[HTML][HTML] Omicron variant (B. 1.1. 529) and its sublineages: What do we know so far amid the emergence of recombinant variants of SARS-CoV-2?

M Dhawan, ARA Saied, S Mitra, FA Alhumaydhi… - Biomedicine & …, 2022 - Elsevier
Since the start of the COVID-19 pandemic, numerous variants of SARS-CoV-2 have been
reported worldwide. The advent of variants of concern (VOCs) raises severe concerns amid …

[HTML][HTML] From genotypes to organisms: State-of-the-art and perspectives of a cornerstone in evolutionary dynamics

S Manrubia, JA Cuesta, J Aguirre, SE Ahnert… - Physics of Life …, 2021 - Elsevier
Understanding how genotypes map onto phenotypes, fitness, and eventually organisms is
arguably the next major missing piece in a fully predictive theory of evolution. We refer to this …

[HTML][HTML] Metabolic fitness landscapes predict the evolution of antibiotic resistance

F Pinheiro, O Warsi, DI Andersson… - Nature Ecology & …, 2021 - nature.com
Bacteria evolve resistance to antibiotics by a multitude of mechanisms. A central, yet
unsolved question is how resistance evolution affects cell growth at different drug levels …

Synonymous edits in the Escherichia coli genome have substantial and condition-dependent effects on fitness

DD Yang, LM Rusch, KA Widney… - Proceedings of the …, 2024 - National Acad Sciences
CRISPR-Cas-based genome editing is widely used in bacteria at scales ranging from
construction of individual mutants to massively parallel libraries. This procedure relies on …

Plasmid-mediated phenotypic noise leads to transient antibiotic resistance in bacteria

JCR Hernandez-Beltran, J Rodríguez-Beltrán… - Nature …, 2024 - nature.com
The rise of antibiotic resistance is a critical public health concern, requiring an
understanding of mechanisms that enable bacteria to tolerate antimicrobial agents. Bacteria …

Recent insights into the genotype–phenotype relationship from massively parallel genetic assays

H Kemble, P Nghe, O Tenaillon - Evolutionary applications, 2019 - Wiley Online Library
With the molecular revolution in Biology, a mechanistic understanding of the genotype–
phenotype relationship became possible. Recently, advances in DNA synthesis and …

Deep mutational scanning of essential bacterial proteins can guide antibiotic development

L Dewachter, AN Brooks, K Noon, C Cialek… - nature …, 2023 - nature.com
Deep mutational scanning is a powerful approach to investigate a wide variety of research
questions including protein function and stability. Here, we perform deep mutational …

Molecular Mechanisms and the Significance of Synonymous Mutations

P Oelschlaeger - Biomolecules, 2024 - mdpi.com
Synonymous mutations result from the degeneracy of the genetic code. Most amino acids
are encoded by two or more codons, and mutations that change a codon to another …

Fitness benefits of a synonymous substitution in an ancient EF-Tu gene depend on the genetic background

KM McGrath, SJ Russell, E Fer, E Garmendia… - Journal of …, 2024 - Am Soc Microbiol
Synonymous mutations are changes to DNA sequence, which occur within translated genes
but which do not affect the protein sequence. Although often referred to as silent mutations …

Genome-wide association study of gastric cancer- and duodenal ulcer-derived Helicobacter pylori strains reveals discriminatory genetic variations and novel …

VP Tuan, K Yahara, HDQ Dung, TT Binh… - Microbial …, 2021 - microbiologyresearch.org
Genome-wide association studies (GWASs) can reveal genetic variations associated with a
phenotype in the absence of any hypothesis of candidate genes. The problem of false …