Job Title
Professor in Biomedicine
Department
WMS - Microbiology and Infection
Phone
024 7615 0392
Web Link
Research Interests
I have been Professor of Microbial Genomics at the University of Warwick since April 2013.
NB: From April 2017, I will be Research Leader at the Quadram Institute and Professor of Microbial Genomics at the University of East Anglia.
To find out more about me, please visit my personal academic web site
- Jones, Jana, Higham, Thomas F.G., Chivall, David, Bianucci, Raffaella, Kay, Gemma L., Pallen, Mark J., Oldfield, Ron, Ugliano, Federica, 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
- Mokrousov, Igor, 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., Antonio, Martin, 2017. Whole-genome sequencing illuminates the evolution and spread of multidrug-resistant tuberculosis in Southwest Nigeria. PLoS One, 12 (9)
- Card, Roderick M., Cawthraw, Shaun A., Nunez-Garcia, Javier, Ellis, Richard J., Kay, Gemma, Pallen, Mark J., Woodward, Martin J., 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)
- Unnikrishnan, Meera, Constantinidou, Chrystala, Palmer, Tracy, Pallen, Mark J., 2017. The enigmatic Esx proteins : looking beyond mycobacteria. Trends in Microbiology, 25 (3), pp. 192-204
- 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., Fullam, Elizabeth, 2017. Identification of the anti-mycobacterial functional properties of piperidinol derivatives. British Journal of Pharmacology, 174 (14), pp. 2183-2193
- Higgins, P. G., Chan, J. Z.-M., Seifert, H., Pallen, Mark J., Millard, Andrew D., 2016. Draft genome sequences of 11 clinical isolates of Acinetobacter baumannii. Genome Announcements, 4 (2)
- Smith, Oliver, Momber, G., Bates, R., Garwood, P., Fitch, S., Pallen, Mark J., Gaffney, V., 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
- Kay, Gemma L., Sergeant, Martin J., Zhou, Zhemin, Chan, Jacqueline, Millard, Andrew D., Quick, Joshua, Szikossy, Ildikó, Pap, Ildiko´, Spigelman, Mark, Loman, Nicholas J., Achtman, Mark, Donoghue, Helen D., Pallen, Mark J., 2015. Eighteenth-century genomes show that mixed infections were common at time of peak tuberculosis in Europe. Nature Communications, 6, pp. 1-9
- Kay, Gemma L., Millard, Andrew D., Sergeant, Martin J., Midzi, Nicholas, Gwisai, Reggis, Mduluza, Takafira, Ivens, Alasdair, Nausch, Norman, Mutapi, Francisca, Pallen, Mark J., 2015. Differences in the faecal microbiome in Schistosoma haematobium infected children vs. uninfected children. PLoS Neglected Tropical Diseases, 9 (6)
- Smith, Oliver, Momber, G., Bates, R., Garwood, P., Fitch, S., Pallen, Mark J., Gaffney, V., Allaby, Robin G., 2015. Response to comment on "Sedimentary DNA from a submerged site reveals wheat in the British Isles 8000 years ago". Science, 349 (6245), pp. 247-247
- Loman, Nicholas J., Pallen, Mark J., 2015. Twenty years of bacterial genome sequencing. Nature Reviews Microbiology
- Hänsch, Stephanie, Cilli, Elisabetta, Catalano, Giulioilda, Gruppioni, Giorgio, Bianucci, Raffaella, Stenseth, Nils C., Bramanti, Barbara, Pallen, Mark J., 2015. The pla gene, encoding plasminogen activator, is not specific to Yersinia pestis. BMC Research Notes, 8 (1), pp. 1-3
- Millard, Andrew D., Westblade, Lars, LiPuma, John J., Vavikolanu, Kranthi, Read, Timothy, Pallen, Mark J., Burd, Eileen, Constantinidou, Chrystala, 2015. Genome Sequence of the Pandoraea apista LMG 16407 Type Strain. Journal of Bacteriology, 3 (6), pp. e01300-e01315
