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For: Zhang N, Huang T, Cai YD. Discriminating between deleterious and neutral non-frameshifting indels based on protein interaction networks and hybrid properties. Mol Genet Genomics 2014;290:343-52. [PMID: 25248637 DOI: 10.1007/s00438-014-0922-5] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2014] [Accepted: 09/12/2014] [Indexed: 02/06/2023]
Number Cited by Other Article(s)
1
Yang Z, Wu Y, Liu H, He L, Deng X. AMYGNN: A Graph Convolutional Neural Network-Based Approach for Predicting Amyloid Formation from Polypeptides. J Chem Inf Model 2024;64:1751-1762. [PMID: 38408296 DOI: 10.1021/acs.jcim.3c02035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/28/2024]
2
Fan X, Pan H, Tian A, Chung WK, Shen Y. SHINE: protein language model-based pathogenicity prediction for short inframe insertion and deletion variants. Brief Bioinform 2023;24:bbac584. [PMID: 36575831 PMCID: PMC9851320 DOI: 10.1093/bib/bbac584] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Revised: 11/04/2022] [Accepted: 11/29/2022] [Indexed: 12/29/2022]  Open
3
Jan A, Hayat M, Wedyan M, Alturki R, Gazzawe F, Ali H, Alarfaj FK. Target-AMP: Computational prediction of antimicrobial peptides by coupling sequential information with evolutionary profile. Comput Biol Med 2022;151:106311. [PMID: 36410097 DOI: 10.1016/j.compbiomed.2022.106311] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Revised: 11/02/2022] [Accepted: 11/13/2022] [Indexed: 11/18/2022]
4
Xia Q, Shu Z, Ye T, Zhang M. Identification and Analysis of the Blood lncRNA Signature for Liver Cirrhosis and Hepatocellular Carcinoma. Front Genet 2020;11:595699. [PMID: 33365048 PMCID: PMC7750531 DOI: 10.3389/fgene.2020.595699] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Accepted: 10/13/2020] [Indexed: 12/12/2022]  Open
5
Wu Z, Shou L, Wang J, Huang T, Xu X. The Methylation Pattern for Knee and Hip Osteoarthritis. Front Cell Dev Biol 2020;8:602024. [PMID: 33240895 PMCID: PMC7677303 DOI: 10.3389/fcell.2020.602024] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Accepted: 10/22/2020] [Indexed: 01/08/2023]  Open
6
Cheng Q, Li J, Fan F, Cao H, Dai ZY, Wang ZY, Feng SS. Identification and Analysis of Glioblastoma Biomarkers Based on Single Cell Sequencing. Front Bioeng Biotechnol 2020;8:167. [PMID: 32195242 PMCID: PMC7066068 DOI: 10.3389/fbioe.2020.00167] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Accepted: 02/19/2020] [Indexed: 12/16/2022]  Open
7
Yao Y, Gu Y, Yang M, Cao D, Wu F. The Gene Expression Biomarkers for Chronic Obstructive Pulmonary Disease and Interstitial Lung Disease. Front Genet 2019;10:1154. [PMID: 31824564 PMCID: PMC6879656 DOI: 10.3389/fgene.2019.01154] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Accepted: 10/22/2019] [Indexed: 01/01/2023]  Open
8
Chen L, Li D, Shao Y, Wang H, Liu Y, Zhang Y. Identifying Microbiota Signature and Functional Rules Associated With Bacterial Subtypes in Human Intestine. Front Genet 2019;10:1146. [PMID: 31803234 PMCID: PMC6872643 DOI: 10.3389/fgene.2019.01146] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2019] [Accepted: 10/21/2019] [Indexed: 12/12/2022]  Open
9
Zhang GL, Pan LL, Huang T, Wang JH. The transcriptome difference between colorectal tumor and normal tissues revealed by single-cell sequencing. J Cancer 2019;10:5883-5890. [PMID: 31737124 PMCID: PMC6843882 DOI: 10.7150/jca.32267] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2018] [Accepted: 06/17/2019] [Indexed: 12/29/2022]  Open
10
