[HTML][HTML] Antibiotic resistance in microbes: History, mechanisms, therapeutic strategies and future prospects

TM Uddin, AJ Chakraborty, A Khusro… - Journal of infection and …, 2021 - Elsevier
Antibiotics have been used to cure bacterial infections for more than 70 years, and these low-
molecular-weight bioactive agents have also been used for a variety of other medicinal …

[HTML][HTML] Next-generation sequencing: insights to advance clinical investigations of the microbiome

CR Wensel, JL Pluznick, SL Salzberg… - The Journal of clinical …, 2022 - Am Soc Clin Investig
Next-generation sequencing (NGS) technology has advanced our understanding of the
human microbiome by allowing for the discovery and characterization of unculturable …

KEGG for taxonomy-based analysis of pathways and genomes

M Kanehisa, M Furumichi, Y Sato… - Nucleic acids …, 2023 - academic.oup.com
Abstract KEGG (https://www. kegg. jp) is a manually curated database resource integrating
various biological objects categorized into systems, genomic, chemical and health …

Ensembl 2023

FJ Martin, MR Amode, A Aneja… - Nucleic acids …, 2023 - academic.oup.com
Abstract Ensembl (https://www. ensembl. org) has produced high-quality genomic resources
for vertebrates and model organisms for more than twenty years. During that time, our …

[HTML][HTML] Extending and improving metagenomic taxonomic profiling with uncharacterized species using MetaPhlAn 4

A Blanco-Míguez, F Beghini, F Cumbo, LJ McIver… - Nature …, 2023 - nature.com
Metagenomic assembly enables new organism discovery from microbial communities, but it
can only capture few abundant organisms from most metagenomes. Here we present …

The UCSC genome browser database: 2023 update

LR Nassar, GP Barber, A Benet-Pagès… - Nucleic acids …, 2023 - academic.oup.com
Abstract The UCSC Genome Browser (https://genome. ucsc. edu) is an omics data
consolidator, graphical viewer, and general bioinformatics resource that continues to serve …

OrthoDB v11: annotation of orthologs in the widest sampling of organismal diversity

D Kuznetsov, F Tegenfeldt, M Manni… - Nucleic Acids …, 2023 - academic.oup.com
OrthoDB provides evolutionary and functional annotations of genes in a diverse sampling of
eukaryotes, prokaryotes, and viruses. Genomics continues to accelerate our exploration of …

IMG/VR v4: an expanded database of uncultivated virus genomes within a framework of extensive functional, taxonomic, and ecological metadata

AP Camargo, S Nayfach, IMA Chen… - Nucleic acids …, 2023 - academic.oup.com
Viruses are widely recognized as critical members of all microbiomes. Metagenomics
enables large-scale exploration of the global virosphere, progressively revealing the …

[HTML][HTML] A joint NCBI and EMBL-EBI transcript set for clinical genomics and research

J Morales, S Pujar, JE Loveland, A Astashyn, R Bennett… - Nature, 2022 - nature.com
Comprehensive genome annotation is essential to understand the impact of clinically
relevant variants. However, the absence of a standard for clinical reporting and browser …

Acute inflammatory response via neutrophil activation protects against the development of chronic pain

M Parisien, LV Lima, C Dagostino… - Science translational …, 2022 - science.org
The transition from acute to chronic pain is critically important but not well understood. Here,
we investigated the pathophysiological mechanisms underlying the transition from acute to …