- Webber, Mark A., Whitehead, Rebekah N., Mount, Manuella, Loman, Nicholas J., Pallen, Mark J., Piddock, Laura J. V., 2015. Parallel evolutionary pathways to antibiotic resistance selected by biocide exposure. Journal of antimicrobial chemotherapy, 70 (8), pp. 2241-2248
- Bruce, A. G., Thouless, M. E., Haines, A. S., Pallen, Mark J., Grundhoff, A., Rose, T. N., 2015. Complete genome sequence of MneRV2, the pig-tailed macaque RV2 rhadinovirus, and evolutionary relationship with rhesus macaque RRV and human herpesvirus 8/KSHV. Journal of Virology, 89 (7), pp. 3888-3909
- Sergeant, Martin J., Constantinidou, Chrystala, Cogan, Tristan A., Bedford, Michael R., Penn, Charles W., Pallen, Mark J., 2014. Extensive microbial and functional diversity within the chicken cecal microbiome. PLoS ONE, 9 (3)
- Doughty, Emma L., Sergeant, Martin J., Ifedayo, Adetifa M. O., Antonio, Martin, Pallen, Mark J., 2014. Culture-independent detection and characterisation of Mycobacterium tuberculosis and M. africanum in sputum samples using shotgun metagenomics on a benchtop sequencer. PeerJ PrePrints
- Quick, Joshua, Constantinidou, Chrystala, Pallen, Mark J., Oppenheim, Beryl, Loman, Nicholas J., 2014. Draft genome sequence of Elizabethkingia meningoseptica isolated from a traumatic wound. Genome Announcements, 2 (3)
- Kay, Gemma L., Sergeant, Martin J., Giuffra, Valentina, Bandiera, Pasquale, Milanese, Marco, Bramanti, Barbara, Bianucci, Raffaella, Pallen, Mark J., 2014. Recovery of a medieval Brucella melitensis genome using shotgun metagenomics. mBio, 5 (4)
- Quick, Joshua, Cumley, Nicola, Wearn, Christopher M., Niebel, Marc, Constantinidou, Chrystala, Thomas, Christopher M., Pallen, Mark J., Moiemen, Naiem S., Bamford, Amy, Oppenheim, Beryl, Loman, Nicholas J., 2014. Seeking the source of Pseudomonas aeruginosa infections in a recently opened hospital : an observational study using whole-genome sequencing. BMJ Open, 4 (11)
- Bingle, Lewis E. H., Constantinidou, Chrystala, Shaw, Robert K., Islam, Md. Shahidul, Patel, Mala, Snyder, Lori A. S., Lee, David J., Penn, C. W., Busby, Stephen J. W., Pallen, Mark J., 2014. Microarray analysis of the ler regulon in enteropathogenic and enterohaemorrhagic escherichia coli strains. PLoS One, 9 (1)
- Halachev, Mihail R., Chan, Jacqueline, Constantinidou, Chrystala, Cumley, Nicola, Bradley, Craig, Smith-Banks, Matthew, Oppenheim, Beryl, Pallen, Mark J., 2014. Genomic epidemiology of a protracted hospital outbreak caused by multidrug-resistant Acinetobacter baumannii in Birmingham, England. Genome Medicine, 6 (11), pp. 1-13
- Pallen, Mark J., 2014. Diagnostic metagenomics : potential applications to bacterial, viral and parasitic infections. Parasitology, 141 (14), pp. 1856-1862
- Remuiñán, Modesto J., Pérez-Herrán, Esther, Rullás, Joaquín, Alemparte, Carlos, Martínez-Hoyos, María, Dow, David J., Afari, Johnson, Mehta, Nalini, Esquivias, Jorge, Jiménez, Elena, Ortega-Muro, Fátima, Fraile-Gabaldón, María Teresa, Spivey, Vickey L., Loman, Nicholas J., Pallen, Mark J., Constantinidou, Chrystala, Minick, Douglas J., Cacho, Mónica, Rebollo-López, María José, González, Carolina et al (Select to open full list), 2013. Tetrahydropyrazolo[1,5-a]Pyrimidine-3-Carboxamide and N-Benzyl-6',7'-Dihydrospiro[Piperidine-4,4'-Thieno[3,2-c]Pyran] analogues with bactericidal efficacy against Mycobacterium tuberculosis targeting MmpL3. PLoS One, 8 (4)
