Codon Pair Bias Is a Direct Consequence of Dinucleotide Bias

Kunec, Dusan, Osterrieder, Nikolaus·2016·Cell Reports
DOI 10.1016/j.celrep.2015.12.011

Cited by (160)

Items 101–160 of 160

  1. Bias at the third nucleotide of codon pairs in virus and host genomes
    Ewan P. Plant, Zhiping Ye · 2022 · Scientific Reports
  2. A detailed analysis of synonymous codon usage in human bocavirus
    Snawar Hussain, Sahibzada Tasleem Rasool, Afzal Haq Asif · 2018 · Archives of Virology
  3. Genomic Signatures Among Acanthamoeba polyphaga Entoorganisms Unveil Evidence of Coevolution
    Víctor Serrano-Solís, Paulo Eduardo Toscano Soares, Sávio Torres de Farías · 2018 · Journal of Molecular Evolution
  4. Comprehensive Genomics Investigation of Neboviruses Reveals Distinct Codon Usage Patterns and Host Specificity
    Rahul Kaushik, Naveen Kumar, Pragya D. Yadav, S. Sircar, Anita Shete-Aich, Ankur Singh, S. Tomar, Thomas Launey, Y. Malik · 2024 · Microorganisms
  5. Human parainfluenza virus 3 vaccine candidates attenuated by codon-pair deoptimization are immunogenic and protective in hamsters
    Sharmin Afroz, Sirle Saul, Jin Dai, Sonja R. Surman, Xueqiao Liu, Hong-Su Park, Cyril Le Nouën, Matthias Lingemann, Bibha Dahal, John Robert Coleman et al. · 2024 · Proceedings of the National Academy of Sciences
  6. Codon usage pattern in Gnetales evolved in close accordance with the Gnetifer hypothesis
    Aasim Majeed, Harpreet Kaur, Amitozdeep Kaur · 2021 · Botanical Journal of the Linnean Society
  7. Mapping evolutionary paradigm of bovine viral diarrhea virus Npro associated with different organizations of nucleotide
    Xili Feng, Zeyu Liu, Xiaoting Ren, Lele An, Xiao‐xia Ma · 2025 · Virulence
  8. Distinct codon usage signatures reflecting evolutionary and pathogenic adaptation in the Acinetobacter baumannii complex
    Ujwal Dahal, Anuj Sharma, Karan Paul · 2025 · European Journal of Clinical Microbiology & Infectious Diseases
  9. Strategies and Patterns of Codon Bias in Molluscum Contagiosum Virus
    Rahul Raveendran Nair, Manikandan Mohan, Gudepalya Renukaiah Rudramurthy, Reethu Vivekanandam, Panayampalli Subbian Satheshkumar · 2021 · Pathogens
