Items where Author is "Pallen, Mark"

Oren, Aharon, Kostovski, Marko and Pallen, Mark J. ORCID: https://orcid.org/0000-0003-1807-3657 (2024) Proposal to add a Note to Rule 8 of the International Code of Nomenclature of Prokaryotes to clarify the meaning of the term ‘stem’. International Journal of Systematic and Evolutionary Microbiology, 74 (9). ISSN 1466-5026

Pallen, Mark J. ORCID: https://orcid.org/0000-0003-1807-3657 (2024) The dynamic history of prokaryotic phyla: Discovery, diversity and division. International Journal of Systematic and Evolutionary Microbiology, 74 (9). ISSN 1466-5026

Pallen, Mark J. ORCID: https://orcid.org/0000-0003-1807-3657 (2024) Valid publication of names for bacterial species from the chicken gut. International Journal of Systematic and Evolutionary Microbiology, 74 (7). ISSN 1466-5026

Ereqat, Suheir, Alikhan, Nabil-Fareed, Al-Jawabreh, Amer, Matthews, Michaela, Al-Jawabreh, Ahmed, de Oliveira Martins, Leonardo, Trotter, Alexander J., Al-Kaila, Mai, Page, Andrew J., Pallen, Mark J. ORCID: https://orcid.org/0000-0003-1807-3657 and Nasereddin, Abedelmajeed (2024) Epidemiological characterization and genetic variation of the SARS-CoV-2 Delta variant in Palestine. Pathogens, 13 (6). ISSN 2076-0817

Pallen, Mark J. ORCID: https://orcid.org/0000-0003-1807-3657 (2024) Formation of prokaryote names from personal names: A review of current practice and a proposal to emend Appendix 9 of the International Code of Nomenclature of Prokaryotes. International Journal of Systematic and Evolutionary Microbiology, 74 (1). ISSN 1466-5026

Pallen, Mark J. ORCID: https://orcid.org/0000-0003-1807-3657 (2023) Use of connecting vowels after stems ending in the same vowel:a proposal to emend Appendix 9 of the International Code of Nomenclature of Prokaryotes. International Journal of Systematic and Evolutionary Microbiology, 73 (12). ISSN 1466-5026

Pallen, Mark J. ORCID: https://orcid.org/0000-0003-1807-3657 (2023) Request for an Opinion on the standing and retention of Firmicutes as a phylum name. International Journal of Systematic and Evolutionary Microbiology, 73 (7). ISSN 1466-5026

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

Ravi, Anuradha, Troncoso-Rey, Perla, Ahn-Jarvis, Jennifer, Corbin, Kendall R., Harris, Suzanne, Harris, Hannah, Aydin, Alp, Kay, Gemma L., Le Viet, Thanh, Gilroy, Rachel, Pallen, Mark J. ORCID: https://orcid.org/0000-0003-1807-3657, Page, Andrew J., O'Grady, Justin and Warren, Frederick J. (2022) Hybrid metagenome assemblies link carbohydrate structure with function in the human gut microbiome. Communications Biology, 5. ISSN 2399-3642

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

Foster-Nyarko, Ebenezer and Pallen, Mark J. ORCID: https://orcid.org/0000-0003-1807-3657 (2022) The microbial ecology of Escherichia coli in the vertebrate gut. FEMS Microbiology Reviews, 46 (3). ISSN 0168-6445

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 (2022) 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 (2022) Metagenomic investigation of the equine faecal microbiome reveals extensive taxonomic diversity. PeerJ, 10. ISSN 2167-8359

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 (2022) Remarkable genomic diversity among Escherichia isolates recovered from healthy chickens. PeerJ, 10. ISSN 2167-8359

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 (2021) Leviviricetes: expanding and restructuring the taxonomy of bacteria-infecting single-stranded RNA viruses. Microbial Genomics, 7 (11). ISSN 2057-5858

Pallen, M. J. ORCID: https://orcid.org/0000-0003-1807-3657 (2021) Bacterial nomenclature in the era of genomics. New Microbes and New Infections, 44. ISSN 2052-2975

Pallen, Mark J. ORCID: https://orcid.org/0000-0003-1807-3657 (2021) The status Candidatus for uncultured taxa of Bacteria and Archaea: SWOT analysis. International Journal of Systematic and Evolutionary Microbiology, 71 (9). ISSN 1466-5026

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. (2021) 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. ISSN 1664-302X

Konings, Frank, Perkins, Mark D., Kuhn, Jens H., Pallen, Mark J. ORCID: https://orcid.org/0000-0003-1807-3657, Alm, Erik J., Archer, Brett N., Barakat, Amal, Bedford, Trevor, Bhiman, Jinal N., Caly, Leon, Carter, Lisa L., Cullinane, Anne, de Oliveira, Tulio, Druce, Julian, El Masry, Ihab, Evans, Roger, Gao, George F., Gorbalenya, Alexander E., Hamblion, Esther, Herring, Belinda L., Hodcroft, Emma, Holmes, Edward C., Kakkar, Manish, Khare, Shagun, Koopmans, Marion P.G., Korber, Bette, Leite, Juliana, MacCannell, Duncan, Marklewitz, Marco, Maurer-Stroh, Sebastian, Rico, Jairo Andres Mendez, Munster, Vincent J., Neher, Richard, Munnink, Bas Oude, Pavlin, Boris I., Peiris, Malik, Poon, Leo, Pybus, Oliver, Rambaut, Andrew, Resende, Paola, Subissi, Lorenzo, Thiel, Volker, Tong, Suxiang, van der Werf, Sylvie, von Gottberg, Anne, Ziebuhr, John and Van Kerkhove, Maria D. (2021) SARS-CoV-2 Variants of Interest and Concern naming scheme conducive for global discourse. Nature Microbiology, 6 (7). pp. 821-823. ISSN 2058-5276