- Solez, Kim, Bernier, Ashlyn, Crichton, Joel, Graves, Heather, Kuttikat, Preeti, Lockwood, Ross, Marovitz, William F, Monroe, Damon, Pallen, Mark J., Pandya, Shawna, Pearce, David, Saleh, Abdullah, Sandhu, Neelam, Sergi, Consolato, Tuszynski, Jack, Waugh, Earle, White, Jonathan, Woodside, Michael, Wyndham, Roger, Zaiane, Osmar et al (Select to open full list), 2013. Bridging the gap between the technological singularity and mainstream medicine : highlighting a course on technology and the future of medicine. Global Journal of Health Science, 5 (6), pp. 112-125
- Gladstone, Rebecca A., Loman, Nicholas J., Constantinidou, Chrystala, Tocheva, Anna S., Jefferies, Johanna M. C., Faust, Saul N., O'Connor, Leigh, Chan, Jacqueline, Pallen, Mark J., Clarke, Stuart C., 2013. Clonal expansion within pneumococcal serotype 6C after use of seven-valent vaccine. PLoS One, 8 (5)
- Loman, Nicholas J., Constantinidou, Chrystala, Christner, Martin, Rohde, Holger, Chan, Jacqueline, Quick, Joshua, Weir, Jacqueline C., Quince, Christopher, Smith, Geoffrey, Betley, Jason R., Aepfelbacher, Martin, Pallen, Mark J., 2013. A culture-independent sequence-based metagenomics approach to the investigation of an outbreak of Shiga-Toxigenic Escherichia coli O104:H4. JAMA: The Journal of the American Medical Association, 309 (14), pp. 1502-1510
- Snyder, L. A., Loman, Nicholas J., Faraj, L. A., Levi, K., Weinstock, G., Boswell, T. C., Pallen, Mark J., Ala Aldeen, D. A., 2013. Epidemiological investigation of Pseudomonas aeruginosa isolates from a six-year-long hospital outbreak using high-throughput whole genome sequencing. Euro surveillance : bulletin Europeen sur les maladies transmissibles = European communicable disease bulletin, 18 (42)
- Robinson, Esther R., Walker, Timothy M., Pallen, Mark J., 2013. Genomics and outbreak investigation : from sequence to consequence. Genome Medicine, 5 (4)
- Chan, Jacqueline, Halachev, Mihail R., Loman, Nicholas J., Constantinidou, Chrystala, Pallen, Mark J., 2012. Defining bacterial species in the genomic era : insights from the genus Acinetobacter. BMC Microbiology, 12 (1)
- Williams, Tiffany M., Loman, Nicholas J., Ebruke, Chinelo, Musher, Daniel M., Adegbola, Richard A., Pallen, Mark J., Weinstock, George M., Antonio, Martin, 2012. Genome analysis of a highly virulent serotype 1 strain of streptococcus pneumoniae from West Africa. PLoS One, 7 (10)
- Islam, Md. Shahidul, Shaw, Robert K., Frankel, Gad, Pallen, Mark J., Busby, Stephen J. W., 2012. Translation of a minigene in the 5' leader sequence of the enterohaemorrhagic Escherichia coli LEE1 transcription unit affects expression of the neighbouring downstream gene. Biochemical Journal, 441 (1), pp. 247-253
- Van Wyhe, John, Pallen, Mark J., 2012. The ?Annie Hypothesis' : did the death of His daughter cause Darwin to ?Give up Christianity'?. Centaurus, 54 (2), pp. 105-123
- Loman, Nicholas J., Constantinidou, Chrystala, Chan, Jacqueline, Halachev, Mihail R., Sergeant, Martin J., Penn, Charles W., Robinson, Esther R., Pallen, Mark J., 2012. High-throughput bacterial genome sequencing : an embarrassment of choice, a world of opportunity. Nature Reviews Microbiology, 10 (9), pp. 599-606
