Journal Club Bot (@JC_pathogenomic) profile picture

Journal Club Bot

@JC_pathogenomic

I'm a Bot. I post interesting papers. Maintained by @happy_khan

 Somewhere in the ether.
github.com/happykhan/journalbot
Joined December 2014
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Coding-Complete Genome Sequences of 40 SARS-CoV-2 Omicron XBB, XBB.1, and XBB.2 Sublineage Strains in Bangladesh. ncbi.nlm.nih.gov/pubmed/3677…
Coding-Complete Genome Sequences of 40 SARS-CoV-2 Omicron XBB, XBB.1, and XBB.2 Sublineage Strains...

Coding-Complete Genome Sequences of 40 SARS-CoV-2 Omicron XBB, XBB.1, and XBB.2 Sublineage Strains...

Here, we report the coding-complete genome sequences of 40 severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) strains of the newly emerged recombinant Omicron variants XBB, XBB.1, and...

pubmed.ncbi.nlm.nih.gov
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Factors associated with plasmid antibiotic resistance gene carriage revealed using large-scale multivariable analysis. ncbi.nlm.nih.gov/pubmed/3678…
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Global disparities in SARS-CoV-2 genomic surveillance. ncbi.nlm.nih.gov/pubmed/3638…
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De novo identification of microbial contaminants in low microbial biomass microbiomes with Squeegee. ncbi.nlm.nih.gov/pubmed/3635…
De novo identification of microbial contaminants in low microbial biomass microbiomes with Squeegee...

De novo identification of microbial contaminants in low microbial biomass microbiomes with Squeegee...

Computational analysis of host-associated microbiomes has opened the door to numerous discoveries relevant to human health and disease. However, contaminant sequences in metagenomic samples can...

pubmed.ncbi.nlm.nih.gov
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Repeated out-of-Africa expansions of Helicobacter pylori driven by replacement of deleterious mutations. ncbi.nlm.nih.gov/pubmed/3636…
Repeated out-of-Africa expansions of Helicobacter pylori driven by replacement of deleterious...

Repeated out-of-Africa expansions of Helicobacter pylori driven by replacement of deleterious...

Helicobacter pylori lives in the human stomach and has a population structure resembling that of its host. However, H. pylori from Europe and the Middle East trace substantially more ancestry from...

pubmed.ncbi.nlm.nih.gov
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Cov2clusters: genomic clustering of SARS-CoV-2 sequences. ncbi.nlm.nih.gov/pubmed/3625…
New rules for genomics-informed COVID-19 responses-Lessons learned from the first waves of the Omicron variant in Australia. bit.ly/3ErKGGO
GyrB in silico mining in 27151 global gonococcal genomes from 1928-2021 combined with zoliflodacin in vitro testing of 71 international gonococcal isolates with different GyrB, ParC and ParE substitutions confirms high susceptibility. bit.ly/3O3kdm8
Structural and Genomic Evolution of RRNPPA Systems and Their Pheromone Signaling. bit.ly/3GtMkJJ
Impact of host age on viral and bacterial communities in a waterbird population. bit.ly/3AaY93e
Impact of host age on viral and bacterial communities in a waterbird population - PubMed

Impact of host age on viral and bacterial communities in a waterbird population - PubMed

Wildlife harbour pathogens that can harm human or livestock health and are the source of most emerging infectious diseases. It is rarely considered how changes in wildlife population age-structures...

pubmed.ncbi.nlm.nih.gov
MIDAS2: Metagenomic Intra-species Diversity Analysis System. bit.ly/3toMFp1
MIDAS2: Metagenomic Intra-species Diversity Analysis System - PubMed

MIDAS2: Metagenomic Intra-species Diversity Analysis System - PubMed

Supplementary data are available at Bioinformatics online.

pubmed.ncbi.nlm.nih.gov
Genome-wide association studies identify an association of transferrin binding protein B variation and invasive serogroup Y meningococcal disease in older adults. bit.ly/3g45r28
kmdiff, large-scale and user-friendly differential k-mer analyses. bit.ly/3EqMxvy
Prevalence and risk factors of bacterial enteric pathogens in men who have sex with men: a cross-sectional study at the UK's largest sexual health service. bit.ly/3WQdmAF
Prevalence and risk factors of bacterial enteric pathogens in men who have sex with men: A cross-...

Prevalence and risk factors of bacterial enteric pathogens in men who have sex with men: A cross-...

One in ten MSM had a BEP detected and most did not report symptoms. MphA carriage was common, particularly among those with BEPs. Bacterial STI treatment might contribute to selection of resistant...

pubmed.ncbi.nlm.nih.gov
CARD 2023: expanded curation, support for machine learning,and resistome prediction at the Comprehensive Antibiotic Resistance Database. bit.ly/3hDMNyx
CARD 2023: expanded curation, support for machine learning, and resistome prediction at the...

CARD 2023: expanded curation, support for machine learning, and resistome prediction at the...

The Comprehensive Antibiotic Resistance Database (CARD; card.mcmaster.ca) combines the Antibiotic Resistance Ontology (ARO) with curated AMR gene (ARG) sequences and resistance-conferring mutations...

pubmed.ncbi.nlm.nih.gov
COVID-19 cluster size and transmission rates in schools from crowdsourced case reports. bit.ly/3EnW06O
Phylodynamic signatures in the emergence of community-associated MRSA. bit.ly/3G7BeJT
Swiss public health measures associated with reduced SARS-CoV-2 transmission using genome data. bit.ly/3DRm4Wy
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The Anglo-Saxon migration and the formation of the early English gene pool. bit.ly/3AqUPBt
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Genomic population structure associated with repeated escape of Salmonella enterica ATCC14028s from the laboratory into nature. bit.ly/2XY7Hyz
Genomic population structure associated with repeated escape of Salmonella enterica ATCC14028s from...

Genomic population structure associated with repeated escape of Salmonella enterica ATCC14028s from...

Salmonella enterica serovar Typhimurium strain ATCC14028s is commercially available from multiple national type culture collections, and has been widely used since 1960 for quality control of growth...

pubmed.ncbi.nlm.nih.gov
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