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Number of items: 61.
2020
Frentrup, Martinique, Zhou, Zhemin, Steglich, Matthias, Meier-Kolthoff, Jan P., Göker, Markus, Riedel, Thomas, Bunk, Boyke, Spröer, Cathrin, Overmann, Jörg, Blaschitz, Marion et al.
(2020)
A publicly accessible database for Clostridioides difficile genome sequences supports tracing of transmission chains and epidemics.
Microbial Genomics
.
doi:10.1099/mgen.0.000410
(In Press)
Achtman, Mark and Zhou, Zhemin (2020) Metagenomics of the modern and historical human oral microbiome with phylogenetic studies on Streptococcus mutans and Streptococcus sobrinus. Philosophical Transactions of the Royal Society B: Biological Sciences . doi:https://doi.org/10.1101/842542 (In Press)
Zhou, Zhemin, Charlesworth, Jane and Achtman, Mark (2020) Accurate reconstruction of bacterial pan- and core genomes with PEPPAN. Genome Research . (In Press)
2019
Agama Study Group (Including: Zhou, Zhemin, Alikhan, Nabil-Fareed, Mohamed, Khaled, Fan, Yulei, Achtman, Mark and Tyne, William). (2019) The EnteroBase user's guide, with case studies on Salmonella transmissions, Yersinia pestis phylogeny and Escherichia core genomic diversity. Genome Research . 251678.119. doi:10.1101/gr.251678.119
Zhou, Zhemin, Alikhan, Nabil-Fareed, Mohamed, Khaled, Fan, Yulei, the Agama Study Group, and Achtman, Mark (2019) Data for The user’s guide to comparative genomics with EnteroBase. [Dataset]
Chen, Lihong, Song, Nan, Liu, Bo, Zhang, Nan, Alikhan, Nabil-Fareed, Zhou, Zhemin, Zhou, Yanyan, Zhou, Siyu, Zheng, Dandan, Chen, Mingxing, Hapeshi, Alexia, Healey, Joseph R. J., Waterfield, Nicholas R., Yang, Jian and Yang, Guowei (2019) Genome-wide identification and characterization of a superfamily of bacterial extracellular contractile injection systems. Cell Reports, 29 (2). 511-521.e2. doi:10.1016/j.celrep.2019.08.096
2018
Zhou, Zhemin, Alikhan, Nabil-Fareed, Sergeant, Martin J., Luhmann, Nina, Vaz, Cátia, Francisco, Alexandre P. , Carriço, João André and Achtman, Mark (2018) GrapeTree : visualization of core genomic relationships among 100,000 bacterial pathogens. Genome Research, 28 (10). pp. 1395-1404. doi:10.1101/gr.232397.117
Zhou, Zhemin, Lundstrøm, Inge, Tran-Dien, Alicia, Duchêne, Sebastián, Alikhan, Nabil-Fareed, Sergeant, Martin J., Langridge, Gemma, Fotakis, Anna K., Nair, Satheesh, Stenøien, Hans K., Hamre, Stian S., Casjens, Sherwood, Christophersen, Axel, Quince, Christopher , Thomson, Nicholas R., Weill, François-Xavier, Ho, Simon Y. W., Gilbert, M. Thomas P. and Achtman, Mark (2018) Pan-genome analysis of ancient and modern Salmonella enterica demonstrates genomic stability of the invasive Para C lineage for millennia. Current Biology, 28 (15). pp. 2420-2428. doi:10.1016/j.cub.2018.05.058
Zhou, Zhemin, Alikhan, Nabil-Fareed, Sergeant, Martin J., Luhmann, Nina, Vaz, Cátia, Francisco, Alexandre P., Carriço, João André and Achtman, Mark (2018) GrapeTree: visualization of core genomic relationships among 100,000 bacterial pathogens. Genome Research, 28 (9). pp. 1395-1404. doi:10.1101/gr.232397.117
Pearce, Madison E., Alikhan, Nabil-Fareed, Dallman, Timothy J., Zhou, Zhemin, Grant, Kathie and Maiden, Martin C. J. (2018) Comparative analysis of core genome MLST and SNP typing within a European Salmonella serovar Enteritidis outbreak. International Journal of Food Microbiology, 274 . pp. 1-11. doi:10.1016/j.ijfoodmicro.2018.02.023
