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The Black Queen Hypothesis: Evolution of Dependencies through Adaptive Gene Loss

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Ten years of pan-genome analyses

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PGAP: pan-genomes analysis pipeline

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Linking pangenomes and metagenomes: the Prochlorococcus metapangenome

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EDGAR: A software framework for the comparative analysis of prokaryotic genomes

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Why prokaryotes have pangenomes

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Structure and dynamics of the pan-genome of Streptococcus pneumoniae and closely related species

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Pan-genomics in the human genome era

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The 3,000 rice genomes project: new opportunities and challenges for future rice research

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Computational pan-genomics: status, promises and challenges

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The cyanobacterial genome core and the origin of photosynthesis

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Pangenome Graphs

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Pan-genome sequence analysis using Panseq: an online tool for the rapid analysis of core and accessory genomic regions

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panX: pan-genome analysis and exploration

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Tailed giant Tupanvirus possesses the most complete translational apparatus of the known virosphere

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PPanGGOLiN: Depicting microbial diversity via a partitioned pangenome graph

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The Pseudomonas aeruginosa Pan-Genome Provides New Insights on Its Population Structure, Horizontal Gene Transfer, and Pathogenicity

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Towards plant pangenomics

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Building pangenome graphs

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Graphtyper enables population-scale genotyping using pangenome graphs

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Pangenomics Comes of Age: From Bacteria to Plant and Animal Applications

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PanGP: A tool for quickly analyzing bacterial pan-genome profile

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Gain and Loss of Multiple Genes During the Evolution of Helicobacter pylori

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Extensive variation within the pan-genome of cultivated and wild sorghum

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Pan-genome of the dominant human gut-associated archaeon, Methanobrevibacter smithii , studied in twins

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PanOCT: automated clustering of orthologs using conserved gene neighborhood for pan-genomic analysis of bacterial strains and closely related species

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Genomes of three tomato pathogens within the Ralstonia solanacearum species complex reveal significant evolutionary divergence

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Comparative genomics of the bacterial genus Listeria: Genome evolution is characterized by limited gene acquisition and limited gene loss

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The evolution of the Escherichia coli phylogeny

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The Balance of Driving Forces During Genome Evolution in ProkaryotesPreprint

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Characterization of the core and accessory genomes of Pseudomonas aeruginosa using bioinformatic tools Spine and AGEnt

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Pangenome analyses of the wheat pathogen Zymoseptoria tritici reveal the structural basis of a highly plastic eukaryotic genome

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ODGI: understanding pangenome graphs

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Combined Analysis of Variation in Core, Accessory and Regulatory Genome Regions Provides a Super-Resolution View into the Evolution of Bacterial Populations

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Legionella pneumophila pangenome reveals strain-specific virulence factors

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RPAN: rice pan-genome browser for ∼3000 rice genomes

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Comparative genomics of the core and accessory genomes of 48 Sinorhizobiumstrains comprising five genospecies

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Pangenome analysis provides insight into the evolution of the orange subfamily and a key gene for citric acid accumulation in citrus fruits

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GET_PHYLOMARKERS, a Software Package to Select Optimal Orthologous Clusters for Phylogenomics and Inferring Pan-Genome Phylogenies, Used for a Critical Geno-Taxonomic Revision of the Genus Stenotrophomonas

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Phylogenomics and the Dynamic Genome Evolution of the Genus Streptococcus

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The Infinitely Many Genes Model for the Distributed Genome of Bacteria

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A Reference Pan-Genome Approach to Comparative Bacterial Genomics: Identification of Novel Epidemiological Markers in Pathogenic Campylobacter

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Endosymbiotic gene transfer from prokaryotic pangenomes: Inherited chimerism in eukaryotes

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Too Much Eukaryote LGT

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The Core- and Pan-Genomic Analyses of the Genus Comamonas: From Environmental Adaptation to Potential Virulence

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Essential Genes in the Core Genome of the Human Pathogen Streptococcus pyogenes

