Virus-host coevolution: common patterns of nucleotide motif usage in Flaviviridae and their hosts
Open accessAbstract
Virus-host biological interaction is a continuous coevolutionary process involving both host immune system and viral escape mechanisms. Flaviviridae family is composed of fast evolving RNA viruses that infects vertebrate (mammals and birds) and/or invertebrate (ticks and mosquitoes) organisms. These host groups are very distinct life forms separated by a long evolutionary time, so lineage-specific anti-viral mechanisms are likely to have evolved. Flaviviridae viruses which infect a single host lineage would be subjected to specific host-induced pressures and, therefore, selected by them. In this work we compare the genomic evolutionary patterns of Flaviviridae viruses and their hosts in an attempt to uncover coevolutionary processes inducing common features in such disparate groups. Especially, we have analyzed dinucleotide and codon usage patterns in the coding regions of vertebrate and invertebrate organisms as well as in Flaviviridae viruses which specifically infect one or both host types. The two host groups posses very distinctive dinucleotide and codon usage patterns. A pronounced CpG under-representation was found in the vertebrate group, possibly induced by the methylation-deamination process, as well as a prominent TpA decrease. The invertebrate group displayed only a TpA frequency reduction bias. Flaviviridae viruses mimicked host nucleotide motif usage in a host-specific manner. Vertebrate-infecting viruses possessed under-representation of CpG and TpA, and insect-only viruses displayed only a TpA under-representation bias. Single-host Flaviviridae members which persistently infect mammals or insect hosts (Hepacivirus and insect-only Flavivirus, respectively) were found to posses a codon usage profile more similar to that of their hosts than to related Flaviviridae. We demonstrated that vertebrates and mosquitoes genomes are under very distinct lineage-specific constraints, and Flaviviridae viruses which specifically infect these lineages appear to be subject to the same evolutionary pressures that shaped their host coding regions, evidencing the lineage-specific coevolutionary processes between the viral and host groups.
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Integrity signals
Registry
Cites
Statistics
Claims the paper makes
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Claims other papers make about this one
Each is checked against this paper’s own text: does it say what the citing paper says it does?
Suppression of CpG dinucleotides in these and many other small viruses occurs at all three possible codon locations, not only at the codon pair boundary.
“Suppression of CpG dinucleotides in these and many other small viruses occurs at all three possible codon locations, not only at the codon pair boundary.”
From Codon Pair Bias Is a Direct Consequence of Dinucleotide Bias (2016) · cites this paper as Lobo et al., 2009
The Codon Usage Similarity section (page unavailable) reports under-representation of CpG-containing codons in vertebrate-infecting viruses, supporting suppression within codons, not just at codon boundaries. The Dinucleotide Composition Analysis section reports broader viral CpG depletion, but the paper does not establish suppression separately at all three codon locations across the many small viruses claimed; it also notes viral groups with little CpG bias. (LLM, conf=0.86)
Experimental — accuracy not yet measuredThe two groups of viruses are exposed to different selection pressures and the pressure is imposed by the respective hosts.
“suggesting that the two groups of viruses are exposed to different selection pressures and that the pressure is imposed by the respective hosts (Lobo et al., 2009).”
From Codon Pair Bias Is a Direct Consequence of Dinucleotide Bias (2016) · cites this paper as Lobo et al., 2009
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
Cites
R: A Language and Environment for Statistical Computing
R Core Team (2000) · doi:10.32614/r.manuals · Cited by 355,706 · see citing works
MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) Software Version 4.0
Tamura, K., Dudley, J. T., Nei, M., & Kumar, S. (2007) · Molecular Biology and Evolution · doi:10.1093/molbev/msm092 · Cited by 28,734 · see citing works
Pruitt, K. D., Tatusova, T. A., & Maglott, D. R. (2006) · Nucleic Acids Research · doi:10.1093/nar/gkl842 · Cited by 4,441 · see citing works
Mutation of the mouse klotho gene leads to a syndrome resembling ageing
Kuro-o, M., Matsumura, Y., Aizawa, H., Kawaguchi, H., Suga, T., Utsugi, T., Ohyama, Y., Kurabayashi, M., Kaname, T., Kume, E., et al. (1997) · Nature · doi:10.1038/36285 · Cited by 3,837 · see citing works
Bird, A. (2007) · Nature · doi:10.1038/nature05913 · Cited by 3,011 · see citing works
Lauer, G. M., & Walker, B. D. (2001) · New England Journal of Medicine · doi:10.1056/nejm200107053450107 · Cited by 3,010 · see citing works
Multiple Sequence Alignment Using ClustalW and ClustalX
Thompson, J., Gibson, T. J., & Higgins, D. G. (2002) · Current Protocols in Bioinformatics · doi:10.1002/0471250953.bi0203s00 · Cited by 2,989 · see citing works
Endoplasmic reticulum stress: cell life and death decisions
Xu, C. (2005) · Journal of Clinical Investigation · doi:10.1172/jci26373 · Cited by 2,260 · see citing works
Molecular Cloning and Disease Association of Hepatitis G Virus: A Transfusion-Transmissible Agent
Linnen, J., Wages, J., Keck, Z., Fry, K. E., Krawczyński, K., Alter, H. J., Koonin, E. V., Gallagher, M. L., Alter, M. J., Hadziyannis, S. J., et al. (1996) · Science · doi:10.1126/science.271.5248.505 · Cited by 1,339 · see citing works
DNA methylation and the frequency of CpG in animal DNA
Bird, A. P. (1980) · Nucleic Acids Research · doi:10.1093/nar/8.7.1499 · Cited by 1,175 · see citing works
Guzmán, M. G., & Kourí, G. (2002) · The Lancet Infectious Diseases · doi:10.1016/s1473-3099(01)00171-2 · Cited by 1,170 · see citing works
R Development Core Team (2010): R: A language and environment for statistical computing
Dalgaard, P. (2010) · Cited by 951 · see citing works
The Aedes aegypti Toll Pathway Controls Dengue Virus Infection
Xi, Z., Ramirez, J. L., & Dimopoulos, G. (2008) · PLoS Pathogens · doi:10.1371/journal.ppat.1000098 · Cited by 928 · see citing works
Transmission of Hepatitis C by Intrahepatic Inoculation with Transcribed RNA
Kolykhalov, A. A., Agapov, E. V., Blight, K. J., Mihalik, K., Feinstone, S. M., & Rice, C. M. (1997) · Science · doi:10.1126/science.277.5325.570 · Cited by 733 · see citing works
RNA Interference Directs Innate Immunity Against Viruses in Adult Drosophila
Wang, X.-H., Aliyari, R., Li, W.-X., Li, H.-W., Kim, K., Carthew, R. W., Atkinson, P. W., & Ding, S. (2006) · Science · doi:10.1126/science.1125694 · Cited by 726 · see citing works
Benson, D. A., Karsch‐Mizrachi, I., Lipman, D. J., Ostell, J., & Sayers, E. W. (2008) · Nucleic Acids Research · doi:10.1093/nar/gkn723 · Cited by 688 · see citing works
