Evolution of the genome and the genetic code: selection at the dinucleotide level by methylation and polyribonucleotide cleavage

A comprehensive set of sequence analysis programs for the VAX

Devereux, J., Haeberli, P. E., & Smithies, O. (1984) · Nucleic Acids Research · doi:10.1093/nar/12.1part1.387 · Cited by 14,222 · see citing works

A conserved AU sequence from the 3′ untranslated region of GM-CSF mRNA mediates selective mRNA degradation

Shaw, G. D., & Kamen, R. (1986) · Cell · doi:10.1016/0092-8674(86)90341-7 · Cited by 3,946 · see citing works

Identification of a common nucleotide sequence in the 3'-untranslated region of mRNA molecules specifying inflammatory mediators.

Caput, D., Beutler, B., Hartog, K., Thayer, R. M., Brown-Shimer, S. L., & Cerami, A. (1986) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.83.6.1670 · Cited by 1,516 · 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

The CpG dinucleotide and human genetic disease

Cooper, D. N., & Youssoufian, H. (1988) · Human Genetics · doi:10.1007/bf00278187 · Cited by 936 · see citing works

The sex-determining region of the human Y chromosome encodes a finger protein

Page, D. C., Mosher, R. A., Simpson, E. M., Fisher, E., Mardon, G., Pollack, J. R., McGillivray, B. C., de la Chapelle, A., & Brown, L. G. (1987) · Cell · doi:10.1016/0092-8674(87)90595-2 · Cited by 832 · see citing works

Synthetic oligonucleotide probes deduced from amino acid sequence data

Lathe, R. (1985) · Journal of Molecular Biology · doi:10.1016/0022-2836(85)90276-1 · Cited by 762 · see citing works

Enzymatic Synthesis of Deoxyribonucleic Acid

Josse, J., Kaiser, A. D., & Kornberg, A. (1961) · Journal of Biological Chemistry · doi:10.1016/s0021-9258(18)64321-2 · Cited by 756 · see citing works

BIOLOGICAL CATALYSIS BY RNA

Cech, T. R., & Bass, B. (1986) · Annual Review of Biochemistry · doi:10.1146/annurev.bi.55.070186.003123 · Cited by 560 · see citing works

Enzymatic Synthesis of Deoxyribonucleic Acid

Swartz, M. N., Trautner, T. A., & Kornberg, A. (1962) · Journal of Biological Chemistry · doi:10.1016/s0021-9258(19)73967-2 · Cited by 476 · see citing works

Recurrent mutations in haemophilia A give evidence for CpG mutation hotspots

Youssoufian, H., Kazazian, H. H., Phillips, D. G., Aronis, S., Tsiftis, G., Brown, V. A., & Antonarakis, S. E. (1986) · Nature · doi:10.1038/324380a0 · Cited by 262 · see citing works

Cotranslational insertion of selenocysteine into formate dehydrogenase from Escherichia coli directed by a UGA codon.

Zinoni, F., Birkmann, A., Leinfelder, W., & Böck, A. (1987) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.84.10.3156 · Cited by 237 · see citing works

NATURAL VARIATION IN THE GENETIC CODE

Fox, T. D. (1987) · Annual Review of Genetics · doi:10.1146/annurev.ge.21.120187.000435 · Cited by 158 · see citing works

Doublet frequencies in evolutionary distinct groups

Nussinov, R. (1984) · Nucleic Acids Research · doi:10.1093/nar/12.3.1749 · Cited by 150 · see citing works

Nearest neighbor nucleotide patterns. Structural and biological implications.

Nussinov, R. (1981) · Journal of Biological Chemistry · doi:10.1016/s0021-9258(19)68865-4 · Cited by 77 · see citing works

Strong doublet preferences in nucleotide sequences and DNA geometry

Nussinov, R. (1984) · Journal of Molecular Evolution · doi:10.1007/bf02257371 · Cited by 67 · see citing works

CpG frequency in large DNA segments

Lennon, G. G., & Fraser, N. W. (1983) · Journal of Molecular Evolution · doi:10.1007/bf02099976 · Cited by 20 · see citing works

Codon usage in Homo sapiens: Evidence for a coding pattern on the non-coding strand and evolutionary implications of dinucleotide discrimination

Alff-Steinberger, C. (1987) · Journal of Theoretical Biology · doi:10.1016/s0022-5193(87)80254-0 · Cited by 18 · see citing works

Doublet frequencies in the DNA of genetic code limit organisms

Elton, R. A. (1973) · Journal of Molecular Evolution · doi:10.1007/bf01654097 · Cited by 9 · see citing works

Dinucleotide frequencies in different reading frame positions of coding bacterial DNA sequences.