  10. Analyzing the Evolution and Host Adaptation of the Rabies Virus from the Perspective of Codon Usage Bias
    Gen Li, Xuhong Chen, Xin Li et al. · 2023 · Transboundary and Emerging Diseases
  11. HIV long-term non-progressors share similar features with simian immunodeficiency virus infection of chimpanzees
    Ayan Roy, Surajit Basak · 2020 · Journal of Biomolecular Structure and Dynamics
  12. Virus Eradication and Synthetic Biology: Changes with SARS-CoV-2?
    Jean‐Nicolas Tournier, Joseph P. Kononchik · 2021 · Viruses
  13. Evolutionary paradigm of distinct viral coding regions of BVDV associated with different nucleotide usage patterns
    Le-le An, Zeyu Liu, Xiaoting Ren, Y. J. Mo, Jianhua Zhou · 2025 · BMC Veterinary Research
  14. An interplay between compositional constraint and natural selection dictates the codon usage pattern among select Galliformes
    Indrani Sarkar, Saurabh Singh Rathore, Ram Pratap Singh · 2021 · Biosystems
  15. An Insight into Codon Pattern Analysis of Autophagy Genes Associated with Virus Infection
    Shailja Singhal, Utsang Kumar, Taha Alqahtani, Igor Vladimirovich Rzhepakovsky, Rekha Khandia, Megha Katare Pandey, Saud Alqahtani, Hanan M. Alharbi, Mohammad Amjad Kamal · 2023 · Current Pharmaceutical Design
  16. Codon Pattern and Context Analysis in Genes Triggering Alzheimer’s Disease and Latent Tau Protein Aggregation Post-Anesthesia Exhibited Unique Molecular Patterns Associated with Functional Aspects
    Liyuan Jiao, Ziye Jing, Wenjie Zhang, Xuesen Su, Hualei Yan, Shouyuan Tian · 2024 · Journal of Alzheimer s Disease
  17. Genome recoding: a review of basic concepts, current research and future prospects of virus attenuation for controlling plant viral diseases
    Vinay Satish Kumar, Tanya Singh · 2020 · Journal of Plant Biochemistry and Biotechnology
  18. Codon usage analysis in selected virulence genes of Staphylococcal species
    Pinky Arora, Shubham Kumar, Chandra Sekhar Mukhopadhyay, Sandeep Kaur · 2025 · Current Genetics
  19. De-Coding the Contributions of the Viral RNAs to Alphaviral Pathogenesis
    Autumn T. LaPointe, Kevin J. Sokoloski · 2021 · Pathogens
  20. Molecular insights into codon usage analysis of mitochondrial fission and fusion gene: relevance to neurodegenerative diseases
    Rekha Khandia, Megha Katare Pandey, R. K. Garg, Azmat Ali Khan, Igor Spartakovich Baklanov, Amer M. Alanazi, Prakash Nepali, Pankaj Gurjar, Om Prakash Choudhary · 2024 · Annals of Medicine and Surgery
  21. Viral attenuation by engineered protein fragmentation
    Daniel J. Garry, Andrew D. Ellington, Ian J. Molineux · 2018 · Virus Evolution
  22. Molecular features similarities between SARS-CoV-2, SARS, MERS and key human genes could favour the viral infections and trigger collateral effects
    Lucas L. Maldonado, Laura Kamenetzky · 2020 · bioRxiv (Cold Spring Harbor Laboratory)
  23. CodonTranslator: a conditional codon language model for codon optimization across life domains
    Yanshuo Chen, Yuming Zhang, Joshua Li, Boxue Tian, Heng Huang · 2025 · bioRxiv (Cold Spring Harbor Laboratory)
  24. CocoVax: a web server for codon-based deoptimization of viral genes in live attenuated vaccine design
    Jiaxuan Li, Shimin Shuai · 2025 · Nucleic Acids Research
  25. Mapping evolutionary paradigm of Oropouche virus driven by dinucleotide bias and context-dependent codon bias
    Xuanye Yang, Zeyu Liu, Xiaoting Ren · 2025 · Virulence
  26. Broad beta-CoV immunity and transmission blockade by a single-dose live-attenuated vaccine with atypical codon usage
    Nigeer Te, Alex W. H. Chin, Hao-Gao Gu, Janice Zhirong Jia, Yi Huang, Samuel M. S. Cheng, Chee-Wah Tan, Jin-Cun Zhao, Kenrie Pui Yan Hui, Michael Chi Wai Chan et al. · 2026 · Proceedings of the National Academy of Sciences of the United States of America
