Research Projects

Wellcome Trust Investigator Award - Deep evolutionary history of bacterial pathogens

with Mark Achtman, Christopher Quince, Zhemin Zhou, Nina Luhmann, Sandra Bedarida, William Tyne, Jane Charlesworth

Funded by: Wellcome Trust, 01-09-2016 - 31-08-2021

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EnteroBase: A Powerful, User-Friendly Online Resource for Analyzing and Visualizing Genomic Variation within Escherichia coli and Salmonella enterica

with Mark Achtman, Khaled Mohamed, Yulei Fan, Andrew Millard, Funded by: BBSRC, 01-04-2014 - 31-10-2019

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Recent Publications

• Zhou, Zhemin, Alikhan, Nabil-Fareed, Mohamed, Khaled, Agama Study Group, Achtman, Mark. 2019. The user’s guide to comparative genomics with EnteroBase. Three case studies: micro-clades within Salmonella enterica serovar Agama, ancient and modern populations of Yersinia pestis, and core genomic diversity of all Escherichia. Preprint bioRxiv.
• Zhou, Zhemin, Alikhan, Nabil-Fareed, Sergeant, Martin J., Luhmann, Nina, Vaz, Cátia, Francisco, Alexandre P., Carriço, João André, Achtman, Mark. 2018. GrapeTree : visualization of core genomic relationships among 100,000 bacterial pathogens. Genome Research, 28 (10), pp. 1395-1404
• Zhou, Zhemin, Lundstrà¸m, Inge, Tran-Dien, Alicia, Duchàªne, Sebastián, Alikhan, Nabil-Fareed, Sergeant, Martin J., Langridge, Gemma, Fotakis, Anna K., Nair, Satheesh, Stenà¸ien, 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., 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
• Zhou, Zhemin, Luhmann, Nina, Alikhan, Nabil-Fareed, Quince, Christopher, Achtman, Mark. 2018. Accurate reconstruction of microbial strains from metagenomic sequencing using representative reference genomes. RECOMB 2018 : International Conference on Research in Computational Molecular Biology, Paris, 21-24 Apr 2018, Published in Lecture Notes in Computer Science, pp. 225-240
• Alikhan, Nabil-Fareed, Zhou, Zhemin, Sergeant, Martin J., Achtman, Mark. 2018. A genomic overview of the population structure of Salmonella. PLoS Genetics, 14 (4)
• Achtman, Mark. 2016. How old are bacterial pathogens?. Proceeding of the Royal Society B, 286 (1836)
• 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, Fookes, Maria, Doublet, Benoà®t, Zhou, Zhemin, Feltwell, Theresa, Ellington, Matthew J., Herrera, Silvia, Gilmour, Matthew, Cloeckaert, Axel, Achtman, Mark, Parkhill, Julian, Wain, John, De Pinna, Elizabeth, Weill, François-Xavier, Peters, Tansy, Thomson, Nick. 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), pp. e00527-16
• Earl, Joshua. P.l., de Vries, Stefan, P.W., Powell, Evan, Schultz, Matthew P., Hermans, Peter, W.M., Hill, Darryl, J., Zhou, Zhemin, Constantinidou, Chrystala, I., Hu, Fen Z., Bootsma, Hester, J., Ehrlich, Garth, D. (2016) Comparative Genomic Analyses of the Moraxella catarrhalis Serosensitive and Seroresistant Lineages Demonstrate Their Independent Evolution, Genome Biology and Evolution, Volume 8, Issue 4, 1 April 2016, Pages 955–974
• Kay, Gemma L., Sergeant, Martin J., Zhou, Zhemin, Chan, Jacqueline, Millard, Andrew D., Quick, Joshua, Szikossy, Ildikó, Pap, Ildikó, 1951-‏ , 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. ISSN 2041-1723
• 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. ISSN 1553-7390
• Kay, Gemma L., Millard, Andrew D., Sergeant, Martin J., Midzi, Nicholas, Gwisai, Reggis, Mduluza, Takafira, Ivens, Alasdair, Nausch, Norman, Mutapi, Francisca and Pallen, Mark J.. (2015) Differences in the faecal microbiome in Schistosoma haematobium infected children vs. uninfected children. PLoS Neglected Tropical Diseases, 9 (6). e0003861. ISSN 1935-2727
• Kevei, Zoltan, King, Robert C., Mohareb, Fady, Sergeant, Martin J., Awan, Sajjad Zahoor and Thompson, Andrew J.. (2015) Resequencing at >=40-fold depth of the parental genomes of a Solanum Lycopersicum x S. pimpinellifolium recombinant inbred line population and characterization of frame-shift indels that are highly likely to perturb protein function. G3 : genes, genomes, genetics, 5 (5). pp. 971-981. ISSN 2160-1836
• Kay, Gemma L., Sergeant, Martin J., Zhou, Zhemin, Chan, Jacqueline, Millard, Andrew D., Quick, Joshua, Szikossy, Ildikó, Pap, Ildikó, 1951-‏ , 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. ISSN 2041-1723

View Mark Achtman Publications on the University of Warwick Publication service.

View Zhemin Zhou Publications on the University of Warwick Publication service.

Professor Mark Achtman
Professor in Bacterial Population Genetics

 

Dr. Zhemin Zhou 
Senior Research Fellow in Microbial Bioinformatics

 

Dr. Nina Luhmann 
Research Fellow in Computational Biology

 

Dr. Sandra Bedarida
Research Fellow in Ancient DNA of Microbial Pathogens

 

Dr. William Tyne

Research Associate

 

Dr. Khaled Mohamed

Research Fellow, Software development for EnteroBase

 

Dr. Yulei Fan
Research Fellow, Software development for EnteroBase

 

Dr. Jane Charlesworth
Senior Research Fellow in Pathogen Evolution