Santibanez‐Koref, M., & Jg, R. (1986) · PubMed · Cited by 5 · see citing works

Ten years of AFLP in ecology and evolution: why so few animals?

Bensch, S., & Åkesson, M. (2005) · Molecular Ecology · doi:10.1111/j.1365-294x.2005.02655.x · Cited by 675 · see citing works

Compositional biases of bacterial genomes and evolutionary implications

Karlin, S., Mrázek, J., & Campbell, A. (1997) · Journal of Bacteriology · doi:10.1128/jb.179.12.3899-3913.1997 · Cited by 442 · see citing works

The mutational spectrum of single base-pair substitutions causing human genetic disease: patterns and predictions

Cooper, D. N., & Krawczak, M. (1990) · Human Genetics · doi:10.1007/bf00276326 · Cited by 387 · see citing works

Over- and under-representation of short oligonucleotides in DNA sequences.

Burge, C., Campbell, A., & Karlin, S. (1992) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.89.4.1358 · Cited by 368 · see citing works

COMPARATIVE DNA ANALYSIS ACROSS DIVERSE GENOMES

Karlin, S., Campbell, A., & Mrázek, J. (1998) · Annual Review of Genetics · doi:10.1146/annurev.genet.32.1.185 · Cited by 363 · see citing works

Genomic signature: characterization and classification of species assessed by chaos game representation of sequences

Deschavanne, P., Giron, A., Vilain, J., Fagot, G., & Fertil, B. (1999) · Molecular Biology and Evolution · doi:10.1093/oxfordjournals.molbev.a026048 · Cited by 343 · see citing works

Evidence for selection on synonymous mutations affecting stability of mRNA secondary structure in mammals

Chamary, J., & Hurst, L. D. (2005) · Genome biology · doi:10.1186/gb-2005-6-9-r75 · Cited by 332 · see citing works

Translational Blockade Imposed by Cytokine-Derived UA-Rich Sequences

Kruys, V., Marinx, O., Shaw, G. D., Deschamps, J., & Huez, G. (1989) · Science · doi:10.1126/science.2672333 · Cited by 328 · see citing works

Why is CpG suppressed in the genomes of virtually all small eukaryotic viruses but not in those of large eukaryotic viruses?

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

DNA methylation and cancer

Jones, P. A. (2002) · Oncogene · doi:10.1038/sj.onc.1205597 · Cited by 321 · see citing works

Evolutionary Basis of Codon Usage and Nucleotide Composition Bias in Vertebrate DNA Viruses

Shackelton, L. A., Parrish, C. R., & Holmes, E. C. (2006) · Journal of Molecular Evolution · doi:10.1007/s00239-005-0221-1 · Cited by 307 · 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

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

Structure and Function of the Human Immunodeficiency Virus Leader RNA

Berkhout, B. (1996) · Progress in nucleic acid research and molecular biology · doi:10.1016/s0079-6603(08)60359-1 · Cited by 231 · see citing works

Global dinucleotide signatures and analysis of genomic heterogeneity

Karlin, S. (1998) · Current Opinion in Microbiology · doi:10.1016/s1369-5274(98)80095-7 · Cited by 212 · 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

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

Chance and Statistical Significance in Protein and DNA Sequence Analysis

Karlin, S., & Brendel, V. (1992) · Science · doi:10.1126/science.1621093 · Cited by 185 · see citing works

RNA virus attenuation by codon pair deoptimisation is an artefact of increases in CpG/UpA dinucleotide frequencies

Tulloch, F., Atkinson, N. J., Evans, D. J., Ryan, M. D., & Simmonds, P. (2014) · eLife · doi:10.7554/elife.04531 · Cited by 178 · see citing works

Genome-Scale Compositional Comparisons in EukaryotesPreprint

Gentles, A. J., & Karlin, S. (2001) · Genome Research · doi:10.1101/gr.163101 · Cited by 171 · see citing works

Genetic inactivation of poliovirus infectivity by increasing the frequencies of CpG and UpA dinucleotides within and across synonymous capsid region codons

Burns, C. C., Campagnoli, R., Shaw, J., Vincent, A., Jorba, J., & Kew, O. (2009) · Journal of Virology · doi:10.1128/jvi.00508-09 · Cited by 170 · see citing works

Heterogeneity of genomes: measures and values.

