A genomic overview of the population structure of Salmonella

por Alikhan, Nabil-Fareed, Zhou, Zhemin, Sergeant, Martin J., Achtman, Mark
Publicado en PLoS Genet (2018)

The EnteroBase user's guide, with case studies on Salmonella transmissions, Yersinia pestis phylogeny, and Escherichia core genomic diversity

por Zhou, Zhemin, Alikhan, Nabil-Fareed, Mohamed, Khaled, Fan, Yulei, Achtman, Mark
Publicado en Genome Res (2020)

ICTV Virus Taxonomy Profile: Herelleviridae

por Barylski, Jakub, Kropinski, Andrew M., Alikhan, Nabil-Fareed, Adriaenssens, Evelien M.
Publicado en J Gen Virol (2020)

BLAST Ring Image Generator (BRIG): simple prokaryote genome comparisons

por Alikhan, Nabil-Fareed, Petty, Nicola K, Ben Zakour, Nouri L, Beatson, Scott A
Publicado 2011

Comparison of classical multi-locus sequence typing software for next-generation sequencing data

por Page, Andrew J., Alikhan, Nabil-Fareed, Carleton, Heather A., Seemann, Torsten, Keane, Jacqueline A., Katz, Lee S.
Publicado en Microb Genom (2017)

Comparative analysis of core genome MLST and SNP typing within a European Salmonella serovar Enteritidis outbreak

por Pearce, Madison E., Alikhan, Nabil-Fareed, Dallman, Timothy J., Zhou, Zhemin, Grant, Kathie, Maiden, Martin C.J.
Publicado en Int J Food Microbiol (2018)

GrapeTree: visualization of core genomic relationships among 100,000 bacterial pathogens

por Zhou, Zhemin, Alikhan, Nabil-Fareed, Sergeant, Martin J., Luhmann, Nina, Vaz, Cátia, Francisco, Alexandre P., Carriço, João André, Achtman, Mark
Publicado en Genome Res (2018)

Evolution of Salmonella enterica serotype Typhimurium driven by anthropogenic selection and niche adaptation

por Bawn, Matt, Alikhan, Nabil-Fareed, Thilliez, Gaëtan, Kirkwood, Mark, Wheeler, Nicole E., Petrovska, Liljana, Dallman, Timothy J., Adriaenssens, Evelien M., Hall, Neil, Kingsley, Robert A.
Publicado en PLoS Genet (2020)

Genomic diversity of Escherichia coli from healthy children in rural Gambia

por Foster-Nyarko, Ebenezer, Alikhan, Nabil-Fareed, Ikumapayi, Usman N., Sarwar, Golam, Okoi, Catherine, Tientcheu, Peggy-Estelle Maguiagueu, Defernez, Marianne, O’Grady, Justin, Antonio, Martin, Pallen, Mark J.
Publicado en PeerJ (2021)

Genomic diversity of Escherichia coli isolates from backyard chickens and guinea fowl in the Gambia

por Foster-Nyarko, Ebenezer, Alikhan, Nabil-Fareed, Ravi, Anuradha, Thomson, Nicholas M., Jarju, Sheikh, Kwambana-Adams, Brenda A., Secka, Arss, O’Grady, Justin, Antonio, Martin, Pallen, Mark John
Publicado en Microb Genom (2020)

Genomic diversity of Escherichia coli isolates from non-human primates in the Gambia

por Foster-Nyarko, Ebenezer, Alikhan, Nabil-Fareed, Ravi, Anuradha, Thilliez, Gaëtan, Thomson, Nicholas M., Baker, David, Kay, Gemma, Cramer, Jennifer D., O’Grady, Justin, Antonio, Martin, Pallen, Mark J.
Publicado en Microb Genom (2020)

Genome-wide Identification and Characterization of a Superfamily of Bacterial Extracellular Contractile Injection Systems

por 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, Waterfield, Nicholas R., Yang, Jian, Yang, Guowei
Publicado en Cell Rep (2019)

Mechanisms Involved in Acquisition of bla(NDM) Genes by IncA/C(2) and IncFII(Y) Plasmids

por Wailan, Alexander M., Sidjabat, Hanna E., Yam, Wan Keat, Alikhan, Nabil-Fareed, Petty, Nicola K., Sartor, Anna L., Williamson, Deborah A., Forde, Brian M., Schembri, Mark A., Beatson, Scott A., Paterson, David L., Walsh, Timothy R., Partridge, Sally R.
Publicado en Antimicrob Agents Chemother (2016)

