| Year |
Citation |
Score |
| 2023 |
Zhou Z, Charlesworth J, Achtman M. HierCC: a multi-level clustering scheme for population assignments based on core genome MLST. Bioinformatics (Oxford, England). 37: 3645-3646. PMID 33823553 DOI: 10.1093/bioinformatics/btab234 |
0.645 |
|
| 2022 |
Achtman M, Zhou Z, Charlesworth J, Baxter L. EnteroBase: hierarchical clustering of 100 000s of bacterial genomes into species/subspecies and populations. Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences. 377: 20210240. PMID 35989609 DOI: 10.1098/rstb.2021.0240 |
0.66 |
|
| 2022 |
Holt KE, Aanensen DM, Achtman M. Genomic population structures of microbial pathogens. Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences. 377: 20210230. PMID 35989608 DOI: 10.1098/rstb.2021.0230 |
0.406 |
|
| 2021 |
Achtman M, Van den Broeck F, Cooper KK, Lemey P, Parker CT, Zhou Z. Genomic population structure associated with repeated escape of Salmonella enterica ATCC14028s from the laboratory into nature. Plos Genetics. 17: e1009820. PMID 34570761 DOI: 10.1371/journal.pgen.1009820 |
0.628 |
|
| 2021 |
Moodley Y, Brunelli A, Ghirotto S, Klyubin A, Maady AS, Tyne W, Muñoz-Ramirez ZY, Zhou Z, Manica A, Linz B, Achtman M. 's historical journey through Siberia and the Americas. Proceedings of the National Academy of Sciences of the United States of America. 118. PMID 34161258 DOI: 10.1073/pnas.2015523118 |
0.601 |
|
| 2020 |
Achtman M, Zhou Z, Alikhan NF, Tyne W, Parkhill J, Cormican M, Chiou CS, Torpdahl M, Litrup E, Prendergast DM, Moore JE, Strain S, Kornschober C, Meinersmann R, Uesbeck A, et al. Genomic diversity of The UoWUCC 10K genomes project. Wellcome Open Research. 5: 223. PMID 33614977 DOI: 10.12688/wellcomeopenres.16291.2 |
0.688 |
|
| 2020 |
Achtman M, Wain J, Weill FX, Nair S, Zhou Z, Sangal V, Krauland MG, Hale JL, Harbottle H, Uesbeck A, Dougan G, Harrison LH, Brisse S. Correction: Multilocus Sequence Typing as a Replacement for Serotyping in Salmonella enterica. Plos Pathogens. 16: e1009040. PMID 33085727 DOI: 10.1371/journal.ppat.1009040 |
0.503 |
|
| 2020 |
Zhou Z, Charlesworth J, Achtman M. Accurate reconstruction of bacterial pan- and core genomes with PEPPAN. Genome Research. 30: 1667-1679. PMID 33055096 DOI: 10.1101/gr.260828.120 |
0.603 |
|
| 2020 |
Achtman M, Zhou Z. Metagenomics of the modern and historical human oral microbiome with phylogenetic studies on and . Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences. 375: 20190573. PMID 33012228 DOI: 10.1098/rstb.2019.0573 |
0.648 |
|
| 2020 |
Frentrup M, Zhou Z, Steglich M, Meier-Kolthoff JP, Göker M, Riedel T, Bunk B, Spröer C, Overmann J, Blaschitz M, Indra A, von Müller L, Kohl TA, Niemann S, Seyboldt C, ... ... Achtman M, et al. A publicly accessible database for genome sequences supports tracing of transmission chains and epidemics. Microbial Genomics. PMID 32726198 DOI: 10.1099/mgen.0.000410 |
0.647 |
|
| 2020 |
Key FM, Posth C, Esquivel-Gomez LR, Hübler R, Spyrou MA, Neumann GU, Furtwängler A, Sabin S, Burri M, Wissgott A, Lankapalli AK, Vågene ÅJ, Meyer M, Nagel S, Tukhbatova R, ... ... Achtman M, et al. Emergence of human-adapted Salmonella enterica is linked to the Neolithization process. Nature Ecology & Evolution. PMID 32094538 DOI: 10.1038/S41559-020-1106-9 |
0.624 |
|
| 2019 |
Zhou Z, Alikhan NF, Mohamed K, Fan Y, Achtman M. The EnteroBase user's guide, with case studies on transmissions, phylogeny and core genomic diversity. Genome Research. PMID 31809257 DOI: 10.1101/gr.251678.119 |
