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For: Ma W, Zhang L, Zeng P, Huang C, Li J, Geng B, Yang J, Kong W, Zhou X, Cui Q. An analysis of human microbe-disease associations. Brief Bioinform 2016;18:85-97. [PMID: 26883326 DOI: 10.1093/bib/bbw005] [Citation(s) in RCA: 122] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2015] [Revised: 12/22/2015] [Indexed: 02/07/2023]  Open
Number Cited by Other Article(s)
1
Lu Y, Hui F, Zhou G, Xia J. MicrobiomeNet: exploring microbial associations and metabolic profiles for mechanistic insights. Nucleic Acids Res 2024:gkae944. [PMID: 39441071 DOI: 10.1093/nar/gkae944] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2024] [Revised: 09/30/2024] [Accepted: 10/08/2024] [Indexed: 10/25/2024]  Open
2
Yang M, Wang Z, Yan Z, Wang W, Zhu Q, Jin C. DNASimCLR: a contrastive learning-based deep learning approach for gene sequence data classification. BMC Bioinformatics 2024;25:328. [PMID: 39402441 PMCID: PMC11476100 DOI: 10.1186/s12859-024-05955-8] [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: 02/29/2024] [Accepted: 10/09/2024] [Indexed: 10/19/2024]  Open
3
Wang S, Liu JX, Li F, Wang J, Gao YL. M3HOGAT: A Multi-View Multi-Modal Multi-Scale High-Order Graph Attention Network for Microbe-Disease Association Prediction. IEEE J Biomed Health Inform 2024;28:6259-6267. [PMID: 39012741 DOI: 10.1109/jbhi.2024.3429128] [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: 07/18/2024]
4
Chen H, Chen K. Predicting disease-associated microbes based on similarity fusion and deep learning. Brief Bioinform 2024;25:bbae550. [PMID: 39504483 PMCID: PMC11540060 DOI: 10.1093/bib/bbae550] [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: 06/05/2024] [Revised: 09/15/2024] [Accepted: 10/14/2024] [Indexed: 11/08/2024]  Open
5
Shi K, Huang K, Li L, Liu Q, Zhang Y, Zheng H. Predicting microbe-disease association based on graph autoencoder and inductive matrix completion with multi-similarities fusion. Front Microbiol 2024;15:1438942. [PMID: 39355422 PMCID: PMC11443509 DOI: 10.3389/fmicb.2024.1438942] [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: 05/27/2024] [Accepted: 08/02/2024] [Indexed: 10/03/2024]  Open
6
Chen Z, Zhang L, Li J, Chen H. Microbe-disease associations prediction by graph regularized non-negative matrix factorization with L 2 , 1 $$ {L}_{2,1} $$ norm regularization terms. J Cell Mol Med 2024;28:e18553. [PMID: 39239860 PMCID: PMC11377990 DOI: 10.1111/jcmm.18553] [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: 05/15/2024] [Revised: 06/19/2024] [Accepted: 07/09/2024] [Indexed: 09/07/2024]  Open
7
Zhu H, Hao H, Yu L. Identification of microbe-disease signed associations via multi-scale variational graph autoencoder based on signed message propagation. BMC Biol 2024;22:172. [PMID: 39148051 PMCID: PMC11328394 DOI: 10.1186/s12915-024-01968-0] [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: 04/23/2024] [Accepted: 08/01/2024] [Indexed: 08/17/2024]  Open
8
Jacob T, Sindhu S, Hasan A, Malik MZ, Arefanian H, Al-Rashed F, Nizam R, Kochumon S, Thomas R, Bahman F, Shenouda S, Wilson A, Akther N, Al-Roub A, Abukhalaf N, Albeloushi S, Abu-Farha M, Al Madhoun A, Alzaid F, Thanaraj TA, Koistinen HA, Tuomilehto J, Al-Mulla F, Ahmad R. Soybean oil-based HFD induces gut dysbiosis that leads to steatosis, hepatic inflammation and insulin resistance in mice. Front Microbiol 2024;15:1407258. [PMID: 39165573 PMCID: PMC11334085 DOI: 10.3389/fmicb.2024.1407258] [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: 03/26/2024] [Accepted: 07/09/2024] [Indexed: 08/22/2024]  Open
9
Chen J, Zhu Y, Yuan Q. Predicting potential microbe-disease associations based on dual branch graph convolutional network. J Cell Mol Med 2024;28:e18571. [PMID: 39086148 PMCID: PMC11291560 DOI: 10.1111/jcmm.18571] [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: 05/15/2024] [Revised: 06/15/2024] [Accepted: 06/27/2024] [Indexed: 08/02/2024]  Open
