The grammar of the pangenome: terms, concepts, methods, and emerging patterns—a general framework for comparative genomics and genome biology

Prokka: rapid prokaryotic genome annotation

Seemann, T. (2014) · Bioinformatics · doi:10.1093/bioinformatics/btu153 · Cited by 18,937

Cd-hit: Accelerated for clustering the next-generation sequencing data

Fu, L., Niu, B., Zhu, Z., Wu, S., & Li, W. (2012) · Bioinformatics · doi:10.1093/bioinformatics/bts565 · Cited by 11,175

Shifting the genomic gold standard for the prokaryotic species definition

Richter, M., & Rossello-Mora, R. A. (2009) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0906412106 · Cited by 6,343

Roary: rapid large-scale prokaryote pan genome analysis

Page, A. J., Cummins, C. A., Hunt, M., Wong, V. K., Reuter, S., Holden, M. T. G., Fookes, M., Falush, D., Keane, J. A., & Parkhill, J. (2015) · Bioinformatics · doi:10.1093/bioinformatics/btv421 · Cited by 5,736

progressiveMauve: Multiple Genome Alignment with Gene Gain, Loss and Rearrangement

Darling, A. E., Mau, B., & Perna, N. T. (2010) · PLoS ONE · doi:10.1371/journal.pone.0011147 · Cited by 3,848

ClustVis: a web tool for visualizing clustering of multivariate data using Principal Component Analysis and heatmap

Metsalu, T., & Vilo, J. (2015) · Nucleic Acids Research · doi:10.1093/nar/gkv468 · Cited by 3,770

An efficient algorithm for large-scale detection of protein families

Enright, A. J. (2002) · Nucleic Acids Research · doi:10.1093/nar/30.7.1575 · Cited by 3,536

Genome analysis of multiple pathogenic isolates of Streptococcus agalactiae : Implications for the microbial “pan-genome”

Tettelin, H., Masignani, V., Cieslewicz, M. J., Donati, C., Medini, D., Ward, N. L., Angiuoli, S. V., Crabtree, J., Jones, A. L., Durkin, A. S., et al. (2005) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0506758102 · Cited by 2,728

Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea

The Genome Standards Consortium, Bowers, R. M., Kyrpides, N. C., Stepanauskas, R., Harmon-Smith, M., Doud, D., Reddy, T. B. K., Schulz, F., Jarett, J., Rivers, A. R., et al. (2017) · Nature Biotechnology · doi:10.1038/nbt.3893 · Cited by 2,624

The Harvest suite for rapid core-genome alignment and visualization of thousands of intraspecific microbial genomes

Treangen, T. J., Ondov, B., Koren, S., & Phillippy, A. M. (2014) · Genome biology · doi:10.1186/s13059-014-0524-x · Cited by 1,670

Toward Automatic Reconstruction of a Highly Resolved Tree of Life

Ciccarelli, F. D., Doerks, T., von Mering, C., Creevey, C. J., Snel, B., & Bork, P. (2006) · Science · doi:10.1126/science.1123061 · Cited by 1,663

Producing polished prokaryotic pangenomes with the Panaroo pipeline

Tonkin‐Hill, G. Q., MacAlasdair, N., Ruis, C., Weimann, A., Horesh, G., Lees, J. A., Gladstone, R. A., Lo, S. W., Beaudoin, C. A., Floto, R. A., et al. (2020) · Genome biology · doi:10.1186/s13059-020-02090-4 · Cited by 1,365

The microbial pan-genome

Medini, D., Donati, C., Tettelin, H., Masignani, V., & Rappuoli, R. (2005) · Current Opinion in Genetics & Development · doi:10.1016/j.gde.2005.09.006 · Cited by 1,307

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

Morris, J., Lenski, R. E., & Zinser, E. R. (2012) · mBio · doi:10.1128/mbio.00036-12 · Cited by 1,231

A draft human pangenome reference.

Liao, W.-W., Asri, M., Ebler, J., Doerr, D., Haukness, M., Hickey, G., Lu, S., Lucas, J. K., Monlong, J., Abel, H. J., et al. (2023) · Nature · doi:10.1038/s41586-023-05896-x · Cited by 1,129

Comparative genomics: the bacterial pan-genome

Tettelin, H., Riley, D., Cattuto, C., & Medini, D. (2008) · Current Opinion in Microbiology · doi:10.1016/j.mib.2008.09.006 · Cited by 1,120

Genome evolution across 1,011 Saccharomyces cerevisiae isolates

Peter, J., De Chiara, M., Friedrich, A., Yue, J.-X., Pflieger, D., Bergström, A., Sigwalt, A., Barre, B., Freel, K., Llored, A., et al. (2018) · Nature · doi:10.1038/s41586-018-0030-5 · Cited by 1,117

BPGA- an ultra-fast pan-genome analysis pipeline

Chaudhari, N. M., Gupta, V. K., & Dutta, C. (2016) · Scientific Reports · doi:10.1038/srep24373 · Cited by 993

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

Contreras‐Moreira, B., & Vinuesa, P. (2013) · Applied and Environmental Microbiology · doi:10.1128/aem.02411-13 · Cited by 908

Minimum information about a marker gene sequence (MIMARKS) and minimum information about any (x) sequence (MIxS) specifications

Yilmaz, P., Kottmann, R., Field, D., Knight, R. D., Cole, J. R., Amaral‐Zettler, L., Gilbert, J. A., Karsch‐Mizrachi, I., Johnston, A., Cochrane, G., et al. (2011) · Nature Biotechnology · doi:10.1038/nbt.1823 · Cited by 802

Experimental Determination and System Level Analysis of Essential Genes in Escherichia coli MG1655

Gerdes, S., Scholle, M. D., Campbell, J. W., Balázsi, G., Ravasz, E., Daugherty, M. D., Somera, A. L., Kyrpides, N. C., Anderson, I., Gelfand, M. S., et al. (2003) · Journal of Bacteriology · doi:10.1128/jb.185.19.5673-5684.2003 · Cited by 741

What are Bacterial Species?

