Origin and evolution of the genetic code: The universal enigma

Cited by (392)

Items 101–200 of 392

1. Genetic Code Evolution Investigated through the Synthesis and Characterisation of Proteins from Reduced‐Alphabet Libraries
   Matilda Newton, Dana J. Morrone, Kun‐Hwa Lee, Burckhard Seelig · 2018 · ChemBioChem
2. Origin of Life: The Point of No Return
   Dimiter Kunnev · 2020 · Life
3. Phenotypic mutations contribute to protein diversity and shape protein evolution
   Maria Luisa Romero Romero, Cedric Landerer, Jonas Poehls, Ágnes Tóth-Petróczy · 2022 · Protein Science
4. On the Organizational Dynamics of the Genetic Code
   Zhang Zhang, Jun Myoung Yu · 2011 · Genomics Proteomics & Bioinformatics
5. Energy mapping of the genetic code and genomic domains: implications for code evolution and molecular Darwinism
   Horst H. KLUMP, Jens Völker, Kenneth J. Breslauer · 2020 · Quarterly Reviews of Biophysics
6. Primal Eukaryogenesis: On the Communal Nature of Precellular States, Ancestral to Modern Life
   Richard Egel · 2012 · Life
7. The Origin of Genetic Code and Translation in the Framework of Current Concepts on the Origin of Life
   Liya G. Kondratyeva, Marina S. Dyachkova, Alexey Vladimirovich Galchenko · 2022 · Biochemistry (Moscow)
8. AARS Online: A collaborative database on the structure, function, and evolution of the aminoacyl‐ tRNA synthetases
   2024
9. Cells as semantic systems
   Dennis Görlich, Stefan Artmann, Peter Dittrich · 2011 · Biochimica et Biophysica Acta (BBA) - General Subjects
10. Complete Quantum Information in the DNA Genetic Code
    Michel R. P. Planat, Raymond Aschheim, Marcelo M. Amaral, Fang Fang, Klee Irwin · 2020 · Symmetry
11. Theory of the Origin, Evolution, and Nature of Life
    Erik D. Andrulis · 2011 · Life
12. Multidimensional Phylogenetic Metrics Identify Class I Aminoacyl-tRNA Synthetase Evolutionary Mosaicity and Inter-Modular Coupling
    Charles W. Carter, Alex Popinga, Remco Bouckaert, Peter R. Wills · 2022 · International Journal of Molecular Sciences
13. Theories of the origin of the genetic code: Strong corroboration for the coevolution theory
    Massimo Di Giulio · 2024 · Biosystems
14. Comparison of the Frequency of Functional SH3 Domains with Different Limited Sets of Amino Acids Using mRNA Display
    Junko Tanaka, Hiroshi Yanagawa, Nobuhide Doi · 2011 · PLoS ONE
15. The Plausibility of RNA-Templated Peptides: Simultaneous RNA Affinity for Adjacent Peptide Side Chains
    Rebecca M. Turk-MacLeod, Deepa Puthenvedu, Irene H. Majerfeld, Michael Yarus · 2012 · Journal of Molecular Evolution
16. Inclusion of the fitness sharing technique in an evolutionary algorithm to analyze the fitness landscape of the genetic code adaptability
    José Carlos Almeida Santos, Ángel Monteagudo · 2017 · BMC Bioinformatics
17. Integrated entropy-based approach for analyzing exons and introns in DNA sequences
    Junyi Li, Li Zhang, Huinian Li, Yuan Ping, Qingzhe Xu, Rongjie Wang, Renjie Tan, Zhen Wang, Bo Liu, Yadong Wang · 2019 · BMC Bioinformatics
18. On models of the genetic code generated by binary dichotomic algorithms
    Markus Gumbel, Elena Fimmel, Alberto Danielli, Lutz Strüngmann · 2014 · Biosystems
19. The genetic code is very close to a global optimum in a model of its origin taking into account both the partition energy of amino acids and their biosynthetic relationships
    Franco Caldararo, Massimo Di Giulio · 2022 · Biosystems
20. Horizontal transfer of code fragments between protocells can explain the origins of the genetic code without vertical descent