0.672 |
|
| 2018 |
Cho H, Berger B, Peng J, Galitzine C, Vitek O, Beltran PMJ, Cristea IM, Görtler F, Solbrig S, Wettig T, Oefner PJ, Spang R, Altenbuchinger M, Basso RS, Hochbaum D, ... ... Achtman M, et al. Principles of Systems Biology, No. 31. Cell Systems. 7: 133-135. PMID 30138580 DOI: 10.1016/J.Cels.2018.08.005 |
0.44 |
|
| 2018 |
Zhou Z, Alikhan NF, Sergeant MJ, Luhmann N, Vaz C, Francisco AP, Carriço JA, Achtman M. GrapeTree: Visualization of core genomic relationships among 100,000 bacterial pathogens. Genome Research. PMID 30049790 DOI: 10.1101/gr.232397.117 |
0.586 |
|
| 2018 |
Zhou Z, Lundstrøm I, Tran-Dien A, Duchêne S, Alikhan NF, Sergeant MJ, Langridge G, Fotakis AK, Nair S, Stenøien HK, Hamre SS, Casjens S, Christophersen A, Quince C, Thomson NR, ... ... Achtman M, et al. Pan-genome Analysis of Ancient and Modern Salmonella enterica Demonstrates Genomic Stability of the Invasive Para C Lineage for Millennia. Current Biology : Cb. PMID 30033331 DOI: 10.1016/J.Cub.2018.05.058 |
0.611 |
|
| 2018 |
Alikhan NF, Zhou Z, Sergeant MJ, Achtman M. A genomic overview of the population structure of Salmonella. Plos Genetics. 14: e1007261. PMID 29621240 DOI: 10.1371/journal.pgen.1007261 |
0.661 |
|
| 2016 |
Connor TR, Owen SV, Langridge G, Connell S, Nair S, Reuter S, Dallman TJ, Corander J, Tabing KC, Le Hello S, Fookes M, Doublet B, Zhou Z, Feltwell T, Ellington MJ, ... ... Achtman M, et al. What's in a Name? Species-Wide Whole-Genome Sequencing Resolves Invasive and Noninvasive Lineages of Salmonella enterica Serotype Paratyphi B. Mbio. 7. PMID 27555304 DOI: 10.1128/Mbio.00527-16 |
0.615 |
|
| 2015 |
Achtman M, Zhou Z, Didelot X. Formal Comment to Pettengill: The Time to Most Recent Common Ancestor Does Not (Usually) Approximate the Date of Divergence. Plos One. 10: e0134435. PMID 26274924 DOI: 10.1371/journal.pone.0134435 |
0.587 |
|
| 2015 |
Kay GL, Sergeant MJ, Zhou Z, Chan JZ, Millard A, Quick J, Szikossy I, Pap I, Spigelman M, Loman NJ, Achtman M, Donoghue HD, Pallen MJ. Eighteenth-century genomes show that mixed infections were common at time of peak tuberculosis in Europe. Nature Communications. 6: 6717. PMID 25848958 DOI: 10.1038/ncomms7717 |
0.539 |
|
| 2015 |
Didelot X, Pang B, Zhou Z, McCann A, Ni P, Li D, Achtman M, Kan B. The role of china in the global spread of the current cholera pandemic. Plos Genetics. 11: e1005072. PMID 25768799 DOI: 10.1371/journal.pgen.1005072 |
0.598 |
|
| 2014 |
Achtman M, Zhou Z. Distinct genealogies for plasmids and chromosome. Plos Genetics. 10: e1004874. PMID 25521852 DOI: 10.1371/journal.pgen.1004874 |
0.434 |
|
| 2014 |
Zhou Z, McCann A, Weill FX, Blin C, Nair S, Wain J, Dougan G, Achtman M. Transient Darwinian selection in Salmonella enterica serovar Paratyphi A during 450 years of global spread of enteric fever. Proceedings of the National Academy of Sciences of the United States of America. 111: 12199-204. PMID 25092320 DOI: 10.1073/pnas.1411012111 |
0.62 |
|
| 2014 |
Cui Y, Yang X, Xiao X, Anisimov AP, Li D, Yan Y, Zhou D, Rajerison M, Carniel E, Achtman M, Yang R, Song Y. Genetic variations of live attenuated plague vaccine strains (Yersinia pestis EV76 lineage) during laboratory passages in different countries. Infection, Genetics and Evolution : Journal of Molecular Epidemiology and Evolutionary Genetics in Infectious Diseases. 26: 172-9. PMID 24905600 DOI: 10.1016/j.meegid.2014.05.023 |
0.361 |
|
| 2014 |