Dostert, C., Jouanguy, E., Irving, P., Troxler, L., Galiana-Arnoux, D., Hétru, C., Hoffmann, J. A., & Imler, J. (2005) · Nature Immunology · doi:10.1038/ni1237 · Cited by 648 · see citing works
Structure and function of type II restriction endonucleases
Pingoud, A. (2001) · Nucleic Acids Research · doi:10.1093/nar/29.18.3705 · Cited by 641 · see citing works
Variability of hepatitis C virus
Peter Simmonds, K. (1995) · Hepatology · doi:10.1002/hep.1840210243 · Cited by 565 · see citing works
Monath, T. P. C. (2001) · The Lancet Infectious Diseases · doi:10.1016/s1473-3099(01)00016-0 · Cited by 542 · see citing works
The evolution of RNAi as a defence against viruses and transposable elements
Obbard, D. J., Gordon, K. H. J., Buck, A. H., & Jiggins, F. M. (2008) · Philosophical Transactions of the Royal Society B Biological Sciences · doi:10.1098/rstb.2008.0168 · Cited by 521 · see citing works
Kobayashi, I. (2001) · Nucleic Acids Research · doi:10.1093/nar/29.18.3742 · Cited by 513 · see citing works
Estimating metazoan divergence times with a molecular clock
Peterson, K. J., Lyons, J. B., Nowak, K. S., Takacs, C. M., Wargo, M. J., & McPeek, M. A. (2004) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0401670101 · Cited by 461 · see citing works
Antiviral Signaling Through Pattern Recognition Receptors
Kawai, T., & Akira, S. (2006) · The Journal of Biochemistry · doi:10.1093/jb/mvm032 · Cited by 452 · see citing works
Knight, R. D., Freeland, S. J., & Landweber, L. F. (2001) · Genome biology · doi:10.1186/gb-2001-2-4-research0010 · Cited by 439 · see citing works
Molecules consolidate the placental mammal tree
Springer, M. S. (2004) · Trends in Ecology & Evolution · doi:10.1016/j.tree.2004.05.006 · Cited by 408 · see citing works
The Toll pathway is important for an antiviral response in Drosophila
Zambon, R. A., Nandakumar, M., Vakharia, V. N., & Wu, L. P. (2005) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0409181102 · Cited by 402 · see citing works
Gaunt, M. W., Sall, A. A., de Lamballerie, X. N., Falconar, A. K. I., Dzhivanian, T. I., & Gould, E. A. (2001) · Journal of General Virology · doi:10.1099/0022-1317-82-8-1867 · Cited by 334 · see citing works
Karlin, S., Doerfler, W., & Cardon, L. R. (1994) · Journal of Virology · doi:10.1128/jvi.68.5.2889-2897.1994 · Cited by 326 · see citing works
RNAi is an antiviral immune response against a dsRNA virus in Drosophila melanogaster
Zambon, R. A., Vakharia, V. N., & Wu, L. P. (2006) · Cellular Microbiology · doi:10.1111/j.1462-5822.2006.00688.x · Cited by 302 · see citing works
Patterns of Evolution and Host Gene Mimicry in Influenza and Other RNA Viruses
Greenbaum, B. D., Levine, A. J., Bhanot, G. V., & Rabadán, R. (2008) · PLoS Pathogens · doi:10.1371/journal.ppat.1000079 · Cited by 279 · see citing works
Weaver, S. C., Brault, A. C., Kang, W., & Holland, J. J. (1999) · Journal of Virology · doi:10.1128/jvi.73.5.4316-4326.1999 · Cited by 266 · see citing works
The 2–5 A system: Modulation of viral and cellular processes through acceleration of RNA degradation
Player, M. R., & Torrence, P. F. (1998) · Pharmacology & Therapeutics · doi:10.1016/s0163-7258(97)00167-8 · Cited by 264 · see citing works
Compositional differences within and between eukaryotic genomes
Karlin, S., & Mrázek, J. (1997) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.94.19.10227 · Cited by 264 · see citing works
Persistent Hepatitis C Virus Infection In Vitro: Coevolution of Virus andHost
Zhong, J., Gastaminza, P., Chung, J., Stamataki, Z., Isogawa, M., Cheng, G., McKeating, J. A., & Chisari, F. V. (2006) · Journal of Virology · doi:10.1128/jvi.01307-06 · Cited by 253 · see citing works
Hepatitis C virus, ER stress, and oxidative stress
Tardif, K. D., Waris, G., & Siddiqui, A. (2005) · Trends in Microbiology · doi:10.1016/j.tim.2005.02.004 · Cited by 239 · see citing works
Strand compositional asymmetry in bacterial and large viral genomes
Mrázek, J., & Karlin, S. (1998) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.95.7.3720 · Cited by 239 · see citing works
Pervasive CpG suppression in animal mitochondrial genomes
Cardon, L. R., Burge, C., Clayton, D. A., & Karlin, S. (1994) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.91.9.3799 · Cited by 238 · see citing works
Arbovirus evolution in vivo is constrained by host alternation
Coffey, L. L., Vasilakis, N., Brault, A. C., Powers, A. M., Tripet, F., & Weaver, S. C. (2008) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0712130105 · Cited by 215 · see citing works
Bauhofer, O., Summerfield, A., Sakoda, Y., Tratschin, J.-D., Hofmann‐Apitius, M., & Ruggli, N. (2007) · Journal of Virology · doi:10.1128/jvi.02032-06 · Cited by 205 · see citing works
A periodic pattern of mRNA secondary structure created by the genetic code
Shabalina, S. A. (2006) · Nucleic Acids Research · doi:10.1093/nar/gkl287 · Cited by 202 · see citing works
Genetic characterization of a new insect flavivirus isolated from Culex pipiens mosquito in Japan
Hoshino, K., Isawa, H., Tsuda, Y., Yano, K., Sasaki, T., Yuda, M., Takasaki, T., Kobayashi, M., & Sawabe, K. (2006) · Virology · doi:10.1016/j.virol.2006.09.039 · Cited by 197 · see citing works
Replication of Arboviruses in Insect Vectors
Mellor, P. S. (2000) · Journal of Comparative Pathology · doi:10.1053/jcpa.2000.0434 · Cited by 175 · see citing works
Cook, S., & Holmes, E. C. (2005) · Archives of Virology · doi:10.1007/s00705-005-0626-6 · Cited by 165 · see citing works
Small RNAs in viral infection and host defense
Mlotshwa, S., Pruss, G. J., & Vance, V. B. (2008) · Trends in Plant Science · doi:10.1016/j.tplants.2008.04.009 · Cited by 154 · see citing works
Effect of Alternating Passage on Adaptation of Sindbis Virus to Vertebrate and Invertebrate Cells
Greene, I. P., Wang, E., Deardorff, E. R., Milleron, R. S., Domingo, E., & Weaver, S. C. (2005) · Journal of Virology · doi:10.1128/jvi.79.22.14253-14260.2005 · Cited by 147 · see citing works
RNase L Plays a Role in the Antiviral Response to West Nile Virus
Scherbik, S. V., Paranjape, J. M., Stockman, B. M., Silverman, R. H., & Brinton, M. A. (2006) · Journal of Virology · doi:10.1128/jvi.80.6.2987-2999.2006 · Cited by 147 · see citing works
Reading the viral signature by Toll-like receptors and other pattern recognition receptors
Mogensen, T. H., & Paludan, S. R. (2005) · Journal of Molecular Medicine · doi:10.1007/s00109-004-0620-6 · Cited by 146 · see citing works
Repair of deaminated bases in DNA
Kow, Y. W. (2002) · Free Radical Biology and Medicine · doi:10.1016/s0891-5849(02)00902-4 · Cited by 143 · see citing works
Hepatitis C virus envelope proteins regulate CHOP via induction of the unfolded protein response
Chan, S., & Egan, P. A. (2005) · The FASEB Journal · doi:10.1096/fj.04-3455fje · Cited by 143 · see citing works
Dinucleotide and stop codon frequencies in single-stranded RNA viruses.