Karlin, S., Ladunga, I., & Blaisdell, B. E. (1994) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.91.26.12837 · Cited by 169 · see citing works

Analysis of Nipah Virus Codon Usage and Adaptation to Hosts

Khandia, R., Singhal, S., Kumar, U., Ansari, A. I., Tiwari, R., Dhama, K., Das, J., Munjal, A. K., & Singh, R. K. (2019) · Frontiers in Microbiology · doi:10.3389/fmicb.2019.00886 · Cited by 163 · 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

Codon Usage Bias Covaries With Expression Breadth and the Rate of Synonymous Evolution in Humans, but This Is Not Evidence for Selection

Urrutia, A. O., & Hurst, L. D. (2001) · Genetics · doi:10.1093/genetics/159.3.1191 · Cited by 158 · 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

Analysis of CpG suppression in methylated and nonmethylated species.

Schorderet, D. F., & Gartler, S. M. (1992) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.89.3.957 · Cited by 146 · see citing works

Sequences in the Coding Region of Clotting Factor VIII Act as Dominant Inhibitors of RNA Accumulation and Protein Production

Lynch, C. M., Israel, D. I., Kaufman, R. J., & Miller, A. D. (1993) · Human Gene Therapy · doi:10.1089/hum.1993.4.3-259 · Cited by 132 · 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

Spontaneous deamination of cytosine and 5-methylcytosine residues in DNA and replacement of 5-methylcytosine residues with cytosine residues

Ehrlich, M., Zhang, X., & Inamdar, N. M. (1990) · Mutation Research/Reviews in Genetic Toxicology · doi:10.1016/0165-1110(90)90019-8 · Cited by 127 · 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

Mammalian Mutation Pressure, Synonymous Codon Choice, and mRNA Degradation

Duan, J., & Antezana, M. A. (2003) · Journal of Molecular Evolution · doi:10.1007/s00239-003-2519-1 · Cited by 119 · see citing works

Codon usage and codon pair patterns in non-grass monocot genomes

Mazumdar, P., Othman, R. Y., Mebus, K., Ramakrishnan, N., & Harikrishna, J. A. (2017) · Annals of Botany · doi:10.1093/aob/mcx112 · Cited by 117 · see citing works

Preference of simple sequence repeats in coding and non-coding regions of Arabidopsis thaliana

Zhang, L., Yuan, D., Yu, S., Li, Z., Cao, Y., Miao, Z., Qian, H., & Tang, K. (2004) · Bioinformatics · doi:10.1093/bioinformatics/bth043 · Cited by 116 · see citing works

Structural and compositional features of untranslated regions of eukaryotic mRNAs

Pesole, G., Liuni, S., Grillo, G., & Saccone, C. (1997) · Gene · doi:10.1016/s0378-1119(97)00407-1 · Cited by 108 · see citing works

Large scale comparative codon-pair context analysis unveils general rules that fine-tune evolution of mRNA primary structure

Moura, G., Pinheiro, M., Arrais, J., Gomes, A. C., Carreto, L., Freitas, A., Oliveira, J. L., & Santos, M. A. S. (2007) · PLoS ONE · doi:10.1371/journal.pone.0000847 · Cited by 107 · 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

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

Modelling mutational and selection pressures on dinucleotides in eukaryotic phyla –selection against CpG and UpA in cytoplasmically expressed RNA and in RNA viruses

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

DNA sequence abnormalities of human glucose-6-phosphate dehydrogenase variants

Beutler, E., Kühl, W., Gelbart, T., & Forman, L. (1991) · Journal of Biological Chemistry · doi:10.1016/s0021-9258(20)64298-3 · Cited by 89 · see citing works

Analysis of seed phorbol-ester and curcin content together with genetic diversity in multiple provenances of Jatropha curcas L. from Madagascar and Mexico

He, W., King, A. J., Khan, M. A., Cuevas, J. A., Ramiaramanana, D., & Graham, I. A. (2011) · Plant Physiology and Biochemistry · doi:10.1016/j.plaphy.2011.07.006 · Cited by 88 · see citing works

The Covariation Between TpA Deficiency, CpG Deficiency, and G+C Content of Human Isochores Is Due to a Mathematical Artifact

