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For: Pavesi A. Origin and evolution of overlapping genes in the family Microviridae. J Gen Virol 2006;87:1013-1017. [PMID: 16528052 DOI: 10.1099/vir.0.81375-0] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]  Open
Number Cited by Other Article(s)
1
Iqbal S, Begum F. Identification and characterization of integrated prophages and CRISPR-Cas system in Bacillus subtilis RS10 genome. Braz J Microbiol 2024;55:537-542. [PMID: 38216797 PMCID: PMC10920515 DOI: 10.1007/s42770-024-01249-6] [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: 07/05/2023] [Accepted: 01/04/2024] [Indexed: 01/14/2024]  Open
2
Kirchberger PC, Ochman H. Microviruses: A World Beyond phiX174. Annu Rev Virol 2023;10:99-118. [PMID: 37774127 DOI: 10.1146/annurev-virology-100120-011239] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/01/2023]
3
W B Jr M, A S R, P M, F B. Cellular and Natural Viral Engineering in Cognition-Based Evolution. Commun Integr Biol 2023;16:2196145. [PMID: 37153718 PMCID: PMC10155641 DOI: 10.1080/19420889.2023.2196145] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Accepted: 03/23/2023] [Indexed: 05/10/2023]  Open
4
Pley C, Lourenço J, McNaughton AL, Matthews PC. Spacer Domain in Hepatitis B Virus Polymerase: Plugging a Hole or Performing a Role? J Virol 2022;96:e0005122. [PMID: 35412348 PMCID: PMC9093120 DOI: 10.1128/jvi.00051-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Accepted: 03/14/2022] [Indexed: 11/25/2022]  Open
5
Watson AK, Lopez P, Bapteste E. Hundreds of out-of-frame remodelled gene families in the E. coli pangenome. Mol Biol Evol 2021;39:6430988. [PMID: 34792602 PMCID: PMC8788219 DOI: 10.1093/molbev/msab329] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]  Open
6
Computational methods for inferring location and genealogy of overlapping genes in virus genomes: approaches and applications. Curr Opin Virol 2021;52:1-8. [PMID: 34798370 PMCID: PMC8594276 DOI: 10.1016/j.coviro.2021.10.009] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2021] [Revised: 10/21/2021] [Accepted: 10/22/2021] [Indexed: 12/02/2022]
7
Khan MSI, Gao X, Liang K, Mei S, Zhan J. Virulent Drexlervirial Bacteriophage MSK, Morphological and Genome Resemblance With Rtp Bacteriophage Inhibits the Multidrug-Resistant Bacteria. Front Microbiol 2021;12:706700. [PMID: 34504479 PMCID: PMC8421802 DOI: 10.3389/fmicb.2021.706700] [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: 05/07/2021] [Accepted: 06/14/2021] [Indexed: 11/13/2022]  Open
8
Pavesi A. Origin, Evolution and Stability of Overlapping Genes in Viruses: A Systematic Review. Genes (Basel) 2021;12:genes12060809. [PMID: 34073395 PMCID: PMC8227390 DOI: 10.3390/genes12060809] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Revised: 05/22/2021] [Accepted: 05/24/2021] [Indexed: 12/11/2022]  Open
9
Li M, Lin H, Wang L, Wang J. Complete genome sequence of the extreme-pH-resistant Salmonella bacteriophage αα of the family Microviridae. Arch Virol 2020;166:325-329. [PMID: 33221988 DOI: 10.1007/s00705-020-04880-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2020] [Accepted: 09/29/2020] [Indexed: 12/01/2022]
10
Circular Single-Stranded DNA Virus (Microviridae: Gokushovirinae: Jodiemicrovirus) Associated with the Pathobiome of the Flat-Back Mud Crab, Eurypanopeus depressus. Microbiol Resour Announc 2019;8:8/47/e01026-19. [PMID: 31753941 PMCID: PMC6872883 DOI: 10.1128/mra.01026-19] [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: 01/02/2023]  Open
11
Affram Y, Zapata JC, Gholizadeh Z, Tolbert WD, Zhou W, Iglesias-Ussel MD, Pazgier M, Ray K, Latinovic OS, Romerio F. The HIV-1 Antisense Protein ASP Is a Transmembrane Protein of the Cell Surface and an Integral Protein of the Viral Envelope. J Virol 2019;93:e00574-19. [PMID: 31434734 PMCID: PMC6803264 DOI: 10.1128/jvi.00574-19] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2019] [Accepted: 08/14/2019] [Indexed: 12/13/2022]  Open
12
The Evolution and Expression Pattern of Human Overlapping lncRNA and Protein-coding Gene Pairs. Sci Rep 2017;7:42775. [PMID: 28344339 PMCID: PMC5366806 DOI: 10.1038/srep42775] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2016] [Accepted: 01/13/2017] [Indexed: 12/27/2022]  Open