RIMA, B. K., & McFerran, N. V. (1997) · Journal of General Virology · doi:10.1099/0022-1317-78-11-2859 · Cited by 131 · see citing works
Sang, R. C., Gichogo, A., Gachoya, J., Dunster, M., Ofula, V., Hunt, A. R., Crabtree, M. B., Miller, B. R., & Dunster, L. M. (2003) · Archives of Virology · doi:10.1007/s00705-003-0018-8 · Cited by 130 · see citing works
Bukh, J., Apgar, C. L., & Yanagi, M. (1999) · Virology · doi:10.1006/viro.1999.9941 · Cited by 128 · see citing works
Pattern Recognition Receptors: From the Cell Surface to Intracellular Dynamics
Altenbach, D., & Robatzek, S. (2007) · Molecular Plant-Microbe Interactions · doi:10.1094/mpmi-20-9-1031 · Cited by 123 · see citing works
Cammisa-Parks, H., Cisar, L. A., Kane, A., & Stollar, V. (1992) · Virology · doi:10.1016/0042-6822(92)90575-a · Cited by 121 · see citing works
Billoir, F., de Micco, P., Tolou, H. J., de Chesse, R., de Lamballerie, X. N., & Gould, E. A. (2000) · Journal of General Virology · doi:10.1099/0022-1317-81-3-781 · Cited by 120 · see citing works
A target on the move: Innate and adaptive immune escape strategies of hepatitis C virus
Thimme, R., Lohmann, V., & Weber, F. (2006) · Antiviral Research · doi:10.1016/j.antiviral.2005.12.001 · Cited by 118 · see citing works
Forde, S. E., Thompson, J. N., Holt, R. D., & Bohannan, B. J. M. (2008) · Evolution · doi:10.1111/j.1558-5646.2008.00411.x · Cited by 115 · see citing works
Iqbal, M., Poole, E. L., Goodbourn, S., & McCauley, J. W. (2003) · Journal of Virology · doi:10.1128/jvi.78.1.136-145.2004 · Cited by 112 · see citing works
Evolution of Base Composition and Codon Usage Bias in the Genus Flavivirus
Jenkins, G. M., Pagel, M. D., Gould, E. A., Zanotto, P. M. D. A., & Holmes, E. C. (2001) · Journal of Molecular Evolution · doi:10.1007/s002390010168 · Cited by 111 · see citing works
Gregorio, G. V., Choudhuri, K., Yuan-fang Ma, A., Pensati, P., Iorio, R. F., Grant, P. R., Garson, J. A., Bogdanos, D. P., Vegnente, A., Mieli‐Vergani, G., et al. (2003) · Clinical & Experimental Immunology · doi:10.1046/j.1365-2249.2003.02229.x · Cited by 111 · see citing works
Cell-specific adaptation of two flaviviruses following serial passage in mosquito cell culture
Ciota, A. T., Lovelace, A. O., Ngo, K. A., Le, A. N., Maffei, J. G., Franke, M. A., Payne, A. F., Jones, S. A., Kauffman, E. B., & Kramer, L. D. (2006) · Virology · doi:10.1016/j.virol.2006.08.005 · Cited by 110 · see citing works
Novella, I. S., Clarke, D. K., Quer, J., Duarte, E. A., Lee, C. H., Weaver, S. C., Elena, S. F., Moyá, A., Domingo, E., & Holland, J. J. (1995) · Journal of Virology · doi:10.1128/jvi.69.11.6805-6809.1995 · Cited by 109 · see citing works
Diverse functions of RNase L and implications in pathology
Bisbal, C., & Silverman, R. H. (2007) · Biochimie · doi:10.1016/j.biochi.2007.02.006 · Cited by 104 · see citing works
Presence and role of cytosine methylation in DNA viruses of animals
Hoelzer, K., Shackelton, L. A., & Parrish, C. R. (2008) · Nucleic Acids Research · doi:10.1093/nar/gkn121 · Cited by 103 · see citing works
Genome-scale relationships between cytosine methylation and dinucleotide abundances in animals
Simmen, M. W. (2008) · Genomics · doi:10.1016/j.ygeno.2008.03.009 · Cited by 101 · see citing works
Seago, J. E., Hilton, L. S., Reid, E., Doceul, V., Jeyatheesan, J., Moganeradj, K., McCauley, J. W., Charleston, B., & Goodbourn, S. (2007) · Journal of General Virology · doi:10.1099/vir.0.82934-0 · Cited by 98 · see citing works
Fascination with 2-5A-Dependent RNase: A Unique Enzyme That Functions in Interferon Action*
Silverman, R. H. (1994) · Journal of Interferon Research · doi:10.1089/jir.1994.14.101 · Cited by 93 · see citing works
Searching NCBI Databases Using Entrez
Gibney, G., & Baxevanis, A. D. (2011) · Current Protocols in Bioinformatics · doi:10.1002/0471250953.bi0103s34 · Cited by 83 · see citing works
Schweizer, M., Mätzener, P., Pfaffen, G., Stalder, H., & Peterhans, E. (2006) · Journal of Virology · doi:10.1128/jvi.02443-05 · Cited by 83 · see citing works
A call to arms: coevolution of animal viruses and host innate immune responses
Marques, J. T., & Carthew, R. W. (2007) · Trends in Genetics · doi:10.1016/j.tig.2007.04.004 · Cited by 82 · see citing works
The universal virus database ICTVdB
Büchen-Osmond, C. (2003) · Computing in Science & Engineering · doi:10.1109/mcise.2003.1196303 · Cited by 74 · see citing works
Genome sequence analysis of Tamana bat virus and its relationship with the genus Flavivirus
de Lamballerie, X. N., Crochu, S., Billoir, F., Neyts, J. H., de Micco, P., Holmes, E. C., & Gould, E. A. (2002) · Journal of General Virology · doi:10.1099/0022-1317-83-10-2443 · Cited by 74 · see citing works
Ticks Associated with Macquarie Island Penguins Carry Arboviruses from Four Genera
Major, L. D., Linn, M. L., Slade, R., Schroder, W. A., Hyatt, A. D., Gardner, J., Cowley, J. A., & Suhrbier, A. (2009) · PLoS ONE · doi:10.1371/journal.pone.0004375 · Cited by 72 · see citing works
Clinical application of CpG-, non-CpG-, and antisense oligodeoxynucleotides as immunomodulators.