- Kochar, M., Crosatti, M., Harrison, E. M., Rieck, B., Chan, J., Constantinidou, Chrystala, Pallen, Mark J., Ou, H.-Y., Rajakumar, Kumar, 2012. Deletion of TnAbaR23 results in both expected and unexpected antibiogram changes in a multidrug-resistant acinetobacter baumannii strain. Antimicrobial Agents and Chemotherapy, volume 56 (4), pp. 1845-1853
- Abrahams, Katherine A., Cox, Jonathan A. G., Spivey, Vickey L., Loman, Nicholas J., Pallen, Mark J., Constantinidou, Chrystala, Fernández, Raquel, Alemparte, Carlos, Remuiñán, Modesto J., Barros, David, Ballell, Lluis, Besra, Gurdyal S., 2012. Identification of novel Imidazo[1,2-a]pyridine inhibitors targeting M. tuberculosis QcrB. PLoS One, 7 (12)
- Constantinidou, Chrystala, Sergeant, Martin J., Cogan, Tristan, Penn, Charles W., Pallen, Mark J., 2012. High-throughput sequencing of 16S rRNA gene amplicons : effects of extraction procedure, primer length and annealing temperature. PLoS One, 7 (5)
- Chan, Jacqueline, Pallen, Mark J., Oppenheim, Beryl, Constantinidou, Chrystala, 2012. Genome sequencing in clinical microbiology. Nature Biotechnology, 30 (11), pp. 1068-1071
- Loman, Nicholas J., Misra, Raju V., Dallman, Timothy J, Constantinidou, Chrystala, Gharbia, Saheer E, Wain, John, Pallen, Mark J., 2012. Performance comparison of benchtop high-throughput sequencing platforms. Nature Biotechnology, 30 (6), pp. 562-562
- Loman, Nicholas J., Misra, Raju V., Dallman, Timothy J., Constantinidou, Chrystala, Gharbia, Saheer E., Wain, John, Pallen, Mark J., 2012. Performance comparison of benchtop high-throughput sequencing platforms. Nature Biotechnology, 30 (5), pp. 434-439
- Chan, Jacqueline, Pallen, Mark J., Oppenheim, Beryl, Constantinidou, Chrystala, 2012. Genome sequencing in clinical microbiology. Nature Biotechnology, 30 (11), pp. 1068-1071
- Chan, Jacqueline, Halachev, Mihail R., Yates, Emma, Smith, Grace, Pallen, Mark J., 2012. Whole-genome sequence of the emerging pathogen mycobacterium abscessus strain 47J26. Journal of Bacteriology, 194 (2), pp. 549-549
- Ricci, V., Loman, Nicholas J., Pallen, Mark J., Ivens, Alasdair, Fookes, M., Langridge, G. C., Wain, J., Piddock, Laura J. V., 2011. The TCA cycle is not required for selection or survival of multidrug-resistant Salmonella. Journal of Antimicrobial Chemotherapy, 67 (3), pp. 589-599
- Halachev, Mihail R., Loman, Nicholas J., Pallen, Mark J., 2011. Calculating orthologs in bacteria and archaea : a divide and conquer approach. PLoS One, 6 (12)
- Pallen, Mark J., Loman, Nicholas J., 2011. Are diagnostic and public health bacteriology ready to become branches of genomic medicine?. Genome Medicine, 3 (8)
- Islam, Md. Shahidul, Pallen, Mark J., Busby, Stephen J. W., 2011. A cryptic promoter in theLEE1regulatory region of enterohaemorrhagicEscherichia coli: promoter specificity in AT-rich gene regulatory regions. Biochemical Journal, 436 (3), pp. 681-686
- Islam, Md. Shahidul, Pallen, Mark J., Busby, Stephen J. W., 2011. A cryptic promoter in theLEE1regulatory region of enterohaemorrhagicEscherichia coli: promoter specificity in AT-rich gene regulatory regions. Biochemical Journal, 436 (3), pp. 681-686
- Hornsey, M., Loman, Nicholas J., Wareham, D. W., Ellington, M. J., Pallen, Mark J., Turton, J. F., Underwood, A., Gaulton, T., Thomas, C. P., Doumith, M., Livermore, D. M., Woodford, N., 2011. Whole-genome comparison of two Acinetobacter baumannii isolates from a single patient, where resistance developed during tigecycline therapy. Journal of Antimicrobial Chemotherapy, 66 (7), pp. 1499-1503