Duret, L., & Galtier, N. (2000) · Molecular Biology and Evolution · doi:10.1093/oxfordjournals.molbev.a026261 · Cited by 85 · see citing works

Identification of mRNA that encodes an alternative form of H-CAM(CD44) in lymphoid and nonlymphoid tissues

Goldstein, L. A., & Butcher, E. C. (1990) · Immunogenetics · doi:10.1007/bf00241632 · Cited by 83 · see citing works

The impact of intragenic CpG content on gene expression

Bauer, A. P., Leikam, D., Krinner, S., Notka, F., Ludwig, C., Längst, G., & Wagner, R. (2010) · Nucleic Acids Research · doi:10.1093/nar/gkq115 · Cited by 79 · see citing works

Surviving with low genetic diversity: the case of albatrosses

Milot, E., Weimerskirch, H., Duchesne, P., & Bernatchez, L. (2007) · Proceedings of the Royal Society B Biological Sciences · doi:10.1098/rspb.2006.0221 · Cited by 79 · see citing works

Sequence Requirements for Apolipoprotein B RNA Editing in Transfected rat Hepatoma Cells

Davies, M., Wallis, S. C., Driscoll, D. M., Wynne, J., Williams, G., Powell, L. M., & Scott, J. (1989) · Journal of Biological Chemistry · doi:10.1016/s0021-9258(18)80008-4 · Cited by 79 · see citing works

Genomic and evolutionary comparison between SARS-CoV-2 and other human coronaviruses

Chen, Z., Boon, S. S., Wang, M. H., Chan, R. W. Y., & Chan, P. K. S. (2020) · Journal of Virological Methods · doi:10.1016/j.jviromet.2020.114032 · Cited by 76 · see citing works

Zika Virus Attenuation by Codon Pair Deoptimization Induces Sterilizing Immunity in Mouse Models

Li, P., Ke, X., Wang, T., Tan, Z., Luo, D., Miao, Y., Sun, J., Zhang, Y., Liu, Y., Hu, Q., et al. (2018) · Journal of Virology · doi:10.1128/jvi.00701-18 · Cited by 74 · see citing works

Endonucleolytic cleavage of a maternal homeo box mRNA in Xenopus oocytes.Preprint

Brown, B. D., & Harland, R. M. (1990) · Genes & Development · doi:10.1101/gad.4.11.1925 · Cited by 74 · see citing works

A Genomic Schism in Birds Revealed by Phylogenetic Analysis of DNA Strings

Edwards, S. V., Fertil, B., Giron, A., & Deschavanne, P. (2002) · Systematic Biology · doi:10.1080/10635150290102285 · Cited by 71 · see citing works

UU/UA Dinucleotide Frequency Reduction in Coding Regions Results in Increased mRNA Stability and Protein Expression

Al‐Saif, M., & Khabar, K. S. A. (2012) · Molecular Therapy · doi:10.1038/mt.2012.29 · Cited by 69 · see citing works

WORDUP: an efficient algorithm for discovering statistically significant patterns in DNA sequences

Pesole, G., Prunella, N., Liuni, S., Attimonelli, M., & Saccone, C. (1992) · Nucleic Acids Research · doi:10.1093/nar/20.11.2871 · 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

Genes from Nine Genomes Are Separated into Their Organisms in the Dinucleotide Composition Space

Nakashima, H. (1998) · DNA Research · doi:10.1093/dnares/5.5.251 · Cited by 63 · see citing works

Discovery of Novel Crustacean and Cephalopod Flaviviruses: Insights into the Evolution and Circulation of Flaviviruses between Marine Invertebrate and Vertebrate Hosts

Parry, R. H., & Sassan Asgari, B. (2019) · Journal of Virology · doi:10.1128/jvi.00432-19 · Cited by 62 · see citing works

Antisense Oligonucleotides Containing an Internal, Non-Nucleotide-Based Linker Promote Site-Specific Cleavage of RNA

Reynolds, M. A., Beck, T., Say, P. B., Schwartz, D. A., Dwyer, B. P., Daily, W. J., Vaghefi, M. M., Metzler, M. D., Klem, R. E., & Arnold, L. J. (1996) · Nucleic Acids Research · doi:10.1093/nar/24.4.760 · Cited by 62 · see citing works

Identification and Manipulation of the Molecular Determinants Influencing Poliovirus Recombination

