COVID‐19: A systematic review and update on prevention, diagnosis, and treatment

H Aghamirza Moghim Aliabadi… - MedComm, 2022 - Wiley Online Library
Since the rapid onset of the COVID‐19 or SARS‐CoV‐2 pandemic in the world in 2019,
extensive studies have been conducted to unveil the behavior and emission pattern of the …

A comprehensive review of the analysis and integration of omics data for SARS-CoV-2 and COVID-19

Z Zhu, S Zhang, P Wang, X Chen, J Bi… - Briefings in …, 2022 - academic.oup.com
Since the first report of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in
December 2019, over 100 million people have been infected by COVID-19, millions of …

Hapo-G, haplotype-aware polishing of genome assemblies with accurate reads

JM Aury, B Istace - NAR genomics and bioinformatics, 2021 - academic.oup.com
Single-molecule sequencing technologies have recently been commercialized by Pacific
Biosciences and Oxford Nanopore with the promise of sequencing long DNA fragments …

Altered infective competence of the human gut microbiome in COVID-19

L de Nies, V Galata, C Martin-Gallausiaux… - Microbiome, 2023 - Springer
Abstract Background Infections with SARS-CoV-2 have a pronounced impact on the
gastrointestinal tract and its resident microbiome. Clear differences between severe cases of …

Pervasive tandem duplications and convergent evolution shape coral genomes

B Noel, F Denoeud, A Rouan, C Buitrago-López… - Genome Biology, 2023 - Springer
Background Over the last decade, several coral genomes have been sequenced allowing a
better understanding of these symbiotic organisms threatened by climate change …

A new profiling approach for DNA sequences based on the nucleotides' physicochemical features for accurate analysis of SARS-CoV-2 genomes

S Akbari Rokn Abadi, A Mohammadi, S Koohi - BMC genomics, 2023 - Springer
Background The prevalence of the COVID-19 disease in recent years and its widespread
impact on mortality, as well as various aspects of life around the world, has made it important …

[HTML][HTML] Enhancing metagenomic classification with compression-based features

JM Silva, JR Almeida - Artificial Intelligence in Medicine, 2024 - Elsevier
Metagenomics is a rapidly expanding field that uses next-generation sequencing technology
to analyze the genetic makeup of environmental samples. However, accurately identifying …

New evaluation methods of read mapping by 17 aligners on simulated and empirical NGS data: an updated comparison of DNA-and RNA-Seq data from Illumina and …

L Donato, C Scimone, C Rinaldi, R D'Angelo… - Neural Computing and …, 2021 - Springer
Abstract During the last (15) years, improved omics sequencing technologies have
expanded the scale and resolution of various biological applications, generating high …

RabbitTClust: enabling fast clustering analysis of millions of bacteria genomes with MinHash sketches

X Xu, Z Yin, L Yan, H Zhang, B Xu, Y Wei, B Niu… - Genome Biology, 2023 - Springer
We present RabbitTClust, a fast and memory-efficient genome clustering tool based on
sketch-based distance estimation. Our approach enables efficient processing of large-scale …

A “Four Core Genotypes” rat model to distinguish mechanisms underlying sex-biased phenotypes and diseases

AP Arnold, X Chen, MN Grzybowski, JM Ryan… - bioRxiv, 2023 - biorxiv.org
Background We have generated a rat model similar to the Four Core Genotypes mouse
model, allowing comparison of XX and XY rats with the same type of gonad. The model …