Zhou, Zhemin, Lundstrøm, Inge, Dien, Alicia Tran, Duchêne, Sebastián, Alikhan, Nabil-Fareed, Sergeant, Martin J., Langridge, Gemma, Fotakis, Anna K., Nair, Satheesh, Stenøien, Hans K., Hamre, Stian S., Casjens, Sherwood, Quince, Christopher , Christophersen, Axel, Thomson, Nicholas R., Weill, François-Xavier, Ho, Simon, Gilbert, M. Thomas P. and Achtman, Mark (2018) Data for Millennia of genomic stability within the invasive Para C Lineage of Salmonella enterica. Archive package of additional figures, tables and data. [Dataset]
Zhou, Zhemin, Lundstrøm, Inge, Dien, Alicia Tran, Duchêne, Sebastián, Alikhan, Nabil-Fareed, Sergeant, Martin J., Langridge, Gemma, Fotakis, Anna K., Nair, Satheesh, Stenøien, Hans K., Hamre, Stian S., Casjens, Sherwood, Quince, Christopher , Christophersen, Axel, Thomson, Nicholas R., Weill, François-Xavier, Ho, Simon, Gilbert, M. Thomas P. and Achtman, Mark (2018) Data for Millennia of genomic stability within the invasive Para C Lineage of Salmonella enterica: Concoct 1. [Dataset]
Zhou, Zhemin, Lundstrøm, Inge, Dien, Alicia Tran, Duchêne, Sebastián, Alikhan, Nabil-Fareed, Sergeant, Martin J., Langridge, Gemma, Fotakis, Anna K., Nair, Satheesh, Stenøien, Hans K., Hamre, Stian S., Casjens, Sherwood, Quince, Christopher , Christophersen, Axel, Thomson, Nicholas R., Weill, François-Xavier, Ho, Simon, Gilbert, M. Thomas P. and Achtman, Mark (2018) Data for Millennia of genomic stability within the invasive Para C Lineage of Salmonella enterica: Concoct 2. [Dataset]
Zhou, Zhemin, Lundstrøm, Inge, Dien, Alicia Tran, Duchêne, Sebastián, Alikhan, Nabil-Fareed, Sergeant, Martin J., Langridge, Gemma, Fotakis, Anna K., Nair, Satheesh, Stenøien, Hans K., Hamre, Stian S., Casjens, Sherwood, Quince, Christopher , Christophersen, Axel, Thomson, Nicholas R., Weill, François-Xavier, Ho, Simon, Gilbert, M. Thomas P. and Achtman, Mark (2018) Data for Millennia of genomic stability within the invasive Para C Lineage of Salmonella enterica: Concoct 3. [Dataset]
Zhou, Zhemin, Lundstrøm, Inge, Dien, Alicia Tran, Duchêne, Sebastián, Alikhan, Nabil-Fareed, Sergeant, Martin J., Langridge, Gemma, Fotakis, Anna K., Nair, Satheesh, Stenøien, Hans K., Hamre, Stian S., Casjens, Sherwood, Quince, Christopher , Christophersen, Axel, Thomson, Nicholas R., Weill, François-Xavier, Ho, Simon, Gilbert, M. Thomas P. and Achtman, Mark (2018) Data for Millennia of genomic stability within the invasive Para C Lineage of Salmonella enterica: Concoct 4. [Dataset]
Zhou, Zhemin, Lundstrøm, Inge, Dien, Alicia Tran, Duchêne, Sebastián, Alikhan, Nabil-Fareed, Sergeant, Martin J., Langridge, Gemma, Fotakis, Anna K., Nair, Satheesh, Stenøien, Hans K., Hamre, Stian S., Casjens, Sherwood, Quince, Christopher , Christophersen, Axel, Thomson, Nicholas R., Weill, François-Xavier, Ho, Simon, Gilbert, M. Thomas P. and Achtman, Mark (2018) Data for Millennia of genomic stability within the invasive Para C Lineage of Salmonella enterica: Concoct 5. [Dataset]