Dorn, A., & Kippenberger, S. (2008) · PubMed · Cited by 72 · see citing works
Host Range Specificity of Flaviviruses: Correlation with In Vitro Replication
Kuno, G. (2007) · Journal of Medical Entomology · doi:10.1093/jmedent/41.5.93 · Cited by 70 · see citing works
Bacon, B. R., & Bisceglie, A. M. D. (2001) · New England Journal of Medicine · doi:10.1056/nejm200111083451914 · Cited by 67 · see citing works
Hepatitis C virus RNA: Dinucleotide frequencies and cleavage by RNase L
Washenberger, C. L., Han, J.-Q., Kechris, K. J., Jha, B. K., Silverman, R. H., & Barton, D. J. (2007) · Virus Research · doi:10.1016/j.virusres.2007.05.020 · Cited by 63 · see citing works
Han, J.-Q., Wroblewski, G., Xu, Z., Silverman, R. H., & Barton, D. J. (2004) · Journal of Interferon & Cytokine Research · doi:10.1089/jir.2004.24.664 · Cited by 62 · see citing works
Inhibition of Viruses by RNA Interference
Stram, Y., & Kuzntzova, L. (2006) · Virus Genes · doi:10.1007/s11262-005-6914-0 · Cited by 62 · see citing works
Unapparent virus infection and host fitness in three weedy grass species
Remold, S. K. (2002) · Journal of Ecology · doi:10.1046/j.1365-2745.2002.00731.x · Cited by 55 · see citing works
Skew of Mononucleotide Frequencies, Relative Abundance of Dinucleotides, and DNA Strand Asymmetry
Shioiri, C., & Takahata, N. (2001) · Journal of Molecular Evolution · doi:10.1007/s002390010226 · Cited by 52 · see citing works
Pervasive properties of the genomic signature
Jernigan, R. W., & Baran, R. H. (2002) · BMC Genomics · doi:10.1186/1471-2164-3-23 · Cited by 48 · see citing works
Yomo, T., & Ohno, S. (1989) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.86.21.8452 · Cited by 45 · see citing works
Modulation of Toll‐like Receptor 9 Responses through Synthetic Immunostimulatory Motifs of DNA
Agrawal, S., & Kandimalla, E. R. (2003) · Annals of the New York Academy of Sciences · doi:10.1196/annals.1281.005 · Cited by 43 · see citing works
Molecular cloning and disease association of hepatitis G virus: a transfusion-transmissible agent
(1997) · Transfusion Medicine Reviews · doi:10.1016/s0887-7963(97)80026-0 · Cited by 43 · see citing works
Ngoye virus: a novel evolutionary lineage within the genus Flavivirus
Grard, G., Lemasson, J., Sylla, M., Dubot, A., Cook, S., Molez, J.-F., Pourrut, X., Charrel, R. N., Gonzalez, J., Munderloh, U. G., et al. (2006) · Journal of General Virology · doi:10.1099/vir.0.82071-0 · Cited by 39 · see citing works
Immunoglobulin mimicry by Hepatitis C Virus envelope protein E2
Hu, Y., Rocheleau, L., Larke, B., Chui, L., Lee, B. E., Ma, M. M., Liu, S., Omlin, T., Pelchat, M., & Brown, E. G. (2005) · Virology · doi:10.1016/j.virol.2004.11.041 · Cited by 35 · see citing works
CpG and TpA frequencies in the plant system
Bougraa, M., & Perrin, P. (1987) · Nucleic Acids Research · doi:10.1093/nar/15.14.5729 · Cited by 34 · see citing works
Molecules consolidate the placental mammal tree
Springer, M. S. (2004) · Trends in Ecology & Evolution · doi:10.1016/s0169-5347(04)00142-9 · Cited by 31 · see citing works
Gender-specific selection on codon usage in plant genomes
Whittle, C.-A., Malik, M. R., & Krochko, J. E. (2007) · BMC Genomics · doi:10.1186/1471-2164-8-169 · Cited by 28 · see citing works
Relationship between Retroviral Replication and RNA Interference MachineriesPreprint
Moelling, K., Matskevich, A. A., & Jung-Shiu, J. (2006) · Cold Spring Harbor Symposia on Quantitative Biology · doi:10.1101/sqb.2006.71.010 · Cited by 24 · see citing works
Billoir, F., de Chesse, R., Tolou, H. J., de Micco, P., Gould, E. A., & de Lamballerie, X. N. (2000) · Journal of General Virology · doi:10.1099/0022-1317-81-9-2339 · Cited by 21 · see citing works
Viral Pathogenesis, Modulation of Immune Receptor Signaling and Treatment
Kim, W. M., & Sigalov, A. B. (2008) · Advances in experimental medicine and biology · doi:10.1007/978-0-387-09789-3_22 · Cited by 20 · see citing works
Further progress in ICTVdB, a universal virus database.
Büchen-Osmond, C. (1997) · PubMed · Cited by 17 · see citing works
Searching NCBI Databases Using Entrez
Baxevanis, A. D. (2008) · Current Protocols in Bioinformatics · doi:10.1002/0471250953.bi0103s24 · Cited by 13 · see citing works
Flagged first, then by citations
2 of the 98 references couldn’t be matched to a known paper.
Research works printed but not linked: 2
- [16]Belshaw R de Oliveira T Markowitz S Rambaut A 2009 The RNA virus database. Nucleic Acids Res 37 D431 435 18948277 PMC2686580
- [86]Benson DA Karsch-Mizrachi I Lipman DJ Ostell J Sayers EW 2008 GenBank. Nucleic Acids Res PMC2686462 18940867
Cited by
Sorted by citations
Bente, D. A., Forrester, N. L., Watts, D. M., McAuley, A. J., Whitehouse, C. A., & Bray, M. (2013) · Antiviral Research · doi:10.1016/j.antiviral.2013.07.006 · Cited by 1,150 · see citing works
Randhawa, G. S., Soltysiak, M. P. M., El Roz, H., de Souza, C. P. E., Hill, K. A., & Kari, L. (2020) · PLOS ONE · doi:10.1371/journal.pone.0232391 · Cited by 1,023 · see citing works
Blitvich, B., & Firth, A. (2015) · Viruses · doi:10.3390/v7041927 · Cited by 323 · see citing works
Genome-Wide Analysis of Codon Usage and Influencing Factors in Chikungunya Viruses
Butt, A. M., Nasrullah, I., & Tong, Y. (2014) · PLoS ONE · doi:10.1371/journal.pone.0090905 · Cited by 208 · see citing works
Atkinson, N. J., Witteveldt, J., Evans, D. J., & Simmonds, P. (2014) · Nucleic Acids Research · doi:10.1093/nar/gku075 · Cited by 192 · see citing works
Predicting reservoir hosts and arthropod vectors from evolutionary signatures in RNA virus genomes
Babayan, S. A., Orton, R. J., & Streicker, D. G. (2018) · Science · doi:10.1126/science.aap9072 · Cited by 192 · see citing works
Hess, A. M., Prasad, A. N., Ptitsyn, A. A., Ebel, G. D., Olson, K. E., Bárbácioru, C., Monighetti, C. K., & Campbell, C. L. (2011) · BMC Microbiology · doi:10.1186/1471-2180-11-45 · Cited by 191 · see citing works
Emerging Role of Zika Virus in Adverse Fetal and Neonatal Outcomes
Panchaud, A., Stojanov, M., Ammerdorffer, A., Vouga, M., & Baud, D. (2016) · Clinical Microbiology Reviews · doi:10.1128/cmr.00014-16 · Cited by 171 · see citing works
Molecular evolution of the insect-specific flaviviruses
Cook, S., Moureau, G., Kitchen, A., Gould, E. A., de Lamballerie, X. N., Holmes, E. C., & Harbach, R. E. (2011) · Journal of General Virology · doi:10.1099/vir.0.036525-0 · Cited by 168 · see citing works
Codon Pair Bias Is a Direct Consequence of Dinucleotide Bias
Kunec, D., & Osterrieder, N. (2016) · Cell Reports · doi:10.1016/j.celrep.2015.12.011 · Cited by 159 · see citing works
“viruses are exposed to different selection pressures and that the pressure is imposed by the respective hosts (Lobo et al., 2009).”
