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References from Unitig-centered pan-genome machine learning approach for predicting antibiotic resistance and discovering novel resistance genes in bacterial strains. Local targets link to admitted publications; unresolved targets remain external evidence.
10.1126/science.aag0822
10.1126/science.aag0822 · External reference
Validating the AMRFinder tool and resistance gene database by using antimicrobial resistance genotype-phenotype correlations in a collection of isolates
10.1128/aac.00483-19 · 2019 · External reference
Contrasting approaches to genome-wide association studies impact the detection of resistance mechanisms in Staphylococcus aureus
2019 · External reference
CARD 2020: antibiotic resistome surveillance with the comprehensive antibiotic resistance database
2020 · External reference
ResFinder 4.0 for predictions of phenotypes from genotypes
10.1093/jac/dkaa345 · 2020 · External reference
Genome-wide association study reveals genetic markers for antimicrobial resistance in Mycoplasma bovis
10.1128/spectrum.00262-21 · 2021 · External reference
Antimicrobial resistance genetic factor identification from whole-genome sequence data using deep feature selection
2019 · External reference
Predicting antimicrobial susceptibilities for Escherichia coli and Klebsiella pneumoniae isolates using whole genomic sequence data
10.1093/jac/dkt180 · 2013 · External reference
Prediction of Staphylococcus aureus antimicrobial resistance by whole-genome sequencing
10.1128/jcm.03117-13 · 2014 · External reference
Rapid antibiotic-resistance predictions from genome sequence data for Staphylococcus aureus and Mycobacterium tuberculosis
10.1038/ncomms10063 · 2015 · External reference
Whole-genome sequencing for prediction of Mycobacterium tuberculosis drug susceptibility and resistance: a retrospective cohort study
10.1016/s1473-3099(15)00062-6 · 2015 · External reference
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Identifying lineage effects when controlling for population structure improves power in bacterial association studies
10.1038/nmicrobiol.2016.41 · 2016 · External reference
Sequence element enrichment analysis to determine the genetic basis of bacterial phenotypes
10.1038/ncomms12797 · 2016 · External reference
Association mapping from sequencing reads using k-mers
10.7554/elife.32920 · 2018 · External reference
Characterizing the genetic basis of bacterial phenotypes using genome-wide association studies: a new direction for bacteriology
2014 · External reference
10.1038/nrg.2016.132
10.1038/nrg.2016.132 · External reference
A fast and agnostic method for bacterial genome-wide association studies: Bridging the gap between k-mers and genetic events
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A practical comparison of de novo genome assembly software tools for next-generation sequencing technologies
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The PATRIC bioinformatics resource center: expanding data and analysis capabilities
2020 · External reference
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10.1016/s1473-3099(15)00424-7 · 2016 · External reference
Phylogenetic distribution of CRISPR-Cas systems in antibiotic-resistant Pseudomonas aeruginosa
10.1128/mbio.01796-15 · 2015 · External reference
10.1128/mmbr.00027-10
10.1128/mmbr.00027-10 · External reference
Correlation between phenotypic antibiotic susceptibility and the resistome in Pseudomonas aeruginosa
10.1016/j.ijantimicag.2017.02.026 · 2017 · External reference
Predicting antimicrobial resistance in Pseudomonas aeruginosa with machine learning‐enabled molecular diagnostics
10.15252/emmm.201910264 · 2020 · External reference
Trimmomatic: a flexible trimmer for Illumina sequence data
10.1093/bioinformatics/btu170 · 2014 · External reference
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Compacting de Bruijn graphs from sequencing data quickly and in low memory
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GATB: genome assembly & analysis tool box
10.1093/bioinformatics/btu406 · 2014 · External reference
Antimicrobial treatment of Pseudomonas aeruginosa severe sepsis
10.3390/antibiotics11101432 · 2022 · External reference
Improving MGMT methylation status prediction of glioblastoma through optimizing radiomics features using genetic algorithm-based machine learning approach
2022 · External reference
Feature selection stability and accuracy of prediction models for genomic prediction of residual feed intake in pigs using machine learning
10.3389/fgene.2021.611506 · 2021 · External reference
10.1016/j.csbj.2022.12.046 · Admitted local publication
Enhancing predictions of antimicrobial resistance of pathogens by expanding the potential resistance gene repertoire using a pan-genome-based feature selection approach
2022 · External reference
A pan-genome-based machine learning approach for predicting antimicrobial resistance activities of the Escherichia coli strains
10.1093/bioinformatics/bty276 · 2018 · External reference
Exploiting genomics to mitigate the public health impact of antimicrobial resistance
10.1186/s13073-022-01020-2 · 2022 · External reference
CD-HIT: accelerated for clustering the next-generation sequencing data
10.1093/bioinformatics/bts565 · 2012 · External reference
CARD 2023: expanded curation, support for machine learning, and resistome prediction at the comprehensive antibiotic resistance database
10.1093/nar/gkac920 · 2023 · External reference
Comparative genomics: the bacterial pan-genome
10.1016/j.mib.2008.09.006 · 2008 · External reference
10.1073/pnas.0506758102
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10.1016/b978-0-12-817076-2.00005-6
10.1016/b978-0-12-817076-2.00005-6 · 2020 · External reference
First steps in the analysis of prokaryotic pan-genomes
10.1177/1177932220938064 · 2020 · External reference
Computational pan-genomics: status, promises and challenges.
