Bioinformatics and the Cell: Modern Computational Approaches in Genomics, Proteomics and Transcriptomics
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The codon optimization applied to BNT-162b2 and mRNA-1273 leads to a much increased CAI and ITE for the two vaccine mRNAs.
“The codon optimization applied to BNT-162b2 and mRNA-1273 leads to a much increased codon adaptation index (CAI) [21,22] and index of translation efficiency (ITE) [11,36] for the two vaccine mRNAs.”
From Detailed Dissection and Critical Evaluation of the Pfizer/BioNTech and Moderna mRNA Vaccines (2021) · cites this paper as [36]
Efficient translation initiation in mammalian species depends mainly on the Kozak consensus.
“Efficient translation initiation in mammalian species depends mainly on two factors [40,41]: (1) the Kozak consensus [42,43,44], and (2) the secondary structure that may embed the Kozak consensus to obscure these essential translation initiation signals [9,41,45].”
From Detailed Dissection and Critical Evaluation of the Pfizer/BioNTech and Moderna mRNA Vaccines (2021) · cites this paper as [41]
The position weight matrix of site-specific nucleotide frequencies flanking the start codon AUG for all protein-coding genes from human Chr01 shows a pattern consistent with the GCCRCCAUGG consensus.
“The associated position weight matrix [23,24,47,48], using intron nucleotide frequencies (0.26398, 0.21777, 0.22622 and 0.29203 for A, C, G, and T, respectively) as background frequencies, shows a site-specific pattern consistent with the GCCRCCAUGG consensus.”
From Detailed Dissection and Critical Evaluation of the Pfizer/BioNTech and Moderna mRNA Vaccines (2021) · cites this paper as [24]
Efficient translation initiation in mammalian species depends mainly on the secondary structure that may embed the Kozak consensus to obscure essential translation initiation signals.
“Efficient translation initiation in mammalian species depends mainly on two factors [40,41]: (1) the Kozak consensus [42,43,44], and (2) the secondary structure that may embed the Kozak consensus to obscure these essential translation initiation signals [9,41,45].”
From Detailed Dissection and Critical Evaluation of the Pfizer/BioNTech and Moderna mRNA Vaccines (2021) · cites this paper as [41]
The codon optimization in the previous section suffers from the lack of consideration for translation accuracy.
“The codon optimization in the previous section suffers from the lack of consideration for translation accuracy [36,37].”
From Detailed Dissection and Critical Evaluation of the Pfizer/BioNTech and Moderna mRNA Vaccines (2021) · cites this paper as [36]
Highly expressed genes in diverse bacterial species strongly prefer UAA codons even in strongly GC-rich genomes with an overwhelming majority of stop codons being UGA.
“Highly expressed genes in diverse bacterial species strongly prefer UAA codons even in strongly GC-rich genomes with an overwhelming majority of stop codons being UGA [74,75].”
From Detailed Dissection and Critical Evaluation of the Pfizer/BioNTech and Moderna mRNA Vaccines (2021) · cites this paper as [75]
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Detailed Dissection and Critical Evaluation of the Pfizer/BioNTech and Moderna mRNA Vaccines
Xia, X. (2021) · Vaccines · doi:10.3390/vaccines9070734 · Cited by 201 · see citing works
Self-citation
- Authors
- Xia, X.
- Affiliations
- University of Ottawa (CA)
- Corresponding author
- Xia, Xuhua
- ORCID
- Xia, Xuhua
- Venue
- Springer eBooks
- Publisher
- Springer International Publishing
- Published
- 2018
- OpenAlex
- W4237408630
- Cited by
- 34
- References
- 0
- Citations by year
- 2026: 2 · 2025: 3 · 2024: 5 · 2023: 4 · 2022: 2 · 2021: 3 · 2020: 7 · 2019: 6 · 2018: 2
- FWCI
- 4.43
- Type
- book
- Language
- en
- Open access
- closed
- Licence
- www.springer.com/tdm (tdm)
- Locations
- Springer eBooks (publishedVersion)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genetics, Bioinformatics, and Biomedical Research
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Bioinformatics and Genomic Networks
- Keywords
- bioinformatics, molecular biology, cell biology, computational biology, mathematical modeling in biology
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.
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