Zhou, Zhemin, Lundstrøm, Inge, Dien, Alicia Tran, Duchêne, Sebastián, Alikhan, Nabil-Fareed, Sergeant, Martin J., Langridge, Gemma, Fotakis, Anna K., Nair, Satheesh, Stenøien, Hans K., Hamre, Stian S., Casjens, Sherwood, Quince, Christopher , Christophersen, Axel, Thomson, Nicholas R., Weill, François-Xavier, Ho, Simon, Gilbert, M. Thomas P. and Achtman, Mark (2018) Data for Millennia of genomic stability within the invasive Para C Lineage of Salmonella enterica: Concoct 6. [Dataset]
Zhou, Zhemin, Lundstrøm, Inge, Dien, Alicia Tran, Duchêne, Sebastián, Alikhan, Nabil-Fareed, Sergeant, Martin J., Langridge, Gemma, Fotakis, Anna K., Nair, Satheesh, Stenøien, Hans K., Hamre, Stian S., Casjens, Sherwood, Quince, Christopher , Christophersen, Axel, Thomson, Nicholas R., Weill, François-Xavier, Ho, Simon, Gilbert, M. Thomas P. and Achtman, Mark (2018) Data for Millennia of genomic stability within the invasive Para C Lineage of Salmonella enterica: Concoct 7. [Dataset]
Zhou, Zhemin, Lundstrøm, Inge, Dien, Alicia Tran, Duchêne, Sebastián, Alikhan, Nabil-Fareed, Sergeant, Martin J., Langridge, Gemma, Fotakis, Anna K., Nair, Satheesh, Stenøien, Hans K., Hamre, Stian S., Casjens, Sherwood, Quince, Christopher , Christophersen, Axel, Thomson, Nicholas R., Weill, François-Xavier, Ho, Simon, Gilbert, M. Thomas P. and Achtman, Mark (2018) Data for Millennia of genomic stability within the invasive Para C Lineage of Salmonella enterica: Concoct 8. [Dataset]
Zhou, Zhemin, Lundstrøm, Inge, Dien, Alicia Tran, Duchêne, Sebastián, Alikhan, Nabil-Fareed, Sergeant, Martin J., Langridge, Gemma, Fotakis, Anna K., Nair, Satheesh, Stenøien, Hans K., Hamre, Stian S., Casjens, Sherwood, Quince, Christopher , Christophersen, Axel, Thomson, Nicholas R., Weill, François-Xavier, Ho, Simon, Gilbert, M. Thomas P. and Achtman, Mark (2018) Data for Millennia of genomic stability within the invasive Para C Lineage of Salmonella enterica: ParaC Pan-genome 1. [Dataset]
Zhou, Zhemin, Lundstrøm, Inge, Dien, Alicia Tran, Duchêne, Sebastián, Alikhan, Nabil-Fareed, Sergeant, Martin J., Langridge, Gemma, Fotakis, Anna K., Nair, Satheesh, Stenøien, Hans K., Hamre, Stian S., Casjens, Sherwood, Quince, Christopher , Christophersen, Axel, Thomson, Nicholas R., Weill, François-Xavier, Ho, Simon, Gilbert, M. Thomas P. and Achtman, Mark (2018) Data for Millennia of genomic stability within the invasive Para C Lineage of Salmonella enterica: ParaC Pan-genome 2. [Dataset]
Zhou, Zhemin, Lundstrøm, Inge, Dien, Alicia Tran, Duchêne, Sebastián, Alikhan, Nabil-Fareed, Sergeant, Martin J., Langridge, Gemma, Fotakis, Anna K., Nair, Satheesh, Stenøien, Hans K., Hamre, Stian S., Casjens, Sherwood, Quince, Christopher , Christophersen, Axel, Thomson, Nicholas R., Weill, François-Xavier, Ho, Simon, Gilbert, M. Thomas P. and Achtman, Mark (2018) Data for Millennia of genomic stability within the invasive Para C Lineage of Salmonella enterica: ParaC Pan-genome 3. [Dataset]
Zhou, Zhemin, Lundstrøm, Inge, Dien, Alicia Tran, Duchêne, Sebastián, Alikhan, Nabil-Fareed, Sergeant, Martin J., Langridge, Gemma, Fotakis, Anna K., Nair, Satheesh, Stenøien, Hans K., Hamre, Stian S., Casjens, Sherwood, Quince, Christopher , Christophersen, Axel, Thomson, Nicholas R., Weill, François-Xavier, Ho, Simon, Gilbert, M. Thomas P. and Achtman, Mark (2018) Data for Millennia of genomic stability within the invasive Para C Lineage of Salmonella enterica: ParaC Pan-genome 4. [Dataset]