2018 · External reference
Effects of the order of exposure to antimicrobials on the incidence of multidrug-resistant Pseudomonas aeruginosa
10.1038/s41598-023-35256-8 · 2023 · External reference
Epidemiology and treatment of multidrug-resistant and extensively drug-resistant Pseudomonas aeruginosa infections
10.1128/cmr.00031-19 · 2019 · External reference
10.1016/j.biotechadv.2018.11.013
10.1016/j.biotechadv.2018.11.013 · External reference
Virulence characteristics and an action mode of antibiotic resistance in multidrug-resistant Pseudomonas aeruginosa
10.1038/s41598-018-37422-9 · 2019 · External reference
Mobile genetic elements associated with antimicrobial resistance
10.1128/cmr.00088-17 · 2018 · External reference
10.1111/1574-6976.12067
10.1111/1574-6976.12067 · External reference
Copy‐out—paste‐in transposition of IS911: a major transposition pathway
2015 · External reference
Antimicrobial resistance and molecular characterization of gene cassettes from class 1 integrons in Pseudomonas aeruginosa strains
10.1089/mdr.2019.0406 · 2020 · External reference
Integron activity accelerates the evolution of antibiotic resistance
10.7554/elife.62474 · 2021 · External reference
10.1126/science.1128393
10.1126/science.1128393 · External reference
Key components of the eight classes of type IV secretion systems involved in bacterial conjugation or protein secretion
10.1093/nar/gku194 · 2014 · External reference
A component of the Xanthomonadaceae type IV secretion system combines a VirB7 motif with a N0 domain found in outer membrane transport proteins
10.1371/journal.ppat.1002031 · 2011 · External reference
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10.15252/embj.201796629
10.15252/embj.201796629 · External reference
Mobile genetic elements of Vibrio cholerae and the evolution of its antimicrobial resistance
2021 · External reference
A novel type II secretion system in Pseudomonas aeruginosa
10.1046/j.1365-2958.2002.02759.x · 2002 · External reference
Protein secretion systems in Pseudomonas aeruginosa: a wealth of pathogenic weapons
10.1016/j.ijmm.2010.08.005 · 2010 · External reference
10.1016/j.resmic.2012.07.007
10.1016/j.resmic.2012.07.007 · External reference
Reevaluation, using intact cells, of the exclusion limit and role of porin OprF in Pseudomonas aeruginosa outer membrane permeability
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Gram-negative antibiotic resistance: there is a price to pay
10.1186/cc6820 · 2008 · External reference
Antibacterial-resistant Pseudomonas aeruginosa: clinical impact and complex regulation of chromosomally encoded resistance mechanisms
10.1128/cmr.00040-09 · 2009 · External reference
10.1038/nature02122
10.1038/nature02122 · External reference
Pseudomonas aeruginosa: pathogenesis, virulence factors, antibiotic resistance, interaction with host, technology advances and emerging therapeutics
10.1038/s41392-022-01056-1 · 2022 · External reference
10.1093/femsre/fux020
10.1093/femsre/fux020 · External reference
Pseudomonas aeruginosa: multi-drug-resistance development and treatment options
2013 · External reference
10.1126/science.288.5469.1251
10.1126/science.288.5469.1251 · External reference
Genetic diversity of multidrug-resistant pseudomonas aeruginosa isolates carrying bla VIM–2 and bla KPC–2 genes that spread on different genetic environment in Colombia
2021 · External reference
Virulence factors of Pseudomonas aeruginosa and antivirulence strategies to combat its drug resistance
10.3389/fcimb.2022.926758 · 2022 · External reference
10.3390/ijms22063128
10.3390/ijms22063128 · External reference
10.2217/fmb-2021-0158
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Characterization of the virulence of Pseudomonas aeruginosa strains causing ventilator-associated pneumonia
2020 · External reference
Prevalence of different virulence factors and their association with antimicrobial resistance among Pseudomonas aeruginosa clinical isolates from Egypt
10.1186/s12866-023-02897-8 · 2023 · External reference
10.3390/app13074238
10.3390/app13074238 · External reference
10.1016/j.bbapap.2008.11.005
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Understanding antibiotic resistance via outer membrane permeability
10.2147/idr.s156995 · 2018 · External reference
Mechanisms of antibiotic resistance
10.1128/9781555819286.ch17 · 2016 · External reference
Mechanisms of bacterial resistance to antibiotics
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Antibiotic resistance mechanisms in bacteria: relationships between resistance determinants of antibiotic producers, environmental bacteria, and clinical pathogens
10.3389/fmicb.2018.02928 · 2018 · External reference
10.1038/s41579-022-00820-y
10.1038/s41579-022-00820-y · External reference
The building blocks of antimicrobial resistance in Pseudomonas aeruginosa: implications for current resistance-breaking therapies
10.3389/fcimb.2021.665759 · 2021 · External reference
Multidrug adaptive resistance of Pseudomonas aeruginosa swarming cells
10.1128/aac.01999-19 · 2020 · External reference
10.1016/j.bioflm.2021.100056 · 2021 · Admitted local publication
Broad-spectrum adaptive antibiotic resistance associated with Pseudomonas aeruginosa mucin-dependent surfing motility
2018 · External reference