Runckel, C., Westesson, O., Andino, R., & DeRisi, J. L. (2013) · PLoS Pathogens · doi:10.1371/journal.ppat.1003164 · Cited by 61 · see citing works

CpG and UpA dinucleotides in both coding and non-coding regions of echovirus 7 inhibit replication initiation post-entry

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

Regions of extreme synonymous codon selection in mammalian genes

Schattner, P. (2006) · Nucleic Acids Research · doi:10.1093/nar/gkl095 · Cited by 54 · see citing works

New insights into the interplay between codon bias determinants in plants

Camiolo, S., Melito, S., & Porceddu, A. (2015) · DNA Research · doi:10.1093/dnares/dsv027 · Cited by 54 · see citing works

Predicting RAD-seq Marker Numbers across the Eukaryotic Tree of Life

Herrera, S., Reyes-Herrera, P. H., & Shank, T. M. (2015) · Genome Biology and Evolution · doi:10.1093/gbe/evv210 · Cited by 52 · see citing works

Information contents and dinucleotide compositions of plant intron sequences vary with evolutionary origin

White, O. R., Soderlund, C. A., Shanmugan, P., & Fields, C. (1992) · Plant Molecular Biology · doi:10.1007/bf00040537 · Cited by 52 · see citing works

DNA Methylation and cancer

Spruck, C., Rideout, W. M., & Jones, P. A. (1993) · Birkhäuser Basel eBooks · doi:10.1007/978-3-0348-9118-9_22 · Cited by 52 · see citing works

Genomic signature is preserved in short DNA fragments

Deschavanne, P., Giron, A., Vilain, J., Dufraigne, C., & Fertil, B. (2002) · IEEE International Symposium on Bio-Informatics and Biomedical Engineering (BIBE) · doi:10.1109/bibe.2000.889603 · Cited by 48 · see citing works

Measuring codon usage bias

Roth, A. C., Anisimova, M. O., & Cannarozzi, G. M. (2012) · Oxford University Press eBooks · doi:10.1093/acprof:osobl/9780199601165.003.0013 · Cited by 47 · see citing works

Genome-Wide Characterization and Linkage Mapping of Simple Sequence Repeats in Mei (Prunus mume Sieb. et Zucc.)

Sun, L., Yang, W., Zhang, Q., Cheng, T., Pan, H., Xu, Z., Zhang, J., & Chen, C. (2013) · PLoS ONE · doi:10.1371/journal.pone.0059562 · Cited by 46 · see citing works

Application of Transcriptional and Posttranscriptional Reporter Constructs to the Analysis of Tumor Necrosis Factor Gene Regulation

Beutler, B. (1992) · The American Journal of the Medical Sciences · doi:10.1097/00000441-199202000-00015 · Cited by 45 · see citing works

Heterogeneity of Genome and Proteome Content in Bacteria, Archaea, and Eukaryotes

Karlin, S., Brocchieri, L., Trent, J. D., Blaisdell, B. E., & Mrázek, J. (2002) · Theoretical Population Biology · doi:10.1006/tpbi.2002.1606 · Cited by 43 · see citing works

Evolution of the sequence composition of Flaviviruses

Schubert, A. M., & Putonti, C. (2009) · Infection Genetics and Evolution · doi:10.1016/j.meegid.2009.11.004 · Cited by 42 · see citing works

Intercodon dinucleotides affect codon choice in plant genes

Amicis, F. D. (2000) · Nucleic Acids Research · doi:10.1093/nar/28.17.3339 · Cited by 41 · see citing works

The dinucleotide composition of the Zika virus genome is shaped by conflicting evolutionary pressures in mammalian hosts and mosquito vectors

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

Context-Dependent Codon Bias and Messenger RNA Longevity in the Yeast Transcriptome

Carlini, D. B. (2005) · Molecular Biology and Evolution · doi:10.1093/molbev/msi135 · Cited by 39 · see citing works

Low levels of expression of wild type Bacillus thuringiensis var. kurstaki cryIA (c) sequences in transgenic walnut somatic embryos

Dandekar, A. M., McGranahan, G. H., Vail, P. V., Uratsu, S. L., Leslie, C. A., & Tebbets, J. S. (1994) · Plant Science · doi:10.1016/0168-9452(94)90232-1 · Cited by 39 · see citing works

CpG Dinucleotide Frequencies Reveal the Role of Host Methylation Capabilities in Parvovirus Evolution

Upadhyay, M., Samal, J., Kandpal, M., Vasaikar, S. V., Biswas, B., Gomes, J., & Vivekanandan, P. (2013) · Journal of Virology · doi:10.1128/jvi.02515-13 · Cited by 38 · see citing works

Tumor necrosis factor-alpha mRNA expression in lipopolysaccharide-stimulated rat kidney. Chronological analysis of localization.