Pagel KA, Antaki D, Lian A, Mort M, Cooper DN, Sebat J, Iakoucheva LM, Mooney SD, Radivojac P. Pathogenicity and functional impact of non-frameshifting insertion/deletion variation in the human genome. PLoS Comput Biol 2019;15:e1007112. [PMID: 31199787 PMCID: PMC6594643 DOI: 10.1371/journal.pcbi.1007112] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2018] [Revised: 06/26/2019] [Accepted: 05/17/2019] [Indexed: 11/19/2022]  Open
11
Deng M, Lv XD, Fang ZX, Xie XS, Chen WY. The blood transcriptional signature for active and latent tuberculosis. Infect Drug Resist 2019;12:321-328. [PMID: 30787624 PMCID: PMC6363485 DOI: 10.2147/idr.s184640] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]  Open
12
Sheng M, Dong Z, Xie Y. Identification of tumor-educated platelet biomarkers of non-small-cell lung cancer. Onco Targets Ther 2018;11:8143-8151. [PMID: 30532555 PMCID: PMC6241732 DOI: 10.2147/ott.s177384] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]  Open
13
The early detection of asthma based on blood gene expression. Mol Biol Rep 2018;46:217-223. [PMID: 30421126 DOI: 10.1007/s11033-018-4463-6] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2018] [Accepted: 11/01/2018] [Indexed: 01/10/2023]
14
Lin H, Qiu X, Zhang B, Zhang J. Identification of the predictive genes for the response of colorectal cancer patients to FOLFOX therapy. Onco Targets Ther 2018;11:5943-5955. [PMID: 30271178 PMCID: PMC6149834 DOI: 10.2147/ott.s167656] [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] [Indexed: 12/11/2022]  Open
15
Pan X, Hu X, Zhang YH, Chen L, Zhu L, Wan S, Huang T, Cai YD. Identification of the copy number variant biomarkers for breast cancer subtypes. Mol Genet Genomics 2018;294:95-110. [PMID: 30203254 DOI: 10.1007/s00438-018-1488-4] [Citation(s) in RCA: 55] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2018] [Accepted: 09/03/2018] [Indexed: 01/07/2023]
16
Li J, Lan CN, Kong Y, Feng SS, Huang T. Identification and Analysis of Blood Gene Expression Signature for Osteoarthritis With Advanced Feature Selection Methods. Front Genet 2018;9:246. [PMID: 30214455 PMCID: PMC6125376 DOI: 10.3389/fgene.2018.00246] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2018] [Accepted: 06/22/2018] [Indexed: 12/15/2022]  Open
17
Niu M, Li Y, Wang C, Han K. RFAmyloid: A Web Server for Predicting Amyloid Proteins. Int J Mol Sci 2018;19:ijms19072071. [PMID: 30013015 PMCID: PMC6073578 DOI: 10.3390/ijms19072071] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2018] [Revised: 07/10/2018] [Accepted: 07/12/2018] [Indexed: 12/22/2022]  Open
18
Zhang TM, Huang T, Wang RF. Cross talk of chromosome instability, CpG island methylator phenotype and mismatch repair in colorectal cancer. Oncol Lett 2018;16:1736-1746. [PMID: 30008861 PMCID: PMC6036478 DOI: 10.3892/ol.2018.8860] [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] [Received: 12/12/2017] [Accepted: 05/22/2018] [Indexed: 12/20/2022]  Open
19
Huang T, Shu Y, Cai YD. Genetic differences among ethnic groups. BMC Genomics 2015;16:1093. [PMID: 26690364 PMCID: PMC4687076 DOI: 10.1186/s12864-015-2328-0] [Citation(s) in RCA: 108] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2015] [Accepted: 12/15/2015] [Indexed: 12/12/2022]  Open
20
Computational approaches to study the effects of small genomic variations. J Mol Model 2015;21:251. [PMID: 26350246 DOI: 10.1007/s00894-015-2794-y] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2015] [Accepted: 08/23/2015] [Indexed: 10/23/2022]
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