- Clarke, D. J., Chaudhuri, R. R., Martin, H. M., Campbell, B. J., Rhodes, J. M., Constantinidou, Chrystala, Pallen, Mark J., Loman, Nicholas J., Cunningham, A. F., Browning, D. F., Henderson, I. R., 2011. Complete genome sequence of the Crohn's disease-associated adherent-invasive escherichia coliStrain HM605. Journal of Bacteriology, 193 (17)
- Shaw, Robert K., Lasa, Iñigo, García, Begoña M., Pallen, Mark J., Hinton, Jay C. D., Berger, Cedric N., Frankel, Gad, 2011. Cellulose mediates attachment of Salmonella enterica Serovar Typhimurium to tomatoes. Environmental Microbiology Reports, 3 (5), pp. 569-573
- Rohde, Holger, Qin, Junjie, Cui, Yujun, Li, Dongfang, Loman, Nicholas J., Hentschke, Moritz, Chen, Wentong, Pu, Fei, Peng, Yangqing, Li, Junhua, Xi, Feng, Li, Shenghui, Li, Yin, Zhang, Zhaoxi, Yang, Xianwei, Zhao, Meiru, Wang, Peng, Guan, Yuanlin, Cen, Zhong, Zhao, Xiangna et al (Select to open full list), 2011. Open-source genomic analysis of shiga-toxin?producing E. coli O104:H4. New England Journal Of Medicine, 365 (8), pp. 718-724
- Pallen, Mark J., 2011. Time to recognise that mitochondria are bacteria?. Trends in Microbiology, 19 (2), pp. 58-64
- Zarrilli, R., Giannouli, M., Rocco, F., Loman, Nicholas J., Haines, A. S., Constantinidou, Chrystala, Pallen, Mark J., Triassi, M., Di Nocera, P. P., 2011. Genome sequences of three acinetobacter baumannii strains assigned to the multilocus sequence typing genotypes ST2, ST25, and ST78. Journal of Bacteriology, 193 (9), pp. 2359-2360
- Younis, R., Bingle, L. E. H., Rollauer, S., Munera, D., Busby, S. J., Johnson, S., Deane, J. E., Lea, S. M., Frankel, G., Pallen, Mark J., 2010. SepL resembles an aberrant effector in binding to a class 1 Type III secretion chaperone and carrying an N-Terminal secretion signal. Journal of Bacteriology, 192 (22), pp. 6093-6098
- Shukla, Anshuman, Pallen, Mark J., Anthony, Mark, White, Scott A., 2010. The homodimeric GBS1074 fromStreptococcus agalactiae. Acta Crystallographica Section F Structural Biology and Crystallization Communications, 66 (11), pp. 1421-1425
- Crossman, L. C., Chaudhuri, R. R., Beatson, S. A., Wells, T. J., Desvaux, M., Cunningham, A. F., Petty, N. K., Mahon, V., Brinkley, C., Hobman, J. L., Savarino, S. J., Turner, S. M., Pallen, Mark J., Penn, C. W., Parkhill, J., Turner, A. K., Johnson, T. J., Thomson, N. R., Smith, S. G. J., Henderson, I. 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
- Loman, Nicholas J., Pallen, Mark J., 2010. EntrezAJAX : direct web browser access to the Entrez Programming Utilities. Source Code for Biology and Medicine, volume 5 (1)
- Pallen, Mark J., Loman, Nicholas J., Penn, Charles W., 2010. High-throughput sequencing and clinical microbiology : progress, opportunities and challenges. Current Opinion in Microbiology, 13 (5), pp. 625-631
- Chaudhuri, R. R., Sebaihia, Mohammed, Hobman, Jon L., Webber, Mark A., Leyton, Denisse L., Goldberg, Martin D., Cunningham, Adam F., Scott-Tucker, Anthony, Ferguson, Paul R., Thomas, Christopher M., Frankel, Gad, Tang, Christoph M., Dudley, Edward G., Roberts, Ian, Rasko, David A., Pallen, Mark J., Parkhill, Julian, Nataro, James P., Thomson, Nicholas R., Henderson, Ian R., 2010. Complete genome sequence and comparative metabolic profiling of the prototypical enteroaggregative escherichia coli strain 042. PLoS One, 5 (1)
