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For: Le TD, Zhang J, Liu L, Liu H, Li J. miRLAB: An R Based Dry Lab for Exploring miRNA-mRNA Regulatory Relationships. PLoS One 2015;10:e0145386. [PMID: 26716983 PMCID: PMC4696828 DOI: 10.1371/journal.pone.0145386] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2015] [Accepted: 12/03/2015] [Indexed: 11/19/2022]  Open
Number Cited by Other Article(s)
1
Anuarbekov A, Kléma J. Utilizing RNA-seq data in monotone iterative generalized linear model to elevate prior knowledge quality of the circRNA-miRNA-mRNA regulatory axis. BMC Bioinformatics 2025;26:139. [PMID: 40426030 DOI: 10.1186/s12859-025-06161-w] [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: 02/25/2025] [Accepted: 05/07/2025] [Indexed: 05/29/2025]  Open
2
Zhang J, Liu L, Wei X, Zhao C, Luo Y, Li J, Le TD. Scanning sample-specific miRNA regulation from bulk and single-cell RNA-sequencing data. BMC Biol 2024;22:218. [PMID: 39334271 PMCID: PMC11438147 DOI: 10.1186/s12915-024-02020-x] [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: 01/15/2024] [Accepted: 09/24/2024] [Indexed: 09/30/2024]  Open
3
Evidence that Transcriptional Alterations in Sarcoptes scabiei Are under Tight Post-Transcriptional (microRNA) Control. Int J Mol Sci 2022;23:ijms23179719. [PMID: 36077116 PMCID: PMC9456212 DOI: 10.3390/ijms23179719] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Revised: 08/19/2022] [Accepted: 08/23/2022] [Indexed: 11/16/2022]  Open
4
Li Q, Chen W, Mao X. Characterization of microRNA and gene expression in the cochlea of an echolocating bat (Rhinolophus affinis). Ecol Evol 2022;12:e9025. [PMID: 35784079 PMCID: PMC9217883 DOI: 10.1002/ece3.9025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Revised: 05/15/2022] [Accepted: 05/26/2022] [Indexed: 11/25/2022]  Open
5
Analysing miRNA-Target Gene Networks in Inflammatory Bowel Disease and Other Complex Diseases Using Transcriptomic Data. Genes (Basel) 2022;13:genes13020370. [PMID: 35205414 PMCID: PMC8872053 DOI: 10.3390/genes13020370] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Revised: 02/11/2022] [Accepted: 02/14/2022] [Indexed: 02/01/2023]  Open
6
Wani N, Barh D, Raza K. Modular network inference between miRNA-mRNA expression profiles using weighted co-expression network analysis. J Integr Bioinform 2021;18:20210029. [PMID: 34800012 PMCID: PMC8709739 DOI: 10.1515/jib-2021-0029] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 10/20/2021] [Accepted: 10/28/2021] [Indexed: 12/14/2022]  Open
7
Cifuentes-Bernal AM, Pham VV, Li X, Liu L, Li J, Le TD. A pseudotemporal causality approach to identifying miRNA-mRNA interactions during biological processes. Bioinformatics 2021;37:807-814. [PMID: 33070184 DOI: 10.1093/bioinformatics/btaa899] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Revised: 09/02/2020] [Accepted: 10/06/2020] [Indexed: 12/19/2022]  Open
8
Xiong C, Sun S, Jiang W, Ma L, Zhang J. ASDmiR: A Stepwise Method to Uncover miRNA Regulation Related to Autism Spectrum Disorder. Front Genet 2020;11:562971. [PMID: 33173536 PMCID: PMC7591752 DOI: 10.3389/fgene.2020.562971] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2020] [Accepted: 08/31/2020] [Indexed: 12/14/2022]  Open
9
Hearn J, Clark J, Wilson PJ, Little TJ. Daphnia magna modifies its gene expression extensively in response to caloric restriction revealing a novel effect on haemoglobin isoform preference. Mol Ecol 2020;29:3261-3276. [PMID: 32687619 DOI: 10.1111/mec.15557] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Revised: 07/03/2020] [Accepted: 07/13/2020] [Indexed: 12/16/2022]
10
Wang P, Li Q, Sun N, Gao Y, Liu JS, Deng K, He J. MiRACLe: an individual-specific approach to improve microRNA-target prediction based on a random contact model. Brief Bioinform 2020;22:5868068. [PMID: 34020537 DOI: 10.1093/bib/bbaa117] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2020] [Revised: 04/30/2020] [Accepted: 05/16/2020] [Indexed: 12/13/2022]  Open
11
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
12
