VAMPr: VAriant Mapping and Prediction of antibiotic resistance via explainable features and machine learning

Parallelization of MAFFT for large-scale multiple sequence alignments

(2018) Tsukasa Nakamura et al.   BIOINFORMATICS

Practical issues in implementing whole-genome-sequencing in routine diagnostic microbiology

(2018) J.W.A. Rossen et al.   CLINICAL MICROBIOLOGY AND INFECTION

Predictable Phenotypes of Antibiotic Resistance Mutations

(2018) M. Knopp et al.   mBio

Developing an in silico minimum inhibitory concentration panel test for Klebsiella pneumoniae

(2018) Marcus Nguyen et al.   Scientific Reports

Prediction of Susceptibility to First-Line Tuberculosis Drugs by DNA Sequencing

(2018)   NEW ENGLAND JOURNAL OF MEDICINE

Applying Rapid Whole-Genome Sequencing To Predict Phenotypic Antimicrobial Susceptibility Testing Results among Carbapenem-Resistant Klebsiella pneumoniae Clinical Isolates

(2018) Pranita D. Tamma et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

Bacteremia due to carbapenem-resistant Enterobacteriaceae in neutropenic patients with hematologic malignancies

(2016) Michael J. Satlin et al.   JOURNAL OF INFECTION

Antimicrobial Resistance Prediction in PATRIC and RAST

(2016) James J. Davis et al.   Scientific Reports

Antimicrobial resistance: a priority for global health action

(2015) Arthur Chioro et al.   BULLETIN OF THE WORLD HEALTH ORGANIZATION

The Resistome of Pseudomonas aeruginosa in Relationship to Phenotypic Susceptibility

(2014) Veronica N. Kos et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

Fast and sensitive protein alignment using DIAMOND

(2014) Benjamin Buchfink et al.   NATURE METHODS

PATRIC, the bacterial bioinformatics database and analysis resource

(2013) Alice R. Wattam et al.   NUCLEIC ACIDS RESEARCH

CD-HIT: accelerated for clustering the next-generation sequencing data

(2012) Limin Fu et al.   BIOINFORMATICS

Identification of acquired antimicrobial resistance genes

(2012) E. Zankari et al.   JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY

SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing

(2012) Anton Bankevich et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

PATRIC: the Comprehensive Bacterial Bioinformatics Resource with a Focus on Human Pathogenic Species

(2011) Joseph J. Gillespie et al.   INFECTION AND IMMUNITY

KEGG for integration and interpretation of large-scale molecular data sets

(2011) M. Kanehisa et al.   NUCLEIC ACIDS RESEARCH

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

Antibacterial-Resistant Pseudomonas aeruginosa: Clinical Impact and Complex Regulation of Chromosomally Encoded Resistance Mechanisms

(2009) P. D. Lister et al.   CLINICAL MICROBIOLOGY REVIEWS