Zhou, Zhemin, Lundstrøm, Inge, Dien, Alicia Tran, Duchêne, Sebastián, Alikhan, Nabil-Fareed, Sergeant, Martin J., Langridge, Gemma, Fotakis, Anna K., Nair, Satheesh, Stenøien, Hans K., Hamre, Stian S., Casjens, Sherwood, Quince, Christopher , Christophersen, Axel, Thomson, Nicholas R., Weill, François-Xavier, Ho, Simon, Gilbert, M. Thomas P. and Achtman, Mark (2018) Data for Millennia of genomic stability within the invasive Para C Lineage of Salmonella enterica: ParaC Pan-genome 5. [Dataset]
Zhou, Zhemin, Lundstrøm, Inge, Dien, Alicia Tran, Duchêne, Sebastián, Alikhan, Nabil-Fareed, Sergeant, Martin J., Langridge, Gemma, Fotakis, Anna K., Nair, Satheesh, Stenøien, Hans K., Hamre, Stian S., Casjens, Sherwood, Quince, Christopher , Christophersen, Axel, Thomson, Nicholas R., Weill, François-Xavier, Ho, Simon, Gilbert, M. Thomas P. and Achtman, Mark (2018) Data for Millennia of genomic stability within the invasive Para C Lineage of Salmonella enterica: ParaC Pan-genome 6. [Dataset]
Zhou, Zhemin, Lundstrøm, Inge, Dien, Alicia Tran, Duchêne, Sebastián, Alikhan, Nabil-Fareed, Sergeant, Martin J., Langridge, Gemma, Fotakis, Anna K., Nair, Satheesh, Stenøien, Hans K., Hamre, Stian S., Casjens, Sherwood, Quince, Christopher , Christophersen, Axel, Thomson, Nicholas R., Weill, François-Xavier, Ho, Simon, Gilbert, M. Thomas P. and Achtman, Mark (2018) Data for Millennia of genomic stability within the invasive Para C Lineage of Salmonella enterica: ParaC Pan-genome 7. [Dataset]
Zhou, Zhemin, Lundstrøm, Inge, Dien, Alicia Tran, Duchêne, Sebastián, Alikhan, Nabil-Fareed, Sergeant, Martin J., Langridge, Gemma, Fotakis, Anna K., Nair, Satheesh, Stenøien, Hans K., Hamre, Stian S., Casjens, Sherwood, Quince, Christopher , Christophersen, Axel, Thomson, Nicholas R., Weill, François-Xavier, Ho, Simon, Gilbert, M. Thomas P. and Achtman, Mark (2018) Data for Millennia of genomic stability within the invasive Para C Lineage of Salmonella enterica: ParaC Pan-genome 8. [Dataset]
Zhou, Zhemin, Lundstrøm, Inge, Dien, Alicia Tran, Duchêne, Sebastián, Alikhan, Nabil-Fareed, Sergeant, Martin J., Langridge, Gemma, Fotakis, Anna K., Nair, Satheesh, Stenøien, Hans K., Hamre, Stian S., Casjens, Sherwood, Quince, Christopher , Christophersen, Axel, Thomson, Nicholas R., Weill, François-Xavier, Ho, Simon, Gilbert, M. Thomas P. and Achtman, Mark (2018) Data for Millennia of genomic stability within the invasive Para C Lineage of Salmonella enterica: ParaC genome SNPs 1. [Dataset]
Zhou, Zhemin, Lundstrøm, Inge, Dien, Alicia Tran, Duchêne, Sebastián, Alikhan, Nabil-Fareed, Sergeant, Martin J., Langridge, Gemma, Fotakis, Anna K., Nair, Satheesh, Stenøien, Hans K., Hamre, Stian S., Casjens, Sherwood, Quince, Christopher , Christophersen, Axel, Thomson, Nicholas R., Weill, François-Xavier, Ho, Simon, Gilbert, M. Thomas P. and Achtman, Mark (2018) Data for Millennia of genomic stability within the invasive Para C Lineage of Salmonella enterica: ParaC genome SNPs 2. [Dataset]
Zhou, Zhemin, Lundstrøm, Inge, Dien, Alicia Tran, Duchêne, Sebastián, Alikhan, Nabil-Fareed, Sergeant, Martin J., Langridge, Gemma, Fotakis, Anna K., Nair, Satheesh, Stenøien, Hans K., Hamre, Stian S., Casjens, Sherwood, Quince, Christopher , Christophersen, Axel, Thomson, Nicholas R., Weill, François-Xavier, Ho, Simon, Gilbert, M. Thomas P. and Achtman, Mark (2018) Data for Millennia of genomic stability within the invasive Para C Lineage of Salmonella enterica: ParaC genome SNPs 3. [Dataset]
