:16. [PMID: 30626319 PMCID: PMC6327428 DOI: 10.1186/s12859-018-2586-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2018] [Accepted: 12/17/2018] [Indexed: 12/24/2022]  Open
57
Navarro C, Martínez V, Blanco A, Cano C. ProphTools: general prioritization tools for heterogeneous biological networks. Gigascience 2018;6:1-8. [PMID: 29186475 PMCID: PMC5751048 DOI: 10.1093/gigascience/gix111] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2017] [Accepted: 11/09/2017] [Indexed: 12/17/2022]  Open
58
Tu Z, Xiong J, Xiao R, Shao L, Yang X, Zhou L, Yuan W, Wang M, Yin Q, Wu Y, Pan S, Leng J, Jiang D, He C, Zhang Q. Loss of miR-146b-5p promotes T cell acute lymphoblastic leukemia migration and invasion via the IL-17A pathway. J Cell Biochem 2018;120:5936-5948. [PMID: 30362152 DOI: 10.1002/jcb.27882] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2018] [Accepted: 09/21/2018] [Indexed: 12/25/2022]
59
Kang SD, Chatterjee S, Alam S, Salzberg AC, Milici J, van der Burg SH, Meyers C. Effect of Productive Human Papillomavirus 16 Infection on Global Gene Expression in Cervical Epithelium. J Virol 2018;92:e01261-18. [PMID: 30045992 PMCID: PMC6158420 DOI: 10.1128/jvi.01261-18] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2018] [Accepted: 07/20/2018] [Indexed: 12/29/2022]  Open
60
Burton M, Abanobi C, Wang KTC, Ma Y, Rasche ME. Substrate Specificity Analysis of Dihydrofolate/Dihydromethanopterin Reductase Homologs in Methylotrophic α-Proteobacteria. Front Microbiol 2018;9:2439. [PMID: 30364315 PMCID: PMC6193120 DOI: 10.3389/fmicb.2018.02439] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2018] [Accepted: 09/24/2018] [Indexed: 12/22/2022]  Open
61
Xiong Y, Yuan L, Chen L, Zhu Y, Zhang S, Liu X, Xiao Y, Wang X. Identifying a Novel Biomarker TOP2A of Clear Cell Renal Cell Carcinoma (ccRCC) Associated with Smoking by Co-Expression Network Analysis. J Cancer 2018;9:3912-3922. [PMID: 30410595 PMCID: PMC6218786 DOI: 10.7150/jca.25900] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2018] [Accepted: 08/26/2018] [Indexed: 12/16/2022]  Open
62
Chen PF, Wang F, Nie JY, Feng JR, Liu J, Zhou R, Wang HL, Zhao Q. Co-expression network analysis identified CDH11 in association with progression and prognosis in gastric cancer. Onco Targets Ther 2018;11:6425-6436. [PMID: 30323620 PMCID: PMC6174304 DOI: 10.2147/ott.s176511] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]  Open
63
Oakley RH, Campen MJ, Paffett ML, Chen X, Wang Z, Parry TL, Hillhouse C, Cidlowski JA, Willis MS. Muscle-specific regulation of right ventricular transcriptional responses to chronic hypoxia-induced hypertrophy by the muscle ring finger-1 (MuRF1) ubiquitin ligase in mice. BMC MEDICAL GENETICS 2018;19:175. [PMID: 30241514 PMCID: PMC6150973 DOI: 10.1186/s12881-018-0670-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/19/2018] [Accepted: 08/21/2018] [Indexed: 01/05/2023]
64
Yang J, Zhang S, Zhang J, Dong J, Wu J, Zhang L, Guo P, Tang S, Zhao Z, Wang H, Zhao Y, Zhang W, Wu F. Identification of key genes and pathways using bioinformatics analysis in septic shock children. Infect Drug Resist 2018;11:1163-1174. [PMID: 30147344 PMCID: PMC6098424 DOI: 10.2147/idr.s157269] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]  Open
65
Cyclic Enterobacterial Common Antigen Maintains the Outer Membrane Permeability Barrier of Escherichia coli in a Manner Controlled by YhdP. mBio 2018;9:mBio.01321-18. [PMID: 30087168 PMCID: PMC6083912 DOI: 10.1128/mbio.01321-18] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]  Open
66
Zhou T, Wang Y, Qian D, Liang Q, Wang B. Over-expression of TOP2A as a prognostic biomarker in patients with glioma. INTERNATIONAL JOURNAL OF CLINICAL AND EXPERIMENTAL PATHOLOGY 2018;11:1228-1237. [PMID: 31938217 PMCID: PMC6958105] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 12/07/2017] [Accepted: 01/19/2018] [Indexed: 06/10/2023]
67
Chen X, Yang JR, Guan NN, Li JQ. GRMDA: Graph Regression for MiRNA-Disease Association Prediction. Front Physiol 2018. [PMID: 29515453 PMCID: PMC5826195 DOI: 10.3389/fphys.2018.00092] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]  Open
68
Yuan L, Chen L, Qian K, Wang G, Lu M, Qian G, Cao X, Jiang W, Xiao Y, Wang X. A novel correlation between ATP5A1 gene expression and progression of human clear cell renal cell carcinoma identified by co‑expression analysis. Oncol Rep 2018;39:525-536. [PMID: 29207195 PMCID: PMC5783621 DOI: 10.3892/or.2017.6132] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2017] [Accepted: 11/30/2017] [Indexed: 01/12/2023]  Open