BackgroundMethodInfluentialKenney, J. L., Solberg, O. D., Langevin, S. A., & Brault, A. C. (2014) · Journal of General Virology · doi:10.1099/vir.0.068031-0 · Cited by 156 · see citing works
G-quadruplex forming sequences in the genome of all known human viruses: A comprehensive guide
Lavezzo, E., Berselli, M., Frasson, I., Perrone, R., Palù, G., Brazzale, A. R., Richter, S. N., & Toppo, S. (2018) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1006675 · Cited by 151 · see citing works
Newman, C. M., Cerutti, F., Anderson, T. K., Hamer, G. L., Walker, E. D., Kitron, U. D., Ruiz, M. O., Brawn, J. D., & Goldberg, T. L. (2011) · Vector-Borne and Zoonotic Diseases · doi:10.1089/vbz.2010.0144 · Cited by 140 · see citing works
Inferring the hosts of coronavirus using dual statistical models based on nucleotide composition
Tang, Q., Song, Y., Shi, M., Cheng, Y., Zhang, W., & Xia, X.-Q. (2015) · Scientific Reports · doi:10.1038/srep17155 · Cited by 122 · see citing works
Nasrullah, I., Butt, A. M., Tahir, S., Idrees, M., & Tong, Y. (2015) · BMC Evolutionary Biology · doi:10.1186/s12862-015-0456-4 · Cited by 121 · see citing works
Dinucleotide Composition in Animal RNA Viruses Is Shaped More by Virus Family than by Host Species
Giallonardo, F. D., Schlub, T. E., Shī, M., & Holmes, E. C. (2017) · Journal of Virology · doi:10.1128/jvi.02381-16 · Cited by 119 · see citing works
Vertebrate Reservoirs of Arboviruses: Myth, Synonym of Amplifier, or Reality?
Kuno, G., Mackenzie, J., Junglen, S., Hubálek, Z., Plyusnin, A., & Gubler, D. J. (2017) · Viruses · doi:10.3390/v9070185 · Cited by 117 · see citing works
CpG Usage in RNA Viruses: Data and Hypotheses
Cheng, X., Virk, N., Chen, W., Shu-qin, J., Shu-xian, J., Sun, Y., & Wu, X. (2013) · PLoS ONE · doi:10.1371/journal.pone.0074109 · Cited by 116 · see citing works
Schweizer, M., & Peterhans, E. (2013) · Annual Review of Animal Biosciences · doi:10.1146/annurev-animal-022513-114209 · Cited by 115 · see citing works
The Distribution of Synonymous Codon Choice in the Translation Initiation Region of Dengue Virus
Zhou, J.-H., Zhang, J., Sun, D., Ma, Q., Chen, H.-T., Ma, L.-N., Ding, Y., & Liu, Y. (2013) · PLoS ONE · doi:10.1371/journal.pone.0077239 · Cited by 99 · see citing works
Functional RNA during Zika virus infection
Göertz, G. P., Abbo, S. R., Fros, J. J., & Pijlman, G. P. (2017) · Virus Research · doi:10.1016/j.virusres.2017.08.015 · Cited by 95 · see citing works
Peter Simmonds, K., Xia, W., Baillie, J. K., & McKinnon, K. I. M. (2013) · BMC Genomics · doi:10.1186/1471-2164-14-610 · Cited by 92 · see citing works
Genome-wide analysis of codon usage bias in Ebolavirus
Cristina, J., Moreno, P., Moratorio, G., & Musto, H. (2014) · Virus Research · doi:10.1016/j.virusres.2014.11.005 · Cited by 86 · see citing works
Use of Nucleotide Composition Analysis To Infer Hosts for Three Novel Picorna-Like Viruses
Kapoor, A., Simmonds, P., Lipkin, W., Zaidi, S. S., & Delwart, E. (2010) · Journal of Virology · doi:10.1128/jvi.00601-10 · Cited by 87 · see citing works
Mechanisms underlying the inhibition of interferon signaling by viruses
Devasthanam, A. S. (2014) · Virulence · doi:10.4161/viru.27902 · Cited by 79 · see citing works
A detailed comparative analysis on the overall codon usage patterns in West Nile virus
Moratorio, G., Iriarte, A., Moreno, P., Musto, H., & Cristina, J. (2013) · Infection Genetics and Evolution · doi:10.1016/j.meegid.2013.01.001 · Cited by 79 · see citing works
Maruyama, S. R., de Castro-Jorge, L. A., Ribeiro, J. M. C., Gardinassi, L. G., Garcia, G. R., Brandão, L. G., Rodrigues, A. R., Okada, M. I., Abrão, E. P., Ferreira, B. R., et al. (2014) · Memórias do Instituto Oswaldo Cruz · doi:10.1590/0074-0276130166 · Cited by 76 · see citing works
Colmant, A. M. G., Hobson‐Peters, J., Bielefeldt‐Ohmann, H., van den Hurk, A. F., Hall‐Mendelin, S., Chow, W. K., Johansen, C. A., Fros, J. J., Peter Simmonds, K., Watterson, D., et al. (2017) · mSphere · doi:10.1128/msphere.00262-17 · Cited by 75 · see citing works
Nucleotide composition of the Zika virus RNA genome and its codon usage
van Hemert, F. J., & Berkhout, B. (2016) · Virology Journal · doi:10.1186/s12985-016-0551-1 · Cited by 71 · see citing works
Coordinated Rates of Evolution between Interacting Plastid and Nuclear Genes in Geraniaceae
Zhang, J., Ruhlman, T. A., Sabir, J. S. M., Blazier, J. C., & Jansen, R. K. (2015) · The Plant Cell · doi:10.1105/tpc.114.134353 · Cited by 67 · see citing works
Predicting host taxonomic information from viral genomes: A comparison of feature representations
Young, F., Rogers, S., & Robertson, D. L. (2020) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1007894 · Cited by 63 · see citing works
Chen, Y. (2013) · BioMed Research International · doi:10.1155/2013/406342 · Cited by 63 · see citing works
Viral Genome Size Distribution Does not Correlate with the Antiquity of the Host Lineages
Campillo-Balderas, J. A., Lazcano, A., & Becerra, A. (2015) · Frontiers in Ecology and Evolution · doi:10.3389/fevo.2015.00143 · Cited by 62 · see citing works
Parry, R. H., & Sassan Asgari, B. (2019) · Journal of Virology · doi:10.1128/jvi.00432-19 · Cited by 62 · see citing works