Yoon S, Nguyen HCT, Jo W, Kim J, Chi SM, Park J, Kim SY, Nam D. Biclustering analysis of transcriptome big data identifies condition-specific microRNA targets. Nucleic Acids Res 2019;47:e53. [PMID: 30820547 PMCID: PMC6511842 DOI: 10.1093/nar/gkz139] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2018] [Accepted: 02/19/2019] [Indexed: 12/26/2022]  Open
13
Borgmästars E, de Weerd HA, Lubovac-Pilav Z, Sund M. miRFA: an automated pipeline for microRNA functional analysis with correlation support from TCGA and TCPA expression data in pancreatic cancer. BMC Bioinformatics 2019;20:393. [PMID: 31311505 PMCID: PMC6636046 DOI: 10.1186/s12859-019-2974-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2018] [Accepted: 06/28/2019] [Indexed: 12/14/2022]  Open
14
Pham VV, Zhang J, Liu L, Truong B, Xu T, Nguyen TT, Li J, Le TD. Identifying miRNA-mRNA regulatory relationships in breast cancer with invariant causal prediction. BMC Bioinformatics 2019;20:143. [PMID: 30876399 PMCID: PMC6419852 DOI: 10.1186/s12859-019-2668-x] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Accepted: 02/05/2019] [Indexed: 12/14/2022]  Open
15
Xu T, Su N, Liu L, Zhang J, Wang H, Zhang W, Gui J, Yu K, Li J, Le TD. miRBaseConverter: an R/Bioconductor package for converting and retrieving miRNA name, accession, sequence and family information in different versions of miRBase. BMC Bioinformatics 2018;19:514. [PMID: 30598108 PMCID: PMC6311916 DOI: 10.1186/s12859-018-2531-5] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]  Open
16
Graham AM, Barreto FS. Novel microRNAs are associated with population divergence in transcriptional response to thermal stress in an intertidal copepod. Mol Ecol 2018;28:584-599. [PMID: 30548575 DOI: 10.1111/mec.14973] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2018] [Revised: 11/09/2018] [Accepted: 11/13/2018] [Indexed: 12/29/2022]
17
Ma G, Wang T, Korhonen PK, Ang CS, Williamson NA, Young ND, Stroehlein AJ, Hall RS, Koehler AV, Hofmann A, Gasser RB. Molecular alterations during larval development of Haemonchus contortus in vitro are under tight post-transcriptional control. Int J Parasitol 2018;48:763-772. [PMID: 29792880 DOI: 10.1016/j.ijpara.2018.03.008] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Revised: 03/20/2018] [Accepted: 03/26/2018] [Indexed: 12/23/2022]
18
Drago-García D, Espinal-Enríquez J, Hernández-Lemus E. Network analysis of EMT and MET micro-RNA regulation in breast cancer. Sci Rep 2017;7:13534. [PMID: 29051564 PMCID: PMC5648819 DOI: 10.1038/s41598-017-13903-1] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2016] [Accepted: 09/27/2017] [Indexed: 12/13/2022]  Open
19
Wang L, Michoel T. Efficient and accurate causal inference with hidden confounders from genome-transcriptome variation data. PLoS Comput Biol 2017;13:e1005703. [PMID: 28821014 PMCID: PMC5576763 DOI: 10.1371/journal.pcbi.1005703] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2017] [Revised: 08/30/2017] [Accepted: 07/26/2017] [Indexed: 02/07/2023]  Open
20
Paces J, Nic M, Novotny T, Svoboda P. Literature review of baseline information to support the risk assessment of RNAi‐based GM plants. ACTA ACUST UNITED AC 2017. [PMCID: PMC7163844 DOI: 10.2903/sp.efsa.2017.en-1246] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
21
Russo F, Belling K, Jensen AB, Scoyni F, Brunak S, Pellegrini M. MicroRNAs, Regulatory Networks, and Comorbidities: Decoding Complex Systems. Methods Mol Biol 2017;1580:281-295. [PMID: 28439840 DOI: 10.1007/978-1-4939-6866-4_19] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/05/2023]
22
Lee M, Lee H. DMirNet: Inferring direct microRNA-mRNA association networks. BMC SYSTEMS BIOLOGY 2016;10:125. [PMID: 28105958 PMCID: PMC5249041 DOI: 10.1186/s12918-016-0373-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
23
Walsh CJ, Hu P, Batt J, Dos Santos CC. Discovering MicroRNA-Regulatory Modules in Multi-Dimensional Cancer Genomic Data: A Survey of Computational Methods. Cancer Inform 2016;15:25-42. [PMID: 27721651 PMCID: PMC5051584 DOI: 10.4137/cin.s39369] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2016] [Revised: 08/14/2016] [Accepted: 08/16/2016] [Indexed: 12/20/2022]  Open
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