10
Zhang C, Zhang Z, Zhang F, Zeng B, Liu X, Wang L. A computational model for potential microbe-disease association detection based on improved graph convolutional networks and multi-channel autoencoders. Front Microbiol 2024;15:1435408. [PMID: 39144226 PMCID: PMC11322764 DOI: 10.3389/fmicb.2024.1435408] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2024] [Accepted: 07/05/2024] [Indexed: 08/16/2024]  Open
11
Kochumon S, Malik MZ, Sindhu S, Arefanian H, Jacob T, Bahman F, Nizam R, Hasan A, Thomas R, Al-Rashed F, Shenouda S, Wilson A, Albeloushi S, Almansour N, Alhamar G, Al Madhoun A, Alzaid F, Thanaraj TA, Koistinen HA, Tuomilehto J, Al-Mulla F, Ahmad R. Gut Dysbiosis Shaped by Cocoa Butter-Based Sucrose-Free HFD Leads to Steatohepatitis, and Insulin Resistance in Mice. Nutrients 2024;16:1929. [PMID: 38931284 PMCID: PMC11207001 DOI: 10.3390/nu16121929] [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: 04/15/2024] [Revised: 06/05/2024] [Accepted: 06/07/2024] [Indexed: 06/28/2024]  Open
12
Chen R, Xie G, Lin Z, Gu G, Yu Y, Yu J, Liu Z. Predicting Microbe-Disease Associations Based on a Linear Neighborhood Label Propagation Method with Multi-order Similarity Fusion Learning. Interdiscip Sci 2024;16:345-360. [PMID: 38436840 DOI: 10.1007/s12539-024-00607-0] [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: 08/11/2023] [Revised: 01/04/2024] [Accepted: 01/05/2024] [Indexed: 03/05/2024]
13
Chen Z, Zhang L, Li J, Fu M. MLFLHMDA: predicting human microbe-disease association based on multi-view latent feature learning. Front Microbiol 2024;15:1353278. [PMID: 38371933 PMCID: PMC10869561 DOI: 10.3389/fmicb.2024.1353278] [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: 12/10/2023] [Accepted: 01/17/2024] [Indexed: 02/20/2024]  Open
14
Zhu H, Hao H, Yu L. Identifying disease-related microbes based on multi-scale variational graph autoencoder embedding Wasserstein distance. BMC Biol 2023;21:294. [PMID: 38115088 PMCID: PMC10731776 DOI: 10.1186/s12915-023-01796-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2023] [Accepted: 12/05/2023] [Indexed: 12/21/2023]  Open
15
Lu S, Liang Y, Li L, Miao R, Liao S, Zou Y, Yang C, Ouyang D. Predicting potential microbe-disease associations based on auto-encoder and graph convolution network. BMC Bioinformatics 2023;24:476. [PMID: 38097930 PMCID: PMC10722760 DOI: 10.1186/s12859-023-05611-7] [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: 10/25/2023] [Accepted: 12/11/2023] [Indexed: 12/17/2023]  Open
16
Santangelo B, Bada M, Hunter L, Lozupone C. Hypothesizing mechanistic links between microbes and disease using knowledge graphs. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.01.569645. [PMID: 38106100 PMCID: PMC10723325 DOI: 10.1101/2023.12.01.569645] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2023]
17
Sánchez-Valle J, Valencia A. Molecular bases of comorbidities: present and future perspectives. Trends Genet 2023;39:773-786. [PMID: 37482451 DOI: 10.1016/j.tig.2023.06.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Revised: 06/12/2023] [Accepted: 06/12/2023] [Indexed: 07/25/2023]
18
Shen Y, Gao Y, Shi J, Huang Z, Dai R, Fu Y, Zhou Y, Kong W, Cui Q. MicroRNA-disease Network Analysis Repurposes Methotrexate for the Treatment of Abdominal Aortic Aneurysm in Mice. GENOMICS, PROTEOMICS & BIOINFORMATICS 2023;21:1030-1042. [PMID: 36030000 PMCID: PMC10928436 DOI: 10.1016/j.gpb.2022.08.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Revised: 07/15/2022] [Accepted: 08/19/2022] [Indexed: 06/15/2023]
19