Fros, J. J., Dietrich, I., Alshaikhahmed, K., Passchier, T. C., Evans, D. J., & Peter Simmonds, K. (2017) · eLife · doi:10.7554/elife.29112 · Cited by 58 · see citing works
Analysis of codon usage bias of Crimean-Congo hemorrhagic fever virus and its adaptation to hosts
Rahman, S. U., Yao, X., Li, X., Chen, D., & Tao, S. (2017) · Infection Genetics and Evolution · doi:10.1016/j.meegid.2017.11.027 · Cited by 59 · see citing works
Kolekar, P. S., Kale, M. M., & Kulkarni‐Kale, U. (2012) · Molecular Phylogenetics and Evolution · doi:10.1016/j.ympev.2012.07.003 · Cited by 58 · see citing works
Goldberg, T. L., Bennett, A. J., Kityo, R., Kuhn, J. H., & Chapman, C. A. (2017) · Scientific Reports · doi:10.1038/s41598-017-05236-w · Cited by 55 · see citing works
Tse, H., Chan, W.-M., Li, K. S. M., Lau, S. K. P., Woo, P. C. Y., & Yuen, K. (2012) · PLoS ONE · doi:10.1371/journal.pone.0034987 · Cited by 53 · see citing works
Severson, D. W., & Behura, S. K. (2016) · Insects · doi:10.3390/insects7040058 · Cited by 53 · see citing works
Sequence-Specific Sensing of Nucleic Acids
Vabret, N., Bhardwaj, N., & Greenbaum, B. D. (2017) · Trends in Immunology · doi:10.1016/j.it.2016.10.006 · Cited by 45 · see citing works
A detailed comparative analysis of codon usage bias in Zika virus
Cristina, J., Fajardo, Á., Sóñora, M., Moratorio, G., & Musto, H. (2016) · Virus Research · doi:10.1016/j.virusres.2016.06.022 · Cited by 51 · see citing works
Codon usage roles in human papillomavirus
Zhao, K., & Chen, J. (2011) · Reviews in Medical Virology · doi:10.1002/rmv.707 · Cited by 46 · see citing works
Xia, H., Beck, A. S., Gargılı, A., Forrester, N. L., Barrett, A. D. T., & Bente, D. A. (2016) · Scientific Reports · doi:10.1038/srep35819 · Cited by 46 · see citing works
Transmission bottlenecks and RNAi collectively influence tick-borne flavivirus evolution
Grubaugh, N. D., Rückert, C., Armstrong, P. M., Bransfield, A. B., Anderson, J. F., Ebel, G. D., & Brackney, D. E. (2016) · Virus Evolution · doi:10.1093/ve/vew033 · Cited by 45 · see citing works
Segundo, F. D.-S., Medina, G. N., Ramírez-Medina, E., Velázquez-Salinas, L., Koster, M. J., Grubman, M. J., & Santos, T. D. L. (2015) · Journal of Virology · doi:10.1128/jvi.02167-15 · Cited by 48 · see citing works
Wu, L., Pappas, N., Wijesekara, Y., Piedade, G. J., Brussaard, C. P. D., & Dutilh, B. E. (2024) · Genome biology · doi:10.1186/s13059-024-03236-4 · Cited by 42 · see citing works
Goñi, N., Iriarte, A., Comas, V., Sóñora, M., Moreno, P., Moratorio, G., Musto, H., & Cristina, J. (2012) · Virology Journal · doi:10.1186/1743-422x-9-263 · Cited by 42 · see citing works
Molecular Basis for Arbovirus Transmission by Aedes aegypti Mosquitoes
Alonso-Palomares, L. A., Moreno‐García, M., Lanz‐Mendoza, H., & Salazar, M. I. (2018) · Intervirology · doi:10.1159/000499128 · Cited by 42 · see citing works
Oberemok, V. V., Laikova, K. V., Yurchenko, K. A., Marochkin, N. A., Фомочкина, И. И., & Kubyshkin, A. V. (2020) · Inflammation Research · doi:10.1007/s00011-020-01377-3 · Cited by 40 · see citing works
Fros, J. J., Visser, I., Tang, B., Yan, K., Nakayama, E., Visser, T. M., Koenraadt, C. J. M., van Oers, M. M., Pijlman, G. P., Suhrbier, A., et al. (2021) · PLoS Biology · doi:10.1371/journal.pbio.3001201 · Cited by 40 · see citing works
Codon usage and codon context bias in Xanthophyllomyces dendrorhous
Baeza, M., Alcaı́no, J., Barahona, S., Sepúlveda, D., & Cifuentes, V. (2015) · BMC Genomics · doi:10.1186/s12864-015-1493-5 · Cited by 39 · see citing works
Dating the origin of the genus Flavivirus in the light of Beringian biogeography
Pettersson, J. H. ‐., & Fiz-Palacios, O. (2014) · Journal of General Virology · doi:10.1099/vir.0.065227-0 · Cited by 39 · see citing works
Co-circulation of Aedes flavivirus, Culex flavivirus, and Quang Binh virus in Shanghai, China
Fang, Y., Zhang, Y., Zhou, Z., Shi, W., Xia, S., Li, Y., Wu, J., Liu, Q., & Lin, G.-Y. (2018) · Infectious Diseases of Poverty · doi:10.1186/s40249-018-0457-9 · Cited by 38 · see citing works
A detailed comparative analysis on the overall codon usage patterns in Hepatitis A virus
Andrea, L. D., Pintó, R. M., Bosch, A., Musto, H., & Cristina, J. (2011) · Virus Research · doi:10.1016/j.virusres.2011.01.012 · Cited by 37 · see citing works
Discovery of Mwinilunga alphavirus: A novel alphavirus in Culex mosquitoes in Zambia
Torii, S., Orba, Y., Hang’ombe, B. M., Mweene, A. S., Wada, Y., Anindita, P. D., Phongphaew, W., Qiu, Y., Kajihara, M., Mori‐Kajihara, A., et al. (2018) · Virus Research · doi:10.1016/j.virusres.2018.04.005 · Cited by 36 · see citing works
Host Taxon Predictor - A Tool for Predicting Taxon of the Host of a Newly Discovered Virus
Gałan, W., Bąk, M., & Jakubowska, M. (2019) · Scientific Reports · doi:10.1038/s41598-019-39847-2 · Cited by 35 · see citing works
Effects of Arbovirus Multi-Host Life Cycles on Dinucleotide and Codon Usage Patterns
Sexton, N. R., & Ebel, G. D. (2019) · Viruses · doi:10.3390/v11070643 · Cited by 35 · see citing works
Compositional biases in RNA viruses: Causes, consequences and applications
Gaunt, E. R., & Digard, P. (2021) · Wiley Interdisciplinary Reviews - RNA · doi:10.1002/wrna.1679 · Cited by 34 · see citing works
RNA editing by the host ADAR system affects the molecular evolution of the Zika virus
