Pallen, Mark J. ORCID: https://orcid.org/0000-0003-1807-3657, Rodriguez-R, Luis M. and Alikhan, Nabil-Fareed
(2022)
Naming the unnamed: over 65,000 Candidatus names for unnamed Archaea and Bacteria in the Genome Taxonomy Database.
International Journal of Systematic and Evolutionary Microbiology, 72 (9).
ISSN 1466-5026
Merhi, Georgi, Trotter, Alexander J., de Olivera Martins, Leonardo, Koweyes, Jad, Le-Viet, Thanh, Naja, Hala Abou, Al Buaini, Mona, Prosolek, Sophie J., Alikhan, Nabil-Fareed, Lott, Martin, Tohmeh, Tatiana, Badran, Bassam, Jupp, Orla, Gardner, Sarah, Felgate, Matthew, Makin, Kate, Wilkinson, Janine, Stanley, Rachael, Sesay, Abdul K., Webber, Mark, Davidson, Rosemary ORCID: https://orcid.org/0000-0002-6624-4011, Ghosn, Nada, Pallen, Mark
ORCID: https://orcid.org/0000-0003-1807-3657, Hasan, Hamad, Page, Andrew J. and Tokajian, Sima
(2022)
Replacement of the Alpha variant of SARS-CoV-2 by the Delta variant in Lebanon between April and June 2021.
Microbial Genomics, 8 (7).
ISSN 2057-5858
Kumar, Bhaskar ORCID: https://orcid.org/0000-0001-5705-1384, Lam, Stephen
ORCID: https://orcid.org/0000-0003-1040-938X, Adam, Mina, Gilroy, Rachel and Pallen, Mark J.
ORCID: https://orcid.org/0000-0003-1807-3657
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The oesophageal microbiome and cancer: Hope or hype?
Trends in Microbiology, 30 (4).
pp. 322-329.
ISSN 0966-842X
Gilroy, Rachel, Leng, Joy, Ravi, Anuradha, Adriaenssens, Evelien M., Oren, Aharon, Baker, Dave, La Ragione, Roberto M., Proudman, Christopher and Pallen, Mark J. ORCID: https://orcid.org/0000-0003-1807-3657
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Metagenomic investigation of the equine faecal microbiome reveals extensive taxonomic diversity.
PeerJ, 10.
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Thomson, Nicholas M., Gilroy, Rachel, Getino, Maria, Foster-Nyarko, Ebenezer, Van Vliet, Arnoud H. M., La Ragione, Roberto M. and Pallen, Mark J. ORCID: https://orcid.org/0000-0003-1807-3657
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Remarkable genomic diversity among Escherichia isolates recovered from healthy chickens.
PeerJ, 10.
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Crossfield, Matthew, Gilroy, Rachel, Ravi, Anuradha, Baker, David, La Ragione, Roberto M. and Pallen, Mark J. ORCID: https://orcid.org/0000-0003-1807-3657
(2022)
Archaeal and bacterial metagenome-assembled genome sequences derived from pig feces.
Microbiology Resource Announcements, 11 (1).
Callanan, Julie, Stockdale, Stephen R., Adriaenssens, Evelien M., Kuhn, Jens H., Rumnieks, Janis, Pallen, Mark J. ORCID: https://orcid.org/0000-0003-1807-3657, Shkoporov, Andrey N., Draper, Lorraine A., Ross, R. Paul and Hill, Colin
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Leviviricetes: expanding and restructuring the taxonomy of bacteria-infecting single-stranded RNA viruses.
Microbial Genomics, 7 (11).
ISSN 2057-5858
Stubberfield, Emma, Sheldon, Jonathan, Card, Roderick M., Abuoun, Manal, Rogers, Jon, Williamson, Susanna, Kay, Gemma L., Pallen, Mark J. ORCID: https://orcid.org/0000-0003-1807-3657 and Anjum, Muna F.
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Whole-genome sequencing of Brachyspira hyodysenteriae isolates from England and Wales reveals similarities to European isolates and mutations associated with reduced sensitivity to antimicrobials.