Zhou, Zhemin, Lundstrøm, Inge, Dien, Alicia Tran, Duchêne, Sebastián, Alikhan, Nabil-Fareed, Sergeant, Martin J., Langridge, Gemma, Fotakis, Anna K., Nair, Satheesh, Stenøien, Hans K., Hamre, Stian S., Casjens, Sherwood, Quince, Christopher , Christophersen, Axel, Thomson, Nicholas R., Weill, François-Xavier, Ho, Simon, Gilbert, M. Thomas P. and Achtman, Mark (2018) Data for Millennia of genomic stability within the invasive Para C Lineage of Salmonella enterica: ParaC genome SNPs 4. [Dataset]
Zhou, Zhemin, Lundstrøm, Inge, Dien, Alicia Tran, Duchêne, Sebastián, Alikhan, Nabil-Fareed, Sergeant, Martin J., Langridge, Gemma, Fotakis, Anna K., Nair, Satheesh, Stenøien, Hans K., Hamre, Stian S., Casjens, Sherwood, Quince, Christopher , Christophersen, Axel, Thomson, Nicholas R., Weill, François-Xavier, Ho, Simon, Gilbert, M. Thomas P. and Achtman, Mark (2018) Data for Millennia of genomic stability within the invasive Para C Lineage of Salmonella enterica: Salmonella supertree 1. [Dataset]
Zhou, Zhemin, Lundstrøm, Inge, Dien, Alicia Tran, Duchêne, Sebastián, Alikhan, Nabil-Fareed, Sergeant, Martin J., Langridge, Gemma, Fotakis, Anna K., Nair, Satheesh, Stenøien, Hans K., Hamre, Stian S., Casjens, Sherwood, Quince, Christopher , Christophersen, Axel, Thomson, Nicholas R., Weill, François-Xavier, Ho, Simon, Gilbert, M. Thomas P. and Achtman, Mark (2018) Data for Millennia of genomic stability within the invasive Para C Lineage of Salmonella enterica: Salmonella supertree 2. [Dataset]
Zhou, Zhemin, Lundstrøm, Inge, Dien, Alicia Tran, Duchêne, Sebastián, Alikhan, Nabil-Fareed, Sergeant, Martin J., Langridge, Gemma, Fotakis, Anna K., Nair, Satheesh, Stenøien, Hans K., Hamre, Stian S., Casjens, Sherwood, Quince, Christopher , Christophersen, Axel, Thomson, Nicholas R., Weill, François-Xavier, Ho, Simon, Gilbert, M. Thomas P. and Achtman, Mark (2018) Data for Millennia of genomic stability within the invasive Para C Lineage of Salmonella enterica: Salmonella supertree 3. [Dataset]
Zhou, Zhemin, Lundstrøm, Inge, Dien, Alicia Tran, Duchêne, Sebastián, Alikhan, Nabil-Fareed, Sergeant, Martin J., Langridge, Gemma, Fotakis, Anna K., Nair, Satheesh, Stenøien, Hans K., Hamre, Stian S., Casjens, Sherwood, Quince, Christopher , Christophersen, Axel, Thomson, Nicholas R., Weill, François-Xavier, Ho, Simon, Gilbert, M. Thomas P. and Achtman, Mark (2018) Data for Millennia of genomic stability within the invasive Para C Lineage of Salmonella enterica: ancestral reconstruction 1. [Dataset]
Zhou, Zhemin, Lundstrøm, Inge, Dien, Alicia Tran, Duchêne, Sebastián, Alikhan, Nabil-Fareed, Sergeant, Martin J., Langridge, Gemma, Fotakis, Anna K., Nair, Satheesh, Stenøien, Hans K., Hamre, Stian S., Casjens, Sherwood, Quince, Christopher , Christophersen, Axel, Thomson, Nicholas R., Weill, François-Xavier, Ho, Simon, Gilbert, M. Thomas P. and Achtman, Mark (2018) Data for Millennia of genomic stability within the invasive Para C Lineage of Salmonella enterica: ancestral reconstruction 2. [Dataset]
