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Number Cited by Other Article(s)
1
Yang B, Li J, Li X, Liu S. Gene regulatory network inference based on novel ensemble method. Brief Funct Genomics 2024;23:866-878. [PMID: 39324652 DOI: 10.1093/bfgp/elae036] [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: 03/11/2024] [Revised: 08/09/2024] [Accepted: 09/06/2024] [Indexed: 09/27/2024]  Open
2
Dong H, Ma B, Meng Y, Wu Y, Liu Y, Zeng T, Huang J. GRNMOPT: Inference of gene regulatory networks based on a multi-objective optimization approach. Comput Biol Chem 2024;113:108223. [PMID: 39340962 DOI: 10.1016/j.compbiolchem.2024.108223] [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: 06/17/2024] [Revised: 08/21/2024] [Accepted: 09/20/2024] [Indexed: 09/30/2024]
3
Nourisa J, Passemiers A, Shakeri F, Omidi M, Helmholz H, Raimondi D, Moreau Y, Tomforde S, Schlüter H, Luthringer-Feyerabend B, Cyron CJ, Aydin RC, Willumeit-Römer R, Zeller-Plumhoff B. Gene regulatory network analysis identifies MYL1, MDH2, GLS, and TRIM28 as the principal proteins in the response of mesenchymal stem cells to Mg2+ ions. Comput Struct Biotechnol J 2024;23:1773-1785. [PMID: 38689715 PMCID: PMC11058716 DOI: 10.1016/j.csbj.2024.04.033] [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: 12/15/2023] [Revised: 04/12/2024] [Accepted: 04/12/2024] [Indexed: 05/02/2024]  Open
4
Karamveer, Uzun Y. Approaches for Benchmarking Single-Cell Gene Regulatory Network Methods. Bioinform Biol Insights 2024;18:11779322241287120. [PMID: 39502448 PMCID: PMC11536393 DOI: 10.1177/11779322241287120] [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: 05/17/2024] [Accepted: 09/10/2024] [Indexed: 11/08/2024]  Open
5
Wang Y, Zheng P, Cheng YC, Wang Z, Aravkin A. WENDY: Covariance dynamics based gene regulatory network inference. Math Biosci 2024;377:109284. [PMID: 39168402 DOI: 10.1016/j.mbs.2024.109284] [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: 03/25/2024] [Revised: 06/25/2024] [Accepted: 08/16/2024] [Indexed: 08/23/2024]
6
Emadi M, Boroujeni FZ, Pirgazi J. Improved Fuzzy Cognitive Maps for Gene Regulatory Networks Inference Based on Time Series Data. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2024;21:1816-1829. [PMID: 38963747 DOI: 10.1109/tcbb.2024.3423383] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/06/2024]
7
Wei PJ, Bao JJ, Gao Z, Tan JY, Cao RF, Su Y, Zheng CH, Deng L. MEFFGRN: Matrix enhancement and feature fusion-based method for reconstructing the gene regulatory network of epithelioma papulosum cyprini cells by spring viremia of carp virus infection. Comput Biol Med 2024;179:108835. [PMID: 38996550 DOI: 10.1016/j.compbiomed.2024.108835] [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: 03/01/2024] [Revised: 06/05/2024] [Accepted: 06/29/2024] [Indexed: 07/14/2024]
8
Peng H, Xu J, Liu K, Liu F, Zhang A, Zhang X. EIEPCF: accurate inference of functional gene regulatory networks by eliminating indirect effects from confounding factors. Brief Funct Genomics 2024;23:373-383. [PMID: 37642217 DOI: 10.1093/bfgp/elad040] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Revised: 07/07/2023] [Accepted: 08/14/2023] [Indexed: 08/31/2023]  Open
9
Wu S, Jin K, Tang M, Xia Y, Gao W. Inference of Gene Regulatory Networks Based on Multi-view Hierarchical Hypergraphs. Interdiscip Sci 2024;16:318-332. [PMID: 38342857 DOI: 10.1007/s12539-024-00604-3] [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: 08/16/2023] [Revised: 11/26/2023] [Accepted: 01/03/2024] [Indexed: 02/13/2024]
