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For: El-Athman R, Knezevic D, Fuhr L, Relógio A. A Computational Analysis of Alternative Splicing across Mammalian Tissues Reveals Circadian and Ultradian Rhythms in Splicing Events. Int J Mol Sci 2019;20:E3977. [PMID: 31443305 PMCID: PMC6721216 DOI: 10.3390/ijms20163977] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Revised: 08/03/2019] [Accepted: 08/10/2019] [Indexed: 02/07/2023]  Open
Number Cited by Other Article(s)
1
Bowazolo C, Morse D. Ribosome profiling in the Symbiodiniacean dinoflagellate Fugacium kawagutii shows coordinated protein synthesis of enzymes in different pathways at different times of day. Mol Microbiol 2023;120:462-471. [PMID: 37545098 DOI: 10.1111/mmi.15137] [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: 04/25/2023] [Revised: 07/19/2023] [Accepted: 07/21/2023] [Indexed: 08/08/2023]
2
Larriba Y, Mason IC, Saxena R, Scheer FAJL, Rueda C. CIRCUST: A novel methodology for temporal order reconstruction of molecular rhythms; validation and application towards a daily rhythm gene expression atlas in humans. PLoS Comput Biol 2023;19:e1011510. [PMID: 37769026 PMCID: PMC10564179 DOI: 10.1371/journal.pcbi.1011510] [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: 02/12/2023] [Revised: 10/10/2023] [Accepted: 09/12/2023] [Indexed: 09/30/2023]  Open
3
Khan AH, Bagley JR, LaPierre N, Gonzalez-Figueroa C, Spencer TC, Choudhury M, Xiao X, Eskin E, Jentsch JD, Smith DJ. Genetic pathways regulating the longitudinal acquisition of cocaine self-administration in a panel of inbred and recombinant inbred mice. Cell Rep 2023;42:112856. [PMID: 37481717 PMCID: PMC10530068 DOI: 10.1016/j.celrep.2023.112856] [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: 11/16/2022] [Revised: 06/06/2023] [Accepted: 07/10/2023] [Indexed: 07/25/2023]  Open
4
Hesse J, Müller T, Relógio A. An integrative mathematical model for timing treatment toxicity and Zeitgeber impact in colorectal cancer cells. NPJ Syst Biol Appl 2023;9:27. [PMID: 37353516 DOI: 10.1038/s41540-023-00287-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Accepted: 06/05/2023] [Indexed: 06/25/2023]  Open
5
Zhu B, Liu S. Preservation of ∼12-h ultradian rhythms of gene expression of mRNA and protein metabolism in the absence of canonical circadian clock. Front Physiol 2023;14:1195001. [PMID: 37324401 PMCID: PMC10267751 DOI: 10.3389/fphys.2023.1195001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Accepted: 05/19/2023] [Indexed: 06/17/2023]  Open
6
Zhu B, Liu S. Preservation of ∼12-hour ultradian rhythms of gene expression of mRNA and protein metabolism in the absence of canonical circadian clock. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.01.538977. [PMID: 37205336 PMCID: PMC10187213 DOI: 10.1101/2023.05.01.538977] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
7
Ludwig M, Basti A, Yalçin M, Schulte JH, Relógio A. Molecular characterization of the circadian clock in paediatric leukaemia patients: a prospective study protocol. BMC Pediatr 2023;23:105. [PMID: 36870963 PMCID: PMC9985245 DOI: 10.1186/s12887-023-03921-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Accepted: 02/17/2023] [Indexed: 03/06/2023]  Open
8
Asher G, Zhu B. Beyond circadian rhythms: emerging roles of ultradian rhythms in control of liver functions. Hepatology 2023;77:1022-1035. [PMID: 35591797 PMCID: PMC9674798 DOI: 10.1002/hep.32580] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Revised: 04/26/2022] [Accepted: 04/28/2022] [Indexed: 12/08/2022]
9
Comprehensive analysis of the circadian nuclear and cytoplasmic transcriptome in mouse liver. PLoS Genet 2022;18:e1009903. [PMID: 35921362 PMCID: PMC9377612 DOI: 10.1371/journal.pgen.1009903] [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: 10/22/2021] [Revised: 08/15/2022] [Accepted: 07/06/2022] [Indexed: 11/19/2022]  Open
10
Malhan D, Basti A, Relógio A. Transcriptome analysis of clock disrupted cancer cells reveals differential alternative splicing of cancer hallmarks genes. NPJ Syst Biol Appl 2022;8:17. [PMID: 35552415 PMCID: PMC9098426 DOI: 10.1038/s41540-022-00225-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Accepted: 04/04/2022] [Indexed: 12/13/2022]  Open
11
Yalçin M, Mundorf A, Thiel F, Amatriain-Fernández S, Kalthoff IS, Beucke JC, Budde H, Garthus-Niegel S, Peterburs J, Relógio A. It's About Time: The Circadian Network as Time-Keeper for Cognitive Functioning, Locomotor Activity and Mental Health. Front Physiol 2022;13:873237. [PMID: 35547585 PMCID: PMC9081535 DOI: 10.3389/fphys.2022.873237] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Accepted: 03/08/2022] [Indexed: 12/24/2022]  Open
