SARS‐CoV‐2, the pandemic coronavirus: Molecular and structural insights

SB Kadam, GS Sukhramani, P Bishnoi… - Journal of basic …, 2021 - Wiley Online Library
The outbreak of a novel coronavirus associated with acute respiratory disease, called
COVID‐19, marked the introduction of the third spillover of an animal coronavirus (CoV) to …

Determinants of translation efficiency and accuracy

H Gingold, Y Pilpel - Molecular systems biology, 2011 - embopress.org
Proper functioning of biological cells requires that the process of protein expression be
carried out with high efficiency and fidelity. Given an amino‐acid sequence of a protein …

Cross‐species transmission of the newly identified coronavirus 2019‐nCoV

W Ji, W Wang, X Zhao, J Zai, X Li - Journal of medical virology, 2020 - Wiley Online Library
The current outbreak of viral pneumonia in the city of Wuhan, China, was caused by a novel
coronavirus designated 2019‐nCoV by the World Health Organization, as determined by …

From SARS and MERS CoVs to SARS‐CoV‐2: Moving toward more biased codon usage in viral structural and nonstructural genes

M Kandeel, A Ibrahim, M Fayez… - Journal of medical …, 2020 - Wiley Online Library
Background Severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) is an
emerging disease with fatal outcomes. In this study, a fundamental knowledge gap question …

A new and updated resource for codon usage tables

J Athey, A Alexaki, E Osipova, A Rostovtsev… - BMC …, 2017 - Springer
Background Due to the degeneracy of the genetic code, most amino acids can be encoded
by multiple synonymous codons. Synonymous codons naturally occur with different …

PhiSpy: a novel algorithm for finding prophages in bacterial genomes that combines similarity- and composition-based strategies

S Akhter, RK Aziz, RA Edwards - Nucleic acids research, 2012 - academic.oup.com
Prophages are phages in lysogeny that are integrated into, and replicated as part of, the
host bacterial genome. These mobile elements can have tremendous impact on their …

Clinical sequencing uncovers origins and evolution of Lassa virus

KG Andersen, BJ Shapiro, CB Matranga, R Sealfon… - Cell, 2015 - cell.com
Summary The 2013–2015 West African epidemic of Ebola virus disease (EVD) reminds us
of how little is known about biosafety level 4 viruses. Like Ebola virus, Lassa virus (LASV) …

ViralZone: a knowledge resource to understand virus diversity

C Hulo, E De Castro, P Masson… - Nucleic acids …, 2011 - academic.oup.com
The molecular diversity of viruses complicates the interpretation of viral genomic and
proteomic data. To make sense of viral gene functions, investigators must be familiar with …

MARVEL, a tool for prediction of bacteriophage sequences in metagenomic bins

D Amgarten, LPP Braga, AM Da Silva… - Frontiers in genetics, 2018 - frontiersin.org
Here we present MARVEL, a tool for prediction of double-stranded DNA bacteriophage
sequences in metagenomic bins. MARVEL uses a random forest machine learning …

Deeply altered genome architecture in the endoparasitic flowering plant Sapria himalayana Griff.(Rafflesiaceae)

L Cai, BJ Arnold, Z Xi, DE Khost, N Patel, CB Hartmann… - Current Biology, 2021 - cell.com
Summary Despite more than 2,000-fold variation in genome size, key features of genome
architecture are largely conserved across angiosperms. Parasitic plants have elucidated the …