10
Chen Q, Zheng X, Shi H, Zhou Q, Hu H, Sun M, Xu Y, Zhang X. Prediction of influenza outbreaks in Fuzhou, China: comparative analysis of forecasting models. BMC Public Health 2024;24:1399. [PMID: 38796443 PMCID: PMC11127308 DOI: 10.1186/s12889-024-18583-x] [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: 11/18/2023] [Accepted: 04/12/2024] [Indexed: 05/28/2024]  Open
11
Wei PJ, Guo Z, Gao Z, Ding Z, Cao RF, Su Y, Zheng CH. Inference of gene regulatory networks based on directed graph convolutional networks. Brief Bioinform 2024;25:bbae309. [PMID: 38935070 PMCID: PMC11209731 DOI: 10.1093/bib/bbae309] [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: 12/26/2023] [Revised: 05/17/2024] [Indexed: 06/28/2024]  Open
12
Shen B, Coruzzi GM, Shasha D. Bipartite networks represent causality better than simple networks: evidence, algorithms, and applications. Front Genet 2024;15:1371607. [PMID: 38798697 PMCID: PMC11120958 DOI: 10.3389/fgene.2024.1371607] [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: 01/16/2024] [Accepted: 04/17/2024] [Indexed: 05/29/2024]  Open
13
Gan Y, Yu J, Xu G, Yan C, Zou G. Inferring gene regulatory networks from single-cell transcriptomics based on graph embedding. Bioinformatics 2024;40:btae291. [PMID: 38810116 PMCID: PMC11142726 DOI: 10.1093/bioinformatics/btae291] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Revised: 03/06/2024] [Accepted: 05/28/2024] [Indexed: 05/31/2024]  Open
14
Gao Z, Su Y, Xia J, Cao RF, Ding Y, Zheng CH, Wei PJ. DeepFGRN: inference of gene regulatory network with regulation type based on directed graph embedding. Brief Bioinform 2024;25:bbae143. [PMID: 38581416 PMCID: PMC10998536 DOI: 10.1093/bib/bbae143] [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: 01/17/2024] [Revised: 03/02/2024] [Accepted: 03/15/2024] [Indexed: 04/08/2024]  Open
15
Zheng R, Xu Z, Zeng Y, Wang E, Li M. SPIDE: A single cell potency inference method based on the local cell-specific network entropy. Methods 2023;220:90-97. [PMID: 37952704 DOI: 10.1016/j.ymeth.2023.11.006] [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: 07/01/2023] [Revised: 10/25/2023] [Accepted: 11/06/2023] [Indexed: 11/14/2023]  Open
16
Wu Y, Qian B, Wang A, Dong H, Zhu E, Ma B. iLSGRN: inference of large-scale gene regulatory networks based on multi-model fusion. Bioinformatics 2023;39:btad619. [PMID: 37851379 PMCID: PMC10589915 DOI: 10.1093/bioinformatics/btad619] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Revised: 10/04/2023] [Accepted: 10/17/2023] [Indexed: 10/19/2023]  Open
17
Zeng Y, He Y, Zheng R, Li M. Inferring single-cell gene regulatory network by non-redundant mutual information. Brief Bioinform 2023;24:bbad326. [PMID: 37715282 DOI: 10.1093/bib/bbad326] [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: 04/19/2023] [Revised: 07/12/2023] [Accepted: 08/08/2023] [Indexed: 09/17/2023]  Open
18
Gao Z, Tang J, Xia J, Zheng CH, Wei PJ. CNNGRN: A Convolutional Neural Network-Based Method for Gene Regulatory Network Inference From Bulk Time-Series Expression Data. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2023;20:2853-2861. [PMID: 37267145 DOI: 10.1109/tcbb.2023.3282212] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
19
Mbebi AJ, Nikoloski Z. Gene regulatory network inference using mixed-norms regularized multivariate model with covariance selection. PLoS Comput Biol 2023;19:e1010832. [PMID: 37523414 PMCID: PMC10414675 DOI: 10.1371/journal.pcbi.1010832] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 08/10/2023] [Accepted: 07/11/2023] [Indexed: 08/02/2023]  Open