    Tom Froese, Jorge Campos, Kosuke Fujishima, Daisuke Kiga, Nathaniel Virgo · 2018 · Scientific Reports
21. An alternative to the RNA World Hypothesis
    Brian R. Francis · 2011 · Trends in Evolutionary Biology
22. On universal common ancestry, sequence similarity, and phylogenetic structure: the sins of P-values and the virtues of Bayesian evidence
    Theobald, Douglas L · 2011 · Biology Direct
23. Evolving a mitigation of the stress response pathway to change the basic chemistry of life
    Isabella Tolle, Stefan Oehm, Michael Georg Hoesl, Christin Treiber-Kleinke, Lauri Peil, Mihaela Bozukova, Suki Albers, Abdul-Rahman Adamu Bukari, Torsten Semmler, Juri Rappsilber et al. · 2023 · Frontiers in Synthetic Biology
24. Identification of a non-canonical ciliate nuclear genetic code where UAA and UAG code for different amino acids
    Jamie McGowan, Estelle Silvia Kilias, Elisabet Alacid, James Lipscombe, Benjamin H. Jenkins, Karim Gharbi, Gemy Kaithakottil, Iain C. Macaulay, Seanna J. McTaggart, Sally D. Warring et al. · 2023 · PLoS Genetics
25. Computational analysis of amino acids and their sidechain analogs in crowded solutions of RNA nucleobases with implications for the mRNA–protein complementarity hypothesis
    Matea Hajnić, Juan Iregui Osorio, Bojan Žagrović · 2014 · Nucleic Acids Research
26. Single cell transcriptomics reveals UAR codon reassignment in Palmarella salina (Metopida, Armophorea) and confirms Armophorida belongs to APM clade
    Johana Rotterová, Tomáš Pánek, Eric D. Salomaki, Michael Kotyk, Petr Táborský, Martin Kolísko, Ivan Čepička · 2023 · Molecular Phylogenetics and Evolution
27. The non-power model of the genetic code: a paradigm for interpreting genomic information
    Diego Luis Gonzalez, Simone Giannerini, Rodolfo Rosa · 2016 · Philosophical Transactions of the Royal Society A Mathematical Physical and Engineering Sciences
28. The influence of different types of translational inaccuracies on the genetic code structure
    Paweł Błażej, Małgorzata Wnętrzak, Dorota Mackiewicz, Paweł Mackiewicz · 2019 · BMC Bioinformatics
29. Probability of change in life: Amino acid changes in single nucleotide substitutions
    Kwok-Fong Chan, Stelios Koukouravas, Joshua Yi Yeo, Darius Wen‐Shuo Koh, Samuel Ken‐En Gan · 2020 · Biosystems
30. Large-scale in silico mutagenesis experiments reveal optimization of genetic code and codon usage for protein mutational robustness
    Martin Schwersensky, Marianne J. Rooman, Fabrizio Pucci · 2020 · BMC Biology
31. Molecular Codes in Biological and Chemical Reaction Networks
    Dennis Görlich, Peter Dittrich · 2013 · PLoS ONE
32. Thawing out frozen metabolic accidents
    Dario Leister · 2019 · BMC Biology
33. The progene hypothesis: the nucleoprotein world and how life began
    Altstein, Anatoly D. · 2015 · Biology Direct
34. Anticodon sequence determines the impact of mistranslating tRNA Ala variants
    Ecaterina Cozma, Megha Rao, Madison Dusick, Julie L. Genereaux, Ricard A. Rodríguez‐Mias, Judit Villén, Christopher J. Brandl, Matthew D. Berg · 2023 · RNA Biology
35. Structural bioinformatics studies of glutamate transporters and their AlphaFold2 predicted water-soluble QTY variants and uncovering the natural mutations of L->Q, I->T, F->Y and Q->L, T->I and Y->F
    Alper Karagöl, Taner Karagöl, Eva Smorodina, Shuguang Zhang · 2024 · PLoS ONE
36. Data mining algorithm for pre-processing biopharmaceutical drug product manufacturing records
    Gioele Casola, Christian Siegmund, Markus Mattern, Hirokazu Sugiyama · 2018 · Computers & Chemical Engineering