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Evolution of minimal-gene-sets in host-dependent bacteria

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Grapevine pangenome facilitates trait genetics and genomic breeding

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ITEP: An integrated toolkit for exploration of microbial pan-genomes

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The pan-genome: towards a knowledge-based discovery of novel targets for vaccines and antibacterials

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Microbial comparative pan-genomics using binomial mixture models

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Revisiting the Evolution and Taxonomy of Clostridia, a Phylogenomic Update

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

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SplitMEM: a graphical algorithm for pan-genome analysis with suffix skips

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Accurate reconstruction of bacterial pan- and core genomes with PEPPANPreprint

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Analysis of the Pantoea ananatis pan-genome reveals factors underlying its ability to colonize and interact with plant, insect and vertebrate hosts

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Genomic fluidity: an integrative view of gene diversity within microbial populations

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The Need for a Human Pangenome Reference Sequence

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A pangenome analysis pipeline provides insights into functional gene identification in rice

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Evolution of Pan-Genomes of Escherichia coli, Shigella spp., and Salmonella enterica

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

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Bacillus subtilis, the model Gram‐positive bacterium: 20 years of annotation refinement

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Exploring the symbiotic pangenome of the nitrogen-fixing bacterium Sinorhizobium meliloti

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A pangenome reference of wild and cultivated rice

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Pangenome analysis of Bifidobacterium longum and site-directed mutagenesis through by-pass of restriction-modification systems

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Pangenome-wide and molecular evolution analyses of the Pseudomonas aeruginosa species

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Comparative analysis of the Oenococcus oeni pan genome reveals genetic diversity in industrially-relevant pathways

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KinFin: Software for Taxon-Aware Analysis of Clustered Protein Sequences

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Microcystis pangenome reveals cryptic diversity within and across morphospecies

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Analysis of the core genome and pangenome of P seudomonas putida

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Unbiased pangenome graphs

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Probing the pan-genome of Listeria monocytogenes: new insights into intraspecific niche expansion and genomic diversification

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Patterns of Evolutionary Conservation of Essential Genes Correlate with Their Compensability

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PGAT: a multistrain analysis resource for microbial genomes

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Pan-genome analysis of the emerging foodborne pathogen Cronobacterspp. suggests a species-level bidirectional divergence driven by niche adaptation

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The Core and Accessory Genomes of Burkholderia pseudomallei: Implications for Human Melioidosis

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Genome-based approaches to develop vaccines against bacterial pathogens

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PanTools: representation, storage and exploration of pan-genomic data

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A neutral theory of genome evolution and the frequency distribution of genes

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Bloom Filter Trie: an alignment-free and reference-free data structure for pan-genome storage

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Gene Frequency Distributions Reject a Neutral Model of Genome Evolution

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Pangenome Evolution in the Marine BacteriumAlteromonas

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PanExplorer: a web-based tool for exploratory analysis and visualization of bacterial pan-genomes

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Graphical pan-genome analysis with compressed suffix trees and the Burrows–Wheeler transform

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Pangenome graphs and their applications in biodiversity genomics

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Strain Dependent Genetic Networks for Antibiotic-Sensitivity in a Bacterial Pathogen with a Large Pan-Genome

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Piggy: a rapid, large-scale pan-genome analysis tool for intergenic regions in bacteria

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Pathogen comparative genomics in the next-generation sequencing era: genome alignments, pangenomics and metagenomics

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The evolution of metabolic networks of E. coli

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PanFP: pangenome-based functional profiles for microbial communities

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A Brief Review of Software Tools for Pangenomics

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Genetic Competence Drives Genome Diversity in Bacillus subtilis

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Analysis of the Core Genome and Pan-Genome of Autotrophic Acetogenic Bacteria

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Genome update: the 1000th genome-a cautionary tale

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A Large Open Pangenome and a Small Core Genome for Giant Pandoraviruses