Emergence of Resistance to Fluoroquinolones and Third-Generation Cephalosporins in Salmonella Typhi in Lahore, Pakistan

por Rasheed, Farhan, Saeed, Muhammad, Alikhan, Nabil-Fareed, Baker, David, Khurshid, Mohsin, Ainsworth, Emma V., Turner, A. Keith, Imran, Ambereen Anwar, Rasool, Muhammad Hidayat, Saqalein, Muhammad, Nisar, Muhammad Atif, Fayyaz ur Rehman, Muhammad, Wain, John, Yasir, Muhammad, Langridge, Gemma C., Ikram, Aamer
Publicado en Microorganisms (2020)

Extensive microbial diversity within the chicken gut microbiome revealed by metagenomics and culture

por Gilroy, Rachel, Ravi, Anuradha, Getino, Maria, Pursley, Isabella, Horton, Daniel L., Alikhan, Nabil-Fareed, Baker, Dave, Gharbi, Karim, Hall, Neil, Watson, Mick, Adriaenssens, Evelien M., Foster-Nyarko, Ebenezer, Jarju, Sheikh, Secka, Arss, Antonio, Martin, Oren, Aharon, Chaudhuri, Roy R., La Ragione, Roberto, Hildebrand, Falk, Pallen, Mark J.
Publicado en PeerJ (2021)

Genome Sequence of the Emerging Pathogen Aeromonas caviae

por Beatson, Scott A., das Graças de Luna, Maria, Bachmann, Nathan L., Alikhan, Nabil-Fareed, Hanks, Kirstin R., Sullivan, Mitchell J., Wee, Bryan A., Freitas-Almeida, Angela C., dos Santos, Paula A., de Melo, Janyne T. B., Squire, Derrick J. P., Cunningham, Adam F., Fitzgerald, J. Ross, Henderson, Ian R.
Publicado 2011

Pan-genome Analysis of Ancient and Modern Salmonella enterica Demonstrates Genomic Stability of the Invasive Para C Lineage for Millennia

por 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., Achtman, Mark
Publicado en Curr Biol (2018)

Genomic diversity of Salmonella enterica -The UoWUCC 10K genomes project

por Achtman, Mark, Zhou, Zhemin, Alikhan, Nabil-Fareed, Tyne, William, Parkhill, Julian, Cormican, Martin, Chiou, Chien-Shun, Torpdahl, Mia, Litrup, Eva, Prendergast, Deirdre M., Moore, John E., Strain, Sam, Kornschober, Christian, Meinersmann, Richard, Uesbeck, Alexandra, Weill, François-Xavier, Coffey, Aidan, Andrews-Polymenis, Helene, Curtiss 3rd, Roy, Fanning, Séamus
Publicado en Wellcome Open Res (2021)

Molecular Analysis of Asymptomatic Bacteriuria Escherichia coli Strain VR50 Reveals Adaptation to the Urinary Tract by Gene Acquisition

por Beatson, Scott A., Ben Zakour, Nouri L., Totsika, Makrina, Forde, Brian M., Watts, Rebecca E., Mabbett, Amanda N., Szubert, Jan M., Sarkar, Sohinee, Phan, Minh-Duy, Peters, Kate M., Petty, Nicola K., Alikhan, Nabil-Fareed, Sullivan, Mitchell J., Gawthorne, Jayde A., Stanton-Cook, Mitchell, Nhu, Nguyen Thi Khanh, Chong, Teik Min, Yin, Wai-Fong, Chan, Kok-Gan, Hancock, Viktoria, Ussery, David W., Ulett, Glen C., Schembri, Mark A.
Publicado en Infect Immun (2015)

CoronaHiT: high-throughput sequencing of SARS-CoV-2 genomes

por Baker, Dave J., Aydin, Alp, Le-Viet, Thanh, Kay, Gemma L., Rudder, Steven, de Oliveira Martins, Leonardo, Tedim, Ana P., Kolyva, Anastasia, Diaz, Maria, Alikhan, Nabil-Fareed, Meadows, Lizzie, Bell, Andrew, Gutierrez, Ana Victoria, Trotter, Alexander J., Thomson, Nicholas M., Gilroy, Rachel, Griffith, Luke, Adriaenssens, Evelien M., Stanley, Rachael, Charles, Ian G., Elumogo, Ngozi, Wain, John, Prakash, Reenesh, Meader, Emma, Mather, Alison E., Webber, Mark A., Dervisevic, Samir, Page, Andrew J., O’Grady, Justin
Publicado en Genome Med (2021)