PlasmidHostFinder: Prediction of Plasmid Hosts Using Random Forest

Beyond horizontal gene transfer: the role of plasmids in bacterial evolution

(2021) Jerónimo Rodríguez-Beltrán et al.   NATURE REVIEWS MICROBIOLOGY

COPLA, a taxonomic classifier of plasmids

(2021) Santiago Redondo-Salvo et al.   BMC BIOINFORMATICS

SciPy 1.0: fundamental algorithms for scientific computing in Python

(2020) Pauli Virtanen et al.   NATURE METHODS

Prediction of Acquired Antimicrobial Resistance for Multiple Bacterial Species Using Neural Networks

(2020) D. Aytan-Aktug et al.   mSystems

Pathways for horizontal gene transfer in bacteria revealed by a global map of their plasmids

(2020) Santiago Redondo-Salvo et al.   Nature Communications

Understanding and predicting ciprofloxacin minimum inhibitory concentration in Escherichia coli with machine learning

(2020) Bálint Ármin Pataki et al.   Scientific Reports

Universal whole-sequence-based plasmid typing and its utility to prediction of host range and epidemiological surveillance

(2020) James Robertson et al.   Microbial Genomics

Coevolving Plasmids Drive Gene Flow and Genome Plasticity in Host-Associated Intracellular Bacteria

(2020) Stephan Köstlbacher et al.   CURRENT BIOLOGY

Interactive Tree Of Life (iTOL) v4: recent updates and new developments

(2019) Ivica Letunic et al.   NUCLEIC ACIDS RESEARCH

Horizontal Gene Transfer and Its Association with Antibiotic Resistance in the Genus Aeromonas spp.

(2019) J. Manuel Bello-López et al.   Microorganisms

The PATRIC Bioinformatics Resource Center: expanding data and analysis capabilities

(2019) James J Davis et al.   NUCLEIC ACIDS RESEARCH

PlasFlow: predicting plasmid sequences in metagenomic data using genome signatures

(2018) Pawel S Krawczyk et al.   NUCLEIC ACIDS RESEARCH

Rapid and precise alignment of raw reads against redundant databases with KMA

(2018) Philip T. L. C. Clausen et al.   BMC BIOINFORMATICS

Machine learning and structural analysis of Mycobacterium tuberculosis pan-genome identifies genetic signatures of antibiotic resistance

(2018) Erol S. Kavvas et al.   Nature Communications

Prediction of the intestinal resistome by a three-dimensional structure-based method

(2018) Etienne Ruppé et al.   Nature Microbiology

Ordering the mob: Insights into replicon and MOB typing schemes from analysis of a curated dataset of publicly available plasmids

(2017) Alex Orlek et al.   PLASMID

Random Forest Algorithm for the Classification of Neuroimaging Data in Alzheimer's Disease: A Systematic Review

(2017) Alessia Sarica et al.   Frontiers in Aging Neuroscience

Plasmid Classification in an Era of Whole-Genome Sequencing: Application in Studies of Antibiotic Resistance Epidemiology

(2017) Alex Orlek et al.   Frontiers in Microbiology

K-mer Content, Correlation, and Position Analysis of Genome DNA Sequences for the Identification of Function and Evolutionary Features

(2017) Aaron Sievers et al.   Genes

Reference sequence (RefSeq) database at NCBI: current status, taxonomic expansion, and functional annotation

(2015) Nuala A. O'Leary et al.   NUCLEIC ACIDS RESEARCH

The Precision-Recall Plot Is More Informative than the ROC Plot When Evaluating Binary Classifiers on Imbalanced Datasets

(2015) Takaya Saito et al.   PLoS One

RASTtk: A modular and extensible implementation of the RAST algorithm for building custom annotation pipelines and annotating batches of genomes

(2015) Thomas Brettin et al.   Scientific Reports

In SilicoDetection and Typing of Plasmids using PlasmidFinder and Plasmid Multilocus Sequence Typing

(2014) Alessandra Carattoli et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

Broad host range plasmids

(2013) Aayushi Jain et al.   FEMS MICROBIOLOGY LETTERS

Expansion of a Plasmid Classification System for Gram-Positive Bacteria and Determination of the Diversity of Plasmids in Staphylococcus aureus Strains of Human, Animal, and Food Origins

(2012) Carmen Lozano et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

The IncP-1 plasmid backbone adapts to different host bacterial species and evolves through homologous recombination

(2011) Peter Norberg et al.   Nature Communications

ETE: a python Environment for Tree Exploration

(2010) Jaime Huerta-Cepas et al.   BMC BIOINFORMATICS

Prodigal: prokaryotic gene recognition and translation initiation site identification

(2010) Doug Hyatt et al.   BMC BIOINFORMATICS

Predicting Plasmid Promiscuity Based on Genomic Signature

(2010) H. Suzuki et al.   JOURNAL OF BACTERIOLOGY

Selection of representative protein data sets

(2010) Uwe Hobohm et al.   PROTEIN SCIENCE

BLAST+: architecture and applications

(2009) Christiam Camacho et al.   BMC BIOINFORMATICS

Using Mahalanobis distance to compare genomic signatures between bacterial plasmids and chromosomes

(2008) Haruo Suzuki et al.   NUCLEIC ACIDS RESEARCH