Hu X, Liu D, Zhang J, Fan Y, Ouyang T, Luo Y, Zhang Y, Deng L. A comprehensive review and evaluation of graph neural networks for non-coding RNA and complex disease associations. Brief Bioinform 2023;24:bbad410. [PMID: 37985451 DOI: 10.1093/bib/bbad410] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Revised: 10/07/2023] [Accepted: 10/25/2023] [Indexed: 11/22/2023]  Open
20
Peng L, Huang L, Tian G, Wu Y, Li G, Cao J, Wang P, Li Z, Duan L. Predicting potential microbe-disease associations with graph attention autoencoder, positive-unlabeled learning, and deep neural network. Front Microbiol 2023;14:1244527. [PMID: 37789848 PMCID: PMC10543759 DOI: 10.3389/fmicb.2023.1244527] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Accepted: 08/16/2023] [Indexed: 10/05/2023]  Open
21
Peng W, Liu M, Dai W, Chen T, Fu Y, Pan Y. Multi-View Feature Aggregation for Predicting Microbe-Disease Association. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2023;20:2748-2758. [PMID: 34871177 DOI: 10.1109/tcbb.2021.3132611] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
22
Li J, Wei C, Zhou T, Mo C, Wang G, He F, Wang P, Qin L, Peng F. A display and analysis platform for gut microbiomes of minority people and phenotypic data in China. Sci Rep 2023;13:14247. [PMID: 37648696 PMCID: PMC10469205 DOI: 10.1038/s41598-023-36754-5] [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: 06/08/2022] [Accepted: 06/09/2023] [Indexed: 09/01/2023]  Open
23
Wang CY, Kuang X, Wang QQ, Zhang GQ, Cheng ZS, Deng ZX, Guo FB. GMMAD: a comprehensive database of human gut microbial metabolite associations with diseases. BMC Genomics 2023;24:482. [PMID: 37620754 PMCID: PMC10464125 DOI: 10.1186/s12864-023-09599-5] [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: 02/09/2023] [Accepted: 08/17/2023] [Indexed: 08/26/2023]  Open
24
Wang L, Wang Y, Xuan C, Zhang B, Wu H, Gao J. Predicting potential microbe-disease associations based on multi-source features and deep learning. Brief Bioinform 2023;24:bbad255. [PMID: 37406190 DOI: 10.1093/bib/bbad255] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Revised: 05/30/2023] [Accepted: 06/20/2023] [Indexed: 07/07/2023]  Open
25
Karkera N, Acharya S, Palaniappan SK. Leveraging pre-trained language models for mining microbiome-disease relationships. BMC Bioinformatics 2023;24:290. [PMID: 37468830 PMCID: PMC10357883 DOI: 10.1186/s12859-023-05411-z] [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: 05/22/2023] [Accepted: 07/13/2023] [Indexed: 07/21/2023]  Open
26
Wang F, Yang H, Wu Y, Peng L, Li X. SAELGMDA: Identifying human microbe-disease associations based on sparse autoencoder and LightGBM. Front Microbiol 2023;14:1207209. [PMID: 37415823 PMCID: PMC10320730 DOI: 10.3389/fmicb.2023.1207209] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Accepted: 05/18/2023] [Indexed: 07/08/2023]  Open
27
Shen K, Din AU, Sinha B, Zhou Y, Qian F, Shen B. Translational informatics for human microbiota: data resources, models and applications. Brief Bioinform 2023;24:7152256. [PMID: 37141135 DOI: 10.1093/bib/bbad168] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2022] [Revised: 04/07/2023] [Accepted: 04/11/2023] [Indexed: 05/05/2023]  Open
28
Shokri Garjan H, Omidi Y, Poursheikhali Asghari M, Ferdousi R. In-silico computational approaches to study microbiota impacts on diseases and pharmacotherapy. Gut Pathog 2023;15:10. [PMID: 36882861 PMCID: PMC9990230 DOI: 10.1186/s13099-023-00535-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Accepted: 02/21/2023] [Indexed: 03/09/2023]  Open
29
Jiang C, Tang M, Jin S, Huang W, Liu X. KGNMDA: A Knowledge Graph Neural Network Method for Predicting Microbe-Disease Associations. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2023;20:1147-1155. [PMID: 35724280 DOI: 10.1109/tcbb.2022.3184362] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
30
