Codon usage bias

ST Parvathy, V Udayasuriyan, V Bhadana - Molecular biology reports, 2022 - Springer
Codon usage bias is the preferential or non-random use of synonymous codons, a
ubiquitous phenomenon observed in bacteria, plants and animals. Different species have …

SARS coronavirus 2: from genome to infectome

M Rastogi, N Pandey, A Shukla, SK Singh - Respiratory research, 2020 - Springer
Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) belongs to the group of
Betacoronaviruses. The SARS-CoV-2 is closely related to SARS-CoV-1 and probably …

Structural basis of ribosomal frameshifting during translation of the SARS-CoV-2 RNA genome

PR Bhatt, A Scaiola, G Loughran, M Leibundgut… - Science, 2021 - science.org
Programmed ribosomal frameshifting is a key event during translation of the severe acute
respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA genome that allows synthesis of the …

Structural and functional conservation of the programmed− 1 ribosomal frameshift signal of SARS coronavirus 2 (SARS-CoV-2)

JA Kelly, AN Olson, K Neupane, S Munshi… - Journal of Biological …, 2020 - ASBMB
Approximately 17 years after the severe acute respiratory syndrome coronavirus (SARS-
CoV) epidemic, the world is currently facing the COVID-19 pandemic caused by SARS …

Disome and trisome profiling reveal genome-wide targets of ribosome quality control

S Meydan, NR Guydosh - Molecular cell, 2020 - cell.com
The ribosome-associated protein quality control (RQC) system that resolves stalled
translation events is activated when ribosomes collide and form disome, trisome, or higher …

The AAA+ superfamily: a review of the structural and mechanistic principles of these molecular machines

YA Khan, KI White, AT Brunger - Critical reviews in biochemistry …, 2022 - Taylor & Francis
ATPases associated with diverse cellular activities (AAA+ proteins) are a superfamily of
proteins found throughout all domains of life. The hallmark of this family is a conserved …

Galaxy and Apollo as a biologist-friendly interface for high-quality cooperative phage genome annotation

J Ramsey, H Rasche, C Maughmer… - PLOS Computational …, 2020 - journals.plos.org
In the modern genomic era, scientists without extensive bioinformatic training need to apply
high-power computational analyses to critical tasks like phage genome annotation. At the …

Integrated proteogenomic deep sequencing and analytics accurately identify non-canonical peptides in tumor immunopeptidomes

C Chong, M Müller, HS Pak, D Harnett, F Huber… - Nature …, 2020 - nature.com
Efforts to precisely identify tumor human leukocyte antigen (HLA) bound peptides capable of
mediating T cell-based tumor rejection still face important challenges. Recent studies …

Heterogeneous and multiple conformational transition pathways between pseudoknots of the SARS-CoV-2 frameshift element

S Yan, T Schlick - Proceedings of the National Academy of Sciences, 2025 - pnas.org
Frameshifting is an essential mechanism employed by many viruses including
coronaviruses to produce viral proteins from a compact RNA genome. It is facilitated by …

The HCPro from the Potyviridae family: an enviable multitasking Helper Component that every virus would like to have

AA Valli, A Gallo, B Rodamilans… - Molecular plant …, 2018 - Wiley Online Library
RNA viruses have very compact genomes and so provide a unique opportunity to study how
evolution works to optimize the use of very limited genomic information. A widespread viral …