Noiri, E., Kuwata, S., Nosaka, K., Tokunaga, K., Juji, T., Shibata, Y., & Kurokawa, K. (1994) · PubMed Central · Cited by 38 · see citing works

Di.erences in Dinucleotide Frequencies of Human, Yeast, and Escherichia coli Genes

Nakashima, H. (1997) · DNA Research · doi:10.1093/dnares/4.3.185 · Cited by 36 · see citing works

Codon usage bias and its influencing factors for Y-linked genes in human

Choudhury, M. N., Uddin, A., & Chakraborty, S. (2017) · Computational Biology and Chemistry · doi:10.1016/j.compbiolchem.2017.05.005 · Cited by 35 · see citing works

CpG domains downstream of TSSs promote high levels of gene expression

Krinner, S., Heitzer, A. P., Diermeier, S. D., Obermeier, I., Längst, G., & Wagner, R. (2014) · Nucleic Acids Research · doi:10.1093/nar/gkt1358 · Cited by 34 · see citing works

Linkage mapping of AFLP markers in a wild population of great reed warblers: importance of heterozygosity and number of genotyped individuals

Åkesson, M., Hansson, B., Hasselquist, D., & Bensch, S. (2007) · Molecular Ecology · doi:10.1111/j.1365-294x.2007.03290.x · Cited by 34 · see citing works

The Tumor Necrosis Factors: Cachectin and Lymphotoxin

Beutler, B. (1990) · Hospital Practice · doi:10.1080/21548331.1990.11703910 · Cited by 34 · see citing works

Nitric oxide downregulates tumour necrosis factor mRNA in RAW 264.7 cells

Sinha, B. N. M., Eigler, A., Baumann, K., Greten, T. F., Moeller, J., & Endres, S. (1998) · Research in Immunology · doi:10.1016/s0923-2494(98)80297-6 · Cited by 31 · see citing works

Mycobacterium lepromatosis genome exhibits unusually high CpG dinucleotide content and selection is key force in shaping codon usage

Munjal, A. K., Khandia, R., Shende, K., & Das, J. (2020) · Infection Genetics and Evolution · doi:10.1016/j.meegid.2020.104399 · Cited by 30 · see citing works

Genome-wide analysis of the synonymous codon usage patterns in apple

Li, N., Sun, M., Jiang, Z., Shu, H., & Zhang, S. (2016) · Journal of Integrative Agriculture · doi:10.1016/s2095-3119(16)61333-3 · Cited by 29 · see citing works

Evolution of Synonymous Codon Usage Bias in West African and Central African Strains of Monkeypox Virus

Karumathil, S., Raveendran, N. T., Ganesh, D., Kumar, N. S. S., Nair, R. R., & Dirisala, V. R. (2018) · Evolutionary Bioinformatics · doi:10.1177/1176934318761368 · Cited by 29 · see citing works

Analysis of codon usage of severe acute respiratory syndrome corona virus 2 (SARS-CoV-2) and its adaptability in dog

Dutta, R., Buragohain, L., & Borah, P. (2020) · Virus Research · doi:10.1016/j.virusres.2020.198113 · Cited by 29 · see citing works

Mechanisms of Attenuation by Genetic Recoding of Viruses

Gonçalves-Carneiro, D., & Bieniasz, P. D. (2021) · mBio · doi:10.1128/mbio.02238-20 · Cited by 29 · see citing works

Depletion of CpG Dinucleotides in Papillomaviruses and Polyomaviruses: A Role for Divergent Evolutionary Pressures

Upadhyay, M., & Vivekanandan, P. (2015) · PLoS ONE · doi:10.1371/journal.pone.0142368 · Cited by 29 · see citing works

The grammatical rule for all DNA: Junk and coding sequences

Ohno, S., & Yomo, T. (1991) · Electrophoresis · doi:10.1002/elps.1150120203 · Cited by 29 · see citing works

An investigation into inter- and intragenomic variations of graphic genomic signatures