Zhou, Zhemin, Lundstrøm, Inge, Dien, Alicia Tran, Duchêne, Sebastián, Alikhan, Nabil-Fareed, Sergeant, Martin J., Langridge, Gemma, Fotakis, Anna K., Nair, Satheesh, Stenøien, Hans K., Hamre, Stian S., Casjens, Sherwood, Quince, Christopher , Christophersen, Axel, Thomson, Nicholas R., Weill, François-Xavier, Ho, Simon, Gilbert, M. Thomas P. and Achtman, Mark (2018) Data for Millennia of genomic stability within the invasive Para C Lineage of Salmonella enterica: date estimation 1. [Dataset]
Zhou, Zhemin, Lundstrøm, Inge, Dien, Alicia Tran, Duchêne, Sebastián, Alikhan, Nabil-Fareed, Sergeant, Martin J., Langridge, Gemma, Fotakis, Anna K., Nair, Satheesh, Stenøien, Hans K., Hamre, Stian S., Casjens, Sherwood, Quince, Christopher , Christophersen, Axel, Thomson, Nicholas R., Weill, François-Xavier, Ho, Simon, Gilbert, M. Thomas P. and Achtman, Mark (2018) Data for Millennia of genomic stability within the invasive Para C Lineage of Salmonella enterica: date estimation 2. [Dataset]
Zhou, Zhemin, Lundstrøm, Inge, Dien, Alicia Tran, Duchêne, Sebastián, Alikhan, Nabil-Fareed, Sergeant, Martin J., Langridge, Gemma, Fotakis, Anna K., Nair, Satheesh, Stenøien, Hans K., Hamre, Stian S., Casjens, Sherwood, Quince, Christopher , Christophersen, Axel, Thomson, Nicholas R., Weill, François-Xavier, Ho, Simon, Gilbert, M. Thomas P. and Achtman, Mark (2018) Data for Millennia of genomic stability within the invasive Para C Lineage of Salmonella enterica: date estimation 3. [Dataset]
Zhou, Zhemin, Lundstrøm, Inge, Dien, Alicia Tran, Duchêne, Sebastián, Alikhan, Nabil-Fareed, Sergeant, Martin J., Langridge, Gemma, Fotakis, Anna K., Nair, Satheesh, Stenøien, Hans K., Hamre, Stian S., Casjens, Sherwood, Quince, Christopher , Christophersen, Axel, Thomson, Nicholas R., Weill, François-Xavier, Ho, Simon, Gilbert, M. Thomas P. and Achtman, Mark (2018) Data for Millennia of genomic stability within the invasive Para C Lineage of Salmonella enterica: date estimation 4. [Dataset]
Zhou, Zhemin, Lundstrøm, Inge, Dien, Alicia Tran, Duchêne, Sebastián, Alikhan, Nabil-Fareed, Sergeant, Martin J., Langridge, Gemma, Fotakis, Anna K., Nair, Satheesh, Stenøien, Hans K., Hamre, Stian S., Casjens, Sherwood, Quince, Christopher , Christophersen, Axel, Thomson, Nicholas R., Weill, François-Xavier, Ho, Simon, Gilbert, M. Thomas P. and Achtman, Mark (2018) Data for Millennia of genomic stability within the invasive Para C Lineage of Salmonella enterica: workflow. [Dataset]
Zhou, Zhemin, Luhmann, Nina, Alikhan, Nabil-Fareed, Quince, Christopher and Achtman, Mark (2018) Accurate reconstruction of microbial strains from metagenomic sequencing using representative reference genomes. In: RECOMB 2018 : International Conference on Research in Computational Molecular Biology, Paris, 21-24 Apr 2018. Published in: Lecture Notes in Computer Science, 10812 pp. 225-240. ISBN 9783319899299. ISSN 0302-9743. doi:10.1007/978-3-319-89929-9_15
Alikhan, Nabil-Fareed, Zhou, Zhemin, Sergeant, Martin J. and Achtman, Mark (2018) A genomic overview of the population structure of Salmonella. PLoS Genetics, 14 (4). e1007261. doi:10.1371/journal.pgen.1007261
2017
Zhou, Zhemin, Alikhan, Nabil-Fareed, Sergeant, Martin J., Luhmann, Nina, Vaz, Catia, Francisco, Alexandre P., Carrico, Joao Andre and Achtman, Mark (2017) GrapeTree : visualization of core genomic relationships among 100,000 bacterial pathogens. Working Paper. BioRxiv: Cold Spring Harbour.