Reuter S, Connor TR, Barquist L, Walker D, Feltwell T, Harris SR, Fookes M, Hall ME, Petty NK, Fuchs TM, Corander J, Dufour M, Ringwood T, Savin C, Bouchier C, ... ... Achtman M, et al. Parallel independent evolution of pathogenicity within the genus Yersinia. Proceedings of the National Academy of Sciences of the United States of America. 111: 6768-73. PMID 24753568 DOI: 10.1073/Pnas.1317161111 |
0.416 |
|
| 2014 |
Haase JK, Didelot X, Lecuit M, Korkeala H, Achtman M, Leclercq A, Grant K, Wiedmann M, Apfalter P. The ubiquitous nature of Listeria monocytogenes clones: A large-scale Multilocus Sequence Typing study Environmental Microbiology. 16: 405-416. PMID 24274459 DOI: 10.1111/1462-2920.12342 |
0.304 |
|
| 2013 |
Zhou Z, McCann A, Litrup E, Murphy R, Cormican M, Fanning S, Brown D, Guttman DS, Brisse S, Achtman M. Neutral genomic microevolution of a recently emerged pathogen, Salmonella enterica serovar Agona. Plos Genetics. 9: e1003471. PMID 23637636 DOI: 10.1371/Journal.Pgen.1003471 |
0.677 |
|
| 2013 |
Achtman M, Hale J, Murphy RA, Boyd EF, Porwollik S. Population structures in the SARA and SARB reference collections of Salmonella enterica according to MLST, MLEE and microarray hybridization. Infection, Genetics and Evolution : Journal of Molecular Epidemiology and Evolutionary Genetics in Infectious Diseases. 16: 314-25. PMID 23507027 DOI: 10.1016/j.meegid.2013.03.003 |
0.385 |
|
| 2013 |
Holden MT, Hsu LY, Kurt K, Weinert LA, Mather AE, Harris SR, Strommenger B, Layer F, Witte W, de Lencastre H, Skov R, Westh H, Zemlicková H, Coombs G, Kearns AM, ... ... Achtman M, et al. A genomic portrait of the emergence, evolution, and global spread of a methicillin-resistant Staphylococcus aureus pandemic. Genome Research. 23: 653-64. PMID 23299977 DOI: 10.1101/Gr.147710.112 |
0.591 |
|
| 2012 |
Haase JK, Brown DJ, Weill FX, Mather H, Foster G, Brisse S, Wain J, Achtman M. Population genetic structure of 4,12:a:- Salmonella enterica strains from harbor porpoises. Applied and Environmental Microbiology. 78: 8829-33. PMID 23042176 DOI: 10.1128/AEM.02310-12 |
0.347 |
|
| 2012 |
Achtman M, Wain J, Weill FX, Nair S, Zhou Z, Sangal V, Krauland MG, Hale JL, Harbottle H, Uesbeck A, Dougan G, Harrison LH, Brisse S. Multilocus sequence typing as a replacement for serotyping in Salmonella enterica. Plos Pathogens. 8: e1002776. PMID 22737074 DOI: 10.1371/Journal.Ppat.1002776 |
0.58 |
|
| 2012 |
Clark G, Paszkiewicz K, Hale J, Weston V, Constantinidou C, Penn C, Achtman M, McNally A. Genomic analysis uncovers a phenotypically diverse but genetically homogeneous Escherichia coli ST131 clone circulating in unrelated urinary tract infections. The Journal of Antimicrobial Chemotherapy. 67: 868-77. PMID 22258927 DOI: 10.1093/jac/dkr585 |
0.424 |
|
| 2012 |
Shepard SM, Danzeisen JL, Isaacson RE, Seemann T, Achtman M, Johnson TJ. Genome sequences and phylogenetic analysis of K88- and F18-positive porcine enterotoxigenic Escherichia coli. Journal of Bacteriology. 194: 395-405. PMID 22081385 DOI: 10.1128/Jb.06225-11 |
0.423 |
|
| 2011 |
Vogler AJ, Chan F, Wagner DM, Roumagnac P, Lee J, Nera R, Eppinger M, Ravel J, Rahalison L, Rasoamanana BW, Beckstrom-Sternberg SM, Achtman M, Chanteau S, Keim P. Phylogeography and molecular epidemiology of Yersinia pestis in Madagascar. Plos Neglected Tropical Diseases. 5: e1319. PMID 21931876 DOI: 10.1371/Journal.Pntd.0001319 |
0.324 |
|
| 2011 |
Didelot X, Bowden R, Street T, Golubchik T, Spencer C, McVean G, Sangal V, Anjum MF, Achtman M, Falush D, Donnelly P. Recombination and population structure in Salmonella enterica. Plos Genetics. 7: e1002191. PMID 21829375 DOI: 10.1371/Journal.Pgen.1002191 |