Karamichalis, R., Lila Kari, A., Konstantinidis, S., & Kopecki, S. (2015) · BMC Bioinformatics · doi:10.1186/s12859-015-0655-4 · Cited by 27 · see citing works

Relationship of SARS-CoV to other pathogenic RNA viruses explored by tetranucleotide usage profiling

Yap, Y. L., Zhang, X. W., & Danchin, A. (2003) · BMC Bioinformatics · doi:10.1186/1471-2105-4-43 · Cited by 26 · see citing works

Recurrent missense mutations at the first and second base of codon Arg243 in human lipoprotein lipase in patients of different ancestries

Ma, Y., Liu, M., Chitayat, D. A., Bruin, T., Beisiegel†, U., Benlian, P., Foubert, L., Gennes, J. L. D., Funke, H., Forsythe, I. J., et al. (1994) · Human Mutation · doi:10.1002/humu.1380030109 · Cited by 26 · see citing works

Read between the Lines: Diversity of Nontranslational Selection Pressures on Local Codon Usage

Callens, M., Pradier, L., Finnegan, M., Rose, C. J., & Bedhomme, S. (2021) · Genome Biology and Evolution · doi:10.1093/gbe/evab097 · Cited by 25 · see citing works

The analysis of genome composition and codon bias reveals distinctive patterns between avian and mammalian circoviruses which suggest a potential recombinant origin for Porcine circovirus 3

Franzo, G., Segalés, J., Tucciarone, C. M., Cecchinato, M., & Drigo, M. (2018) · PLoS ONE · doi:10.1371/journal.pone.0199950 · Cited by 25 · see citing works

Estrogen regulation of Xenopus laevis .gamma.-fibrinogen gene expression

Pastori, R. L., Moskaitis, J. E., Smith, L. H., & Schoenberg, D. R. (1990) · Biochemistry · doi:10.1021/bi00462a024 · Cited by 25 · see citing works

Cachectin in Tissue Injury, Shock, and Related States

Beutler, B. (1989) · Critical Care Clinics · doi:10.1016/s0749-0704(18)30441-x · Cited by 24 · see citing works

Sequence analysis and compositional properties of untranslated regions of human mRNAs

Pesole, G., Fiormarino, G., & Saccone, C. (1994) · Gene · doi:10.1016/0378-1119(94)90547-9 · Cited by 23 · see citing works

Codon Usage Provides Insights into the Adaptive Evolution of Mycoviruses in Their Associated Fungi Host

Wang, Q., Lyu, X., Chéng, J., Fù, Y., Lin, Y., Abdoulaye, A. H., Jiāng, D., & Xiè, J. (2022) · International Journal of Molecular Sciences · doi:10.3390/ijms23137441 · Cited by 22 · see citing works

A Structural Split in the Human Genome

Tang, C. S.-M., & Epstein, R. J. (2007) · PLoS ONE · doi:10.1371/journal.pone.0000603 · Cited by 22 · see citing works

TNF in Pathophysiology: Biosynthetic Regulation

Beutler, B. (1990) · Journal of Investigative Dermatology · doi:10.1111/1523-1747.ep12874797 · Cited by 22 · see citing works

A nucleoside triphosphate-regulated, 3' exonucleolytic mechanism is involved in turnover of yeast mitochondrial RNAs

Min, J., & Zassenhaus, H. P. (1993) · Journal of Bacteriology · doi:10.1128/jb.175.19.6245-6253.1993 · Cited by 22 · see citing works

Modelling mutational and selection pressures on dinucleotides in eukaryotic phyla –selection against CpG and UpA in cytoplasmically expressed RNA and in RNA viruses

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

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

TA, GT and AC are significantly under-represented in open reading frames of prokaryotic and eukaryotic protein-coding genes

Wang, Y. L., Zeng, Z., Liu, T.-L., Sun, L. V., Yao, Q., & Chen, K. (2019) · Molecular Genetics and Genomics · doi:10.1007/s00438-019-01535-1 · Cited by 4 · see citing works

The Covariation Between TpA Deficiency, CpG Deficiency, and G+C Content of Human Isochores Is Due to a Mathematical Artifact

Duret, L., & Galtier, N. (2000) · Molecular Biology and Evolution · doi:10.1093/oxfordjournals.molbev.a026261 · Cited by 85 · see citing works

Dinucleotide frequencies in different reading frame positions of coding bacterial DNA sequences.

Santibanez‐Koref, M., & Jg, R. (1986) · PubMed · Cited by 5 · see citing works