Shi K, Li L, Wang Z, Chen H, Chen Z, Fang S. Identifying microbe-disease association based on graph convolutional attention network: Case study of liver cirrhosis and epilepsy. Front Neurosci 2023;16:1124315. [PMID: 36741060 PMCID: PMC9892757 DOI: 10.3389/fnins.2022.1124315] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Accepted: 12/31/2022] [Indexed: 01/20/2023]  Open
31
Liu H, Bing P, Zhang M, Tian G, Ma J, Li H, Bao M, He K, He J, He B, Yang J. MNNMDA: Predicting human microbe-disease association via a method to minimize matrix nuclear norm. Comput Struct Biotechnol J 2023;21:1414-1423. [PMID: 36824227 PMCID: PMC9941872 DOI: 10.1016/j.csbj.2022.12.053] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Revised: 12/29/2022] [Accepted: 12/30/2022] [Indexed: 01/03/2023]  Open
32
Hu W, Yang X, Wang L, Zhu X. MADGAN:A microbe-disease association prediction model based on generative adversarial networks. Front Microbiol 2023;14:1159076. [PMID: 37032881 PMCID: PMC10076708 DOI: 10.3389/fmicb.2023.1159076] [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: 02/05/2023] [Accepted: 03/02/2023] [Indexed: 04/11/2023]  Open
33
Yang X, Xu W, Leng D, Wen Y, Wu L, Li R, Huang J, Bo X, He S. Exploring novel disease-disease associations based on multi-view fusion network. Comput Struct Biotechnol J 2023;21:1807-1819. [PMID: 36923471 PMCID: PMC10009443 DOI: 10.1016/j.csbj.2023.02.038] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Revised: 02/02/2023] [Accepted: 02/22/2023] [Indexed: 03/06/2023]  Open
34
Liu JX, Yin MM, Gao YL, Shang J, Zheng CH. MSF-LRR: Multi-Similarity Information Fusion Through Low-Rank Representation to Predict Disease-Associated Microbes. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2023;20:534-543. [PMID: 35085090 DOI: 10.1109/tcbb.2022.3146176] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
35
Gong H, You X, Jin M, Meng Y, Zhang H, Yang S, Xu J. Graph neural network and multi-data heterogeneous networks for microbe-disease prediction. Front Microbiol 2022;13:1077111. [PMID: 36620040 PMCID: PMC9814480 DOI: 10.3389/fmicb.2022.1077111] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2022] [Accepted: 11/30/2022] [Indexed: 12/24/2022]  Open
36
Minadakis G, Tomazou M, Dietis N, Spyrou GM. Vir2Drug: a drug repurposing framework based on protein similarities between pathogens. Brief Bioinform 2022;24:6895455. [PMID: 36513376 PMCID: PMC9851336 DOI: 10.1093/bib/bbac536] [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: 07/19/2022] [Revised: 10/25/2022] [Accepted: 11/08/2022] [Indexed: 12/15/2022]  Open
37
Liu D, Liu J, Luo Y, He Q, Deng L. MGATMDA: Predicting Microbe-Disease Associations via Multi-Component Graph Attention Network. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2022;19:3578-3585. [PMID: 34587092 DOI: 10.1109/tcbb.2021.3116318] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
38
Hua M, Yu S, Liu T, Yang X, Wang H. MVGCNMDA: Multi-view Graph Augmentation Convolutional Network for Uncovering Disease-Related Microbes. Interdiscip Sci 2022;14:669-682. [PMID: 35428964 DOI: 10.1007/s12539-022-00514-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Revised: 03/06/2022] [Accepted: 03/13/2022] [Indexed: 06/14/2023]
39
Yang M, Huang ZA, Gu W, Han K, Pan W, Yang X, Zhu Z. Prediction of biomarker-disease associations based on graph attention network and text representation. Brief Bioinform 2022;23:6651308. [PMID: 35901464 DOI: 10.1093/bib/bbac298] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2022] [Revised: 06/28/2022] [Accepted: 06/30/2022] [Indexed: 02/06/2023]  Open
40
Wang Y, Lei X, Lu C, Pan Y. Predicting Microbe-Disease Association Based on Multiple Similarities and LINE Algorithm. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2022;19:2399-2408. [PMID: 34014827 DOI: 10.1109/tcbb.2021.3082183] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
41