Cohan, F. M. (2002) · Annual Review of Microbiology · doi:10.1146/annurev.micro.56.012302.160634 · Cited by 714

Rapid scoring of genes in microbial pan-genome-wide association studies with Scoary

Brynildsrud, O. B., Bohlin, J., Scheffer, L., & Eldholm, V. (2016) · Genome biology · doi:10.1186/s13059-016-1108-8 · Cited by 708

Phandango: an interactive viewer for bacterial population genomics

Hadfield, J., Croucher, N. J., Goater, R., Abudahab, K., Aanensen, D. M., & Harris, S. R. (2017) · Bioinformatics · doi:10.1093/bioinformatics/btx610 · Cited by 657

Ten years of pan-genome analyses

Vernikos, G. S., Medini, D., Riley, D. R. J., & Tettelin, H. (2014) · Current Opinion in Microbiology · doi:10.1016/j.mib.2014.11.016 · Cited by 628

Determination of the Core of a Minimal Bacterial Gene Set

Gil, R., Silva, F. J., Peretó, J., & Moya, A. (2004) · Microbiology and Molecular Biology Reviews · doi:10.1128/mmbr.68.3.518-537.2004 · Cited by 573

The pangenome of an agronomically important crop plant Brassica oleracea

Golicz, A. A., Bayer, P. E., Barker, G. C., Edger, P. P., Kim, H. R., Martinez, P. A., Chan, C. K., Severn‐Ellis, A. A., McCombie, W. R., Parkin, I. A. P., et al. (2016) · Nature Communications · doi:10.1038/ncomms13390 · Cited by 553

Patterns and Implications of Gene Gain and Loss in the Evolution of Prochlorococcus

Kettler, G. C., Martiny, A. C., Huang, K. H., Zucker, J., Coleman, M. L., Rodrigue, S., Chen, F., Lapidus, A. L., Ferriera, S., Johnson, J. H., et al. (2007) · PLoS Genetics · doi:10.1371/journal.pgen.0030231 · Cited by 552

PGAP: pan-genomes analysis pipeline

Zhao, Y., Wu, J., Yang, J., Sun, S., Xiao, J., & Yu, J. M. (2011) · Bioinformatics · doi:10.1093/bioinformatics/btr655 · Cited by 518

Evolution of plant genome architecture

Wendel, J. F., Jackson, S. A., Meyers, B. C., & Wing, R. A. (2016) · Genome biology · doi:10.1186/s13059-016-0908-1 · Cited by 474

Linking pangenomes and metagenomes: the Prochlorococcus metapangenome

Delmont, T. O., & Eren, A. M. (2018) · PeerJ · doi:10.7717/peerj.4320 · Cited by 453

Why prokaryotes have pangenomes

McInerney, J. O., McNally, A., & O’Connell, M. J. (2017) · Nature Microbiology · doi:10.1038/nmicrobiol.2017.40 · Cited by 415

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

Blom, J., Albaum, S. P., Doppmeier, D., Pühler, A., Vorhölter, F., Zakrzewski, M., & Goesmann, A. (2009) · BMC Bioinformatics · doi:10.1186/1471-2105-10-154 · Cited by 412

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

Donati, C., Hiller, N. L., Tettelin, H., Muzzi, A., Croucher, N. J., Angiuoli, S. V., Oggioni, M. R., Hotopp, J. C. D., Hu, F. Z., Riley, D. R. J., et al. (2010) · Genome biology · doi:10.1186/gb-2010-11-10-r107 · Cited by 407

Pan-genomics in the human genome era

Sherman, R. M., & Salzberg, S. L. (2020) · Nature Reviews Genetics · doi:10.1038/s41576-020-0210-7 · Cited by 375

Estimating the size of the bacterial pan-genome

Lapierre, P., & Gogarten, J. P. (2009) · Trends in Genetics · doi:10.1016/j.tig.2008.12.004 · Cited by 373

Computational pan-genomics: status, promises and challenges

Marschall, T., Marz, M., Abeel, T., Dijkstra, L., Dutilh, B. E., Ghaffaari, A., Kersey, P., Kloosterman, W. P., Mäkinen, V., Novak, A. M., et al. (2016) · Briefings in Bioinformatics · doi:10.1093/bib/bbw089 · Cited by 369

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

Li, J., Wang, J., & Zeigler, R. S. (2014) · GigaScience · doi:10.1186/2047-217x-3-8 · Cited by 362

Evolution of the core and pan-genome of Streptococcus: positive selection, recombination, and genome composition

Tristan, L., & Stanhope, M. J. (2007) · Genome biology · doi:10.1186/gb-2007-8-5-r71 · Cited by 356

The bacterial pangenome as a new tool for analysing pathogenic bacteria

Rouli, L., Merhej, V., Fournier, P., & Raoult, D. (2015) · New Microbes and New Infections · doi:10.1016/j.nmni.2015.06.005 · Cited by 346

The cyanobacterial genome core and the origin of photosynthesis

Mulkidjanian, A. Y., Koonin, E. V., Makarova, K. S., Mekhedov, S. L., Sorokin, A. V., Wolf, Y. I., Dufresne, A., Partensky, F., Burd, H., Kaznadzey, D., et al. (2006) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0605709103 · Cited by 325

Pangenome Graphs

Eizenga, J. M., Novak, A. M., Sibbesen, J. A., Heumos, S., Ghaffaari, A., Hickey, G., Chang, X., Seaman, J. D., Rounthwaite, R., Ebler, J., et al. (2020) · Annual Review of Genomics and Human Genetics · doi:10.1146/annurev-genom-120219-080406 · Cited by 320

panX: pan-genome analysis and exploration

Ding, W., Baumdicker, F., & Neher, R. A. (2017) · Nucleic Acids Research · doi:10.1093/nar/gkx977 · Cited by 318

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

Laing, C., Buchanan, C. J., Taboada, E. N., Zhang, Y., Kropinski, A. M., Villegas, A., Thomas, J. E., & Gannon, V. P. J. (2010) · BMC Bioinformatics · doi:10.1186/1471-2105-11-461 · Cited by 302

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

Freschi, L., Vincent, A. T., Jeukens, J., Emond-Rhéault, J.-G., Kukavica‐Ibrulj, I., Dupont, M.-J., Charette, S. J., Boyle, B., & Lévesque, R. C. (2018) · Genome Biology and Evolution · doi:10.1093/gbe/evy259 · Cited by 302

PPanGGOLiN: Depicting microbial diversity via a partitioned pangenome graph

Gautreau, G., Bazin, A., Gachet, M., Planel, R., Burlot, L., Dubois, M., Perrin, A., Médigue, C., Calteau, A., Cruveiller, S., et al. (2020) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1007732 · Cited by 293