- Snyder, Lori A. S., Loman, Nicholas J., Linton, James D., Langdon, Rebecca R., Weinstock, George M., Wren, Brendan, Pallen, Mark J., 2010. Simple sequence repeats in Helicobacter canadensis and their role in phase variable expression and C-terminal sequence switching. BMC Genomics, 11 (1)
- Lewis, T., Loman, Nicholas J., Bingle, L., Jumaa, P., Weinstock, G. M., Mortiboy, D., Pallen, Mark J., 2010. High-throughput whole-genome sequencing to dissect the epidemiology of Acinetobacter baumannii isolates from a hospital outbreak. Journal of Hospital Infection, 75 (1), pp. 37-41
- Shaw, Robert K., Berger, Cedric N., Pallen, Mark J., Sjöling, Åsa, Frankel, Gad, 2010. Flagella mediate attachment of enterotoxigenic Escherichia coli to fresh salad leaves. Environmental Microbiology Reports, 3 (1), pp. 112-117
- Pallen, Mark J., 2010. FP1.1 High-throughput sequencing as a tool in the discovery, diagnosis and epidemiology of nosocomial pathogens. Journal of Hospital Infection, 76
- Lee, David J., Bingle, Lewis E. H., Heurlier, Karin, Pallen, Mark J., Penn, Charles W., Busby, Stephen J. W., Hobman, Jon L., 2009. Gene doctoring : a method for recombineering in laboratory and pathogenic Escherichia coli strains. BMC Microbiology, 9 (1)
- Woo, Patrick C. Y., Lau, Susanna K. P., Tse, Herman, Teng, Jade L. L., Curreem, Shirly O. T., Tsang, Alan K. L., Fan, Rachel Y. Y., Wong, Gilman K. M., Huang, Yi, Loman, Nicholas J., Snyder, Lori A. S., Cai, James J., Huang, Jian-Dong, Mak, William, Pallen, Mark J., Lok, Si, Yuen, Kwok-Yung, 2009. The complete genome and proteome of laribacter hongkongensis reveal potential mechanisms for adaptations to different temperatures and habitats. PLoS Genetics, 5 (3)
- Snyder, Lori A. S., Cole, Jeff A, Pallen, Mark J., 2009. Comparative analysis of two Neisseria gonorrhoeae genome sequences reveals evidence of mobilization of Correia Repeat Enclosed Elements and their role in regulation. BMC Genomics, 10 (1)
- Snyder, Lori A.S., Loman, Nicholas J., Fütterer, Klaus, Pallen, Mark J., 2009. Bacterial flagellar diversity and evolution : seek simplicity and distrust it?. Trends in Microbiology, 17 (1), pp. 1-5
- Snyder, Lori A. S., Loman, Nicholas J., Pallen, Mark J., Penn, C. W., 2009. Next-generation sequencing?the promise and perils of charting the great microbial unknown. Microbial Ecology, 57 (1), pp. 1-3
- Pallen, Mark J., 2009. Darwin : from the origin of species to the origin of infection. Microbiology Today, 36
- Spear, Abigail M., Loman, Nicholas J., Atkins, Helen S., Pallen, Mark J., 2009. Microbial TIR domains : not necessarily agents of subversion?. Trends in Microbiology, 17 (9), pp. 393-398
- Berger, Cedric N., Shaw, Robert K., Ruiz-Perez, Fernando, Nataro, James P., Henderson, Ian R., Pallen, Mark J., Frankel, Gad, 2009. Interaction of enteroaggregative escherichia coli with salad leaves. Environmental Microbiology Reports, 1 (4), pp. 234-239
- Loman, Nicholas J., Snyder, Lori A. S., Linton, James D., Langdon, Rebecca R., Lawson, A. J., Weinstock, G. M., Wren, B. W., Pallen, Mark J., 2009. Genome sequence of the emerging pathogen helicobacter canadensis. Journal of Bacteriology, 191 (17), pp. 5566-5567