Chen Y, Lei X. Metapath Aggregated Graph Neural Network and Tripartite Heterogeneous Networks for Microbe-Disease Prediction. Front Microbiol 2022;13:919380. [PMID: 35711758 PMCID: PMC9194683 DOI: 10.3389/fmicb.2022.919380] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Accepted: 04/29/2022] [Indexed: 11/25/2022]  Open
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Wang CY, Wen QF, Wang QQ, Kuang X, Dong C, Deng ZX, Guo FB. Discovery of Drug Candidates for Specific Human Disease Based on Natural Products of Gut Microbes. Front Microbiol 2022;13:896740. [PMID: 35783383 PMCID: PMC9240467 DOI: 10.3389/fmicb.2022.896740] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Accepted: 05/19/2022] [Indexed: 11/24/2022]  Open
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Yin MM, Liu JX, Gao YL, Kong XZ, Zheng CH. NCPLP: A Novel Approach for Predicting Microbe-Associated Diseases With Network Consistency Projection and Label Propagation. IEEE TRANSACTIONS ON CYBERNETICS 2022;52:5079-5087. [PMID: 33119529 DOI: 10.1109/tcyb.2020.3026652] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
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Gu W, Yang X, Yang M, Han K, Pan W, Zhu Z. MarkerGenie: an NLP-enabled text-mining system for biomedical entity relation extraction. BIOINFORMATICS ADVANCES 2022;2:vbac035. [PMID: 36699388 PMCID: PMC9710573 DOI: 10.1093/bioadv/vbac035] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Revised: 05/04/2022] [Accepted: 05/09/2022] [Indexed: 01/28/2023]
45
Toor R, Chana I. Exploring diet associations with Covid-19 and other diseases: a Network Analysis-based approach. Med Biol Eng Comput 2022;60:991-1013. [PMID: 35171411 PMCID: PMC8852958 DOI: 10.1007/s11517-022-02505-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Accepted: 01/10/2022] [Indexed: 02/07/2023]
46
Wang L, Tan Y, Yang X, Kuang L, Ping P. Review on predicting pairwise relationships between human microbes, drugs and diseases: from biological data to computational models. Brief Bioinform 2022;23:6553604. [PMID: 35325024 DOI: 10.1093/bib/bbac080] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Revised: 02/14/2022] [Accepted: 02/15/2022] [Indexed: 12/11/2022]  Open
47
Zhao Y, Chen L, Chen L, Huang J, Chen S, Yu Z. Exploration of the Potential Relationship Between Gut Microbiota Remodeling Under the Influence of High-Protein Diet and Crohn's Disease. Front Microbiol 2022;13:831176. [PMID: 35308389 PMCID: PMC8927681 DOI: 10.3389/fmicb.2022.831176] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Accepted: 01/07/2022] [Indexed: 12/20/2022]  Open
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Huang YA, Huang ZA, Li JQ, You ZH, Wang L, Yi HC, Yu CQ. GBDR: a Bayesian model for precise prediction of pathogenic microorganisms using 16S rRNA gene sequences. BMC Genomics 2022;22:916. [PMID: 35296232 PMCID: PMC8925046 DOI: 10.1186/s12864-022-08423-w] [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: 12/26/2021] [Accepted: 02/25/2022] [Indexed: 11/10/2022]  Open
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Xu D, Xu H, Zhang Y, Gao R. Novel Collaborative Weighted Non-negative Matrix Factorization Improves Prediction of Disease-Associated Human Microbes. Front Microbiol 2022;13:834982. [PMID: 35369503 PMCID: PMC8965656 DOI: 10.3389/fmicb.2022.834982] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Accepted: 01/19/2022] [Indexed: 12/14/2022]  Open
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Wang L, Li H, Wang Y, Tan Y, Chen Z, Pei T, Zou Q. MDADP: A webserver integrating database and prediction tools for microbe-disease associations. IEEE J Biomed Health Inform 2022;26:3427-3434. [PMID: 35254998 DOI: 10.1109/jbhi.2022.3156166] [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: 11/07/2022]
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