Piontkivska, H., Frederick, M., Miyamoto, M. M., & Wayne, M. L. (2017) · Ecology and Evolution · doi:10.1002/ece3.3033 · Cited by 33 · see citing works
Fonseca, P. L. C., Ferreira, F. V., da Silva, F. R., Oliveira, L. S., Marques, J. T., Goés‐Neto, A., Aguiar, E. R. G. R., & Gruber, A. (2020) · Viruses · doi:10.3390/v13010009 · Cited by 33 · see citing works
Specific and Nonspecific Host Adaptation during Arboviral Experimental Evolution
Novella, I. S., Presloid, J. B., Smith, S. D., & Wilke, C. O. (2011) · Microbial Physiology · doi:10.1159/000332752 · Cited by 31 · see citing works
Vlachakis, D., Koumandou, V. L., & Κοσσίδα, Σ. (2013) · PeerJ · doi:10.7717/peerj.74 · Cited by 31 · see citing works
Codon usage bias in human cytomegalovirus and its biological implication
Hu, C., Chen, J., Ye, L., Chen, R., Zhang, L., & Xue, X. (2014) · Gene · doi:10.1016/j.gene.2014.05.018 · Cited by 30 · see citing works
Lara-Ramirez, E. E., Salazar, M. I., López-López, M. D. J., Salas-Benito, J. S., Sánchez-Varela, A., & Guo, X. (2014) · BioMed Research International · doi:10.1155/2014/851425 · Cited by 29 · see citing works
Isolation of a novel insect-specific flavivirus with immunomodulatory effects in vertebrate systems
Auguste, A. J., Langsjoen, R. M., Porier, D. L., Erasmus, J. H., Bergren, N. A., Bolling, B. G., Luo, H., Singh, A., Guzmán, H., Popov, V. L., et al. (2021) · Virology · doi:10.1016/j.virol.2021.07.004 · Cited by 28 · see citing works
Behura, S. K., & Severson, D. W. (2013) · BMC Microbiology · doi:10.1186/1471-2180-13-37 · Cited by 29 · see citing works
Newman, C. M., Anderson, T. K., & Goldberg, T. L. (2015) · Journal of Medical Entomology · doi:10.1093/jme/tjv161 · Cited by 28 · see citing works
Ortiz, J. F., MacDonald, M. L., Masterson, P., Uversky, V. N., & Siltberg-Liberles, J. (2013) · Genome Biology and Evolution · doi:10.1093/gbe/evt026 · Cited by 27 · see citing works
Colmant, A. M. G., Hobson‐Peters, J., Slijkerman, T. A. P., Harrison, J. J., Pijlman, G. P., van Oers, M. M., Peter Simmonds, K., Hall, R. A., & Fros, J. J. (2021) · Viruses · doi:10.3390/v13040573 · Cited by 26 · see citing works
da Silva, F. S., Cruz, A. C. R., Medeiros, D. B. D. A., da Silva, S. P., Nunes, M. R. T., Martins, L. C., Chiang, J. O., Lemos, P. D. S., Cunha, G. M., de Araújo, R. F., et al. (2020) · Scientific Reports · doi:10.1038/s41598-020-73790-x · Cited by 25 · see citing works
Haridevamuthu, B., Guru, A., Sudhakaran, G., Murugan, R., Arshad, A., & Arockiaraj, J. (2021) · Reviews in Aquaculture · doi:10.1111/raq.12613 · Cited by 25 · see citing works
Adhya, D., Dutta, K., Kundu, K., & Basu, A. (2013) · Immunobiology · doi:10.1016/j.imbio.2013.04.018 · Cited by 25 · see citing works
High codon adaptation in citrus tristeza virus to its citrus host
Cheng, X., Wu, X., Wang, H., Sun, Y., Qian, Y.-S., & Luo, L. (2012) · Virology Journal · doi:10.1186/1743-422x-9-113 · Cited by 24 · see citing works
Selective Factors Associated with the Evolution of Codon Usage in Natural Populations of Arboviruses
Velázquez-Salinas, L., Zárate, S., Eschbaumer, M., Lobo, F. P., Gladue, D. P., Arzt, J., Novella, I. S., & Rodrı́guez, L. L. (2016) · PLoS ONE · doi:10.1371/journal.pone.0159943 · Cited by 23 · see citing works
Self-citationPriya, S. P., Sakinah, S., Kumari, S., Hamat, R. A., Sekawi, Z., Higuchi, A., Ling, M. P., Nordin, S. A., Benelli, G., & Kumar, S. S. (2017) · Acta Tropica · doi:10.1016/j.actatropica.2017.08.007 · Cited by 22 · see citing works
Lúcio, F. N. M., da Silva, J. E., Marinho, E. M., Mendes, F. R. D. S., Marinho, M. M., & Marinho, E. S. (2020) · International Journal of Research -GRANTHAALAYAH · doi:10.29121/granthaalayah.v8.i1.2020.270 · Cited by 22 · see citing works
Rapid Evolution of Enhanced Zika Virus Virulence during Direct Vertebrate Transmission Chains
Riemersma, K. K., Jaeger, A. S., Crooks, C. M., Braun, K. M., Weger‐Lucarelli, J., Ebel, G. D., Friedrich, T. C., & Aliota, M. T. (2021) · Journal of Virology · doi:10.1128/jvi.02218-20 · Cited by 22 · see citing works
Yu, D., Zhao, Z., Yang, Y., Yu, Q. P., Pan, D., Yuan, L., Huang, Y., & Wang, B. (2023) · Journal of Medical Virology · doi:10.1002/jmv.28672 · Cited by 21 · see citing works
Chen, G., Jiang, J., & Sun, Y. (2024) · GigaScience · doi:10.1093/gigascience/giae059 · Cited by 20 · see citing works
Genetic and codon usage bias analyses of major capsid protein gene in Ranavirus
Tian, H., Hu, Q., Xiao, H., Zeng, L., Meng, Y., & Zhong, L. (2020) · Infection Genetics and Evolution · doi:10.1016/j.meegid.2020.104379 · Cited by 20 · see citing works
Dengue virus preferentially uses human and mosquito non-optimal codons
Castellano, L. A., McNamara, R. J., Pallarés, H. M., Gamarnik, A. V., Alvarez, D. E., & Bazzini, A. (2024) · Molecular Systems Biology · doi:10.1038/s44320-024-00052-7 · Cited by 20 · see citing works
Host influence in the genomic composition of flaviviruses: A multivariate approach
Simón, D., Fajardo, Á., Sóñora, M., Delfraro, A., & Musto, H. (2017) · Biochemical and Biophysical Research Communications · doi:10.1016/j.bbrc.2017.06.088 · Cited by 20 · see citing works
Behura, S. K., & Severson, D. W. (2012) · Infection Genetics and Evolution · doi:10.1016/j.meegid.2012.04.027 · Cited by 19 · see citing works