Zhou, Zhemin, Luhmann, Nina, Alikhan, Nabil-Fareed, Quince, Christopher and Achtman, Mark (2017) Accurate reconstruction of microbial strains using representative reference genomes. Working Paper. BioRxiv: Cold Spring Harbour.
Zhou, Zhemin, Lundstrøm, Inge, Tran-Dien, Alicia, Duchêne, Sebastián, Alikhan, Nabil-Fareed, Sergeant, Martin J., Langridge, Gemma, Fotakis, Anna K., Nair, Satheesh, Stenøien, Hans K., Hamre, Stian S., Casjens, Sherwood, Christophersen, Axel, Quince, Christopher, Thomson, Nicholas R., Weill, François-Xavier, Ho, Simon Y. W., Gilbert, M. Thomas P. and Achtman, Mark (2017) Millennia of genomic stability within the invasive Para C Lineage of Salmonella enterica. Working Paper. BioRxiv: Cold Spring Harbour.
2016
Connor, Thomas R., Owen, Sian V., Langridge, Gemma, Connell, Steve, Nair, Satheesh, Reuter, Sandra, Dallman, Timothy J., Corander, Jukka, Tabing, Kristine C., Le Hello, Simon et al.
(2016)
What’s in a name? Species-wide whole-genome sequencing resolves invasive and noninvasive lineages of salmonella enterica serotype Paratyphi B.
mBio, 7
(4).
e00527-16.
doi:10.1128/mBio.00527-16
2015
Achtman, Mark, Zhou, Zhemin and Didelot, Xavier (2015) Formal comment to Pettengill : the time to most recent common ancestor does not (usually) approximate the date of divergence. PLoS One, 10 (8). pp. 1-11. e0134435. doi:10.1371/journal.pone.0134435
Kay, Gemma L., Sergeant, Martin J., Zhou, Zhemin, Chan, Jacqueline, Millard, Andrew D., Quick, Joshua, Szikossy, Ildikó, Pap, Ildikó, Spigelman, Mark, Loman, Nicholas J., Achtman, Mark, Donoghue, Helen D. and Pallen, Mark J. (2015) Eighteenth-century genomes show that mixed infections were common at time of peak tuberculosis in Europe. Nature Communications, Volume 6 . pp. 1-9. Article number 6717. doi:10.1038/ncomms7717
Didelot, Xavier, Pang, Bo, Zhou, Zhemin, McCann, Angela, Ni, Peixiang, Li, Dongfang, Achtman, Mark and Kan, Biao (2015) The role of China in the global spread of the current cholera pandemic. PLoS Genetics, Volume 11 (Number 3). pp. 1-14. Article number e1005072. doi:10.1371/journal.pgen.1005072
2014
Achtman, Mark and Zhou, Zhemin (2014) Distinct genealogies for plasmids and chromosome. PLoS Genetics, Volume 10 (Number 12). Article number e1004874. doi:10.1371/journal.pgen.1004874
Zhou, Zhemin, McCann, A., Weill, F. -X., Blin, C., Nair, S., Wain, J., Dougan, G. and Achtman, Mark (2014) 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, Volume 111 (Number 33). pp. 12199-12204. doi:10.1073/pnas.1411012111
Zhang, Cuicai, Pang, Bo, Zhou, Zhemin, Wang, Haiyin, Zhou, Haijian, Lu, Xin, Du, Pengcheng, Zhang, Lijuan, Li, Jie, Cui, Zhigang, Chen, Chen, Stokes, H. W. and Kan, Biao (2014) The purifying trend in the chromosomal integron in Vibrio cholerae strains during the seventh pandemic. Infection, Genetics and Evolution , Volume 26 . pp. 241-249. doi:10.1016/j.meegid.2014.05.019