  27. Determination of codon pattern and evolutionary forces acting on genes linked to inflammatory bowel disease
    Rekha Khandia, R. K. Garg, Megha Katare Pandey, Azmat Ali Khan, Sandeep Kumar Dhanda, Abdul Malik, Pankaj Gurjar · 2024 · International Journal of Biological Macromolecules
  28. Insights into genetic architecture and disease associations of genes associated with different human blood group systems using codon usage bias
    Utsang Kumar, Shailja Singhal, Azmat Ali Khan, Amer M. Alanazi, Pankaj Gurjar, Rekha Khandia · 2025 · Journal of Biomolecular Structure and Dynamics
  29. Codon usage bias and nucleotide bias are not influenced by the 5′ flanking but by 3′ and intronic region composition in SCID-associated genes
    Yichun Zou, Quan Shi, Rekha Khandia · 2025 · International Journal of Biological Macromolecules
  30. Suboptimal dengue genome leverages non-canonical translation mechanisms
    Priyanka Mehta, Priti Devi, Sandeep Budhiraja, Bansidhar Tarai, Rajesh Pandey · 2025 · iScience
  31. CodSeqGen: A tool for generating synonymous coding sequences with desired GC-contents
    Abdulrakeeb M. Al-Ssulami, Aqil M. Azmi, Muhammad Hussain · 2019 · Genomics
  32. Methods to Evaluate the Effects of Synonymous Variants
    Brian C. Lin, Katarzyna I. Jankowska, Douglas Meyer, Upendra Katneni · 2022 · Springer eBooks
  33. Not so giant steps on tuning protein production and diminished genomes
    Max Finger‐Bou · 2023
  34. A Porcine Circovirus Vaccine with Enhanced Capabilities
    Oleksandr Kolyvushko · 2016 · NDSU Repository (North Dakota State University)
  35. Molecular determinants of arbovirus transmission by mosquitoes
    Giel P. Göertz · 2019
  36. The G nucleotide guides codon usage bias in genes associated with depression
    Rekha Khandia, Nidhi Puranik, Megha Katare Pandey, Kuldeep Dhama, Azmat Ali Khan, Athanasios T. Alexiou, Gaber El‐Saber Batiha, Mohamed Elsayad · 2022 · Research Square
  37. Current Status of Vaccines Developed for SARS-CoV-2 Infection: A Review
    Carlos Andrés Marín Hoyos, Jean Paul Cappellaro Sánchez, Romel F Gómez, Monica Chavez Vivas · 2022 · Bangladesh Journal of Infectious Diseases
  38. Newcastle Disease Virus Displaying an Ectodomain of Middle East Respiratory Syndrome Coronavirus Spike Protein Elicited Robust Humoral and Cellular Immunity in Mice
    Jaturawitt Prasopsiri, Kanjana Srisutthisamphan, Benjamas Liwnaree et al. · 2024 · Vaccines
  39. Ross River virus genomes from Australia and the Pacific display coincidental and antagonistic codon usage patterns with common vertebrate hosts and a principal vector
    Eugene T. Madzokere, Wesley Freppel, Alyssa T. Pyke et al. · 2025 · Virology
  40. terminator hinders the higher erythropoietin production achieved through Matrix Attachment Region in CHO-K1 cells
    Fatemeh Jalali, Shahriyar Abdoli, Fatemeh T. Shamsabadi, Ahad Yamchi, Anvarsadat Kianmehr, Majid Shahbazi · 2025 · Research Square
  41. Detection and evaluation of clusters within sequential data
    Alexander Van Werde, Albert Senen–Cerda, Gianluca Kosmella · 2025 · Data Mining and Knowledge Discovery
  42. Uncovering position-specific patterns in codon and codon-pair usage in candidate genes associated with blood coagulation diseases
    Nathan J Clement, Nobuko Hamasaki‐Katagiri, Brian Lin, Anton A. Komar, Michael N. DiCuccio, Haim Bar, Chava Kimchi‐Sarfaty · 2025 · NAR Genomics and Bioinformatics
  43. RNA editing signatures and codon adaptation reveal potential translational compatibility between Hendra virus and its natural host Pteropus Alecto
    Aparajita Roy, Supriyo Chakraborty · 2025 · Archives of Microbiology
  44. Additional file 1 of Effect of genome composition and codon bias on infectious bronchitis virus evolution and adaptation to target tissues
    Giovanni Franzo, Claudia Maria Tucciarone, Matteo Legnardi, Mattia Cecchinato · 2021 · Figshare