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

Abrahão, J. S., Silva, L. K. D. F., Silva, L. S., Khalil, J. Y. B., Rodrigues, R. A. L., Arantes, T. S., de Assis, F. L., Boratto, P. V. D. M., Andrade, M. D. S., Kroon, E. G., et al. (2018) · Nature Communications · doi:10.1038/s41467-018-03168-1 · Cited by 289

Evolutionary consequences of antibiotic use for the resistome, mobilome and microbial pangenome

Gillings, M. R. (2013) · Frontiers in Microbiology · doi:10.3389/fmicb.2013.00004 · Cited by 285

Towards plant pangenomics

Golicz, A. A., Batley, J., & Edwards, D. (2015) · Plant Biotechnology Journal · doi:10.1111/pbi.12499 · Cited by 284

Building pangenome graphs

Garrison, E., Guarracino, A., Heumos, S., Villani, F., Bao, Z., Tattini, L., Hagmann, J., Vorbrugg, S., Marco-Sola, S., Kubica, C., et al. (2024) · Nature Methods · doi:10.1038/s41592-024-02430-3 · Cited by 277

Graphtyper enables population-scale genotyping using pangenome graphs

Eggertsson, H. P., Jónsson, H., Kristmundsdóttir, S., Hjartarson, E., Kehr, B., Másson, G., Zink, F., Hjörleifsson, K. E., Jónasdóttir, Á., Jónasdóttir, A., et al. (2017) · Nature Genetics · doi:10.1038/ng.3964 · Cited by 272

The net of life: Reconstructing the microbial phylogenetic networkPreprint

Kunin, V., Goldovsky, L., Darzentas, N., & Ouzounis, C. A. (2005) · Genome Research · doi:10.1101/gr.3666505 · Cited by 269

Comparative genome-scale modelling of Staphylococcus aureus strains identifies strain-specific metabolic capabilities linked to pathogenicity

Bosi, E., Monk, J. M., Aziz, R. K., Fondi, M., Nizet, V., & Palsson, B. Ø. (2016) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1523199113 · Cited by 266

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

Golicz, A. A., Bayer, P. E., Bhalla, P. L., Batley, J., & Edwards, D. (2019) · Trends in Genetics · doi:10.1016/j.tig.2019.11.006 · Cited by 264

Biogeography of the Sulfolobus islandicus pan-genome

Reno, M. L., Held, N. L., Fields, C. J., Burke, P. V., & Whitaker, R. J. (2009) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0808945106 · Cited by 250

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

Zhao, Y., Jia, X., Yang, J., Ling, Y., Zhang, Z., Yu, J. M., Wu, J., & Xiao, J. (2014) · Bioinformatics · doi:10.1093/bioinformatics/btu017 · Cited by 248

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

Gressmann, H., Linz, B., Ghai, R., Pleißner, K., Schlapbach, R., Yamaoka, Y., Kraft, C., Suerbaum, S., Meyer, T. F., & Achtman, M. (2005) · PLoS Genetics · doi:10.1371/journal.pgen.0010043 · Cited by 244

micropan: an R-package for microbial pan-genomics

Snipen, L. G., & Liland, K. H. (2015) · BMC Bioinformatics · doi:10.1186/s12859-015-0517-0 · Cited by 242

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

Hansen, E. E., Lozupone, C., Rey, F. E., Wu, M., Guruge, J. L., Narra, A., Goodfellow, J., Zaneveld, J., McDonald, D. T., Goodrich, J. A., et al. (2011) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1000071108 · Cited by 236

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

Tao, Y., Luo, H., Xu, J., Cruickshank, A., Zhao, X., Teng, F., Hathorn, A., Wu, X., Liu, Y., Shatte, T., et al. (2021) · Nature Plants · doi:10.1038/s41477-021-00925-x · Cited by 236

Genomes in turmoil: quantification of genome dynamics in prokaryote supergenomes

Puigbò, P., Lobkovsky, A. E., Kristensen, D. M., Wolf, Y. I., & Koonin, E. V. (2014) · BMC Biology · doi:10.1186/s12915-014-0066-4 · Cited by 232

The evolution of the Escherichia coli phylogeny

Chaudhuri, R. R., & Henderson, I. R. (2012) · Infection Genetics and Evolution · doi:10.1016/j.meegid.2012.01.005 · Cited by 223

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

Ozer, E. A., Allen, J. P., & Hauser, A. R. (2014) · BMC Genomics · doi:10.1186/1471-2164-15-737 · Cited by 219

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

Fouts, D. E., Brinkac, L. M., Beck, E., Inman, J. M., & Sutton, G. (2012) · Nucleic Acids Research · doi:10.1093/nar/gks757 · Cited by 215

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

Plissonneau, C., Hartmann, F. E., & Croll, D. (2018) · BMC Biology · doi:10.1186/s12915-017-0457-4 · Cited by 209

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

Remenant, B., Coupat-Goutaland, B., Guidot, A., Cellier, G., Wicker, E., Allen, C., Fegan, M., Pruvost, O., Elbaz, M., Calteau, A., et al. (2010) · BMC Genomics · doi:10.1186/1471-2164-11-379 · Cited by 207

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

den Bakker, H. C., Cummings, C. A., Ferreira, V. B., Vatta, P., Orsi, R. H., Degoricija, L., Barker, M., Petrauskene, O., Furtado, M. R., & Wiedmann, M. (2010) · BMC Genomics · doi:10.1186/1471-2164-11-688 · Cited by 207

ODGI: understanding pangenome graphs

Guarracino, A., Heumos, S., Nahnsen, S., Prins, P., & Garrison, E. P. (2022) · Bioinformatics · doi:10.1093/bioinformatics/btac308 · Cited by 206

The Balance of Driving Forces During Genome Evolution in ProkaryotesPreprint

Kunin, V., & Ouzounis, C. A. (2003) · Genome Research · doi:10.1101/gr.1092603 · Cited by 203

Legionella pneumophila pangenome reveals strain-specific virulence factors

D’Auria, G., Jiménez‐Hernández, N., Peris-Bondia, F., Moyá, A., & Latorre, A. (2010) · BMC Genomics · doi:10.1186/1471-2164-11-181 · Cited by 199

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

McNally, A., Oren, Y., Kelly, D. J., Pascoe, B., Dunn, S. J., Sreecharan, T., Vehkala, M., Välimäki, N., Prentice, M. B., Ashour, A., et al. (2016) · PLoS Genetics · doi:10.1371/journal.pgen.1006280 · Cited by 189