Frontiers in Microbiology, 12.
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Gilroy, Rachel, Ravi, Anuradha, Getino, Maria, Pursley, Isabella, Horton, Daniel L., Alikhan, Nabil-Fareed, Baker, Dave, Gharbi, Karim, Hall, Neil ORCID: https://orcid.org/0000-0003-2808-0009, Watson, Mick, Adriaenssens, Evelien M., Foster-Nyarko, Ebenezer, Jarju, Sheikh, Secka, Arss, Antonio, Martin, Oren, Aharon, Chaudhuri, Roy R., La Ragione, Roberto, Hildebrand, Falk and Pallen, Mark J.
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Extensive microbial diversity within the chicken gut microbiome revealed by metagenomics and culture.
PeerJ, 9.
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Pallen, Mark J. ORCID: https://orcid.org/0000-0003-1807-3657, Telatin, Andrea and Oren, Aharon
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The next million names for Archaea and Bacteria.
Trends in Microbiology, 29 (4).
pp. 289-298.
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Foster-Nyarko, Ebenezer, Alikhan, Nabil-Fareed, Ikumapayi, Usman N, Sarwar, Golam, Okoi, Catherine, Tientcheu, Peggy-Estelle Maguiagueu, Defernez, Marianne, O'Grady, Justin, Antonio, Martin and Pallen, Mark J ORCID: https://orcid.org/0000-0003-1807-3657
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Genomic diversity of Escherichia coli from healthy children in rural Gambia.
PeerJ, 9.
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Foster-Nyarko, Ebenezer, Alikhan, Nabil-Fareed, Ravi, Anuradha, Thomson, Nicholas M., Jarju, Sheikh, Kwambana-Adams, Brenda A., Secka, Arss, O'Grady, Justin, Antonio, Martin and Pallen, Mark John ORCID: https://orcid.org/0000-0003-1807-3657
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Genomic diversity of Escherichia coli isolates from backyard chickens and guinea fowl in the Gambia.
Microbial Genomics, 7 (1).
ISSN 2057-5858
Thomson, Nicholas M., Zhang, Chuanzhen, Trampari, Eleftheria and Pallen, Mark J. ORCID: https://orcid.org/0000-0003-1807-3657
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Creation of Golden Gate constructs for gene doctoring.
BMC Biotechnology, 20 (1).
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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 and Pallen, Mark J ORCID: https://orcid.org/0000-0003-1807-3657
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Genomic diversity of Escherichia coli isolates from non-human primates in the Gambia.
Microbial Genomics, 6 (9).
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Hildebrand, Falk, Pallen, Mark J. ORCID: https://orcid.org/0000-0003-1807-3657 and Bork, Peer
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Towards standardisation of naming novel prokaryotic taxa in the age of high-throughput microbiology.
Gut, 69 (7).
pp. 1358-1359.
ISSN 0017-5749
Glendinning, Laura, Stewart, Robert D., Pallen, Mark J. ORCID: https://orcid.org/0000-0003-1807-3657, Watson, Kellie A. and Watson, Mick
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Assembly of hundreds of novel bacterial genomes from the chicken caecum.
Genome Biology, 21 (1).
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Senghore, Madikay, Diarra, Bassirou, Gehre, Florian, Otu, Jacob, Worwui, Archibald, Muhammad, Abdul Khalie, Kwambana-Adams, Brenda, Kay, Gemma L., Sanogo, Moumine, Baya, Bocar, Orsega, Susan, Doumbia, Seydou, Diallo, Souleymane, de Jong, Bouke C., Pallen, Mark J. ORCID: https://orcid.org/0000-0003-1807-3657 and Antonio, Martin
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Evolution of Mycobacterium tuberculosis complex lineages and their role in an emerging threat of multidrug resistant tuberculosis in Bamako, Mali.
Scientific Reports, 10.
