PPanGGOLiN: Depicting microbial diversity via a partitioned pangenome graph

Extensive Unexplored Human Microbiome Diversity Revealed by Over 150,000 Genomes from Metagenomes Spanning Age, Geography, and Lifestyle

(2019) Edoardo Pasolli et al.   CELL

Fast and accurate genomic analyses using genome graphs

(2019) Goran Rakocevic et al.   NATURE GENETICS

Diversity and Function of Capsular Polysaccharide in Acinetobacter baumannii

(2019) Jennifer K. Singh et al.   Frontiers in Microbiology

Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype

(2019) Daehwan Kim et al.   NATURE BIOTECHNOLOGY

The Ecology and Evolution of Pangenomes

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

Bioconda: sustainable and comprehensive software distribution for the life sciences

(2018) Björn Grüning et al.   NATURE METHODS

Pangenomic Definition of Prokaryotic Species and the Phylogenetic Structure of Prochlorococcus spp.

(2018) Mikhail A. Moldovan et al.   Frontiers in Microbiology

Variation graph toolkit improves read mapping by representing genetic variation in the reference

(2018) Erik Garrison et al.   NATURE BIOTECHNOLOGY

A standardized bacterial taxonomy based on genome phylogeny substantially revises the tree of life

(2018) Donovan H Parks et al.   NATURE BIOTECHNOLOGY

Genome Sequencing and Pan-Genome Analysis of 23 Corallococcus spp. Strains Reveal Unexpected Diversity, With Particular Plasticity of Predatory Gene Sets

(2018) Paul G. Livingstone et al.   Frontiers in Microbiology

Rfam 13.0: shifting to a genome-centric resource for non-coding RNA families

(2017) Ioanna Kalvari et al.   NUCLEIC ACIDS RESEARCH

The chromosomal organization of horizontal gene transfer in bacteria

(2017) Pedro H. Oliveira et al.   Nature Communications

Horizontally Acquired Genes Are Often Shared between Closely Related Bacterial Species

(2017) Evgeni Bolotin et al.   Frontiers in Microbiology

Roary: rapid large-scale prokaryote pan genome analysis

(2015) Andrew J. Page et al.   BIOINFORMATICS

micropan: an R-package for microbial pan-genomics

(2015) Lars Snipen et al.   BMC BIOINFORMATICS

Gene Loss Dominates As a Source of Genetic Variation within Clonal Pathogenic Bacterial Species

(2015) Evgeni Bolotin et al.   Genome Biology and Evolution

Clustering of multivariate binary data with dimension reduction via L1-regularized likelihood maximization

(2015) Michio Yamamoto et al.   PATTERN RECOGNITION

A novel method of consensus pan-chromosome assembly and large-scale comparative analysis reveal the highly flexible pan-genome of Acinetobacter baumannii

(2015) Agnes P. Chan et al.   GENOME BIOLOGY

Comparative Whole-Genome Analysis of Clinical Isolates Reveals Characteristic Architecture of Mycobacterium tuberculosis Pangenome

(2015) Vinita Periwal et al.   PLoS One

ForceAtlas2, a Continuous Graph Layout Algorithm for Handy Network Visualization Designed for the Gephi Software

(2014) Mathieu Jacomy et al.   PLoS One

Defining the Estimated Core Genome of Bacterial Populations Using a Bayesian Decision Model

(2014) Andries J. van Tonder et al.   PLoS Computational Biology

GET_HOMOLOGUES, a Versatile Software Package for Scalable and Robust Microbial Pangenome Analysis

(2013) Bruno Contreras-Moreira et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Infernal 1.1: 100-fold faster RNA homology searches

(2013) E. P. Nawrocki et al.   BIOINFORMATICS

Diversity in the Major Polysaccharide Antigen of Acinetobacter Baumannii Assessed by DNA Sequencing, and Development of a Molecular Serotyping Scheme

(2013) Dalong Hu et al.   PLoS One

The Infinitely Many Genes Model for the Distributed Genome of Bacteria

(2012) Franz Baumdicker et al.   Genome Biology and Evolution

Testing the Infinitely Many Genes Model for the Evolution of the Bacterial Core Genome and Pangenome

(2012) R. Eric Collins et al.   MOLECULAR BIOLOGY AND EVOLUTION

From essential to persistent genes: a functional approach to constructing synthetic life

(2012) Carlos G. Acevedo-Rocha et al.   TRENDS IN GENETICS

Ultra-fast sequence clustering from similarity networks with SiLiX

(2011) Vincent Miele et al.   BMC BIOINFORMATICS

Horizontal Transfer, Not Duplication, Drives the Expansion of Protein Families in Prokaryotes

(2011) Todd J. Treangen et al.   PLoS Genetics

Prodigal: prokaryotic gene recognition and translation initiation site identification

(2010) Doug Hyatt et al.   BMC BIOINFORMATICS

Comparison of 61 Sequenced Escherichia coli Genomes

(2010) Oksana Lukjancenko et al.   MICROBIAL ECOLOGY

Microbial comparative pan-genomics using binomial mixture models

(2009) Lars Snipen et al.   BMC GENOMICS

On multivariate binary data clustering and feature weighting

(2009) Nizar Bouguila   COMPUTATIONAL STATISTICS & DATA ANALYSIS

Diversification of the gut symbiont Lactobacillus reuteri as a result of host-driven evolution

(2009) Phaik Lyn Oh et al.   ISME Journal

On the Origins of a Vibrio Species

(2009) Tammi Vesth et al.   MICROBIAL ECOLOGY

Estimating the size of the bacterial pan-genome

(2009) Pascal Lapierre et al.   TRENDS IN GENETICS

Persistence drives gene clustering in bacterial genomes

(2008) Gang Fang et al.   BMC GENOMICS

Comparative genomics: the bacterial pan-genome

(2008) Hervé Tettelin et al.   CURRENT OPINION IN MICROBIOLOGY

Genomics of bacteria and archaea: the emerging dynamic view of the prokaryotic world

(2008) E. V. Koonin et al.   NUCLEIC ACIDS RESEARCH