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. ORCID: https://orcid.org/0000-0003-1807-3657 (2021) Extensive microbial diversity within the chicken gut microbiome revealed by metagenomics and culture. PeerJ, 9. ISSN 2167-8359

Pallen, Mark J. ORCID: https://orcid.org/0000-0003-1807-3657, Telatin, Andrea and Oren, Aharon (2021) The next million names for Archaea and Bacteria. Trends in Microbiology, 29 (4). pp. 289-298. ISSN 0966-842X

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 (2021) Genomic diversity of Escherichia coli from healthy children in rural Gambia. PeerJ, 9. ISSN 2167-8359

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 (2021) 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 (2020) Creation of Golden Gate constructs for gene doctoring. BMC Biotechnology, 20 (1). ISSN 1472-6750

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 (2020) Genomic diversity of Escherichia coli isolates from non-human primates in the Gambia. Microbial Genomics, 6 (9). ISSN 2057-5858

Hildebrand, Falk, Pallen, Mark J. ORCID: https://orcid.org/0000-0003-1807-3657 and Bork, Peer (2020) 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 (2020) Assembly of hundreds of novel bacterial genomes from the chicken caecum. Genome Biology, 21 (1). ISSN 1474-760X

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 (2020) Evolution of Mycobacterium tuberculosis complex lineages and their role in an emerging threat of multidrug resistant tuberculosis in Bamako, Mali. Scientific Reports, 10. ISSN 2045-2322

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 (2019) Loss of microbial diversity and pathogen domination of the gut microbiota in critically ill patients. Microbial Genomics, 5 (9). ISSN 2057-5858

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. (2019) Organization and architecture of AggR‐dependent promoters from Enteroaggregative Escherichia coli. Molecular Microbiology, 111 (2). pp. 534-551. ISSN 0950-382X

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 (2019) Metagenomic profiling of ticks: Identification of novel rickettsial genomes and detection of tick-borne canine parvovirus. PLoS Neglected Tropical Diseases, 13 (1). ISSN 1935-2727

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. (2018) A prehistoric Egyptian mummy: Evidence for an ‘embalming recipe’ and the evolution of early formative funerary treatments. Journal of Archaeological Science, 100. pp. 191-200. ISSN 0305-4403

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). ISSN 1932-6203

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 (2018) Bacterial Flagellins: Does Size Matter? Trends in Microbiology, 26 (7). pp. 575-581. ISSN 0966-842X

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 (2017) Whole-genome sequencing illuminates the evolution and spread of multidrug-resistant tuberculosis in Southwest Nigeria. PLoS One, 12 (9). ISSN 1932-6203

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. (2017) An in vitro chicken gut model demonstrates transfer of a multidrug resistance plasmid from Salmonella to commensal Escherichia coli. mBIO, 8 (4). e00777-17. ISSN 2150-7511

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 (2017) Identification of the anti-mycobacterial functional properties of piperidinol derivatives. British Journal of Pharmacology, 174 (14). pp. 2183-2193. ISSN 0007-1188

Pallen, Mark J. ORCID: https://orcid.org/0000-0003-1807-3657 and Quraishi, Mohammed N. (2017) The gut microbiota and the hepatologist: Will our bugs prove to be the missing link? Digestive Diseases, 35 (4). pp. 377-383. ISSN 0257-2753

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 (2015) Parallel evolutionary pathways to antibiotic resistance selected by biocide exposure. Journal of Antimicrobial Chemotherapy, 70 (8). pp. 2241-2248. ISSN 0305-7453

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 (2015) Eighteenth-century genomes show that mixed infections were common at time of peak tuberculosis in Europe. Nature Communications, 6. ISSN 2041-1723

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 (2015) Sedimentary DNA from a submerged site reveals wheat in the British Isles 8000 years ago. Science, 347 (6225). pp. 998-1001. ISSN 0036-8075

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 (2014) Genomic epidemiology of a protracted hospital outbreak caused by multidrug-resistant Acinetobacter baumannii in Birmingham, England. Genome Medicine, 6 (11). ISSN 1756-994X

Doughty, Emma L, Sergeant, Martin J, Adetifa, Ifedayo, Antonio, Martin and Pallen, Mark J ORCID: https://orcid.org/0000-0003-1807-3657 (2014) Culture-independent detection and characterisation of Mycobacterium tuberculosis and M. africanum in sputum samples using shotgun metagenomics on a benchtop sequencer. PeerJ, 2. ISSN 2167-8359

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 (2014) Extensive microbial and functional diversity within the chicken cecal microbiome. PLoS One, 9 (3). e91941. ISSN 1932-6203

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 (2013) A culture-independent sequence-based metagenomics approach to the investigation of an outbreak of Shiga-toxigenic Escherichia coli O104:H4. JAMA, 309 (14). pp. 1502-1510. ISSN 0098-7484

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. (2010) A commensal gone bad: Complete genome sequence of the prototypical enterotoxigenic Escherichia coli strain H10407. Journal of Bacteriology, 192 (21). pp. 5822-5831. ISSN 0021-9193