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

Sun, C., Hu, Z., Zheng, T., Lu, K.-C., Zhao, Y., Wang, W., Shi, J., Wang, C., Lu, J., Zhang, D., et al. (2016) · Nucleic Acids Research · doi:10.1093/nar/gkw958 · Cited by 181

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

Huang, Y., He, J., Xu, Y., Zheng, W., Wang, S., Chen, P., Zeng, B., Yang, S., Jiang, X., Liu, Z., et al. (2023) · Nature Genetics · doi:10.1038/s41588-023-01516-6 · Cited by 178

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

Sugawara, M., Epstein, B., Badgley, B. D., Unno, T., Xu, L., Reese, J., Gyaneshwar, P., Denny, R. L., Mudge, J., Bharti, A. K., et al. (2013) · Genome biology · doi:10.1186/gb-2013-14-2-r17 · Cited by 175

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

Vinuesa, P., Ochoa-Sánchez, L. E., & Contreras‐Moreira, B. (2018) · Frontiers in Microbiology · doi:10.3389/fmicb.2018.00771 · Cited by 158

The Infinitely Many Genes Model for the Distributed Genome of Bacteria

Baumdicker, F., Hess, W. R., & Pfaffelhuber, P. (2012) · Genome Biology and Evolution · doi:10.1093/gbe/evs016 · Cited by 147

Phylogenomics and the Dynamic Genome Evolution of the Genus Streptococcus

Richards, V. P., Palmer, S. R., Bitar, P. D. P., Qin, X., Weinstock, G. M., Highlander, S. K., Town, C. D., Burne, R. A., & Stanhope, M. J. (2014) · Genome Biology and Evolution · doi:10.1093/gbe/evu048 · Cited by 145

Endosymbiotic gene transfer from prokaryotic pangenomes: Inherited chimerism in eukaryotes

Ku, C., Sathi, S. N., Roettger, M., Garg, S. G., Hazkani‐Covo, E., & Martin, W. F. (2015) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1421385112 · Cited by 143

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

Méric, G., Yahara, K., Mageiros, L., Pascoe, B., Maiden, M. C. J., Jolley, K. A., & Sheppard, S. K. (2014) · PLoS ONE · doi:10.1371/journal.pone.0092798 · Cited by 143

Too Much Eukaryote LGT

Martin, W. F. (2017) · BioEssays · doi:10.1002/bies.201700115 · Cited by 141

The Pangenome

Tettelin, H., & Medini, D. (2020) · Springer eBooks · doi:10.1007/978-3-030-38281-0 · Cited by 140

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

Wu, Y., Zaiden, N., & Cao, B. (2018) · Frontiers in Microbiology · doi:10.3389/fmicb.2018.03096 · Cited by 138

Revisiting the Evolution and Taxonomy of Clostridia, a Phylogenomic Update

Cruz‐Morales, P., Orellana, C. A., Moutafis, G., Moonen, G., Rincón, G., Nielsen, L. K., & Marcellin, E. (2019) · Genome Biology and Evolution · doi:10.1093/gbe/evz096 · Cited by 138

The Need for a Human Pangenome Reference Sequence

Miga, K. H., & Wang, T. (2021) · Annual Review of Genomics and Human Genetics · doi:10.1146/annurev-genom-120120-081921 · Cited by 137

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

Breton, Y. S. L., Belew, A. T., Valdes, K. M., Islam, E., Curry, P., Tettelin, H., Shirtliff, M. E., El-Sayed, N. M., & McIver, K. S. (2015) · Scientific Reports · doi:10.1038/srep09838 · Cited by 135

Grapevine pangenome facilitates trait genetics and genomic breeding

Liu, Z., Wang, N., Su, Y., Long, Q., Peng, Y., Shangguan, L., Zhang, F., Cao, S., Wang, X., Ge, M., et al. (2024) · Nature Genetics · doi:10.1038/s41588-024-01967-5 · Cited by 134

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

Benedict, M. N., Henriksen, J. R., Metcalf, W. W., Whitaker, R. J., & Price, N. D. (2014) · BMC Genomics · doi:10.1186/1471-2164-15-8 · Cited by 133

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

Muzzi, A., Masignani, V., & Rappuoli, R. (2007) · Drug Discovery Today · doi:10.1016/j.drudis.2007.04.008 · Cited by 127

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

Klasson, L. (2003) · Trends in Microbiology · doi:10.1016/j.tim.2003.11.006 · Cited by 127

Microbial comparative pan-genomics using binomial mixture models

Snipen, L. G., Almøy, T., & Ussery, D. W. (2009) · BMC Genomics · doi:10.1186/1471-2164-10-385 · Cited by 126

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

Chan, A. P.-Y., Sutton, G. G., DePew, J., Krishnakumar, R., Choi, Y., Huang, X.-Z., Beck, E., Harkins, D. M., Kim, M., Lesho, E. P., et al. (2015) · Genome biology · doi:10.1186/s13059-015-0701-6 · Cited by 125

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

Wang, J., Wu, Y., Zhang, S., Hu, H., Yuan, Y., Dong, J., Chen, L., Ma, Y., Yang, T., Zhou, L., et al. (2023) · Genome biology · doi:10.1186/s13059-023-02861-9 · Cited by 125

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

Maayer, P. D., Chan, W., Rubagotti, E., Venter, S. N., Toth, I. K., Birch, P. R. J., & Coutinho, T. A. (2014) · BMC Genomics · doi:10.1186/1471-2164-15-404 · Cited by 121

Accurate reconstruction of bacterial pan- and core genomes with PEPPANPreprint

Zhou, Z., Charlesworth, J., & Achtman, M. (2020) · Genome Research · doi:10.1101/gr.260828.120 · Cited by 121

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

Marcus, S., Lee, H., & Schatz, M. C. (2014) · Bioinformatics · doi:10.1093/bioinformatics/btu756 · Cited by 120

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

Kislyuk, A. O., Haegeman, B., Bergman, N. H., & Weitz, J. S. (2011) · BMC Genomics · doi:10.1186/1471-2164-12-32 · Cited by 120

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

Borriss, R., Danchin, A., Harwood, C. R., Médigue, C., Rocha, E. P. C., Sekowska, A., & Vallenet, D. (2017) · Microbial Biotechnology · doi:10.1111/1751-7915.13043 · Cited by 120