20
Shen B, Coruzzi G, Shasha D. EnsInfer: a simple ensemble approach to network inference outperforms any single method. BMC Bioinformatics 2023;24:114. [PMID: 36964499 PMCID: PMC10037858 DOI: 10.1186/s12859-023-05231-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Accepted: 03/15/2023] [Indexed: 03/26/2023]  Open
21
Liu Q, Li J, Dong M, Liu M, Chai Y. Identification of Gene Regulatory Networks Using Variational Bayesian Inference in the Presence of Missing Data. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2023;20:399-409. [PMID: 35061589 DOI: 10.1109/tcbb.2022.3144418] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
22
Inference of gene regulatory networks based on the Light Gradient Boosting Machine. Comput Biol Chem 2022;101:107769. [DOI: 10.1016/j.compbiolchem.2022.107769] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Revised: 08/12/2022] [Accepted: 09/06/2022] [Indexed: 11/23/2022]
23
Mao G, Zeng R, Peng J, Zuo K, Pang Z, Liu J. Reconstructing gene regulatory networks of biological function using differential equations of multilayer perceptrons. BMC Bioinformatics 2022;23:503. [PMID: 36434499 PMCID: PMC9700916 DOI: 10.1186/s12859-022-05055-5] [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: 07/16/2022] [Accepted: 11/14/2022] [Indexed: 11/26/2022]  Open
24
Yang B, Bao W, Chen B. PGRNIG: novel parallel gene regulatory network identification algorithm based on GPU. Brief Funct Genomics 2022;21:441-454. [PMID: 36064791 DOI: 10.1093/bfgp/elac028] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Revised: 07/30/2022] [Accepted: 08/03/2022] [Indexed: 12/14/2022]  Open
25
Lei J, Cai Z, He X, Zheng W, Liu J. An approach of gene regulatory network construction using mixed entropy optimizing context-related likelihood mutual information. Bioinformatics 2022;39:6808612. [PMID: 36342190 PMCID: PMC9805593 DOI: 10.1093/bioinformatics/btac717] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Revised: 09/18/2022] [Accepted: 11/04/2022] [Indexed: 11/09/2022]  Open
26
Chen G, Liu ZP. Inferring causal gene regulatory network via GreyNet: From dynamic grey association to causation. Front Bioeng Biotechnol 2022;10:954610. [PMID: 36237217 PMCID: PMC9551017 DOI: 10.3389/fbioe.2022.954610] [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: 05/27/2022] [Accepted: 08/15/2022] [Indexed: 11/23/2022]  Open
27
Gan Y, Hu X, Zou G, Yan C, Xu G. Inferring Gene Regulatory Networks From Single-Cell Transcriptomic Data Using Bidirectional RNN. Front Oncol 2022;12:899825. [PMID: 35692809 PMCID: PMC9178250 DOI: 10.3389/fonc.2022.899825] [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: 03/19/2022] [Accepted: 04/22/2022] [Indexed: 11/30/2022]  Open
28
Jiang X, Zhang X. RSNET: inferring gene regulatory networks by a redundancy silencing and network enhancement technique. BMC Bioinformatics 2022;23:165. [PMID: 35524190 PMCID: PMC9074326 DOI: 10.1186/s12859-022-04696-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: 09/14/2021] [Accepted: 04/25/2022] [Indexed: 11/29/2022]  Open
29
Saremi M, Amirmazlaghani M. Reconstruction of Gene Regulatory Networks Using Multiple Datasets. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2022;19:1827-1839. [PMID: 33539303 DOI: 10.1109/tcbb.2021.3057241] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
30
Feng H, Zheng R, Wang J, Wu FX, Li M. NIMCE: A Gene Regulatory Network Inference Approach Based on Multi Time Delays Causal Entropy. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2022;19:1042-1049. [PMID: 33035155 DOI: 10.1109/tcbb.2020.3029846] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
