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For: Kong SG, Fan WL, Chen HD, Hsu ZT, Zhou N, Zheng B, Lee HC. Inverse symmetry in complete genomes and whole-genome inverse duplication. PLoS One 2009;4:e7553. [PMID: 19898631 PMCID: PMC2771390 DOI: 10.1371/journal.pone.0007553] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2009] [Accepted: 07/22/2009] [Indexed: 12/18/2022]  Open
Number Cited by Other Article(s)
1
Rosandić M, Vlahović I, Pilaš I, Glunčić M, Paar V. An Explanation of Exceptions from Chargaff's Second Parity Rule/Strand Symmetry of DNA Molecules. Genes (Basel) 2022;13:1929. [PMID: 36360166 PMCID: PMC9689577 DOI: 10.3390/genes13111929] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2022] [Revised: 10/12/2022] [Accepted: 10/17/2022] [Indexed: 11/04/2022]  Open
2
Malhotra N, Seshasayee ASN. Replication-Dependent Organization Constrains Positioning of Long DNA Repeats in Bacterial Genomes. Genome Biol Evol 2022;14:6625829. [PMID: 35776426 PMCID: PMC9297083 DOI: 10.1093/gbe/evac102] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/27/2022] [Indexed: 01/29/2023]  Open
3
Affinity and Correlation in DNA. J 2022. [DOI: 10.3390/j5020016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]  Open
4
Rosandić M, Vlahović I, Paar V. Novel look at DNA and life-Symmetry as evolutionary forcing. J Theor Biol 2019;483:109985. [PMID: 31469987 DOI: 10.1016/j.jtbi.2019.08.016] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2018] [Revised: 06/21/2018] [Accepted: 08/22/2019] [Indexed: 11/20/2022]
5
Cristadoro G, Degli Esposti M, Altmann EG. The common origin of symmetry and structure in genetic sequences. Sci Rep 2018;8:15817. [PMID: 30361485 PMCID: PMC6202410 DOI: 10.1038/s41598-018-34136-w] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2018] [Accepted: 10/09/2018] [Indexed: 12/20/2022]  Open
6
Akhter S, Aziz RK, Kashef MT, Ibrahim ES, Bailey B, Edwards RA. Kullback Leibler divergence in complete bacterial and phage genomes. PeerJ 2017;5:e4026. [PMID: 29204318 PMCID: PMC5712468 DOI: 10.7717/peerj.4026] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2017] [Accepted: 10/22/2017] [Indexed: 12/11/2022]  Open
7
Afreixo V, Rodrigues JMOS, Bastos CAC, Tavares AHMP, Silva RM. Exceptional Symmetry by Genomic Word : A Statistical Analysis. Interdiscip Sci 2016;9:14-23. [PMID: 27866321 DOI: 10.1007/s12539-016-0200-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2016] [Revised: 11/02/2016] [Accepted: 11/04/2016] [Indexed: 01/12/2023]
8
Shporer S, Chor B, Rosset S, Horn D. Inversion symmetry of DNA k-mer counts: validity and deviations. BMC Genomics 2016;17:696. [PMID: 27580854 PMCID: PMC5006273 DOI: 10.1186/s12864-016-3012-8] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2016] [Accepted: 08/11/2016] [Indexed: 01/25/2023]  Open
9
Rosandić M, Vlahović I, Glunčić M, Paar V. Trinucleotide's quadruplet symmetries and natural symmetry law of DNA creation ensuing Chargaff's second parity rule. J Biomol Struct Dyn 2016;34:1383-94. [PMID: 26524490 DOI: 10.1080/07391102.2015.1080628] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
10
Afreixo V, Rodrigues JMOS, Bastos CAC, Silva RM. The exceptional genomic word symmetry along DNA sequences. BMC Bioinformatics 2016;17:59. [PMID: 26842742 PMCID: PMC4738807 DOI: 10.1186/s12859-016-0905-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2015] [Accepted: 01/19/2016] [Indexed: 01/05/2023]  Open
11
Stems and Loops. Evol Bioinform Online 2016. [DOI: 10.1007/978-3-319-28755-3_5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]  Open
12
Srinivasan R, Scolari VF, Lagomarsino MC, Seshasayee ASN. The genome-scale interplay amongst xenogene silencing, stress response and chromosome architecture in Escherichia coli. Nucleic Acids Res 2014;43:295-308. [PMID: 25429971 PMCID: PMC4288151 DOI: 10.1093/nar/gku1229] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]  Open
13
Afreixo V, Rodrigues JMOS, Bastos CAC. Analysis of single-strand exceptional word symmetry in the human genome: new measures. Biostatistics 2014;16:209-21. [PMID: 25190514 DOI: 10.1093/biostatistics/kxu041] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]  Open
14
Provata A, Nicolis C, Nicolis G. DNA viewed as an out-of-equilibrium structure. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2014;89:052105. [PMID: 25353737 DOI: 10.1103/physreve.89.052105] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2013] [Indexed: 05/02/2023]
15
Li S, Yang J. System analysis of synonymous codon usage biases in archaeal virus genomes. J Theor Biol 2014;355:128-39. [PMID: 24685889 PMCID: PMC7094158 DOI: 10.1016/j.jtbi.2014.03.022] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2013] [Revised: 03/11/2014] [Accepted: 03/12/2014] [Indexed: 12/30/2022]
16
Afreixo V, Bastos CA, Garcia SP, Rodrigues JM, Pinho AJ, Ferreira PJ. The breakdown of the word symmetry in the human genome. J Theor Biol 2013;335:153-9. [DOI: 10.1016/j.jtbi.2013.06.032] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2012] [Revised: 05/30/2013] [Accepted: 06/25/2013] [Indexed: 01/13/2023]
17
Patterns of nucleotide asymmetries in plant and animal genomes. Biosystems 2013;111:181-9. [PMID: 23438636 DOI: 10.1016/j.biosystems.2013.02.001] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2012] [Revised: 11/29/2012] [Accepted: 02/07/2013] [Indexed: 11/20/2022]
18
Applying Shannon's information theory to bacterial and phage genomes and metagenomes. Sci Rep 2013;3:1033. [PMID: 23301154 PMCID: PMC3539204 DOI: 10.1038/srep01033] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2012] [Accepted: 11/20/2012] [Indexed: 01/12/2023]  Open
19
Comin M, Verzotto D. Alignment-free phylogeny of whole genomes using underlying subwords. Algorithms Mol Biol 2012;7:34. [PMID: 23216990 PMCID: PMC3549825 DOI: 10.1186/1748-7188-7-34] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2012] [Accepted: 11/29/2012] [Indexed: 11/24/2022]  Open
20
Hart A, Martínez S. Statistical Testing of Chargaff's Second Parity Rule in Bacterial Genome Sequences. STOCH MODELS 2011. [DOI: 10.1080/15326349.2011.567931] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
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