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Ravi, Anuradha, Halstead, Fenella D, Bamford, Amy, Casey, Anna, Thomson, Nicholas M, van Schaik, Willem, Snelson, Catherine, Goulden, Robert, Foster-Nyarko, Ebenezer, Savva, George M, Whitehouse, Tony, Pallen, Mark J ORCID: https://orcid.org/0000-0003-1807-3657 and Oppenheim, Beryl A
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Loss of microbial diversity and pathogen domination of the gut microbiota in critically ill patients.
Microbial Genomics, 5 (9).
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Yasir, Muhammad, Icke, Christopher, Abdelwahab, Radwa, Haycocks, James R., Godfrey, Rita E., Sazinas, Pavelas, Pallen, Mark J. ORCID: https://orcid.org/0000-0003-1807-3657, Henderson, Ian R., Busby, Stephen J. W. and Browning, Douglas F.
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Organization and architecture of AggR‐dependent promoters from Enteroaggregative Escherichia coli.
Molecular Microbiology, 111 (2).
pp. 534-551.
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Ravi, Anuradha, Ereqat, Suheir, Al-Jawabreh, Amer, Abdeen, Ziad, Abu Shamma, Omar, Hall, Holly, Pallen, Mark J. ORCID: https://orcid.org/0000-0003-1807-3657 and Nasereddin, Abedelmajeed
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Metagenomic profiling of ticks: Identification of novel rickettsial genomes and detection of tick-borne canine parvovirus.
PLoS Neglected Tropical Diseases, 13 (1).
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Jones, Jana, Higham, Thomas F.G., Chivall, David, Bianucci, Raffaella, Kay, Gemma L., Pallen, Mark J. ORCID: https://orcid.org/0000-0003-1807-3657, Oldfield, Ron, Ugliano, Federica and Buckley, Stephen A.
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A prehistoric Egyptian mummy: Evidence for an ‘embalming recipe’ and the evolution of early formative funerary treatments.
Journal of Archaeological Science, 100.
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Thomson, Nicholas M., Ferreira, Josie L., Matthews-Palmer, Teige R., Beeby, Morgan and Pallen, Mark J. ORCID: https://orcid.org/0000-0003-1807-3657
(2018)
Giant flagellins form thick flagellar filaments in two species of marine γ-proteobacteria.
PLoS One, 13 (11).
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Thomson, Nicholas M., Rossmann, Florian M., Ferreira, Josie L., Matthews-Palmer, Teige R., Beeby, Morgan and Pallen, Mark J. ORCID: https://orcid.org/0000-0003-1807-3657
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Bacterial Flagellins: Does Size Matter?
Trends in Microbiology, 26 (7).
pp. 575-581.
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Senghore, Madikay, Otu, Jacob, Witney, Adam, Gehre, Florian, Doughty, Emma L., Kay, Gemma L., Butcher, Phillip, Salako, Kayode, Kehinde, Aderemi, Onyejepu, Nneka, Idigbe, Emmanuel, Corrah, Tumani, de Jong, Bouke, Pallen, Mark J. ORCID: https://orcid.org/0000-0003-1807-3657 and Antonio, Martin
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Whole-genome sequencing illuminates the evolution and spread of multidrug-resistant tuberculosis in Southwest Nigeria.
PLoS One, 12 (9).
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Card, Roderick M., Cawthraw, Shaun A., Nunez-Garcia, Javier, Ellis, Richard J., Kay, Gemma, Pallen, Mark J. ORCID: https://orcid.org/0000-0003-1807-3657, Woodward, Martin J. and Anjum, Muna F.
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An in vitro chicken gut model demonstrates transfer of a multidrug resistance plasmid from Salmonella to commensal Escherichia coli.
mBIO, 8 (4).
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Guy, Collette S., Tichauer, Esther, Kay, Gemma L., Phillips, Daniel J., Bailey, Trisha L., Harrison, James, Furze, Christopher M., Millard, Andrew D., Gibson, Matthew I., Pallen, Mark J. ORCID: https://orcid.org/0000-0003-1807-3657 and Fullam, Elizabeth
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Identification of the anti-mycobacterial functional properties of piperidinol derivatives.
British Journal of Pharmacology, 174 (14).
