Prokaryotic RefSeq Genomes
www.ncbi.nlm.nih.gov/refseq/about/prokaryotes/
Oct 1, 2024
4
What is Type Material?
www.ncbi.nlm.nih.gov/datasets/docs/v2/policies-annotation/genome-processing/type-material/
Oct 1, 2024
2
Genomes Selected for RefSeq Annotation
www.ncbi.nlm.nih.gov/datasets/docs/v2/policies-annotation/genome-processing/refseq-selection/
Oct 1, 2024
1
Selecting Reference Genomes
www.ncbi.nlm.nih.gov/datasets/docs/v2/policies-annotation/genome-processing/reference-selection/
Oct 1, 2024
2
CheckM - assessing the quality of genome bins
ecogenomics.github.io/CheckM/
Sep 24, 2024
1
Lateral Transfer of Genes and Gene Fragments in Staphylococcus Extends beyond Mobile Elements
www.ncbi.nlm.nih.gov/pmc/articles/PMC3147504/
Sep 18, 2024
4
Frontiers | Comparative Genomics of Staphylococcus Reveals Determinants of Speciation and Diversification of Antimicrobial Defense
www.frontiersin.org/journals/microbiology/articles/10.3389/fmicb.2018.02753/full
Sep 18, 2024
3
Digital Microbe: a genome-informed data integration framework for team science on emerging model organisms - Scientific Data
www.nature.com/articles/s41597-024-03778-z
Sep 10, 2024
2
Pangenome-spanning epistasis and coselection analysis via de Bruijn graphs
genome.cshlp.org/content/34/7/1081.long
Sep 2, 2024
1
Using average nucleotide identity to improve taxonomic assignments in prokaryotic genomes at the NCBI
www.ncbi.nlm.nih.gov/pmc/articles/PMC6978984/
Aug 28, 2024
11
Rapid and sensitive detection of genome contamination at scale with FCS-GX - Genome Biology
genomebiology.biomedcentral.com/articles/10.1186/s13059-024-03198-7
Aug 28, 2024
7
Generation of accurate, expandable phylogenomic trees with uDance - Nature Biotechnology
www.nature.com/articles/s41587-023-01868-8?fromPaywallRec=false
Aug 22, 2024
2
Community-curated and standardised metadata of published ancient metagenomic samples with AncientMetagenomeDir - Scientific Data
www.nature.com/articles/s41597-021-00816-y?fromPaywallRec=false
Aug 22, 2024
1
Exploring and retrieving sequence and metadata for species across the tree of life with NCBI Datasets - Scientific Data
www.nature.com/articles/s41597-024-03571-y
Aug 22, 2024
1
Mechanisms of host adaptation by bacterial pathogens
academic.oup.com/femsre/article/48/4/fuae019/7713457
Aug 21, 2024
6
On the Origin and Evolution of Thermophily: Reconstruction of Functional Precambrian Enzymes from Ancestors of Bacillus
academic.oup.com/mbe/article/29/2/825/1032046
Aug 20, 2024
4
A genomic timescale of prokaryote evolution: insights into the origin of methanogenesis, phototrophy, and the colonization of land - BMC Ecology and Evolution
bmcecolevol.biomedcentral.com/articles/10.1186/1471-2148-4-44
Aug 20, 2024
8
The Evolutionary Genomics of Host Specificity in Staphylococcus aureus
www.cell.com/trends/microbiology/fulltext/S0966-842X%2819%2930322-1
Aug 19, 2024
2
Molecular Phylogenetics and Temporal Diversification in the Genus Aeromonas Based on the Sequences of Five Housekeeping Genes
journals.plos.org/plosone/article?id=10.1371/journal.pone.0088805
Aug 19, 2024
7
Multiclonal human origin and global expansion of an endemic bacterial pathogen of livestock | PNAS
www.pnas.org/doi/full/10.1073/pnas.2211217119
Aug 19, 2024
4
Phylogenetic relationships among Staphylococcus species and refinement of cluster groups based on multilocus data
www.ncbi.nlm.nih.gov/pmc/articles/PMC3464590/
Aug 19, 2024
10
Metadata in the BioSample Online Repository are Impaired by Numerous Anomalies
arxiv.org/abs/1708.01286
Aug 16, 2024
1
The Impacts of Low Diversity Sequence Data on Phylodynamic Inference during an Emerging Epidemic
www.mdpi.com/1999-4915/13/1/79
Aug 16, 2024
2
Coagulase-Negative Staphylococci
www.ncbi.nlm.nih.gov/pmc/articles/PMC4187637/
Aug 16, 2024
2
Genome-scale rates of evolutionary change in bacteria
www.ncbi.nlm.nih.gov/pmc/articles/PMC5320706/
Aug 16, 2024
18
Underrated <i>Staphylococcus</i> species and their role in antimicrobial resistance spreading
