Research graph
References from Biased sampling driven by bacterial population structure confounds machine learning prediction of antimicrobial resistance. Local targets link to admitted publications; unresolved targets remain external evidence.
Global burden of bacterial antimicrobial resistance in 2019: a systematic analysis
10.1016/s0140-6736(21)02724-0 · 2022 · External reference
Ten recommendations for supporting open pathogen genomic analysis in public health
10.1038/s41591-020-0935-z · 2020 · External reference
Antimicrobial resistance surveillance in the genomic age
10.1111/nyas.13289 · 2017 · External reference
Innovations in genomic antimicrobial resistance surveillance
10.1016/s2666-5247(23)00285-9 · 2023 · External reference
Genomic surveillance for antimicrobial resistance—a One Health perspective
10.1038/s41576-023-00649-y · 2024 · External reference
Machine learning for antimicrobial resistance prediction: current practice, limitations, and clinical perspective
2022 · External reference
Whole-genome phenotype prediction with machine learning: Open problems in bacterial genomics
2025 · External reference
The scope of the antimicrobial resistance challenge
10.1016/s0140-6736(24)00876-6 · 2024 · External reference
A phylogenetic approach to comparative genomics
10.1038/s41576-024-00803-0 · 2025 · External reference
Phylogenies and the comparative method
10.1086/284325 · 1985 · External reference
Identifying lineage effects when controlling for population structure improves power in bacterial association studies
10.1038/nmicrobiol.2016.41 · 2016 · External reference
Microbial genome-wide association studies: lessons from human GWAS
10.1038/nrg.2016.132 · 2017 · External reference
pyseer: a comprehensive tool for microbial pangenome-wide association studies
10.1093/bioinformatics/bty539 · 2018 · External reference
Navigating the pitfalls of applying machine learning in genomics
10.1038/s41576-021-00434-9 · 2022 · External reference
Unresolved reference
2024 · External reference
Roary: rapid large-scale prokaryote pan genome analysis
10.1093/bioinformatics/btv421 · 2015 · External reference
SNP-sites: rapid efficient extraction of SNPs from multi-FASTA alignments
2016 · External reference
LightGBM: a highly efficient gradient boosting decision tree.
2017 · External reference
Prediction of antibiotic resistance in Escherichia coli from large-scale pan-genome data
10.1371/journal.pcbi.1006258 · 2018 · External reference
Evaluation of parameters affecting performance and reliability of machine learning-based antibiotic susceptibility testing from whole genome sequencing data
10.1371/journal.pcbi.1007349 · 2019 · External reference
From local explanations to global understanding with explainable AI for trees
10.1038/s42256-019-0138-9 · 2020 · External reference
ESKAPE pathogens: antimicrobial resistance, epidemiology, clinical impact and therapeutics
10.1038/s41579-024-01054-w · 2024 · External reference
Molecular mechanisms of antibiotic resistance revisited
10.1038/s41579-022-00820-y · 2023 · External reference
Fluoroquinolone resistance: mechanisms, impact on bacteria, and role in evolutionary success
10.1016/j.tim.2014.04.007 · 2014 · External reference
Rapid inference of antibiotic resistance and susceptibility by genomic neighbour typing
10.1038/s41564-019-0656-6 · 2020 · External reference
Assessing computational predictions of antimicrobial resistance phenotypes from microbial genomes
2024 · External reference
A guided tour of phylogenetic comparative methods for studying trait evolution
10.1146/annurev-ecolsys-102221-050754 · 2024 · External reference
Phylogenetics is the new genetics (for most of biodiversity)
10.1016/j.tree.2020.01.005 · 2020 · External reference
Predictive modeling of antibiotic eradication therapy success for new-onset Pseudomonas aeruginosa pulmonary infections in children with cystic fibrosis
10.1371/journal.pcbi.1011424 · 2023 · External reference
A genomic data resource for predicting antimicrobial resistance from laboratory-derived antimicrobial susceptibility phenotypes
10.1093/bib/bbab313 · 2021 · External reference
Velvet: algorithms for de novo short read assembly using de Bruijn graphs
10.1101/gr.074492.107 · 2008 · External reference
CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes
10.1101/gr.186072.114 · 2015 · External reference
Prokka: rapid prokaryotic genome annotation
10.1093/bioinformatics/btu153 · 2014 · External reference
IQ-TREE: a fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies
10.1093/molbev/msu300 · 2015 · External reference
Open-access bacterial population genomics: BIGSdb software, the PubMLST.org website and their applications
10.12688/wellcomeopenres.14826.1 · 2018 · External reference
Interactive Tree Of Life (iTOL) v5: an online tool for phylogenetic tree display and annotation
10.1093/nar/gkab301 · 2021 · External reference
Bifrost: highly parallel construction and indexing of colored and compacted de Bruijn graphs
10.1186/s13059-020-02135-8 · 2020 · External reference
10.25080/majora-8b375195-003
10.25080/majora-8b375195-003 · External reference
Scikit-learn: machine learning in Python
2011 · 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