12
Möller-Levet CS, Laing EE, Archer SN, Dijk DJ. Diurnal and circadian rhythmicity of the human blood transcriptome overlaps with organ- and tissue-specific expression of a non-human primate. BMC Biol 2022;20:63. [PMID: 35264172 PMCID: PMC8905855 DOI: 10.1186/s12915-022-01258-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Accepted: 02/18/2022] [Indexed: 12/14/2022]  Open
13
Yalçin M, Malhan D, Basti A, Peralta AR, Ferreira JJ, Relógio A. A Computational Analysis in a Cohort of Parkinson's Disease Patients and Clock-Modified Colorectal Cancer Cells Reveals Common Expression Alterations in Clock-Regulated Genes. Cancers (Basel) 2021;13:cancers13235978. [PMID: 34885088 PMCID: PMC8657387 DOI: 10.3390/cancers13235978] [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: 08/31/2021] [Revised: 11/18/2021] [Accepted: 11/21/2021] [Indexed: 12/13/2022]  Open
14
Hesse J, Martinelli J, Aboumanify O, Ballesta A, Relógio A. A mathematical model of the circadian clock and drug pharmacology to optimize irinotecan administration timing in colorectal cancer. Comput Struct Biotechnol J 2021;19:5170-5183. [PMID: 34630937 PMCID: PMC8477139 DOI: 10.1016/j.csbj.2021.08.051] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2021] [Revised: 08/30/2021] [Accepted: 08/30/2021] [Indexed: 12/21/2022]  Open
15
Revealing the hidden reality of the mammalian 12-h ultradian rhythms. Cell Mol Life Sci 2021;78:3127-3140. [PMID: 33449146 DOI: 10.1007/s00018-020-03730-5] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Revised: 11/18/2020] [Accepted: 12/04/2020] [Indexed: 12/29/2022]
16
Xu W, Jain MK, Zhang L. Molecular link between circadian clocks and cardiac function: a network of core clock, slave clock, and effectors. Curr Opin Pharmacol 2020;57:28-40. [PMID: 33189913 DOI: 10.1016/j.coph.2020.10.006] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Revised: 09/27/2020] [Accepted: 10/06/2020] [Indexed: 02/08/2023]
17
Pelham JF, Dunlap JC, Hurley JM. Intrinsic disorder is an essential characteristic of components in the conserved circadian circuit. Cell Commun Signal 2020;18:181. [PMID: 33176800 PMCID: PMC7656774 DOI: 10.1186/s12964-020-00658-y] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Accepted: 09/06/2020] [Indexed: 12/12/2022]  Open
18
Hesse J, Malhan D, Yalҫin M, Aboumanify O, Basti A, Relógio A. An Optimal Time for Treatment-Predicting Circadian Time by Machine Learning and Mathematical Modelling. Cancers (Basel) 2020;12:cancers12113103. [PMID: 33114254 PMCID: PMC7690897 DOI: 10.3390/cancers12113103] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Revised: 10/15/2020] [Accepted: 10/20/2020] [Indexed: 02/07/2023]  Open
19
Režen T, Zmrzljak UP, Bensa T, Tomaš TC, Cirnski K, Stojan J, Rozman D. Novel insights into biological roles of inducible cAMP early repressor ICER. Biochem Biophys Res Commun 2020;530:396-401. [PMID: 32534736 DOI: 10.1016/j.bbrc.2020.05.017] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Accepted: 05/03/2020] [Indexed: 11/16/2022]
20
Huang R, Liu X, Li H, Ning H, Zhou PK. PRKCSH Alternative Splicing Involves in Silica-Induced Expression of Epithelial-Mesenchymal Transition Markers and Cell Proliferation. Dose Response 2020;18:1559325820923825. [PMID: 32425726 PMCID: PMC7218327 DOI: 10.1177/1559325820923825] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2020] [Revised: 03/10/2020] [Accepted: 04/09/2020] [Indexed: 12/13/2022]  Open
21
Thalhammer A, Jaudon F, Cingolani LA. Emerging Roles of Activity-Dependent Alternative Splicing in Homeostatic Plasticity. Front Cell Neurosci 2020;14:104. [PMID: 32477067 PMCID: PMC7235277 DOI: 10.3389/fncel.2020.00104] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2020] [Accepted: 04/06/2020] [Indexed: 12/25/2022]  Open
22
Analysis of the Circadian Regulation of Cancer Hallmarks by a Cross-Platform Study of Colorectal Cancer Time-Series Data Reveals an Association with Genes Involved in Huntington's Disease. Cancers (Basel) 2020;12:cancers12040963. [PMID: 32295075 PMCID: PMC7226183 DOI: 10.3390/cancers12040963] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Revised: 04/07/2020] [Accepted: 04/10/2020] [Indexed: 02/06/2023]  Open
23
Tatullo M, Codispoti B, Spagnuolo G, Zavan B. Human Periapical Cyst-Derived Stem Cells Can Be A Smart "Lab-on-A-Cell" to Investigate Neurodegenerative Diseases and the Related Alteration of the Exosomes' Content. Brain Sci 2019;9:E358. [PMID: 31817546 PMCID: PMC6955839 DOI: 10.3390/brainsci9120358] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2019] [Revised: 12/04/2019] [Accepted: 12/04/2019] [Indexed: 12/14/2022]  Open
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