69
Raynal JT, Bastos BL, Vilas-Boas PCB, Sousa TDJ, Costa-Silva M, de Sá MDCA, Portela RW, Moura-Costa LF, Azevedo V, Meyer R. Identification of membrane-associated proteins with pathogenic potential expressed by Corynebacterium pseudotuberculosis grown in animal serum. BMC Res Notes 2018;11:73. [PMID: 29368627 PMCID: PMC5784612 DOI: 10.1186/s13104-018-3180-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2017] [Accepted: 01/16/2018] [Indexed: 11/10/2022]  Open
70
Wang Y, Huang A, Gan L, Bao Y, Zhu W, Hu Y, Ma L, Wei S, Lan Y. Screening of Potential Genes and Transcription Factors of Postoperative Cognitive Dysfunction via Bioinformatics Methods. Med Sci Monit 2018;24:503-510. [PMID: 29374768 PMCID: PMC5791419 DOI: 10.12659/msm.907445] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]  Open
71
Crosara KTB, Moffa EB, Xiao Y, Siqueira WL. Merging in - silico and in vitro salivary protein complex partners using the STRING database: A tutorial. J Proteomics 2018;171:87-94. [DOI: 10.1016/j.jprot.2017.08.002] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2017] [Revised: 07/28/2017] [Accepted: 08/01/2017] [Indexed: 12/20/2022]
72
Chen L, Yuan L, Wang Y, Wang G, Zhu Y, Cao R, Qian G, Xie C, Liu X, Xiao Y, Wang X. Co-expression network analysis identified FCER1G in association with progression and prognosis in human clear cell renal cell carcinoma. Int J Biol Sci 2017;13:1361-1372. [PMID: 29209141 PMCID: PMC5715520 DOI: 10.7150/ijbs.21657] [Citation(s) in RCA: 92] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2017] [Accepted: 09/04/2017] [Indexed: 12/12/2022]  Open
73
Wang X, Zheng Y, Gan L, Wang X, Sang X, Kong X, Zhao J. Liver segmentation from CT images using a sparse priori statistical shape model (SP-SSM). PLoS One 2017;12:e0185249. [PMID: 28981530 PMCID: PMC5628825 DOI: 10.1371/journal.pone.0185249] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2016] [Accepted: 09/09/2017] [Indexed: 11/19/2022]  Open
74
Zhou Z, Liu S, Zhang M, Zhou R, Liu J, Chang Y, Zhao Q. Overexpression of Topoisomerase 2-Alpha Confers a Poor Prognosis in Pancreatic Adenocarcinoma Identified by Co-Expression Analysis. Dig Dis Sci 2017;62:2790-2800. [PMID: 28815403 DOI: 10.1007/s10620-017-4718-4] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/21/2017] [Accepted: 08/08/2017] [Indexed: 01/16/2023]
75
Chen B, Li F, Chen S, Hu R, Chen L. Link prediction based on non-negative matrix factorization. PLoS One 2017;12:e0182968. [PMID: 28854195 PMCID: PMC5576740 DOI: 10.1371/journal.pone.0182968] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2017] [Accepted: 07/27/2017] [Indexed: 02/02/2023]  Open
76
Niu Y, Liu C, Moghimyfiroozabad S, Yang Y, Alavian KN. PrePhyloPro: phylogenetic profile-based prediction of whole proteome linkages. PeerJ 2017;5:e3712. [PMID: 28875072 PMCID: PMC5578374 DOI: 10.7717/peerj.3712] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2017] [Accepted: 07/28/2017] [Indexed: 02/05/2023]  Open
77
An index-based algorithm for fast on-line query processing of latent semantic analysis. PLoS One 2017;12:e0177523. [PMID: 28520747 PMCID: PMC5433746 DOI: 10.1371/journal.pone.0177523] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2016] [Accepted: 04/29/2017] [Indexed: 11/23/2022]  Open
78
Wittouck S, van Noort V. Correlated duplications and losses in the evolution of palmitoylation writer and eraser families. BMC Evol Biol 2017;17:83. [PMID: 28320309 PMCID: PMC5359973 DOI: 10.1186/s12862-017-0932-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2016] [Accepted: 03/09/2017] [Indexed: 12/27/2022]  Open
79
Szklarczyk D, Morris JH, Cook H, Kuhn M, Wyder S, Simonovic M, Santos A, Doncheva NT, Roth A, Bork P, Jensen LJ, von Mering C. The STRING database in 2017: quality-controlled protein-protein association networks, made broadly accessible. Nucleic Acids Res 2016;45:D362-D368. [PMID: 27924014 PMCID: PMC5210637 DOI: 10.1093/nar/gkw937] [Citation(s) in RCA: 5031] [Impact Index Per Article: 559.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2016] [Accepted: 10/06/2016] [Indexed: 02/06/2023]  Open
80
Valentini G, Armano G, Frasca M, Lin J, Mesiti M, Re M. RANKS: a flexible tool for node label ranking and classification in biological networks. Bioinformatics 2016;32:2872-4. [PMID: 27256314 DOI: 10.1093/bioinformatics/btw235] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2016] [Accepted: 04/22/2016] [Indexed: 11/12/2022]  Open
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