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For: Arhondakis S, Clay O, Bernardi G. GC level and expression of human coding sequences. Biochem Biophys Res Commun 2008;367:542-5. [PMID: 18177737 DOI: 10.1016/j.bbrc.2007.12.155] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2007] [Accepted: 12/21/2007] [Indexed: 11/29/2022]
Number Cited by Other Article(s)
1
qPrimerDB: A Powerful and User-Friendly Database for qPCR Primer Design. Methods Mol Biol 2021. [PMID: 34773623 DOI: 10.1007/978-1-0716-1799-1_13] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2024]
2
Blumberg A, Zhao Y, Huang YF, Dukler N, Rice EJ, Chivu AG, Krumholz K, Danko CG, Siepel A. Characterizing RNA stability genome-wide through combined analysis of PRO-seq and RNA-seq data. BMC Biol 2021;19:30. [PMID: 33588838 PMCID: PMC7885420 DOI: 10.1186/s12915-021-00949-x] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Accepted: 01/05/2021] [Indexed: 01/03/2023]  Open
3
Reshetniak S, Ußling J, Perego E, Rammner B, Schikorski T, Fornasiero EF, Truckenbrodt S, Köster S, Rizzoli SO. A comparative analysis of the mobility of 45 proteins in the synaptic bouton. EMBO J 2020;39:e104596. [PMID: 32627850 PMCID: PMC7429486 DOI: 10.15252/embj.2020104596] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Revised: 05/20/2020] [Accepted: 05/29/2020] [Indexed: 02/01/2023]  Open
4
Arhondakis S, Milanesi M, Castrignanò T, Gioiosa S, Valentini A, Chillemi G. Evidence of distinct gene functional patterns in GC-poor and GC-rich isochores in Bos taurus. Anim Genet 2020;51:358-368. [PMID: 32069522 DOI: 10.1111/age.12917] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/20/2020] [Indexed: 01/10/2023]
5
Lu K, Li T, He J, Chang W, Zhang R, Liu M, Yu M, Fan Y, Ma J, Sun W, Qu C, Liu L, Li N, Liang Y, Wang R, Qian W, Tang Z, Xu X, Lei B, Zhang K, Li J. qPrimerDB: a thermodynamics-based gene-specific qPCR primer database for 147 organisms. Nucleic Acids Res 2019;46:D1229-D1236. [PMID: 28977518 PMCID: PMC5753361 DOI: 10.1093/nar/gkx725] [Citation(s) in RCA: 92] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2017] [Accepted: 08/08/2017] [Indexed: 01/09/2023]  Open
6
Mandad S, Rahman RU, Centeno TP, Vidal RO, Wildhagen H, Rammner B, Keihani S, Opazo F, Urban I, Ischebeck T, Kirli K, Benito E, Fischer A, Yousefi RY, Dennerlein S, Rehling P, Feussner I, Urlaub H, Bonn S, Rizzoli SO, Fornasiero EF. The codon sequences predict protein lifetimes and other parameters of the protein life cycle in the mouse brain. Sci Rep 2018;8:16913. [PMID: 30443017 PMCID: PMC6237891 DOI: 10.1038/s41598-018-35277-8] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2018] [Accepted: 11/02/2018] [Indexed: 12/14/2022]  Open
7
Budzinska MA, Shackel NA, Urban S, Tu T. Cellular Genomic Sites of Hepatitis B Virus DNA Integration. Genes (Basel) 2018;9:E365. [PMID: 30037029 PMCID: PMC6071206 DOI: 10.3390/genes9070365] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2018] [Revised: 07/12/2018] [Accepted: 07/12/2018] [Indexed: 12/14/2022]  Open
8
Barton C, Iliopoulos CS, Pissis SP, Arhondakis S. Transcriptome activity of isochores during preimplantation process in human and mouse. FEBS Lett 2016;590:2297-306. [PMID: 27279593 DOI: 10.1002/1873-3468.12245] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2016] [Revised: 05/27/2016] [Accepted: 06/03/2016] [Indexed: 12/17/2022]
9
Kutzner A, Pramanik S, Kim PS, Heese K. All-or-(N)One - an epistemological characterization of the human tumorigenic neuronal paralogous FAM72 gene loci. Genomics 2015;106:278-285. [PMID: 26206078 DOI: 10.1016/j.ygeno.2015.07.003] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2015] [Revised: 05/26/2015] [Accepted: 07/13/2015] [Indexed: 12/21/2022]