13
Saha D, Podder S, Ghosh TC. Overlapping Regions in HIV-1 Genome Act as Potential Sites for Host-Virus Interaction. Front Microbiol 2016;7:1735. [PMID: 27867372 PMCID: PMC5095123 DOI: 10.3389/fmicb.2016.01735] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2016] [Accepted: 10/17/2016] [Indexed: 01/05/2023]  Open
14
Amarillas L, Chaidez C, González-Robles A, Lugo-Melchor Y, León-Félix J. Characterization of novel bacteriophage phiC119 capable of lysing multidrug-resistant Shiga toxin-producing Escherichia coli O157:H7. PeerJ 2016;4:e2423. [PMID: 27672499 PMCID: PMC5028729 DOI: 10.7717/peerj.2423] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2016] [Accepted: 08/09/2016] [Indexed: 12/22/2022]  Open
15
Different patterns of codon usage in the overlapping polymerase and surface genes of hepatitis B virus suggest a de novo origin by modular evolution. J Gen Virol 2015;96:3577-3586. [DOI: 10.1099/jgv.0.000307] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]  Open
16
Wei X, Zhang J. A simple method for estimating the strength of natural selection on overlapping genes. Genome Biol Evol 2014;7:381-90. [PMID: 25552532 PMCID: PMC4316641 DOI: 10.1093/gbe/evu294] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]  Open
17
Overlapping genes: a new strategy of thermophilic stress tolerance in prokaryotes. Extremophiles 2014;19:345-53. [PMID: 25503326 DOI: 10.1007/s00792-014-0720-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2014] [Accepted: 12/01/2014] [Indexed: 12/29/2022]
18
Shukla A, Hilgenfeld R. Acquisition of new protein domains by coronaviruses: analysis of overlapping genes coding for proteins N and 9b in SARS coronavirus. Virus Genes 2014;50:29-38. [PMID: 25410051 PMCID: PMC7089080 DOI: 10.1007/s11262-014-1139-8] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2014] [Accepted: 10/25/2014] [Indexed: 12/02/2022]
19
Doore SM, Baird CD, Roznowski AP, Fane BA. The Evolution of Genes within Genes and the Control of DNA Replication in Microviruses. Mol Biol Evol 2014;31:1421-31. [DOI: 10.1093/molbev/msu089] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]  Open
20
Lo MK, Søgaard TM, Karlin DG. Evolution and structural organization of the C proteins of paramyxovirinae. PLoS One 2014;9:e90003. [PMID: 24587180 PMCID: PMC3934983 DOI: 10.1371/journal.pone.0090003] [Citation(s) in RCA: 25] [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: 12/19/2013] [Accepted: 01/24/2014] [Indexed: 12/21/2022]  Open
21
Labonté JM, Suttle CA. Metagenomic and whole-genome analysis reveals new lineages of gokushoviruses and biogeographic separation in the sea. Front Microbiol 2013;4:404. [PMID: 24399999 PMCID: PMC3871881 DOI: 10.3389/fmicb.2013.00404] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2013] [Accepted: 12/06/2013] [Indexed: 01/20/2023]  Open
22
Rodriguez-Frias F, Buti M, Tabernero D, Homs M. Quasispecies structure, cornerstone of hepatitis B virus infection: mass sequencing approach. World J Gastroenterol 2013;19:6995-7023. [PMID: 24222943 PMCID: PMC3819535 DOI: 10.3748/wjg.v19.i41.6995] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/28/2013] [Revised: 08/23/2013] [Accepted: 09/15/2013] [Indexed: 02/06/2023]  Open
23
Viral proteins originated de novo by overprinting can be identified by codon usage: application to the "gene nursery" of Deltaretroviruses. PLoS Comput Biol 2013;9:e1003162. [PMID: 23966842 PMCID: PMC3744397 DOI: 10.1371/journal.pcbi.1003162] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2012] [Accepted: 06/13/2013] [Indexed: 12/24/2022]  Open
24
Kawano Y, Neeley S, Adachi K, Nakai H. An experimental and computational evolution-based method to study a mode of co-evolution of overlapping open reading frames in the AAV2 viral genome. PLoS One 2013;8:e66211. [PMID: 23826091 PMCID: PMC3691236 DOI: 10.1371/journal.pone.0066211] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2013] [Accepted: 05/07/2013] [Indexed: 02/07/2023]  Open
25