37. Preparation and chromatographic evaluation of the hydrophilic interaction chromatography stationary phase based on nucleosides or nucleotides
    Tingfeng Tang, Dandan Guo, Shaohua Huang · 2020 · Analytical Methods
38. Mapping the Plasticity of the Escherichia coli Genetic Code with Orthogonal Pair-Directed Sense Codon Reassignment
    Margaret A. Schmitt, Wil Biddle, John D. Fisk · 2018 · Biochemistry
39. The Ancient Operational Code is Embedded in the Amino Acid Substitution Matrix and aaRS Phylogenies
    Julia A. Shore, Barbara R. Holland, Jeremy G. Sumner, Kay Nieselt, Peter R. Wills · 2019 · Journal of Molecular Evolution
40. The Relation Between k-Circularity and Circularity of Codes
    Elena Fimmel, Christian J. Michel, François Pirot, Jean‐Sébastien Sereni, Martin Starman, Lutz Strüngmann · 2020 · Bulletin of Mathematical Biology
41. The Genetic Code—More Than Just a Table
    Daniel Berleant, M. White, Eric A. Pierce, E. Tudoreanu, Andras Boeszoermenyi, Yuri Shtridelman, Jed C. Macosko · 2009 · Cell Biochemistry and Biophysics
42. From matter to form: the evolution of the genetic code as semio-poiesis
    Suren Zolyan · 2022 · Semiotica
43. Rare-event sampling analysis uncovers the fitness landscape of the genetic code
    Yuji Omachi, Nen Saito, Chikara Furusawa · 2023 · PLoS Computational Biology
44. Evolution at the Origins of Life?
    Ludo L. J. Schoenmakers, Thomas A. C. Reydon, Andreas Kirschning · 2024 · Life
45. Chapter 9: Life as We Don't Know It
    Natalie M. Grefenstette, Luoth Chou, Stephanie M. Colón‐Santos, Theresa M. Fisher, Veronica Mierzejewski, Ceren Nural, Pritvik Sinhadc, Monica Vidaurri, Lena Vincent, Maggie Meiqi Weng · 2024 · Astrobiology
46. Robust genetic codes enhance protein evolvability
    Hana Rozhoňová, Carlos Martí‐Gómez, David M. McCandlish, Joshua L. Payne · 2024 · PLoS Biology
47. Revisiting the Physico-Chemical Hypothesis of Code Origin: An Analysis Based on Code-Sequence Coevolution in a Finite Population
    Ashutosh Vishwa Bandhu, Neha Aggarwal, Supratim Sengupta · 2013 · Origins of Life and Evolution of Biospheres
48. Proteome‐wide analysis of nonsynonymous single‐nucleotide variations in active sites of human proteins
    Hayley Dingerdissen, Mona Motwani, Konstantinos Karagiannis, Vahan V. Simonyan, Raja Mazumder · 2013 · FEBS Journal
49. Long-term evolution on complex fitness landscapes when mutation is weak
    David M. McCandlish · 2018 · Heredity
50. Optimization Models and the Structure of the Genetic Code
    Jean‐Luc Jestin, Achim Kempf · 2009 · Journal of Molecular Evolution
51. Low Complexity Regions in Proteins and DNA are Poorly Correlated
    Johanna M Enright, Zachery W. Dickson, G. Brian Golding · 2023 · Molecular Biology and Evolution
52. DNA partitions into triplets under tension in the presence of organic cations, with sequence evolutionary age predicting the stability of the triplet phase
    Amirhossein Taghavi, Paul van der Schoot, Joshua T. Berryman · 2017 · Quarterly Reviews of Biophysics
53. Standard Genetic Code vs. Supersymmetry Genetic Code – Alphabetical table vs. physicochemical table
    Marija Rosandić, V. Paar · 2022 · Biosystems
54. Functional variation in the non-coding genome: molecular implications for food security
    Giorgio Gullotta, Arthur Korte, Sebastian Marquardt · 2022 · Journal of Experimental Botany
55. Biophysical Interactions Underpin the Emergence of Information in the Genetic Code
    Aaron Halpern, Lilly R. Bartsch, Kaan Ibrahim, Stuart A. Harrison, Minkoo Ahn, John Christodoulou, Nick J. Lane · 2023 · Life