31
Emerging Machine Learning Techniques for Modelling Cellular Complex Systems in Alzheimer's Disease. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2022;1338:199-208. [PMID: 34973026 DOI: 10.1007/978-3-030-78775-2_24] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
32
Staem5: A novel computational approachfor accurate prediction of m5C site. MOLECULAR THERAPY. NUCLEIC ACIDS 2021;26:1027-1034. [PMID: 34786208 PMCID: PMC8571400 DOI: 10.1016/j.omtn.2021.10.012] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Revised: 08/27/2021] [Accepted: 10/06/2021] [Indexed: 12/25/2022]
33
Lin CX, Li HD, Deng C, Guan Y, Wang J. TissueNexus: a database of human tissue functional gene networks built with a large compendium of curated RNA-seq data. Nucleic Acids Res 2021;50:D710-D718. [PMID: 34850130 PMCID: PMC8728275 DOI: 10.1093/nar/gkab1133] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Revised: 10/10/2021] [Accepted: 11/18/2021] [Indexed: 01/02/2023]  Open
34
Zhao Y, Fang ZY, Lin CX, Deng C, Xu YP, Li HD. RFCell: A Gene Selection Approach for scRNA-seq Clustering Based on Permutation and Random Forest. Front Genet 2021;12:665843. [PMID: 34386033 PMCID: PMC8354212 DOI: 10.3389/fgene.2021.665843] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Accepted: 04/01/2021] [Indexed: 11/13/2022]  Open
35
Gan Y, Xin Y, Hu X, Zou G. Inferring gene regulatory network from single-cell transcriptomic data by integrating multiple prior networks. Comput Biol Chem 2021;93:107512. [PMID: 34044202 DOI: 10.1016/j.compbiolchem.2021.107512] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2021] [Accepted: 05/12/2021] [Indexed: 11/29/2022]
36
He W, Tang J, Zou Q, Guo F. MMFGRN: a multi-source multi-model fusion method for gene regulatory network reconstruction. Brief Bioinform 2021;22:6261916. [PMID: 33939795 DOI: 10.1093/bib/bbab166] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Revised: 03/08/2021] [Accepted: 04/08/2021] [Indexed: 01/05/2023]  Open
37
Xu Y, Li HD, Pan Y, Luo F, Wu FX, Wang J. A Gene Rank Based Approach for Single Cell Similarity Assessment and Clustering. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2021;18:431-442. [PMID: 31369384 DOI: 10.1109/tcbb.2019.2931582] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
38
Zhang Y, Chang X, Liu X. Inference of gene regulatory networks using pseudo-time series data. Bioinformatics 2021;37:2423-2431. [PMID: 33576787 DOI: 10.1093/bioinformatics/btab099] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Revised: 01/18/2021] [Accepted: 02/10/2021] [Indexed: 11/12/2022]  Open
39
Zhao M, He W, Tang J, Zou Q, Guo F. A comprehensive overview and critical evaluation of gene regulatory network inference technologies. Brief Bioinform 2021;22:6128842. [PMID: 33539514 DOI: 10.1093/bib/bbab009] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Revised: 12/11/2020] [Accepted: 01/06/2021] [Indexed: 12/12/2022]  Open
40
Zheng R, Li M, Chen X, Zhao S, Wu FX, Pan Y, Wang J. An Ensemble Method to Reconstruct Gene Regulatory Networks Based on Multivariate Adaptive Regression Splines. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2021;18:347-354. [PMID: 30794516 DOI: 10.1109/tcbb.2019.2900614] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
41