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Pallen, Mark J. ORCID: https://orcid.org/0000-0003-1807-3657 and Quraishi, Mohammed N.
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The gut microbiota and the hepatologist: Will our bugs prove to be the missing link?
Digestive Diseases, 35 (4).
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Webber, Mark A, Whitehead, Rebekah N, Mount, Manuella, Loman, Nick J, Pallen, Mark J ORCID: https://orcid.org/0000-0003-1807-3657 and Piddock, Laura J V
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Parallel evolutionary pathways to antibiotic resistance selected by biocide exposure.
Journal of Antimicrobial Chemotherapy, 70 (8).
pp. 2241-2248.
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Kay, Gemma L., Sergeant, Martin J., Zhou, Zhemin, Chan, Jacqueline Z. -M., Millard, Andrew, Quick, Joshua, Szikossy, Ildiko, Pap, Ildiko, Spigelman, Mark, Loman, Nicholas J., Achtman, Mark, Donoghue, Helen D. and Pallen, Mark J. ORCID: https://orcid.org/0000-0003-1807-3657
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Eighteenth-century genomes show that mixed infections were common at time of peak tuberculosis in Europe.
Nature Communications, 6.
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Smith, Oliver, Momber, Garry, Bates, Richard, Garwood, Paul, Fitch, Simon, Pallen, Mark ORCID: https://orcid.org/0000-0003-1807-3657, Gaffney, Vincent and Allaby, Robin G
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Sedimentary DNA from a submerged site reveals wheat in the British Isles 8000 years ago.
Science, 347 (6225).
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Halachev, Mihail R, Chan, Jacqueline Z-M, Constantinidou, Chrystala I, Cumley, Nicola, Bradley, Craig, Smith-Banks, Matthew, Oppenheim, Beryl and Pallen, Mark J ORCID: https://orcid.org/0000-0003-1807-3657
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Genomic epidemiology of a protracted hospital outbreak caused by multidrug-resistant Acinetobacter baumannii in Birmingham, England.
Genome Medicine, 6 (11).
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Doughty, Emma L, Sergeant, Martin J, Adetifa, Ifedayo, Antonio, Martin and Pallen, Mark J ORCID: https://orcid.org/0000-0003-1807-3657
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Culture-independent detection and characterisation of Mycobacterium tuberculosis and M. africanum in sputum samples using shotgun metagenomics on a benchtop sequencer.
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Sergeant, Martin J, Constantinidou, Chrystala, Cogan, Tristan A, Bedford, Michael R, Penn, Charles W and Pallen, Mark J ORCID: https://orcid.org/0000-0003-1807-3657
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Extensive microbial and functional diversity within the chicken cecal microbiome.
PLoS One, 9 (3).
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Loman, Nicholas J., Constantinidou, Chrystala, Christner, Martin, Chan, Jacqueline Z. M., Quick, Joshua, Weir, Jacqueline C., Quince, Christopher, Smith, Geoffrey P., Betley, Jason R., Aepfelbacher, Martin and Pallen, Mark J. ORCID: https://orcid.org/0000-0003-1807-3657
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A culture-independent sequence-based metagenomics approach to the investigation of an outbreak of Shiga-toxigenic Escherichia coli O104:H4.
JAMA, 309 (14).
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Crossman, Lisa C., Chaudhuri, Roy R., Beatson, Scott A., Wells, Timothy J., Desvaux, Mickael, Cunningham, Adam F., Petty, Nicola K., Mahon, Vivienne, Brinkley, Carl, Hobman, Jon L., Savarino, Stephen J., Turner, Susan M., Pallen, Mark J. ORCID: https://orcid.org/0000-0003-1807-3657, Penn, Charles W., Parkhill, Julian, Turner, A. Keith, Johnson, Timothy J., Thomson, Nicholas R., Smith, Stephen G. J. and Henderson, Ian R.
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A commensal gone bad: Complete genome sequence of the prototypical enterotoxigenic Escherichia coli strain H10407.
Journal of Bacteriology, 192 (21).
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