56. Thermal, Autonomous Replicator Made from Transfer RNA
    Hubert Krammer, Friederike M. Möller, Dieter Braun · 2012 · Physical Review Letters
57. Footprints of a Singular 22-Nucleotide RNA Ring at the Origin of Life
    J. Demongeot, A. Henrion-Caude · 2020 · Biology
58. Coding From Binding? Molecular Interactions at the Heart of Translation
    Bojan Žagrović, Marlene Adlhart, Thomas H Kapral · 2023 · Annual Review of Biophysics
59. Codon sextets with leading role of serine create “ideal” symmetry classification scheme of the genetic code
    Marija Rosandić, V. Paar · 2014 · Gene
60. The shiftability of protein coding genes: the genetic code was optimized for frameshift tolerating
    Xiaolong Wang, Xuxiang Wang, Gang Chen, Jianye Zhang, Yongqiang Liu, Chao Yang · 2015
61. Silent rain: does the atmosphere-mediated connectivity between microbiomes influence bacterial evolutionary rates?
    Matti Jalasvuori · 2020 · FEMS Microbiology Ecology
62. Chapter 1: The Astrobiology Primer 3.0
    Micah J. Schaible, Nadia Szeinbaum, Gonensin Ozan Bozdag, Luoth Chou, Natalie M. Grefenstette, Stephanie M. Colón‐Santos, Laura E. Rodriguez, Marshall J. Styczinski, Jennifer L. Thweatt, Zoe R. Todd et al. · 2024 · Astrobiology
63. Impacts of ribosomal RNA sequence variation on gene expression and phenotype
    Griffin A. Welfer, Ryan A. Brady, S. Kundhavai Natchiar, Zoe L. Watson, Emily J. Rundlet, Jose L. Alejo, Anand Pratap Singh, Nitish K. Mishra, Roger B. Altman, Scott C. Blanchard · 2025 · Philosophical Transactions of the Royal Society B Biological Sciences
64. The 3 31 Nucleotide Minihelix tRNA Evolution Theorem and the Origin of Life
    Lei Lei, Zachary Frome Burton · 2023 · Life
65. The ancient operational code is embedded in the amino acid substitution matrix and aaRS phylogenies
    Julia A. Shore, Barbara R. Holland, Jeremy G. Sumner, Nieselt, K (15719381), Wills, PR (15719384) · 2020 · Figshare
66. On the Contribution of Protein Spatial Organization to the Physicochemical Interconnection between Proteins and Their Cognate mRNAs
    Andreas Beier, Bojan Žagrović, Anton A. Polyansky · 2014 · Life
67. A unified platform for nucleoside analog synthesis
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68. The Standard Genetic Code Facilitates Exploration of the Space of Functional Nucleotide Sequences
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69. Post-transcriptional and translational control of the morphology and virulence in human fungal pathogens
    Aishwarya Rana, Nidhi Gupta, Anil Thakur · 2021 · Molecular Aspects of Medicine
70. The Supersymmetry Genetic Code Table and Quadruplet Symmetries of DNA Molecules Are Unchangeable and Synchronized with Codon-Free Energy Mapping during Evolution
    Marija Rosandić, V. Paar · 2023 · Genes
71. Genetic code and deformation of the 2-dimensional 2-adic metric
    Andrei Yu. Khrennikov, Sergei Vladimirovich Kozyrev · 2011 · P-Adic Numbers Ultrametric Analysis and Applications
72. Linked Mutations at Adjacent Nucleotides Have Shaped Human Population Differentiation and Protein Evolution
    James G. D. Prendergast, Carys Pugh, Sarah E. Harris, David Arthur Hume, Ian J. Deary, Allan Beveridge · 2019 · Genome Biology and Evolution
73. Fundamental role of start/stop regulators in whole DNA and new trinucleotide classification
    Marija Rosandić, V. Paar, Matko Glunčić · 2013 · Gene
74. Metabolic Constraints on the Evolution of Genetic Codes: Did Multiple Preaerobic’ Ecosystem Transitions Entrain Richer Dialects via Serial Endosymbiosis?