- Berger, Cedric N., Shaw, Robert K., Brown, Derek, Mather, H., Clare, Simon, Dougan, G., Pallen, Mark J., Frankel, Gad, 2009. Interaction of salmonella enterica with basil and other salad leaves. The ISME Journal, 3 (2), pp. 261-265
- Bingle, Lewis E. H., Bailey, Christopher M., Pallen, Mark J., 2008. Type VI secretion : a beginner's guide. Current Opinion in Microbiology, 11 (1), pp. 3-8
- Chaudhuri, R. R., Loman, Nicholas J., Snyder, L. A.S., Bailey, C. M., Stekel, D. J., Pallen, Mark J., 2008. xBASE2 : a comprehensive resource for comparative bacterial genomics. Nucleic Acids Research, 36 (Suppl. 1), pp. D543-D546
- Chaudhuri, R. R., Loman, Nicholas J., Snyder, Lori A. S., Bailey, C. M., Stekel, D. J., Pallen, Mark J., 2008. xBASE2 : a comprehensive resource for comparative bacterial genomics. Nucleic Acids Research, 36 (Database), pp. D543-D546
- Shaw, Robert K., Berger, C. N., Feys, B., Knutton, S., Pallen, Mark J., Frankel, Gad, 2008. Enterohemorrhagic escherichia coli exploits EspA filaments for attachment to salad leaves. Applied and Environmental Microbiology, 74 (9), pp. 2908-2914
- Arbeloa, Ana, Bulgin, Richard R., MacKenzie, Georgina, Shaw, Robert K., Pallen, Mark J., Crepin, Valerie F., Berger, Cedric N., Frankel, Gad, 2008. Subversion of actin dynamics by EspM effectors of attaching and effacing bacterial pathogens. Cellular Microbiology, 10 (7), pp. 1429-1441
- Singh, M. P., Shaw, Robert K., Knutton, S., Pallen, Mark J., Crepin, Valerie F., Frankel, Gad, 2008. Identification of amino acid residues within the n-terminal domain of EspA that play a role in EspA filament biogenesis and function. Journal of Bacteriology, 190 (6), pp. 2221-2226
- Loman, Nicholas J., Pallen, Mark J., 2008. XDR-TB genome sequencing : a glimpse of the microbiology of the future. Future Microbiology, 3 (2), pp. 111-113
- Pallen, Mark J., Pearn, Alison, 2013. Darwin and religion. Ruse, Alison (ed.), The Cambridge Encyclopedia of Darwin and Evolutionary Thought, Cambridge, Cambridge University Press
- Pallen, Mark J., 2011. The human microbiome and host?pathogen interactions. In Nelson, Karen (ed.), Metagenomics of the Human Body, New York, Springer-Verlag New York, pp. 43-61
- Pallen, Mark J., 2009. The rough guide to evolution. London, Rough Guides [2009]
- Sagar, Nidhi M., Kay, Gemma L., O'Connell, N., Nwokolo, Chuka U., Bardhan, Karna Dev, Quince, Christopher, Pallen, Mark J., Arasaradnam, Ramesh P., 2016. PWE-061 Dysbiosis in patients with bile acid diarrhoea (BAD) demonstrated using 16S RNA gene sequencing. British Society of Gastroenterology, Annual General Meeting, 20?23 Jun 2016, Published in Gut, pp. A168-A168
- Jones, J., Bianucci, Raffaella, Higham, T. F .G., Kay, G. L., Pallen, Mark J., Oldfield, R., Buckley, S. A., 2015. The prehistoric ?mummy' from Turin?s Egyptian Museum : preliminary scientific investigations. International Congress of Egyptologists XI, Florence, Italy, 23-30 Aug 2015
- Loman, Nicholas J., Manzoor, Susan, Quick, Joshua, Fothergill, J. L., Gossain, Savita, Kenna, D., Turton, J., Walshaw, M., Whitehouse, Joanna L., Pallen, Mark J., Winstanley, Craig, Hawkey, P. M. (Peter M.), Nash, E. F., 2014. 148 Use of whole-genome sequencing to identify transmission of Pseudomonas aeruginosa between cystic fibrosis patients. 37th European Cystic Fibrosis Conference, 11-14 Jun 2014, Published in Journal of Cystic Fibrosis