0.442 |
|
| 2010 |
Morelli G, Song Y, Mazzoni CJ, Eppinger M, Roumagnac P, Wagner DM, Feldkamp M, Kusecek B, Vogler AJ, Li Y, Cui Y, Thomson NR, Jombart T, Leblois R, Lichtner P, ... ... Achtman M, et al. Yersinia pestis genome sequencing identifies patterns of global phylogenetic diversity. Nature Genetics. 42: 1140-3. PMID 21037571 DOI: 10.1038/Ng.705 |
0.398 |
|
| 2010 |
Eppinger M, Worsham PL, Nikolich MP, Riley DR, Sebastian Y, Mou S, Achtman M, Lindler LE, Ravel J. Genome sequence of the deep-rooted Yersinia pestis strain Angola reveals new insights into the evolution and pangenome of the plague bacterium. Journal of Bacteriology. 192: 1685-99. PMID 20061468 DOI: 10.1128/JB.01518-09 |
0.517 |
|
| 2009 |
Kingsley RA, Msefula CL, Thomson NR, Kariuki S, Holt KE, Gordon MA, Harris D, Clarke L, Whitehead S, Sangal V, Marsh K, Achtman M, Molyneux ME, Cormican M, Parkhill J, et al. Epidemic multiple drug resistant Salmonella Typhimurium causing invasive disease in sub-Saharan Africa have a distinct genotype. Genome Research. 19: 2279-87. PMID 19901036 DOI: 10.1101/gr.091017.109 |
0.454 |
|
| 2008 |
Holt KE, Parkhill J, Mazzoni CJ, Roumagnac P, Weill FX, Goodhead I, Rance R, Baker S, Maskell DJ, Wain J, Dolecek C, Achtman M, Dougan G. High-throughput sequencing provides insights into genome variation and evolution in Salmonella Typhi. Nature Genetics. 40: 987-93. PMID 18660809 DOI: 10.1038/ng.195 |
0.411 |
|
| 2008 |
Baker S, Holt K, van de Vosse E, Roumagnac P, Whitehead S, King E, Ewels P, Keniry A, Weill FX, Lightfoot D, van Dissel JT, Sanderson KE, Farrar J, Achtman M, Deloukas P, et al. High-throughput genotyping of Salmonella enterica serovar Typhi allowing geographical assignment of haplotypes and pathotypes within an urban District of Jakarta, Indonesia. Journal of Clinical Microbiology. 46: 1741-6. PMID 18322069 DOI: 10.1128/JCM.02249-07 |
0.341 |
|
| 2007 |
Wirth T, Morelli G, Kusecek B, van Belkum A, van der Schee C, Meyer A, Achtman M. The rise and spread of a new pathogen: seroresistant Moraxella catarrhalis. Genome Research. 17: 1647-56. PMID 17895425 DOI: 10.1101/Gr.6122607 |
0.346 |
|
| 2007 |
Bentley SD, Vernikos GS, Snyder LA, Churcher C, Arrowsmith C, Chillingworth T, Cronin A, Davis PH, Holroyd NE, Jagels K, Maddison M, Moule S, Rabbinowitsch E, Sharp S, Unwin L, ... ... Achtman M, et al. Meningococcal genetic variation mechanisms viewed through comparative analysis of serogroup C strain FAM18. Plos Genetics. 3: e23. PMID 17305430 DOI: 10.1371/Journal.Pgen.0030023 |
0.422 |
|
| 2007 |
Didelot X, Achtman M, Parkhill J, Thomson NR, Falush D. A bimodal pattern of relatedness between the Salmonella Paratyphi A and Typhi genomes: convergence or divergence by homologous recombination? Genome Research. 17: 61-8. PMID 17090663 DOI: 10.1101/gr.5512906 |
0.435 |
|
| 2006 |
Wirth T, Falush D, Lan R, Colles F, Mensa P, Wieler LH, Karch H, Reeves PR, Maiden MC, Ochman H, Achtman M. Sex and virulence in Escherichia coli: an evolutionary perspective. Molecular Microbiology. 60: 1136-51. PMID 16689791 DOI: 10.1111/J.1365-2958.2006.05172.X |
0.342 |
|
| 2005 |
Gressmann H, Linz B, Ghai R, Pleissner K, Schlapbach R, Yamaoka Y, Kraft C, Suerbaum S, Meyer TF, Achtman M. Gain and loss of multiple genes during the evolution of Helicobacter pylori. Plos Genetics. 1: 419-428. PMID 16217547 DOI: 10.1371/Journal.Pgen.0010043 |
0.322 |
|
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