    Rodrick Wallace · 2012 · Lecture notes in computer science
75. Reciprocal Nucleopeptides as the Ancestral Darwinian Self-Replicator
    Eleanor F. Banwell, Bernard M. A. G. Piette, Anne Taormina C, Jonathan G. Heddle · 2017 · Molecular Biology and Evolution
76. Everyone Is a Protagonist: Residue Conformational Preferences in High-Resolution Protein Structures
    Rodrigo Ligabue‐Braun, Bruno Borguesan, Hugo Verli, Mathias J. Krause, Márcio Dorn · 2017 · Journal of Computational Biology
77. Optimality of circular codes versus the genetic code after frameshift errors
    Gopal Krishna Dila, Christian J. Michel, Julie Thompson · 2020 · Biosystems
78. The role of non-standard translation in Candida albicans pathogenesis
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79. On the Origin of Frameshift-Robustness of the Standard Genetic Code
    Haiqing Xu, Jianzhi Zhang · 2021 · Molecular Biology and Evolution
80. Fullerene and the origin of life.
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81. A rationale for the symmetries by base substitutions of degeneracy in the genetic code
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82. Comparison of translation loads for standard and alternative genetic codes
    Stefanie Gabriele Sammet, Ugo Bastolla, Markus Porto · 2010 · BMC Evolutionary Biology
83. Can the Origin of the Genetic Code Be Explained by Direct RNA Templating?
    Stephen C. Meyer, Paul A. Nelson · 2011 · BIO-Complexity
84. Dependence of Binding Free Energies between RNA Nucleobases and Protein Side Chains on Local Dielectric Properties
    Anita de Ruiter, Anton A. Polyansky, Bojan Žagrović · 2017 · Journal of Chemical Theory and Computation
85. The key role of the elongation factors in the origin of the organization of the genetic code
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86. Stability of the genetic code and optimal parameters of amino acids
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87. Phylogenetic analysis of mutational robustness based on codon usage supports that the standard genetic code does not prefer extreme environments
    Ádám Radványi, Ádám Kun · 2021 · Scientific Reports
88. The Genetic Code Assembles via Division and Fusion, Basic Cellular Events
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89. Integrative Perspectives: In Quest of a Coherent Framework for Origins of Life on Earth
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90. Malleable nature of mRNA-protein compositional complementarity and its functional significance
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91. The Standard Genetic Code can Evolve from a Two-Letter GC Code Without Information Loss or Costly Reassignments
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92. Match fitness landscapes for macromolecular interaction networks: Selection for translational accuracy and rate can displace tRNA-binding interfaces of non-cognate aminoacyl-tRNA synthetases
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93. The Origin of Life and Cellular Systems: A Continuum from Prebiotic Chemistry to Biodiversity
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94. Identifying Molecular Organic Codes in Reaction Networks
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95. Triplet-Based Codon Organization Optimizes the Impact of Synonymous Mutation on Nucleic Acid Molecular Dynamics
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96. A search for the physical basis of the genetic code
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97. The novel Ideal Symmetry Genetic Code table – Common purine-pyrimidine symmetry net for all RNA and DNA species
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98. Genome Evolution from Random Ligation of RNAs of Autocatalytic Sets
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99. Reflections on the Origin and Early Evolution of the Genetic Code
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100. RNA polymerase II-binding aptamers in human ACRO1 satellites disrupt transcription in cis
     Jennifer L. Boots, Frederike von Pelchrzim, Adam Weiss, Bob Zimmermann, Theres Friesacher, Maximilian Radtke, Marek Żywicki, Doris Chen, Katarzyna Matylla-Kulińska, Bojan Žagrović et al. · 2020 · Transcription