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

Gordienko, E. N., Kazanov, M. D., & Gelfand, M. S. (2013) · Journal of Bacteriology · doi:10.1128/jb.02285-12 · Cited by 116

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

Collins, R. E., & Higgs, P. G. (2012) · Molecular Biology and Evolution · doi:10.1093/molbev/mss163 · Cited by 116

A pangenome reference of wild and cultivated rice

Guo, D., Li, Y., Lu, H., Zhao, Y., Kurata, N., Wei, X., Wang, A., Wang, Y., Zhan, Q., Fan, D., et al. (2025) · Nature · doi:10.1038/s41586-025-08883-6 · Cited by 116

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

Galardini, M., Mengoni, A., Brilli, M., Pini, F., Fioravanti, A., Lucas, S. M., Lapidus, A. L., Cheng, J., Goodwin, L., Pitluck, S., et al. (2011) · BMC Genomics · doi:10.1186/1471-2164-12-235 · Cited by 113

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

Borneman, A. R., McCarthy, J. M., Chambers, P. J., & Bartowsky, E. J. (2012) · BMC Genomics · doi:10.1186/1471-2164-13-373 · Cited by 112

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

Mosquera-Rendón, J., Rada, A. M., Cárdenas-Brito, S., Corredor, M., Restrepo, E., & Benítez‐Páez, A. (2016) · BMC Genomics · doi:10.1186/s12864-016-2364-4 · Cited by 108

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

O’Callaghan, A. A., Bottacini, F., Motherway, M. O., & van Sinderen, D. (2015) · BMC Genomics · doi:10.1186/s12864-015-1968-4 · Cited by 107

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

Laetsch, D. R., & Blaxter, M. (2017) · G3 Genes Genomes Genetics · doi:10.1534/g3.117.300233 · Cited by 98

Microcystis pangenome reveals cryptic diversity within and across morphospecies

Cai, H., McLimans, C. J., Beyer, J. E., Krumholz, L. R., & Hambright, K. D. (2023) · Science Advances · doi:10.1126/sciadv.add3783 · Cited by 97

Unbiased pangenome graphs

Garrison, E., & Guarracino, A. (2023) · Bioinformatics · doi:10.1093/bioinformatics/btac743 · Cited by 95

Analysis of the core genome and pangenome of P seudomonas putida

Udaondo, Z., Molina, L., Segura, A., Duque, E., & Ramos, J. L. (2015) · Environmental Microbiology · doi:10.1111/1462-2920.13015 · Cited by 94

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

Deng, X., Phillippy, A. M., Li, Z., Salzberg, S. L., & Zhang, W. (2010) · BMC Genomics · doi:10.1186/1471-2164-11-500 · Cited by 91

PGAT: a multistrain analysis resource for microbial genomes

Brittnacher, M., Fong, C. T., Hayden, H. S., Jacobs, M. A., Radey, M. C., & Rohmer, L. (2011) · Bioinformatics · doi:10.1093/bioinformatics/btr418 · Cited by 86

Patterns of Evolutionary Conservation of Essential Genes Correlate with Their Compensability

Bergmiller, T., Ackermann, M., & Silander, O. (2012) · PLoS Genetics · doi:10.1371/journal.pgen.1002803 · Cited by 85

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

Grim, C. J., Kotewicz, M. L., Power, K. A., Gopinath, G., Franco, A. A., Jarvis, K. G., Yan, Q. Q., Jackson, S. A., Sathyamoorthy, V., Hu, L., et al. (2013) · BMC Genomics · doi:10.1186/1471-2164-14-366 · Cited by 84

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

Sim, S. H., Yu, Y., Lin, C. H., Karuturi, R. K. M., Wuthiekanun, V., Tuanyok, A., Chua, H. H., Ong, C., Sivalingam, S. P., Tan, G. G. Y., et al. (2008) · PLoS Pathogens · doi:10.1371/journal.ppat.1000178 · Cited by 84

Genome-based approaches to develop vaccines against bacterial pathogens

Serruto, D., Serino, L., Masignani, V., & Pizza, M. (2009) · Vaccine · doi:10.1016/j.vaccine.2009.01.072 · Cited by 84

Pangenome graphs and their applications in biodiversity genomics

Secomandi, S., Gallo, G. R., Rossi, R., Fernandes, C., Jarvis, E. D., Bonisoli‐Alquati, A., Gianfranceschi, L., & Formenti, G. (2025) · Nature Genetics · doi:10.1038/s41588-024-02029-6 · Cited by 83

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

Anari, S. S., Schranz, M. E., Akdel, M., de Ridder, D., & Smit, S. (2016) · Bioinformatics · doi:10.1093/bioinformatics/btw455 · Cited by 82

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

Holley, G., Wittler, R., & Stoye, J. (2016) · Algorithms for Molecular Biology · doi:10.1186/s13015-016-0066-8 · Cited by 80

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

Thorpe, H. A., Bayliss, S., Sheppard, S. K., & Feil, E. J. (2018) · GigaScience · doi:10.1093/gigascience/giy015 · Cited by 79

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

Haegeman, B., & Weitz, J. S. (2012) · BMC Genomics · doi:10.1186/1471-2164-13-196 · Cited by 78

Gene Frequency Distributions Reject a Neutral Model of Genome Evolution

Lobkovsky, A. E., Wolf, Y. I., & Koonin, E. V. (2013) · Genome Biology and Evolution · doi:10.1093/gbe/evt002 · Cited by 77

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

Dereeper, A., Summo, M., & Meyer, D. F. (2022) · Bioinformatics · doi:10.1093/bioinformatics/btac504 · Cited by 77

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

Hu, B., Xie, G. G., Lo, C., Starkenburg, S. R., & Chain, P. (2011) · Briefings in Functional Genomics · doi:10.1093/bfgp/elr042 · Cited by 74

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

Baier, U., Beller, T., & Ohlebusch, E. (2015) · Bioinformatics · doi:10.1093/bioinformatics/btv603 · Cited by 73

The evolution of metabolic networks of E. coli

Baumler, D. J., Peplinski, R. G., Reed, J. L., Glasner, J. D., & Perna, N. T. (2011) · BMC Systems Biology · doi:10.1186/1752-0509-5-182 · Cited by 73

Pangenome Evolution in the Marine BacteriumAlteromonas

López‐Pérez, M., & Rodríguez‐Valera, F. (2016) · Genome Biology and Evolution · doi:10.1093/gbe/evw098 · Cited by 73

