Coinfinder: detecting significant associations and dissociations in pangenomes

Genome-wide epistasis and co-selection study using mutual information

(2019) Johan Pensar et al.   NUCLEIC ACIDS RESEARCH

Expansion of Thaumarchaeota habitat range is correlated with horizontal transfer of ATPase operons

(2019) Baozhan Wang et al.   ISME Journal

PIRATE: A fast and scalable pangenomics toolbox for clustering diverged orthologues in bacteria

(2019) Sion C Bayliss et al.   GigaScience

The Ecology and Evolution of Pangenomes

(2019) Michael A. Brockhurst et al.   CURRENT BIOLOGY

‘NetShift’: a methodology for understanding ‘driver microbes’ from healthy and disease microbiome datasets

(2018) Bhusan K. Kuntal et al.   ISME Journal

Puzzling Over the Pneumococcal Pangenome

(2018) N. Luisa Hiller et al.   Frontiers in Microbiology

Function-related replacement of bacterial siderophore pathways

(2017) Hilke Bruns et al.   ISME Journal

Toll-like receptor pathway evolution in deuterostomes

(2017) Michael G. Tassia et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The population genetics of pangenomes

(2017) B. Jesse Shapiro   Nature Microbiology

Why prokaryotes have pangenomes

(2017) James O. McInerney et al.   Nature Microbiology

Correlation detection strategies in microbial data sets vary widely in sensitivity and precision

(2016) Sophie Weiss et al.   ISME Journal

ggtree: anrpackage for visualization and annotation of phylogenetic trees with their covariates and other associated data

(2016) Guangchuang Yu et al.   Methods in Ecology and Evolution

Identifying lineage effects when controlling for population structure improves power in bacterial association studies

(2016) Sarah G. Earle et al.   Nature Microbiology

Roary: rapid large-scale prokaryote pan genome analysis

(2015) Andrew J. Page et al.   BIOINFORMATICS

Prokka: rapid prokaryotic genome annotation

(2014) T. Seemann   BIOINFORMATICS

CoPAP: Coevolution of Presence–Absence Patterns

(2013) Ofir Cohen et al.   NUCLEIC ACIDS RESEARCH

Inferring Correlation Networks from Genomic Survey Data

(2012) Jonathan Friedman et al.   PLoS Computational Biology

Genetic Co-Occurrence Network across Sequenced Microbes

(2011) Pan-Jun Kim et al.   PLoS Computational Biology

Selectivity in Mammalian Extinction Risk and Threat Types: a New Measure of Phylogenetic Signal Strength in Binary Traits

(2010) SUSANNE A. FRITZ et al.   CONSERVATION BIOLOGY

The All-Species Living Tree project: A 16S rRNA-based phylogenetic tree of all sequenced type strains

(2008) Pablo Yarza et al.   SYSTEMATIC AND APPLIED MICROBIOLOGY