Simon-Loriere E, Holmes EC, Pagán I. The effect of gene overlapping on the rate of RNA virus evolution. Mol Biol Evol 2013;30:1916-28. [PMID: 23686658 DOI: 10.1093/molbev/mst094] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]  Open
26
Torres C, Fernández MDB, Flichman DM, Campos RH, Mbayed VA. Influence of overlapping genes on the evolution of human hepatitis B virus. Virology 2013;441:40-8. [PMID: 23541083 DOI: 10.1016/j.virol.2013.02.027] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2013] [Revised: 02/05/2013] [Accepted: 02/28/2013] [Indexed: 12/23/2022]
27
A fully decompressed synthetic bacteriophage øX174 genome assembled and archived in yeast. Virology 2012;434:278-84. [DOI: 10.1016/j.virol.2012.09.020] [Citation(s) in RCA: 72] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2012] [Revised: 09/15/2012] [Accepted: 09/21/2012] [Indexed: 11/20/2022]
28
Seligmann H. Overlapping genetic codes for overlapping frameshifted genes in Testudines, and Lepidochelys olivacea as special case. Comput Biol Chem 2012;41:18-34. [DOI: 10.1016/j.compbiolchem.2012.08.002] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2011] [Revised: 03/14/2012] [Accepted: 08/05/2012] [Indexed: 11/29/2022]
29
Zarghani SN, Shams-Bakhsh M, Zand N, Sokhandan-Bashir N, Pazhouhandeh M. Genetic analysis of Iranian population of Potato leafroll virus based on ORF0. Virus Genes 2012;45:567-74. [PMID: 22903753 DOI: 10.1007/s11262-012-0804-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2012] [Accepted: 08/06/2012] [Indexed: 11/25/2022]
30
Sabath N, Wagner A, Karlin D. Evolution of viral proteins originated de novo by overprinting. Mol Biol Evol 2012;29:3767-80. [PMID: 22821011 PMCID: PMC3494269 DOI: 10.1093/molbev/mss179] [Citation(s) in RCA: 101] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]  Open
31
Ma MR, Ha XQ, Ling H, Wang ML, Zhang FX, Zhang SD, Li G, Yan W. The characteristics of the synonymous codon usage in hepatitis B virus and the effects of host on the virus in codon usage pattern. Virol J 2011;8:544. [PMID: 22171933 PMCID: PMC3287100 DOI: 10.1186/1743-422x-8-544] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2011] [Accepted: 12/15/2011] [Indexed: 12/18/2022]  Open
32
Krupovic M, Prangishvili D, Hendrix RW, Bamford DH. Genomics of bacterial and archaeal viruses: dynamics within the prokaryotic virosphere. Microbiol Mol Biol Rev 2011;75:610-35. [PMID: 22126996 PMCID: PMC3232739 DOI: 10.1128/mmbr.00011-11] [Citation(s) in RCA: 158] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]  Open
33
Successful COG8 and PDF overlap is mediated by alterations in splicing and polyadenylation signals. Hum Genet 2011;131:265-74. [PMID: 21805148 DOI: 10.1007/s00439-011-1075-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2011] [Accepted: 07/19/2011] [Indexed: 01/21/2023]
34
Immune-induced evolutionary selection focused on a single reading frame in overlapping hepatitis B virus proteins. J Virol 2011;85:4558-66. [PMID: 21307195 DOI: 10.1128/jvi.02142-10] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]  Open
35
Pagán I, Holmes EC. Long-term evolution of the Luteoviridae: time scale and mode of virus speciation. J Virol 2010;84:6177-87. [PMID: 20375155 PMCID: PMC2876656 DOI: 10.1128/jvi.02160-09] [Citation(s) in RCA: 92] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2009] [Accepted: 03/31/2010] [Indexed: 12/20/2022]  Open
36
Sequence variability and evolution of the terminal overlapping VP5 gene of the infectious bursal disease virus. Virus Genes 2010;41:59-66. [DOI: 10.1007/s11262-010-0485-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2009] [Accepted: 04/15/2010] [Indexed: 10/19/2022]
37
Zhang D, Chen J, Deng L, Mao Q, Zheng J, Wu J, Zeng C, Li Y. Evolutionary selection associated with the multi-function of overlapping genes in the hepatitis B virus. INFECTION GENETICS AND EVOLUTION 2010;10:84-8. [DOI: 10.1016/j.meegid.2009.10.006] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2009] [Revised: 10/10/2009] [Accepted: 10/20/2009] [Indexed: 11/16/2022]
38