A Brief Review of Software Tools for Pangenomics

Xiao, J., Zhang, Z., Wu, J., & Yu, J. M. (2015) · Genomics Proteomics & Bioinformatics · doi:10.1016/j.gpb.2015.01.007 · Cited by 72

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

van Opijnen, T., Dedrick, S., & Bento, J. (2016) · PLoS Pathogens · doi:10.1371/journal.ppat.1005869 · Cited by 72

Genetic Competence Drives Genome Diversity in Bacillus subtilis

Brito, P. H., Chevreux, B., Serra, C. R., Schyns, G., Henriques, A. O., & Pereira‐Leal, J. B. (2017) · Genome Biology and Evolution · doi:10.1093/gbe/evx270 · Cited by 72

PanFP: pangenome-based functional profiles for microbial communities

Jun, S., Robeson, M. S., Hauser, L., Schadt, C. W., & Gorin, A. A. (2015) · BMC Research Notes · doi:10.1186/s13104-015-1462-8 · Cited by 69

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

Shin, J., Song, Y., Jeong, Y., & Cho, B. (2016) · Frontiers in Microbiology · doi:10.3389/fmicb.2016.01531 · Cited by 65

Genome update: the 1000th genome-a cautionary tale

Lagesen, K., Ussery, D. W., & Wassenaar, T. M. (2010) · Microbiology · doi:10.1099/mic.0.038257-0 · Cited by 62 · cited 1×

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

Aherfi, S., Andréani, J., Baptiste, E., Oumessoum, A., Dornas, F. P., Andrade, A. C. D. S. P., Chabrière, É., Abrahão, J. S., Levasseur, A., Raoult, D., et al. (2018) · Frontiers in Microbiology · doi:10.3389/fmicb.2018.01486 · Cited by 60

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

Zhang, Y., & Sievert, S. M. (2014) · Frontiers in Microbiology · doi:10.3389/fmicb.2014.00110 · Cited by 58

Comparative genome analysis of the Lactobacillus brevis species

Feyereisen, M., Mahony, J., Kelleher, P., Roberts, R. J., O’Sullivan, T., Geertman, J.-M. A., & van Sinderen, D. (2019) · BMC Genomics · doi:10.1186/s12864-019-5783-1 · Cited by 57

The Genus Burkholderia: Analysis of 56 Genomic Sequences

Ussery, D. W., Kiil, K., Lagesen, K., Sicheritz‐Pontén, T., Bohlin, J., & Wassenaar, T. M. (2009) · Genome dynamics · doi:10.1159/000235768 · Cited by 57

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

Janssen, P. (2001) · Nucleic Acids Research · doi:10.1093/nar/29.21.4395 · Cited by 57

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

Fullmer, M. S., Soucy, S. M., & Gogarten, J. P. (2015) · Frontiers in Microbiology · doi:10.3389/fmicb.2015.00728 · Cited by 56

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

Bhardwaj, T., & Somvanshi, P. (2017) · Gene · doi:10.1016/j.gene.2017.04.019 · Cited by 55

Building a Pan-Genome Reference for a Population

Nguyen, N. K., Hickey, G., Zerbino, D. R., Raney, B. J., Earl, D. A., Armstrong, J. C., Kent, W. J., Haussler, D. H., & Paten, B. (2015) · Journal of Computational Biology · doi:10.1089/cmb.2014.0146 · Cited by 54

Pangenomics – an avenue to improved industrial starter cultures and probiotics

Garrigues, C., Johansen, E., & Crittenden, R. G. (2012) · Current Opinion in Biotechnology · doi:10.1016/j.copbio.2012.08.009 · Cited by 52

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

Beiko, R. G. (2011) · Biology Direct · doi:10.1186/1745-6150-6-34 · Cited by 52

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

Liu, Y., Chiou, C., & Chen, C.-C. (2016) · Scientific Reports · doi:10.1038/srep36213 · Cited by 51

The pangenome of the genus C lostridium

Udaondo, Z., Duque, E., & Ramos, J. L. (2017) · Environmental Microbiology · doi:10.1111/1462-2920.13732 · Cited by 50

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

Wu, H., Wang, D., & Gao, F. (2020) · Briefings in Bioinformatics · doi:10.1093/bib/bbaa013 · Cited by 49

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

Beavan, A. J. S., Domingo-Sananes, M. R., & McInerney, J. O. (2023) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2304934120 · Cited by 46

Panacus: fast and exact pangenome growth and core size estimation

Parmigiani, L., Garrison, E. P., Stoye, J., Marschall, T., & Doerr, D. (2024) · Bioinformatics · doi:10.1093/bioinformatics/btae720 · Cited by 45

PGAP-X: extension on pan-genome analysis pipeline

Zhao, Y., Sun, C., Zhao, D., Zhang, Y., You, Y., Jia, X., Yang, J., Wang, L., Wang, J., Fu, H., et al. (2018) · BMC Genomics · doi:10.1186/s12864-017-4337-7 · Cited by 44

Ancestral Genome Estimation Reveals the History of Ecological Diversification in Agrobacterium

Lassalle, F., Planel, R., Penel, S., Chapulliot, D., Barbe, V., Dubost, A., Calteau, A., Vallenet, D., Mornico, D., Bigot, T., et al. (2017) · Genome Biology and Evolution · doi:10.1093/gbe/evx255 · Cited by 43

Towards pan-genome read alignment to improve variation calling

Valenzuela, D., Norri, T., Välimäki, N., Pitkänen, E., & Mäkinen, V. (2018) · BMC Genomics · doi:10.1186/s12864-018-4465-8 · Cited by 42

Improving pan-genome annotation using whole genome multiple alignment

Angiuoli, S. V., Hotopp, J. C. D., Salzberg, S. L., & Tettelin, H. (2011) · BMC Bioinformatics · doi:10.1186/1471-2105-12-272 · Cited by 41

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

Cummins, E., Hall, R. J., Connor, C. H., McInerney, J. O., & McNally, A. (2022) · Microbial Genomics · doi:10.1099/mgen.0.000903 · Cited by 41

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

Simm, S., Keller, M., Selymesi, M., & Schleiff, E. (2015) · Frontiers in Microbiology · doi:10.3389/fmicb.2015.00219 · Cited by 40

