[HTML][HTML] In silico methods for predicting functional synonymous variants

BC Lin, U Katneni, KI Jankowska, D Meyer… - Genome Biology, 2023 - Springer
Single nucleotide variants (SNVs) contribute to human genomic diversity. Synonymous
SNVs are previously considered to be “silent,” but mounting evidence has revealed that …

Timing during translation matters: synonymous mutations in human pathologies influence protein folding and function

R Rauscher, Z Ignatova - Biochemical Society Transactions, 2018 - portlandpress.com
Ribosomes translate mRNAs with non-uniform speed. Translation velocity patterns are a
conserved feature of mRNA and have evolved to fine-tune protein folding, expression and …

[HTML][HTML] Effects of codon optimization on coagulation factor IX translation and structure: Implications for protein and gene therapies

A Alexaki, GK Hettiarachchi, JC Athey, UK Katneni… - Scientific reports, 2019 - nature.com
Synonymous codons occur with different frequencies in different organisms, a phenomenon
termed codon usage bias. Codon optimization, a common term for a variety of approaches …

[HTML][HTML] A computational approach to design a polyvalent vaccine against human respiratory syncytial virus

AT Moin, MA Ullah, RB Patil, NA Faruqui, Y Araf… - Scientific Reports, 2023 - nature.com
Abstract Human Respiratory Syncytial Virus (RSV) is one of the leading causes of lower
respiratory tract infections (LRTI), responsible for infecting people from all age groups—a …

Immunoinformatics approach to design novel subunit vaccine against the Epstein-Barr virus

AT Moin, RB Patil, T Tabassum, Y Araf… - Microbiology …, 2022 - Am Soc Microbiol
Epstein-Barr virus (EBV) is a lymphotropic virus responsible for numerous epithelial and
lymphoid cell malignancies, including gastric carcinoma, Hodgkin's lymphoma …

[HTML][HTML] In silico designing and immunoinformatics analysis of a novel peptide vaccine against metallo-beta-lactamase (VIM and IMP) variants

H Motamedi, A Alvandi, M Fathollahi, MM Ari… - PLoS …, 2023 - journals.plos.org
The rapid spread of acquired metallo-beta-lactamases (MBLs) among gram negative
pathogens is becoming a global concern. Improper use of broad-spectrum antibiotics can …

Synonymous variants that disrupt messenger RNA structure are significantly constrained in the human population

JBS Gaither, GE Lammi, JL Li, DM Gordon… - …, 2021 - academic.oup.com
Background The role of synonymous single-nucleotide variants in human health and
disease is poorly understood, yet evidence suggests that this class of “silent” genetic …

A code within a code: how codons fine-tune protein folding in the cell

AA Komar - Biochemistry (Moscow), 2021 - Springer
The genetic code sets the correspondence between the sequence of a given nucleotide
triplet in an mRNA molecule, called a codon, and the amino acid that is added to the …

[HTML][HTML] Association of μ-calpain and calpastatin polymorphisms with meat tenderness in a brahman–angus population

JD Leal-Gutiérrez, MA Elzo, DD Johnson… - Frontiers in …, 2018 - frontiersin.org
Autogenous proteolytic enzymes of the calpain family are implicated in myofibrillar protein
degradation. As a result, the μ-calpain gene and its specific inhibitor, calpastatin, have been …

Synonymous variants: necessary nuance in our understanding of cancer drivers and treatment outcomes

NM Kaissarian, D Meyer… - Journal Of The National …, 2022 - academic.oup.com
Once called “silent mutations” and assumed to have no effect on protein structure and
function, synonymous variants are now recognized to be drivers for some cancers. There …