www.scielo.br/j/gmb/a/gnJk667XwXzmMDfvCKkt8mv/?format=html&lang=en
Aug 15, 2024
13
A molecular portrait of maternal sepsis from Byzantine Troy
elifesciences.org/articles/20983
Aug 15, 2024
6
Plagued by a cryptic clock: insight and issues from the global phylogeny of Yersinia pestis - Communications Biology
www.nature.com/articles/s42003-022-04394-6
Aug 15, 2024
17
Dating the bacterial tree of life based on ancient symbiosis
www.biorxiv.org/content/10.1101/2023.06.18.545440v1.full
Aug 15, 2024
8
The evolution of bacterial pathogens in the Anthropocene
www.sciencedirect.com/science/article/pii/S1567134820304421
Aug 15, 2024
3
Evolution of bacterial virulence
academic.oup.com/femsre/article/41/5/679/3844166
Aug 15, 2024
5
Pathogen Evolution - Microbial Evolution and Co-Adaptation - NCBI Bookshelf
www.ncbi.nlm.nih.gov/books/NBK45713/
Aug 15, 2024
14
Antibiotic‐induced SOS response promotes horizontal dissemination of pathogenicity island‐encoded virulence factors in staphylococci
onlinelibrary-wiley-com.eux.idm.oclc.org/doi/full/10.1111/j.1365-2958.2005.04584.x
Aug 15, 2024
1
Pathogenicity and resistance islands of staphylococci
www-sciencedirect-com.eux.idm.oclc.org/science/article/pii/S1286457901014149?via%3Dihub
Aug 15, 2024
1
Genomic differences between the food-grade Staphylococcus carnosus and pathogenic staphylococcal species - ClinicalKey
www-clinicalkey-com.eux.idm.oclc.org/
Aug 15, 2024
3
What Distinguishes Highly Pathogenic Staphylococci from Medium- and Non-pathogenic?
link-springer-com.eux.idm.oclc.org/chapter/10.1007/82_2012_286
Aug 15, 2024
11
The past, present and future of ancient bacterial DNA
www.ncbi.nlm.nih.gov/pmc/articles/PMC7478633/
Aug 13, 2024
6
The Rise and Fall of the Mycobacterium tuberculosis Complex
www.sciencedirect.com/science/article/pii/B9780123848901000248
Aug 13, 2024
1
Fig. 4: Staphylococcus aureus host species adaptation over time. | Nature Reviews Microbiology
www.nature.com/articles/s41579-023-00852-y/figures/4
Aug 13, 2024
41
Staphylococcus aureus host interactions and adaptation - Nature Reviews Microbiology
www.nature.com/articles/s41579-023-00852-y
Aug 13, 2024
7
Recent human-to-poultry host jump, adaptation, and pandemic spread of Staphylococcus aureus | PNAS
www.pnas.org/doi/full/10.1073/pnas.0909285106
Aug 12, 2024
1
Evolutionary Genomics of Staphylococcus aureus Reveals Insights into the Origin and Molecular Basis of Ruminant Host Adaptation
academic.oup.com/gbe/article/doi/10.1093/gbe/evq031/573716
Aug 12, 2024
15
Bacteriophage-driven emergence and expansion of Staphylococcus aureus in rodent populations
journals.plos.org/plospathogens/article?id=10.1371/journal.ppat.1012378
Aug 12, 2024
3
Horizontal transfer of probable chicken-pathogenicity chromosomal islands between Staphylococcus aureus and Staphylococcus agnetis
www.ncbi.nlm.nih.gov/pmc/articles/PMC10321648/
Aug 11, 2024
5
Emergence of methicillin resistance predates the clinical use of antibiotics - Nature
www.nature.com/articles/s41586-021-04265-w
Aug 11, 2024
3
SaLTy: a novel Staphylococcus aureus Lineage Typer
www.ncbi.nlm.nih.gov/pmc/articles/PMC11165655/
Aug 8, 2024
2
Staphylococcus chromogenes, a Coagulase-Negative Staphylococcus Species That Can Clot Plasma | Journal of Clinical Microbiology
journals.asm.org/doi/10.1128/jcm.03139-15
Aug 6, 2024
1
Submit Raw Reads with Webin-CLI — ENA Documentation 1 documentation
ena-docs.readthedocs.io/en/latest/submit/reads/webin-cli.html
Aug 6, 2024
1
Phylogenomic and genomic analysis reveals unique and shared genetic signatures of Mycobacterium kansasii complex species
www.microbiologyresearch.org/content/journal/mgen/10.1099/mgen.0.001266?s=09
Jul 26, 2024
11
Genomic LLMs Show Superior Performance and Generalization Across Diverse Tasks | NVIDIA Technical Blog
developer.nvidia.com/blog/genomic-llms-show-superior-performance-and-generalization-across-diverse-tasks/
Jul 26, 2024
1