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

Petersen, C., Sørensen, T., Nielsen, M. R., Søndergaard, T. E., Sørensen, J. L., Fitzpatrick, D. A., Frisvad, J. C., & Nielsen, K. L. (2023) · IMA Fungus · doi:10.1186/s43008-023-00108-7 · Cited by 40

PanGraph: scalable bacterial pan-genome graph construction

Noll, N., Molari, M., Shaw, L. P., & Neher, R. A. (2023) · Microbial Genomics · doi:10.1099/mgen.0.001034 · Cited by 40

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

Raquel Hurtado, C., Carhuaricra, D., Soares, S. D. C., Viana, M. V. C., Azevedo, V., Lenin Maturrano, H., & Aburjaile, F. F. (2018) · Gene · doi:10.1016/j.gene.2018.05.084 · Cited by 39

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

Ahmed, O., Rossi, M., Gagie, T., Boucher, C. A., & Langmead, B. (2023) · Genome biology · doi:10.1186/s13059-023-02958-1 · Cited by 38

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

Jandrasits, C., Dąbrowski, P. W., Fuchs, S., & Renard, B. Y. (2018) · BMC Genomics · doi:10.1186/s12864-017-4401-3 · Cited by 36

Comparative Genome Analysis ofFusobacterium nucleatum

Ang, M. Y., Dutta, A., Wee, W. Y., Dymock, D., Paterson, I. C., & Choo, S. W. (2016) · Genome Biology and Evolution · doi:10.1093/gbe/evw199 · Cited by 33

PanWeb: A web interface for pan-genomic analysis

Pantoja, Y., Pinheiro, K. D. C., Veras, A. A. D. O., Araújo, F. A., de Sousa, A. L., Guimarães, L. C., Silva, A., & Ramos, R. T. J. (2017) · PLoS ONE · doi:10.1371/journal.pone.0178154 · Cited by 33

Order and Disorder during Escherichia coli Divergence

Hendrickson, H. L. (2009) · PLoS Genetics · doi:10.1371/journal.pgen.1000335 · Cited by 32

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

Zamani-Dahaj, S. A., Okasha, M., Kosakowski, J., & Higgs, P. G. (2016) · Molecular Biology and Evolution · doi:10.1093/molbev/msw062 · Cited by 32

PanViz: interactive visualization of the structure of functionally annotated pangenomes

Pedersen, T. L., Nookaew, I., Ussery, D. W., & Månsson, M. (2016) · Bioinformatics · doi:10.1093/bioinformatics/btw761 · Cited by 32

Computational comparisons of model genomes

Ouzounis, C. A., Casari, G., Sander, C., Tamames, J., & Valencia, A. (1996) · Trends in biotechnology · doi:10.1016/0167-7799(96)10043-3 · Cited by 31

Pan-Tetris: an interactive visualisation for Pan-genomes

Hennig, A., Bernhardt, J., & Nieselt, K. (2015) · BMC Bioinformatics · doi:10.1186/1471-2105-16-s11-s3 · Cited by 30

PANNOTATOR: an automated tool for annotation of pan-genomes

dos Santos, A. R., Barbosa, E., Fiaux, K. K., Zurita-Turk, M., Chaitankar, V., Kamapantula, B. K., Abdelzaher, A., Ghosh, P., Tiwari, S., Barve, N., et al. (2013) · Genetics and Molecular Research · doi:10.4238/2013.august.16.2 · Cited by 29

Phylogenomic Insight into Salinispora (Bacteria, Actinobacteria) Species Designations

Millán‐Aguiñaga, N., Chavarría, K. L., Ugalde, J. A., Letzel, A.-C., Rouse, G. W., & Jensen, P. R. (2017) · Scientific Reports · doi:10.1038/s41598-017-02845-3 · Cited by 29

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

Rouli, L., Mbengue, M., Robert, C., Ndiaye, M., Scola, B. L., & Raoult, D. (2014) · New Microbes and New Infections · doi:10.1002/nmi2.62 · Cited by 28

A pangenomic study of Bacillus thuringiensis

Fang, Y., Li, Z., Liu, J., Shu, C., Wang, X., Zhang, X., Yu, X., Zhao, D., Liu, G., Hu, S., et al. (2011) · Journal of genetics and genomics/Journal of Genetics and Genomics · doi:10.1016/j.jgg.2011.11.001 · Cited by 28

The diversity of a distributed genome in bacterial populations

Baumdicker, F., Hess, W. R., & Pfaffelhuber, P. (2010) · The Annals of Applied Probability · doi:10.1214/09-aap657 · Cited by 28

Directional gene flow and ecological separation in Yersinia enterocolitica

Reuter, S., Corander, J., de Been, M., Harris, S. R., Cheng, L., Hall, M., Thomson, N. R., & McNally, A. (2015) · Microbial Genomics · doi:10.1099/mgen.0.000030 · Cited by 28

PATO: Pangenome Analysis Toolkit

Fernández-de-Bobadilla, M. D., Talavera-Rodríguez, A., Chacón, L., Baquero, F., Coque, T. M., & Lanza, V. F. (2021) · Bioinformatics · doi:10.1093/bioinformatics/btab697 · Cited by 27

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

Baby, V., Lachance, J., Gagnon, J., Lucier, J., Matteau, D., Knight, T., & Rodrigue, S. (2018) · mSystems · doi:10.1128/msystems.00198-17 · Cited by 26

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

Zhang, X., Liu, Z., Wei, G., Yang, F., & Liu, X. (2018) · Frontiers in Microbiology · doi:10.3389/fmicb.2018.01255 · Cited by 26

The Bacterial Pan-Genome and Reverse Vaccinology

Tettelin, H. (2009) · Genome dynamics · doi:10.1159/000235761 · Cited by 25

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

Halachev, M. R., Loman, N. J., & Pallen, M. J. (2011) · PLoS ONE · doi:10.1371/journal.pone.0028388 · Cited by 25

Comparison of gene clustering criteria reveals intrinsic uncertainty in pangenome analyses

Manzano-Morales, S., Liu, Y., González-Bodí, S., Huerta‐Cepas, J., & Iranzo, J. (2023) · Genome biology · doi:10.1186/s13059-023-03089-3 · Cited by 25

Defining Orthologs and Pangenome Size Metrics

Bosi, E., Fani, R., & Fondi, M. (2014) · Methods in molecular biology · doi:10.1007/978-1-4939-1720-4_13 · Cited by 24