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Pan-genome analyses identify lineage- and niche-specific markers of evolution and adaptation in Epsilonproteobacteria

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Comparative genome analysis of the Lactobacillus brevis species

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The Genus Burkholderia: Analysis of 56 Genomic Sequences

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Strain-specific genes of Helicobacter pylori: distribution, function and dynamics

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Pan-genome analysis of Clostridium botulinum reveals unique targets for drug development

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Building a Pan-Genome Reference for a Population

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Toward a high-quality pan-genome landscape ofBacillus subtilisby removal of confounding strains

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The pan-genome as a shared genomic resource: mutual cheating, cooperation and the black queen hypothesis

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Telling the whole story in a 10,000-genome world

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PGAdb-builder: A web service tool for creating pan-genome allele database for molecular fine typing

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The pangenome of the genus C lostridium

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Pangenomics – an avenue to improved industrial starter cultures and probiotics

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Panacus: fast and exact pangenome growth and core size estimation

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Contingency, repeatability, and predictability in the evolution of a prokaryotic pangenome

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Ancestral Genome Estimation Reveals the History of Ecological Diversification in Agrobacterium

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The Pangenome: Diversity, Dynamics and Evolution of Genomes

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Towards pan-genome read alignment to improve variation calling

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Improving pan-genome annotation using whole genome multiple alignment

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Distinct evolutionary trajectories in the Escherichia coli pangenome occur within sequence types

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The composition of the global and feature specific cyanobacterial core-genomes

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PGAP-X: extension on pan-genome analysis pipeline

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Comparative genomic study of the Penicillium genus elucidates a diverse pangenome and 15 lateral gene transfer events

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Pan-genomic approach shows insight of genetic divergence and pathogenic-adaptation of Pasteurella multocida

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SPUMONI 2: improved classification using a pangenome index of minimizer digests

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PanGraph: scalable bacterial pan-genome graph construction

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seq-seq-pan: building a computational pan-genome data structure on whole genome alignment

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Estimating the Frequency of Horizontal Gene Transfer Using Phylogenetic Models of Gene Gain and Loss

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Comparative Genome Analysis ofFusobacterium nucleatum

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PanWeb: A web interface for pan-genomic analysis

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Order and Disorder during Escherichia coli Divergence

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PanViz: interactive visualization of the structure of functionally annotated pangenomes

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Computational comparisons of model genomes

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Pan-Tetris: an interactive visualisation for Pan-genomes

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PANNOTATOR: an automated tool for annotation of pan-genomes

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Phylogenomic Insight into Salinispora (Bacteria, Actinobacteria) Species Designations

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Genomic analysis of three African strains of Bacillus anthracis demonstrates that they are part of the clonal expansion of an exclusively pathogenic bacterium

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A pangenomic study of Bacillus thuringiensis

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The diversity of a distributed genome in bacterial populations

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Directional gene flow and ecological separation in Yersinia enterocolitica

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PATO: Pangenome Analysis Toolkit

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In Silico Genome-Wide Analysis Reveals the Potential Links Between Core Genome of Acidithiobacillus thiooxidans and Its Autotrophic Lifestyle

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The Bacterial Pan-Genome and Reverse Vaccinology

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Defining Orthologs and Pangenome Size Metrics

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Modules of co-occurrence in the cyanobacterial pan-genome reveal functional associations between groups of ortholog genes

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Inferring the Minimal Genome of Mesoplasma florum by Comparative Genomics and Transposon Mutagenesis

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A graph-based approach for the visualisation and analysis of bacterial pangenomes

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Comparison of gene clustering criteria reveals intrinsic uncertainty in pangenome analyses

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PanFunPro: PAN-genome analysis based on FUNctional PROfiles

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eCAMBer: efficient support for large-scale comparative analysis of multiple bacterial strains

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Challenges in gene-oriented approaches for pangenome content discovery

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Calculating Orthologs in Bacteria and Archaea: A Divide and Conquer Approach

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Opening the pan-genomics box

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