10
Elhaik E, Graur D. A comparative study and a phylogenetic exploration of the compositional architectures of mammalian nuclear genomes. PLoS Comput Biol 2014;10:e1003925. [PMID: 25375262 PMCID: PMC4222635 DOI: 10.1371/journal.pcbi.1003925] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2014] [Accepted: 09/18/2014] [Indexed: 11/18/2022]  Open
11
Rao YS, Chai XW, Wang ZF, Nie QH, Zhang XQ. Impact of GC content on gene expression pattern in chicken. Genet Sel Evol 2013;45:9. [PMID: 23557030 PMCID: PMC3641017 DOI: 10.1186/1297-9686-45-9] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2012] [Accepted: 03/16/2013] [Indexed: 11/21/2022]  Open
12
Frousios K, Iliopoulos CS, Tischler G, Kossida S, Pissis SP, Arhondakis S. Transcriptome map of mouse isochores in embryonic and neonatal cortex. Genomics 2012. [PMID: 23195409 DOI: 10.1016/j.ygeno.2012.11.006] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
13
Chojnowski JL, Braun EL. An unbiased approach to identify genes involved in development in a turtle with temperature-dependent sex determination. BMC Genomics 2012;13:308. [PMID: 22793670 PMCID: PMC3434017 DOI: 10.1186/1471-2164-13-308] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2011] [Accepted: 07/15/2012] [Indexed: 02/08/2023]  Open
14
Arhondakis S, Frousios K, Iliopoulos CS, Pissis SP, Tischler G, Kossida S. Transcriptome map of mouse isochores. BMC Genomics 2011;12:511. [PMID: 22004510 PMCID: PMC3215772 DOI: 10.1186/1471-2164-12-511] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2011] [Accepted: 10/17/2011] [Indexed: 12/28/2022]  Open
15
Ferguson AA, Jiang N. Pack-MULEs: Recycling and reshaping genes through GC-biased acquisition. Mob Genet Elements 2011;1:135-138. [PMID: 22016862 DOI: 10.4161/mge.1.2.16948] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2011] [Revised: 06/13/2011] [Accepted: 06/14/2011] [Indexed: 11/19/2022]  Open
16
Transcriptome sequencing of a highly salt tolerant mangrove species Sonneratia alba using Illumina platform. Mar Genomics 2011;4:129-36. [PMID: 21620334 DOI: 10.1016/j.margen.2011.03.005] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2011] [Revised: 03/19/2011] [Accepted: 03/27/2011] [Indexed: 12/24/2022]
17
Tatarinova TV, Alexandrov NN, Bouck JB, Feldmann KA. GC3 biology in corn, rice, sorghum and other grasses. BMC Genomics 2010;11:308. [PMID: 20470436 PMCID: PMC2895627 DOI: 10.1186/1471-2164-11-308] [Citation(s) in RCA: 105] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2009] [Accepted: 05/16/2010] [Indexed: 11/10/2022]  Open
18
Sabbbia V, Romero H, Musto H, Naya H. Composition Profile of the Human Genome at the Chromosome Level. J Biomol Struct Dyn 2009;27:361-70. [DOI: 10.1080/07391102.2009.10507322] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
19
Bucciarelli G, Di Filippo M, Costagliola D, Alvarez-Valin F, Bernardi G, Bernardi G. Environmental Genomics: A Tale of Two Fishes. Mol Biol Evol 2009;26:1235-43. [DOI: 10.1093/molbev/msp041] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]  Open
20
Mahmud AA, Amore G, Bernardi G. Compositional genome contexts affect gene expression control in sea urchin embryo. PLoS One 2008;3:e4025. [PMID: 19112499 PMCID: PMC2603317 DOI: 10.1371/journal.pone.0004025] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2008] [Accepted: 11/21/2008] [Indexed: 11/18/2022]  Open
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