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Number Cited by Other Article(s)
1
Chee FT, Harun S, Mohd Daud K, Sulaiman S, Nor Muhammad NA. Exploring gene regulation and biological processes in insects: Insights from omics data using gene regulatory network models. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2024;189:1-12. [PMID: 38604435 DOI: 10.1016/j.pbiomolbio.2024.04.002] [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: 11/02/2023] [Revised: 12/18/2023] [Accepted: 04/03/2024] [Indexed: 04/13/2024]
2
Noordally ZB, Hindle MM, Martin SF, Seaton DD, Simpson TI, Le Bihan T, Millar AJ. A phospho-dawn of protein modification anticipates light onset in the picoeukaryote Ostreococcus tauri. JOURNAL OF EXPERIMENTAL BOTANY 2023;74:5514-5531. [PMID: 37481465 PMCID: PMC10540734 DOI: 10.1093/jxb/erad290] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Accepted: 07/20/2023] [Indexed: 07/24/2023]
3
Guo Y, Mofrad MRK, Tepole AB. On modeling the multiscale mechanobiology of soft tissues: Challenges and progress. BIOPHYSICS REVIEWS 2022;3:031303. [PMID: 38505274 PMCID: PMC10903412 DOI: 10.1063/5.0085025] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Accepted: 07/12/2022] [Indexed: 03/21/2024]
4
Lakhova TN, Kazantsev FV, Lashin SA, Matushkin YG. The finding and researching algorithm for potentially oscillating enzymatic systems. Vavilovskii Zhurnal Genet Selektsii 2021;25:318-330. [PMID: 34901728 PMCID: PMC8627878 DOI: 10.18699/vj21.035] [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: 10/13/2020] [Revised: 03/15/2021] [Accepted: 03/18/2021] [Indexed: 11/19/2022]  Open
5
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
6
Kang X, Hajek B, Hanzawa Y. From graph topology to ODE models for gene regulatory networks. PLoS One 2020;15:e0235070. [PMID: 32603340 PMCID: PMC7326199 DOI: 10.1371/journal.pone.0235070] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2020] [Accepted: 06/08/2020] [Indexed: 11/28/2022]  Open
7
A hypergraph-based method for large-scale dynamic correlation study at the transcriptomic scale. BMC Genomics 2019;20:397. [PMID: 31117943 PMCID: PMC6530038 DOI: 10.1186/s12864-019-5787-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Accepted: 05/09/2019] [Indexed: 12/22/2022]  Open
8
Millar AJ, Urquiza U, Freeman PL, Hume A, Plotkin GD, Sorokina O, Zardilis A, Zielinski T. Practical steps to digital organism models, from laboratory model species to 'Crops in silico. JOURNAL OF EXPERIMENTAL BOTANY 2019;70:2403-2418. [PMID: 30615184 DOI: 10.1093/jxb/ery435] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/28/2018] [Accepted: 11/28/2018] [Indexed: 05/20/2023]
9
Shi M, Shen W, Chong Y, Wang HQ. Improving GRN re-construction by mining hidden regulatory signals. IET Syst Biol 2019;11:174-181. [PMID: 29125126 PMCID: PMC8687237 DOI: 10.1049/iet-syb.2017.0013] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]  Open
10
Huynh-Thu VA, Sanguinetti G. Tree-Based Learning of Regulatory Network Topologies and Dynamics with Jump3. Methods Mol Biol 2019;1883:217-233. [PMID: 30547402 DOI: 10.1007/978-1-4939-8882-2_9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
11
Herbach U, Bonnaffoux A, Espinasse T, Gandrillon O. Inferring gene regulatory networks from single-cell data: a mechanistic approach. BMC SYSTEMS BIOLOGY 2017;11:105. [PMID: 29157246 PMCID: PMC5697158 DOI: 10.1186/s12918-017-0487-0] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/12/2017] [Accepted: 11/09/2017] [Indexed: 01/13/2023]
12
Kazantsev F, Akberdin I, Lashin S, Ree N, Timonov V, Ratushny A, Khlebodarova T, Likhoshvai V. MAMMOTh: A new database for curated mathematical models of biomolecular systems. J Bioinform Comput Biol 2017;16:1740010. [PMID: 29172865 DOI: 10.1142/s0219720017400108] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
13
Liu W, Zhu W, Liao B, Chen H, Ren S, Cai L. Improving gene regulatory network structure using redundancy reduction in the MRNET algorithm. RSC Adv 2017. [DOI: 10.1039/c7ra01557g] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]  Open
14
Gene Regulatory Network Inferences Using a Maximum-Relevance and Maximum-Significance Strategy. PLoS One 2016;11:e0166115. [PMID: 27829000 PMCID: PMC5102470 DOI: 10.1371/journal.pone.0166115] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2016] [Accepted: 10/24/2016] [Indexed: 12/18/2022]  Open
15
Yan Y, Qiu S, Jin Z, Gong S, Bai Y, Lu J, Yu T. Detecting subnetwork-level dynamic correlations. Bioinformatics 2016;33:256-265. [PMID: 27667792 DOI: 10.1093/bioinformatics/btw616] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2016] [Revised: 09/07/2016] [Accepted: 09/21/2016] [Indexed: 01/11/2023]  Open
16
Millar AJ. The Intracellular Dynamics of Circadian Clocks Reach for the Light of Ecology and Evolution. ANNUAL REVIEW OF PLANT BIOLOGY 2016;67:595-618. [PMID: 26653934 DOI: 10.1146/annurev-arplant-043014-115619] [Citation(s) in RCA: 93] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
17
Bayesian Computation Methods for Inferring Regulatory Network Models Using Biomedical Data. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2016;939:289-307. [DOI: 10.1007/978-981-10-1503-8_12] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
18
Ocone A, Haghverdi L, Mueller NS, Theis FJ. Reconstructing gene regulatory dynamics from high-dimensional single-cell snapshot data. Bioinformatics 2015;31:i89-96. [PMID: 26072513 PMCID: PMC4765871 DOI: 10.1093/bioinformatics/btv257] [Citation(s) in RCA: 104] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]  Open
19
Huynh-Thu VA, Sanguinetti G. Combining tree-based and dynamical systems for the inference of gene regulatory networks. Bioinformatics 2015;31:1614-22. [PMID: 25573916 PMCID: PMC4426834 DOI: 10.1093/bioinformatics/btu863] [Citation(s) in RCA: 84] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2014] [Revised: 12/05/2014] [Accepted: 12/23/2014] [Indexed: 12/21/2022]  Open
20
Noordally ZB, Millar AJ. Clocks in algae. Biochemistry 2014;54:171-83. [PMID: 25379817 DOI: 10.1021/bi501089x] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
21
Dixon LE, Hodge SK, van Ooijen G, Troein C, Akman OE, Millar AJ. Light and circadian regulation of clock components aids flexible responses to environmental signals. THE NEW PHYTOLOGIST 2014;203:568-577. [PMID: 24842166 PMCID: PMC4286021 DOI: 10.1111/nph.12853] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2013] [Accepted: 03/24/2014] [Indexed: 05/08/2023]
22
Extrapolating In Vitro Results to Predict Human Toxicity. METHODS IN PHARMACOLOGY AND TOXICOLOGY 2014. [DOI: 10.1007/978-1-4939-0521-8_24] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
23
Asif HMS, Sanguinetti G. Simultaneous inference and clustering of transcriptional dynamics in gene regulatory networks. Stat Appl Genet Mol Biol 2013;12:545-57. [PMID: 24051920 DOI: 10.1515/sagmb-2012-0010] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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