Savin, Cyril, Martin, Liliane, Bouchier, Christiane, Filali, Sofia, Chenau, Jérôme, Zhou, Zhemin, Becher, François, Fukushima, Hiroshi, Thomson, Nicholas R., Scholz, Holger C. and Carniel, Elisabeth (2014) The Yersinia pseudotuberculosis complex : characterization and delineation of a new species, Yersinia wautersii. International Journal of Medical Microbiology, 304 (3-4). pp. 452-463. doi:10.1016/j.ijmm.2014.02.002
2013
Jin, Dong, Chen, Chen , Li, Lianqing, Lu, Shan, Li, Zhenjun, Zhou, Zhemin, Jing, Huaiqi, Xu, Yanmei, Du, Pengcheng, Wang, Haiyin, Xiong, Yanwen, Zheng, Han, Bai, Xuemei, Sun, Hui, Wang, Lei , Le, Changyun, Gottschalk, Marcelo and Xu, Jianguo (2013) Dynamics of fecal microbial communities in children with diarrhea of unknown etiology and genomic analysis of associated Streptococcus lutetiensis. BMC Microbiology, 13 (141). doi:10.1186/1471-2180-13-141
Zhou, Zhemin, McCann, Angela, Litrup, Eva, Murphy, Ronan, Cormican, Martin, Fanning, Seamus, Brown, Derek, Guttman, David S., Brisse, Sylvain and Achtman, Mark (2013) Neutral genomic microevolution of a recently emerged pathogen, salmonella enterica serovar agona. PLoS Genetics, 9 (4). e1003471. doi:10.1371/journal.pgen.1003471
2012
Achtman, Mark, Wain, John, Weill, François-Xavier, Nair, Satheesh, Zhou, Zhemin, Sangal, Vartul, Krauland, Mary G., Hale, James L., Harbottle, Heather, Uesbeck, Alexandra, Dougan, Gordon, Harrison, Lee H. and Brisse, Sylvain (2012) Multilocus sequence typing as a replacement for serotyping in salmonella enterica. PLoS Pathogens, Volume 8 (Number 6). Article number e1002776. doi:10.1371/journal.ppat.1002776
Liu, Wei, Fang, Liurong, Li, Mao, Li, Sha, Guo, Shaohua, Luo, Rui, Feng, Zhixin, Li, Bin, Zhou, Zhemin, Shao, Guoqing, Chen, Huanchun and Xiao, Shaobo (2012) Comparative genomics of mycoplasma : analysis of conserved essential genes and diversity of the pan-genome. PLoS One, 7 (4). e35698. doi:10.1371/journal.pone.0035698
Xiong, Jie, Lu, Xingyi, Zhou, Zhemin, Chang, Yue, Yuan, Dongxia, Tian, Miao, Zhou, Zhigang, Wang, Lei, Fu, Chengjie, Orias, Eduardo and Miao, Wei (2012) Transcriptome analysis of the model protozoan, tetrahymena thermophila, using deep RNA sequencing. PLoS One, 7 (2). e30630. doi:10.1371/journal.pone.0030630
Xiong, Yanwen, Wang, Ping, Lan, Ruiting, Ye, Changyun, Wang, Hua, Ren, Jun, Jing, Huaiqi, Wang, Yiting, Zhou, Zhemin, Bai, Xuemei, Cui, Zhigang, Luo, Xia, Zhao, Ailan, Wang, Yan, Zhang, Shaomin, Sun, Hui, Wang, Lei and Xu, Jianguo (2012) A novel escherichia coli O157:H7 clone causing a major hemolytic uremic syndrome outbreak in China. PLoS One, 7 (4). e36144. doi:10.1371/journal.pone.0036144
Liu, B., Hu, B., Zhou, Zhemin, Guo, D., Guo, X., Ding, P., Feng, L. and Wang, L. (2012) A novel non-homologous recombination-mediated mechanism for Escherichia coli unilateral flagellar phase variation. Nucleic Acids Research, 40 (10). pp. 4530-4538. doi:10.1093/nar/gks040
This list was generated on Thu Feb 25 05:31:13 2021 GMT.