Ma, X., Chang, Q., Ma, P., Li, L., Zhou, X., Zhang, D., Li, M., Cao, X., & Ma, Z. (2017) · Gene · doi:10.1016/j.gene.2017.09.045 · Cited by 19 · see citing works
The Genomic Signature of Human Rhinoviruses A, B and C
Megremis, S., Demetriou, P., Makrinioti, H., Manoussaki, A., & Papadopoulos, N. G. (2012) · PLoS ONE · doi:10.1371/journal.pone.0044557 · Cited by 19 · see citing works
Odon, V., Fiddaman, S. R., Smith, A. L., & Peter Simmonds, K. (2022) · RNA · doi:10.1261/rna.079102.122 · Cited by 17 · see citing works
Codon bias of influenza a viruses and their hosts
Fancher, K. C., & Hu, W. (2011) · American Journal of Molecular Biology · doi:10.4236/ajmb.2011.13017 · Cited by 17 · see citing works
Gómez, M. M., Tort, L. F. L., Volotão, E. D. M., Recarey, R., Moratorio, G., Musto, H., Leite, J. P. G., & Cristina, J. (2011) · Infection Genetics and Evolution · doi:10.1016/j.meegid.2011.01.006 · Cited by 17 · see citing works
Homology-Independent Metrics for Comparative Genomics
Coutinho, T. J. D., Franco, G. R., & Lobo, F. P. (2015) · Computational and Structural Biotechnology Journal · doi:10.1016/j.csbj.2015.04.005 · Cited by 17 · see citing works
Self-citationGoz, E., Zafrir, Z., & Tuller, T. (2018) · Bioinformatics · doi:10.1093/bioinformatics/bty351 · Cited by 16 · see citing works
Altering Compositional Properties of Viral Genomes to Design Live-Attenuated Vaccines
Pereira-Gómez, M., Carrau, L., Fajardo, Á., Moreno, P., & Moratorio, G. (2021) · Frontiers in Microbiology · doi:10.3389/fmicb.2021.676582 · Cited by 16 · see citing works
Rice black-streaked dwarf virus Genome in China: Diversification, Phylogeny, and Selection
Zhou, Y. G., Zhang, L., Zhang, X., Zu, H., Di, H., Dong, L., Liu, X., Zeng, X., Weng, J., Wang, Z., et al. (2017) · Plant Disease · doi:10.1094/pdis-12-16-1814-re · Cited by 16 · see citing works
Kumar, N., Kaushik, R., Tennakoon, C., Uversky, V. N., Longhi, S., Zhang, K. Y. J., & Bhatia, S. (2021) · Briefings in Bioinformatics · doi:10.1093/bib/bbab145 · Cited by 16 · see citing works
Zhou, J., Xing, Y., Zhou, Z. C., & Wang, S. (2023) · Frontiers in Microbiology · doi:10.3389/fmicb.2022.967999 · Cited by 14 · see citing works
Deep decoding of codon usage strategies and host adaption preferences of soybean mosaic virus
Jiang, L., Zhang, Q., Xiao, S., & Si, F. (2022) · International Journal of Biological Macromolecules · doi:10.1016/j.ijbiomac.2022.09.179 · Cited by 14 · see citing works
Base composition, adaptation, and evolution of goose astroviruses: codon-based investigation
Guo, F., Yang, J., El‐Aty, A. M. A., Wang, R., & Ju, X. (2023) · Poultry Science · doi:10.1016/j.psj.2023.103029 · Cited by 14 · see citing works
Clustering of low usage codons in the translation initiation region of hepatitis C virus
Zhou, J.-H., Su, J.-H., Chen, H.-T., Zhang, J., Ma, L.-N., Ding, Y., Stipkovits, L., Szathmáry, S., PEJSAK, Z., & Liu, Y. (2013) · Infection Genetics and Evolution · doi:10.1016/j.meegid.2013.03.043 · Cited by 14 · see citing works
Ma, X., FENG, Y.-P., Bai, J., ZHANG, D.-R., LIN, X.-S., & Ma, Z. (2015) · Journal of Genetics · doi:10.1007/s12041-015-0512-2 · Cited by 14 · see citing works
FLAVi: An Enhanced Annotator for Viral Genomes of Flaviviridae
Schneider, A. D. B., Machado, D. J., Guirales-Medrano, S., & Janies, D. A. (2020) · Viruses · doi:10.3390/v12080892 · Cited by 13 · see citing works
- Authors
- Lobo, F. P., Mota, B. E. F., Pena, S. D. J., Azevedo, V., Macedo, A. M., Tauch, A., Machado, C. R., & Franco, G. R.
- Affiliations
- Universidade Federal de Minas Gerais (BR)
- Bielefeld University (DE)
- Corresponding author
- Lobo, Francisco P.
- ORCID
- Venue
- PLoS ONE
- Publisher
- Public Library of Science (PLoS)
- Published
- 2009-07-20
- Volume
- 4
- Issue
- 7
- Pages
- e6282
- ISSN
- 1932-6203 (ISSN-L)
- PMC
- PMC2707012
- OpenAlex
- W1978006472
- Cited by
- 191
- References
- 98
- Citations by year
- 2026: 7 · 2025: 8 · 2024: 18 · 2023: 12 · 2022: 5 · 2021: 17 · 2020: 12 · 2019: 9 · 2018: 10 · 2017: 19 · 2016: 10 · 2015: 14 · 2014: 16 · 2013: 19 · 2012: 6
- FWCI
- 2.02
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Locations
- PLoS ONE (publishedVersion, cc-by)
- Europe PMC (PubMed Central) (publishedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
- Figshare (submittedVersion, cc-by)
- PUB – Publications at Bielefeld University (Bielefeld University) (submittedVersion)
- Publikationen an der Universität Bielefeld (Universität Bielefeld) (submittedVersion)
- Funders
- Coordenação de Aperfeiçoamento de Pessoal de Nível Superior
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA and protein synthesis mechanisms
- Health Sciences › Medicine › Public Health, Environmental and Occupational Health › Mosquito-borne diseases and control
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Evolution and Genetic Dynamics
- Keywords
- host-virus coevolution, Flaviviridae, codon usage bias, host-virus interaction, Hepacivirus, flavivirus, mosquito hosts, vertebrate hosts, DNA methylation
- MeSH terms
- Animals, Base Sequence, Codon, Disease Vectors, Biological Evolution, Phylogeny, Flaviviridae, Host-Pathogen Interactions
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
Are you an author, or do you see a problem with this page? Request a review
