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For: Marttinen P, Croucher NJ, Gutmann MU, Corander J, Hanage WP. Recombination produces coherent bacterial species clusters in both core and accessory genomes. Microb Genom 2015;1:e000038. [PMID: 28348822 PMCID: PMC5320679 DOI: 10.1099/mgen.0.000038] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2015] [Accepted: 10/06/2015] [Indexed: 12/13/2022]  Open
Number Cited by Other Article(s)
1
Horsfield ST, Fok BCT, Fu Y, Turner P, Lees JA, Croucher NJ. Optimizing nanopore adaptive sampling for pneumococcal serotype surveillance in complex samples using the graph-based GNASTy algorithm. Genome Res 2025;35:1025-1040. [PMID: 40037844 PMCID: PMC12047183 DOI: 10.1101/gr.279435.124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2024] [Accepted: 01/30/2025] [Indexed: 03/06/2025]
2
Lee IPA, Eldakar OT, Gogarten JP, Andam CP. Recombination as an enforcement mechanism of prosocial behavior in cooperating bacteria. iScience 2023;26:107344. [PMID: 37554437 PMCID: PMC10405257 DOI: 10.1016/j.isci.2023.107344] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Revised: 04/11/2023] [Accepted: 07/06/2023] [Indexed: 08/10/2023]  Open
3
Azarian T, Martinez PP, Arnold BJ, Qiu X, Grant LR, Corander J, Fraser C, Croucher NJ, Hammitt LL, Reid R, Santosham M, Weatherholtz RC, Bentley SD, O’Brien KL, Lipsitch M, Hanage WP. Frequency-dependent selection can forecast evolution in Streptococcus pneumoniae. PLoS Biol 2020;18:e3000878. [PMID: 33091022 PMCID: PMC7580979 DOI: 10.1371/journal.pbio.3000878] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Accepted: 09/18/2020] [Indexed: 11/30/2022]  Open
4
Gardon H, Biderre-Petit C, Jouan-Dufournel I, Bronner G. A drift-barrier model drives the genomic landscape of a structured bacterial population. Mol Ecol 2020;29:4143-4156. [PMID: 32920913 DOI: 10.1111/mec.15628] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Revised: 08/26/2020] [Accepted: 08/28/2020] [Indexed: 01/05/2023]
5
Iranzo J, Wolf YI, Koonin EV, Sela I. Gene gain and loss push prokaryotes beyond the homologous recombination barrier and accelerate genome sequence divergence. Nat Commun 2019;10:5376. [PMID: 31772262 PMCID: PMC6879757 DOI: 10.1038/s41467-019-13429-2] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2019] [Accepted: 11/07/2019] [Indexed: 02/05/2023]  Open
6
Sipola A, Marttinen P, Corander J. Bacmeta: simulator for genomic evolution in bacterial metapopulations. Bioinformatics 2019;34:2308-2310. [PMID: 29474733 DOI: 10.1093/bioinformatics/bty093] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2017] [Accepted: 02/20/2018] [Indexed: 12/25/2022]  Open
7
Tomczak JM, Węglarz‐Tomczak E. Estimating kinetic constants in the Michaelis–Menten model from one enzymatic assay using Approximate Bayesian Computation. FEBS Lett 2019;593:2742-2750. [DOI: 10.1002/1873-3468.13531] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2019] [Revised: 06/05/2019] [Accepted: 06/27/2019] [Indexed: 01/04/2023]
8
Ding W, Baumdicker F, Neher RA. panX: pan-genome analysis and exploration. Nucleic Acids Res 2019;46:e5. [PMID: 29077859 PMCID: PMC5758898 DOI: 10.1093/nar/gkx977] [Citation(s) in RCA: 167] [Impact Index Per Article: 27.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2016] [Accepted: 10/10/2017] [Indexed: 11/24/2022]  Open
9