- Tacke, D., Gillis, M., Higgins, P. G., Millard, Andrew D., Chan, J. Z. M., Pallen, Mark J., Faetkenheuer, G., Cornely, O. A., Seifert, H., Vehreschild, M. J. G. T., 2014. Use of whole-genome sequencing to investigate the epidemiology of vancomycin-resistant enterococci on an intensive care unit. 24th European Society of Clinical Microbiology and Infectious Diseases (ECCMID) Conference 2014, Barcelona, Spain, 10-14 May 2014
- Quraishi, M. N., Sergeant, Martin J., Kay, Gemma L., Iqbal, Tariq, Constantinidou, Chrystala, Chan, Jacqueline, Trivedi, Palak J., Ferguson, James W., Adams, David H., Pallen, Mark J., Hirschfield, Gideon, 2014. Probing the microbiota in PSC : the gut adherent microbiota of PSC-IBD is distinct to that of IBD and controls. The 65th Annual Meeting of the American Association for the Study of Liver Diseases: The Liver Meeting 2014, Nov 2014, Published in Hepatology, pp. 264A-267A
- Attwood, N., Whitehead, R., Shukla, A., Parikh, R., Pallen, Mark J., Anthony, M., 2007. The WXG100 protein secretion system of streptococcus agalactiae. Neonatal Society 2007 Summer Meeting, Portsmouth, 28-29 Jun 2007, Published in Neonatal Society Abstracts
- Pallen, Mark J., 2013. Reply to Updating benchtop sequencing performance comparison. Nature Biotechnology, Nature Publishing Group, pp. 296-296
- Chan, Jacqueline, Sergeant, Martin J., Lee, Oona Y.-C., Minnikin, David E., Besra, Gurdyal S., Pap, Ilidkó, Spigelman, Mark, Donoghue, Helen D., Pallen, Mark J., 2013. Metagenomic analysis of tuberculosis in a mummy. New England Journal Of Medicine, Massachusetts Medical Society, pp. 289-290
- Foster, Timothy, Roche, Fiona, Pallen, Mark J., Patti, Joseph M., Hutchins, Jeff T., Speziale, Pietro, 2011. Surface proteins from coagulase-negative staphylococci and Staphylococcus aureus that generate cross-reactive monoclonal and polyclonal antibodies.
- Foster, T. J., Roche, F., Patti, J. M., Hutchins, J. T., Speziale, Pietro, Pallen, Mark J., 2011. Cross-reactive monoclonal and polyclonal antibodies which recognize surface proteins from coagulase-negative staphylococci and staphylococcus aureus.
| Title | Funder | Award start | Award end |
|---|---|---|---|
| THE MRC CONSORTIUM FOR MEDICAL MICROBIAL BIOINFORMATICS | MRC | 01 Apr 2014 | 01 Oct 2020 |
| The farm environment: an overlooked reservoir of Mycobacterium bovis? | BBSRC | 01 Apr 2016 | 31 Mar 2020 |
| BBSRC / Achten / EnteroBase: A Powerful, User-Friendly Online Resource for Analyzing and Visualizing Genomic Variation within Escherichia coli and Salmonella enterica | BBSRC | 01 Apr 2014 | 15 Oct 2019 |
| Fellowship - Chris Quince | MRC | 01 Sep 2014 | 31 Aug 2019 |
| Metagenomics characterization of the chicken caecal microbiome from Gambian chickens | BBSRC | 01 Sep 2016 | 31 Dec 2016 |
| Metagenomic characterization of vector-borne pathogens in the West Bank Palestinian territories | BBSRC | 01 Sep 2016 | 31 Dec 2016 |
| the Chicken caecal microbiome: from baselines to biological impact | BBSRC | 01 Oct 2013 | 31 May 2014 |
| The contributions of virulence clones vs. highly transmissible plasmids to the changing epidemiology of carbapenemases in the UK | National Institute for Health Research (DoH) | 30 Jul 2013 | 31 Mar 2014 |
| MRC Transfer from Birmingham University - Acinetobacter baumannii: genomic profiling of an emerging hospital pathogen | MRC | 01 Apr 2013 | 31 Aug 2013 |