  45. Additional file 1 of GenRCA: a user-friendly rare codon analysis tool for comprehensive evaluation of codon usage preferences based on coding sequences in genomes
    Kunjie Fan, Li, Yuanyuan, Zhiwei Chen, Fan, Long · 2024 · Figshare
  46. Additional file 3 of Effect of genome composition and codon bias on infectious bronchitis virus evolution and adaptation to target tissues
    Giovanni Franzo, Claudia Maria Tucciarone, Matteo Legnardi, Mattia Cecchinato · 2021 · Figshare
  47. Additional file 1 of Development of a rabies virus-based retrograde tracer with high trans-monosynaptic efficiency by reshuffling glycoprotein
    Jia, Fan, Li, Li, Liu, Haizhou · 2021 · Figshare
  48. Additional file 6 of Effect of genome composition and codon bias on infectious bronchitis virus evolution and adaptation to target tissues
    Giovanni Franzo, Claudia Maria Tucciarone, Matteo Legnardi, Mattia Cecchinato · 2021 · Figshare
  49. Additional file 5 of Effect of genome composition and codon bias on infectious bronchitis virus evolution and adaptation to target tissues
    Giovanni Franzo, Claudia Maria Tucciarone, Matteo Legnardi, Mattia Cecchinato · 2021 · Figshare
  50. Additional file 7 of Effect of genome composition and codon bias on infectious bronchitis virus evolution and adaptation to target tissues
    Giovanni Franzo, Claudia Maria Tucciarone, Matteo Legnardi, Mattia Cecchinato · 2021 · Figshare
  51. Additional file 4 of Effect of genome composition and codon bias on infectious bronchitis virus evolution and adaptation to target tissues
    Giovanni Franzo, Claudia Maria Tucciarone, Matteo Legnardi, Mattia Cecchinato · 2021 · Figshare
  52. Additional file 2 of Effect of genome composition and codon bias on infectious bronchitis virus evolution and adaptation to target tissues
    Giovanni Franzo, Claudia Maria Tucciarone, Matteo Legnardi, Mattia Cecchinato · 2021 · Figshare
  53. Additional file 2 of GenRCA: a user-friendly rare codon analysis tool for comprehensive evaluation of codon usage preferences based on coding sequences in genomes
    Kunjie Fan, Li, Yuanyuan, Chen, Zhiwei, Fan, Long · 2024 · Figshare
  54. Hierarchical evolution of the proteobacterial essential chaperone SecB reveals non-neutral synonymous evolution under extreme purifying selection
    Ayon Pal, Madhumita G. Chaki · 2026 · Molecular Genetics and Genomics
  55. Splice-Aware Optimization Prevents Pervasive Missplicing of Natural and Synthetic cDNAs
    Mohd Ahmad, Fernando Bellido Molías, Laura Cano-Aroca, Christine Mordstein, Samir F. Watson, Nabid Bhuiyan, Marguerite J. Clarke, Chava Kimchi‐Sarfaty, Upendra Katneni, Eleanor R. Gaunt et al. · 2026 · bioRxiv (Cold Spring Harbor Laboratory)
  56. Increased or decreased numbers of CpG dinucleotide motifs in the genome of influenza A virus do not affect in vitro virus phenotype
    Balasubramanian Susma, Monique I. J. Spronken, Stefan van Nieuwkoop, Bernike Kalverda, Alexander P. Gultyaev, Ron A. M. Fouchier, Bernadette G. van den Hoogen · 2026 · Journal of Virology
  57. Multilayered nucleotide organization reveals purifying selection and host-driven adaptation in CPV and FPV
    Xili Feng, Liwen Xu, C H I Zhang, Jianhua Zhou, Xue Bai · 2026 · BMC Veterinary Research
  58. Directed Evolution in Codon Space
    James Heuschkel, Laura J. Kingsley, Jon M. Reed, Di Li, Matthew John Warner, Noah B. Pefaur, Steven Cramer · 2026 · bioRxiv (Cold Spring Harbor Laboratory)
  59. Selection-Driven Codon Usage in Agamid Mitochondrial Genomes: Climatic and Biogeographic Implications
    Sayed A. M. Amer, M. M. Rana, Fan Liu · 2026 · Biology Bulletin
  60. Comparative analysis of codon usage bias revealed natural selection-driven evolution and host adaptation of infectious haematopoietic necrosis virus
    Yumeng Yang, Fang Liu, Liuyi Yu, He Sun, Adili Abudu, Jianyong Hu, Yue Zhuo, Cui-Lan Hao, Cheng Yue · 2026 · Virus Evolution