Liang JW, Tian FL, Lan ZR, Huang B, Zhuang WZ. Selection characterization on overlapping reading frame of multiple-protein-encoding P gene in Newcastle disease virus. Vet Microbiol 2009;144:257-63. [PMID: 20079581 DOI: 10.1016/j.vetmic.2009.12.029] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2009] [Accepted: 12/21/2009] [Indexed: 01/08/2023]
39
Dickins B, Nekrutenko A. High-resolution mapping of evolutionary trajectories in a phage. Genome Biol Evol 2009;1:294-307. [PMID: 20333199 PMCID: PMC2817424 DOI: 10.1093/gbe/evp029] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/29/2009] [Indexed: 12/11/2022]  Open
40
Overlapping genes produce proteins with unusual sequence properties and offer insight into de novo protein creation. J Virol 2009;83:10719-36. [PMID: 19640978 DOI: 10.1128/jvi.00595-09] [Citation(s) in RCA: 143] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]  Open
41
Sabath N, Landan G, Graur D. A method for the simultaneous estimation of selection intensities in overlapping genes. PLoS One 2008;3:e3996. [PMID: 19098983 PMCID: PMC2601044 DOI: 10.1371/journal.pone.0003996] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2008] [Accepted: 11/21/2008] [Indexed: 11/18/2022]  Open
42
de Groot S, Mailund T, Lunter G, Hein J. Investigating selection on viruses: a statistical alignment approach. BMC Bioinformatics 2008;9:304. [PMID: 18616801 PMCID: PMC2478691 DOI: 10.1186/1471-2105-9-304] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2007] [Accepted: 07/10/2008] [Indexed: 01/14/2023]  Open
43
Delaye L, Deluna A, Lazcano A, Becerra A. The origin of a novel gene through overprinting in Escherichia coli. BMC Evol Biol 2008;8:31. [PMID: 18226237 PMCID: PMC2268670 DOI: 10.1186/1471-2148-8-31] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2007] [Accepted: 01/28/2008] [Indexed: 11/10/2022]  Open
44
McCauley S, de Groot S, Mailund T, Hein J. Annotation of selection strengths in viral genomes. Bioinformatics 2007;23:2978-86. [PMID: 17921171 DOI: 10.1093/bioinformatics/btm472] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]  Open
45
van Hemert FJ, Zaaijer HL, Berkhout B, Lukashov VV. Mosaic amino acid conservation in 3D-structures of surface protein and polymerase of hepatitis B virus. Virology 2007;370:362-72. [PMID: 17935747 DOI: 10.1016/j.virol.2007.08.036] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2007] [Revised: 07/31/2007] [Accepted: 08/25/2007] [Indexed: 12/17/2022]
46
Cai Y, Hartnett B, Gustafsson C, Peccoud J. A syntactic model to design and verify synthetic genetic constructs derived from standard biological parts. Bioinformatics 2007;23:2760-7. [PMID: 17804435 DOI: 10.1093/bioinformatics/btm446] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]  Open
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Kingsford C, Delcher AL, Salzberg SL. A unified model explaining the offsets of overlapping and near-overlapping prokaryotic genes. Mol Biol Evol 2007;24:2091-8. [PMID: 17642473 PMCID: PMC2429982 DOI: 10.1093/molbev/msm145] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]  Open
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Mayrose I, Doron-Faigenboim A, Bacharach E, Pupko T. Towards realistic codon models: among site variability and dependency of synonymous and non-synonymous rates. ACTA ACUST UNITED AC 2007;23:i319-27. [PMID: 17646313 DOI: 10.1093/bioinformatics/btm176] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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Pavesi A. Pattern of nucleotide substitution in the overlapping nonstructural genes of influenza A virus and implication for the genetic diversity of the H5N1 subtype. Gene 2007;402:28-34. [PMID: 17825505 DOI: 10.1016/j.gene.2007.07.013] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2007] [Revised: 07/12/2007] [Accepted: 07/12/2007] [Indexed: 11/24/2022]
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Szklarczyk R, Heringa J, Pond SK, Nekrutenko A. Rapid asymmetric evolution of a dual-coding tumor suppressor INK4a/ARF locus contradicts its function. Proc Natl Acad Sci U S A 2007;104:12807-12. [PMID: 17652172 PMCID: PMC1937548 DOI: 10.1073/pnas.0703238104] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]  Open
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