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

Beck, C., Knoop, H., & Steuer, R. (2018) · PLoS Genetics · doi:10.1371/journal.pgen.1007239 · Cited by 24

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

Harling-Lee, J. D., Gorzynski, J., Yebra, G., Angus, T., Fitzgerald, J. R., & Freeman, T. C. (2022) · BMC Bioinformatics · doi:10.1186/s12859-022-04898-2 · Cited by 24

PanFunPro: PAN-genome analysis based on FUNctional PROfiles

Lukjančenko, O., Thomsen, M. C. F., Larsen, M. V., & Ussery, D. W. (2013) · F1000Research · doi:10.12688/f1000research.2-265.v1 · Cited by 23

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

Woźniak, M., Wong, L., & Tiuryn, J. (2014) · BMC Bioinformatics · doi:10.1186/1471-2105-15-65 · Cited by 23

Challenges in gene-oriented approaches for pangenome content discovery

Bonnici, V., Maresi, E., & Giugno, R. (2020) · Briefings in Bioinformatics · doi:10.1093/bib/bbaa198 · Cited by 23

Decomposition of the pangenome matrix reveals a structure in gene distribution in the Escherichia coli species

Chauhan, S., Ardalani, O., Hyun, J. C., Monk, J. M., Phaneuf, P. V., & Palsson, B. Ø. (2024) · mSphere · doi:10.1128/msphere.00532-24 · Cited by 23

Opening the pan-genomics box

Read, T. D., & Ussery, D. W. (2006) · Current Opinion in Microbiology · doi:10.1016/j.mib.2006.08.010 · Cited by 21

PanCake: A Data Structure for Pangenomes

Ernst, C., & Rahmann, S. (2013) · DROPS (Schloss Dagstuhl – Leibniz Center for Informatics) · doi:10.4230/oasics.gcb.2013.35 · Cited by 21

PanACEA: a bioinformatics tool for the exploration and visualization of bacterial pan-chromosomes

Clarke, T. H., Brinkac, L. M., Inman, J. M., Sutton, G. G., & Fouts, D. E. (2018) · BMC Bioinformatics · doi:10.1186/s12859-018-2250-y · Cited by 21

Ancestral state reconstructions for genomes

Ouzounis, C. A. (2005) · Current Opinion in Genetics & Development · doi:10.1016/j.gde.2005.09.011 · Cited by 19

Genetic variation between Helicobacter pylori strains: gene acquisition or loss?

Garcı́a-Vallvé, S., Janssen, P., & Ouzounis, C. A. (2002) · Trends in Microbiology · doi:10.1016/s0966-842x(02)02446-0 · Cited by 18

RIBAP: a comprehensive bacterial core genome annotation pipeline for pangenome calculation beyond the species level

Lamkiewicz, K., Barf, L.-M., Sachse, K., & Hölzer, M. (2024) · Genome biology · doi:10.1186/s13059-024-03312-9 · Cited by 18

A domain sequence approach to pangenomics: applications to Escherichia coli

Snipen, L. G., & Ussery, D. W. (2012) · F1000Research · doi:10.12688/f1000research.1-19.v2 · Cited by 17

Comparative genomics and genome biology of Campylobacter showae

Hsu, T. Y., Gemmell, M., Franzosa, E. A., Berry, S., Mukhopadhya, I., Hansen, R., Michaud, M., Nielsen, H. L., Miller, W. G., Nielsen, H. I., et al. (2019) · Emerging Microbes & Infections · doi:10.1080/22221751.2019.1622455 · Cited by 16

Machine learning approaches to identify core and dispensable genes in pangenomes

Yocca, A. E., & Edger, P. P. (2021) · The Plant Genome · doi:10.1002/tpg2.20135 · Cited by 15

Randomness in Sequence Evolution Increases over Time

Wang, G., Sun, S., & Zhang, Z. (2016) · PLoS ONE · doi:10.1371/journal.pone.0155935 · Cited by 13

Bacterial Pangenomics

Mengoni, A., Bacci, G., & Fondi, M. (2021) · Methods in molecular biology · doi:10.1007/978-1-0716-1099-2 · Cited by 12

Structure classification of the proteins from Salmonella enterica pangenome revealed novel potential pathogenicity islands

(2024) · doi:10.1038/s41598-024-60991-x · Cited by 11

NGSPanPipe: A Pipeline for Pan-genome Identification in Microbial Strains from Experimental Reads

Kulsum, U., Kapil, A., Singh, H., & Kaur, P. (2018) · Advances in experimental medicine and biology · doi:10.1007/978-981-10-7572-8_4 · Cited by 9

BGDMdocker: a Docker workflow for data mining and visualization of bacterial pan-genomes and biosynthetic gene clusters

Cheng, G., Lü, Q., Ma, L., Zhang, G., Xu, L. Z., & Zhou, Z. (2017) · PeerJ · doi:10.7717/peerj.3948 · Cited by 8

Corekaburra: pan-genome post-processing using core gene synteny

Jespersen, M. G., Hayes, A. J., & Davies, M. R. (2022) · The Journal of Open Source Software · doi:10.21105/joss.04910 · Cited by 7

Panaconda: Application of pan-synteny graph models to genome content analysisPreprint

Warren, A. S., Davis, J. J., Wattam, A. R., Machi, D., Setúbal, J. C., & Heath, L. S. (2017) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/215988 · Cited by 6

On the use and misuse of pangenome and related terms

Edwards, D. (2026) · Nature Communications · doi:10.1038/s41467-026-68624-9 · Cited by 6

Defining the statistical metrics of a pangenome

Μπατζιάκας, Α. Γ. (2017) · Aristotle University of Thessaloniki · doi:10.26262/heal.auth.ir.292653

To the species level and beyond A rationalized approach to study pangenomes

Bruyère, E., Junker, R., Dérozier, S., Chiapello, H., & Gautreau, G. (2024) · HAL

Challenges in gene-oriented approaches for pangenome content discovery

Bonnici, V., Maresi, E., & Giugno, R. (2020) · Briefings in Bioinformatics · doi:10.1093/bib/bbaa198 · Cited by 23

Measuring pangenome diversity at scale

Parmigiani, L. (2026) · Publikationen an der Universität Bielefeld (Universität Bielefeld) · doi:10.4119/unibi/3020699

A Review of Pangenome Tools and Recent Studies

Vernikos, G. S. (2020) · Springer eBooks · doi:10.1007/978-3-030-38281-0_4 · Cited by 48