Yu B, Chen C, Qi R, Zheng R, Skillman-Lawrence PJ, Wang X, Ma A, Gu H. scGMAI: a Gaussian mixture model for clustering single-cell RNA-Seq data based on deep autoencoder. Brief Bioinform 2020;22:6029147. [PMID: 33300547 DOI: 10.1093/bib/bbaa316] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Revised: 10/19/2020] [Indexed: 01/01/2023]  Open
42
Ma B, Fang M, Jiao X. Inference of gene regulatory networks based on nonlinear ordinary differential equations. Bioinformatics 2020;36:4885-4893. [DOI: 10.1093/bioinformatics/btaa032] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Revised: 12/30/2019] [Accepted: 01/15/2020] [Indexed: 01/05/2023]  Open
43
Riggs K, Chen HS, Rotunno M, Li B, Simonds NI, Mechanic LE, Peng B. On the application, reporting, and sharing of in silico simulations for genetic studies. Genet Epidemiol 2020;45:131-141. [PMID: 33063887 PMCID: PMC7984380 DOI: 10.1002/gepi.22362] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Revised: 09/11/2020] [Accepted: 09/14/2020] [Indexed: 12/31/2022]
44
Che D, Guo S, Jiang Q, Chen L. PFBNet: a priori-fused boosting method for gene regulatory network inference. BMC Bioinformatics 2020;21:308. [PMID: 32664870 PMCID: PMC7362553 DOI: 10.1186/s12859-020-03639-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2019] [Accepted: 07/02/2020] [Indexed: 02/08/2023]  Open
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Li F, Chen J, Ge Z, Wen Y, Yue Y, Hayashida M, Baggag A, Bensmail H, Song J. Computational prediction and interpretation of both general and specific types of promoters in Escherichia coli by exploiting a stacked ensemble-learning framework. Brief Bioinform 2020;22:2126-2140. [PMID: 32363397 DOI: 10.1093/bib/bbaa049] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Revised: 02/25/2020] [Accepted: 03/11/2020] [Indexed: 12/12/2022]  Open
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Zheng R, Liang Z, Chen X, Tian Y, Cao C, Li M. An Adaptive Sparse Subspace Clustering for Cell Type Identification. Front Genet 2020;11:407. [PMID: 32425984 PMCID: PMC7212354 DOI: 10.3389/fgene.2020.00407] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2019] [Accepted: 03/31/2020] [Indexed: 01/04/2023]  Open
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Li X, Li W, Zeng M, Zheng R, Li M. Network-based methods for predicting essential genes or proteins: a survey. Brief Bioinform 2020;21:566-583. [PMID: 30776072 DOI: 10.1093/bib/bbz017] [Citation(s) in RCA: 67] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Revised: 01/21/2019] [Accepted: 01/22/2019] [Indexed: 01/03/2025]  Open
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Xiao Q, Zhang N, Luo J, Dai J, Tang X. Adaptive multi-source multi-view latent feature learning for inferring potential disease-associated miRNAs. Brief Bioinform 2020;22:2043-2057. [PMID: 32186712 DOI: 10.1093/bib/bbaa028] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2019] [Revised: 02/16/2020] [Accepted: 01/14/2020] [Indexed: 12/13/2022]  Open
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A Stable, Unified Density Controlled Memetic Algorithm for Gene Regulatory Network Reconstruction Based on Sparse Fuzzy Cognitive Maps. Neural Process Lett 2019. [DOI: 10.1007/s11063-019-10056-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Zhang X, Li T, Wang J, Li J, Chen L, Liu C. Identification of Cancer-Related Long Non-Coding RNAs Using XGBoost With High Accuracy. Front Genet 2019;10:735. [PMID: 31456817 PMCID: PMC6701491 DOI: 10.3389/fgene.2019.00735] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2019] [Accepted: 07/12/2019] [Indexed: 11/14/2022]  Open
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