Lees JA, Harris SR, Tonkin-Hill G, Gladstone RA, Lo SW, Weiser JN, Corander J, Bentley SD, Croucher NJ. Fast and flexible bacterial genomic epidemiology with PopPUNK. Genome Res 2019;29:304-316. [PMID: 30679308 PMCID: PMC6360808 DOI: 10.1101/gr.241455.118] [Citation(s) in RCA: 245] [Impact Index Per Article: 40.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2018] [Accepted: 12/10/2018] [Indexed: 12/02/2022]
10
Järvenpää M, Gutmann MU, Vehtari A, Marttinen P. Gaussian process modelling in approximate Bayesian computation to estimate horizontal gene transfer in bacteria. Ann Appl Stat 2018. [DOI: 10.1214/18-aoas1150] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
11
Abudahab K, Prada JM, Yang Z, Bentley SD, Croucher NJ, Corander J, Aanensen DM. PANINI: Pangenome Neighbour Identification for Bacterial Populations. Microb Genom 2018;5. [PMID: 30465642 PMCID: PMC6521588 DOI: 10.1099/mgen.0.000220] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]  Open
12
Lintusaari J, Gutmann MU, Dutta R, Kaski S, Corander J. Fundamentals and Recent Developments in Approximate Bayesian Computation. Syst Biol 2018;66:e66-e82. [PMID: 28175922 PMCID: PMC5837704 DOI: 10.1093/sysbio/syw077] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2015] [Revised: 08/09/2016] [Accepted: 08/09/2016] [Indexed: 12/16/2022]  Open
13
Corander J, Fraser C, Gutmann MU, Arnold B, Hanage WP, Bentley SD, Lipsitch M, Croucher NJ. Frequency-dependent selection in vaccine-associated pneumococcal population dynamics. Nat Ecol Evol 2017;1:1950-1960. [PMID: 29038424 PMCID: PMC5708525 DOI: 10.1038/s41559-017-0337-x] [Citation(s) in RCA: 90] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2017] [Accepted: 09/01/2017] [Indexed: 12/21/2022]
14
Apagyi KJ, Fraser C, Croucher NJ. Transformation Asymmetry and the Evolution of the Bacterial Accessory Genome. Mol Biol Evol 2017;35:575-581. [PMID: 29211859 PMCID: PMC5850275 DOI: 10.1093/molbev/msx309] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]  Open
15
Mostowy R, Croucher NJ, Andam CP, Corander J, Hanage WP, Marttinen P. Efficient Inference of Recent and Ancestral Recombination within Bacterial Populations. Mol Biol Evol 2017;34:1167-1182. [PMID: 28199698 PMCID: PMC5400400 DOI: 10.1093/molbev/msx066] [Citation(s) in RCA: 114] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]  Open
16
Recombination-Driven Genome Evolution and Stability of Bacterial Species. Genetics 2017;207:281-295. [PMID: 28751420 DOI: 10.1534/genetics.117.300061] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2016] [Accepted: 07/18/2017] [Indexed: 01/21/2023]  Open
17
Marttinen P, Hanage WP. Speciation trajectories in recombining bacterial species. PLoS Comput Biol 2017;13:e1005640. [PMID: 28671999 PMCID: PMC5542674 DOI: 10.1371/journal.pcbi.1005640] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2017] [Revised: 08/03/2017] [Accepted: 06/15/2017] [Indexed: 01/26/2023]  Open
18
David S, Sánchez-Busó L, Harris SR, Marttinen P, Rusniok C, Buchrieser C, Harrison TG, Parkhill J. Dynamics and impact of homologous recombination on the evolution of Legionella pneumophila. PLoS Genet 2017. [PMID: 28650958 PMCID: PMC5507463 DOI: 10.1371/journal.pgen.1006855] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]  Open
19
Shapiro BJ. How clonal are bacteria over time? Curr Opin Microbiol 2016;31:116-123. [PMID: 27057964 DOI: 10.1016/j.mib.2016.03.013] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2016] [Revised: 03/20/2016] [Accepted: 03/22/2016] [Indexed: 11/15/2022]
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