Journal Article

Jones, Jana, Higham, Thomas F.G., Chivall, David, Bianucci, Raffaella, Kay, Gemma L., Pallen, Mark J., 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. doi:10.1016/j.jas.2018.07.011

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. and Antonio, Martin (2017) Whole-genome sequencing illuminates the evolution and spread of multidrug-resistant tuberculosis in Southwest Nigeria. PLoS One, 12 (9). e0184510. doi:10.1371/journal.pone.0184510

Card, Roderick M., Cawthraw, Shaun A., Nunez-Garcia, Javier, Ellis, Richard J., Kay, Gemma, Pallen, Mark J., 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. doi:10.1128/mBio.00777-17

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. and Fullam, Elizabeth (2017) Identification of the anti-mycobacterial functional properties of piperidinol derivatives. British Journal of Pharmacology, 174 (14). pp. 2183-2193. doi:10.1111/bph.13744

Unnikrishnan, Meera, Constantinidou, Chrystala, Palmer, Tracy and Pallen, Mark J. (2017) The enigmatic Esx proteins : looking beyond mycobacteria. Trends in Microbiology, 25 (3). pp. 192-204. doi:10.1016/j.tim.2016.11.004

Higgins, P. G., Chan, J. Z.-M., Seifert, H., Pallen, Mark J. and Millard, Andrew D. (2016) Draft genome sequences of 11 clinical isolates of Acinetobacter baumannii. Genome Announcements, 4 (2). e00269. doi:10.1128/genomeA.00269-16

Millard, Andrew D., Westblade, Lars, LiPuma, John J., Vavikolanu, Kranthi, Read, Timothy, Pallen, Mark J., Burd, Eileen and Constantinidou, Chrystala (2015) Genome Sequence of the Pandoraea apista LMG 16407 Type Strain. Journal of Bacteriology, 3 (6). e01300-e01315. doi:10.1128/genomeA.01300-15

Loman, Nicholas J. and Pallen, Mark J. (2015) Twenty years of bacterial genome sequencing. Nature Reviews Microbiology . doi:10.1038/nrmicro3565

Hänsch, Stephanie, Cilli, Elisabetta, Catalano, Giulioilda, Gruppioni, Giorgio, Bianucci, Raffaella, Stenseth, Nils C., Bramanti, Barbara and Pallen, Mark J. (2015) The pla gene, encoding plasminogen activator, is not specific to Yersinia pestis. BMC Research Notes, 8 (1). pp. 1-3. doi:10.1186/s13104-015-1525-x

Webber, Mark A., Whitehead, Rebekah N., Mount, Manuella, Loman, Nicholas J., Pallen, Mark J. and Piddock, Laura J. V. (2015) Parallel evolutionary pathways to antibiotic resistance selected by biocide exposure. Journal of antimicrobial chemotherapy, Volume 70 (Number 8). pp. 2241-2248. doi:10.1093/jac/dkv109

Smith, Oliver, Momber, G., Bates, R., Garwood, P., Fitch, S., Pallen, Mark J., Gaffney, V. and 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). p. 247. doi:10.1126/science.aab2062

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. doi:10.1371/journal.pntd.0003861

Kay, Gemma L., Sergeant, Martin J., Zhou, Zhemin, Chan, Jacqueline, Millard, Andrew D., Quick, Joshua, Szikossy, Ildikó, Pap, Ildikó, 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. doi:10.1038/ncomms7717

Bruce, A. G., Thouless, M. E. , Haines, A. S., Pallen, Mark J., Grundhoff, A. and 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, Volume 89 (Number 7). pp. 3888-3909. doi:10.1128/JVI.03597-14

Smith, Oliver , Momber, G., Bates, R., Garwood, P., Fitch, S., Pallen, Mark J., Gaffney, V. and Allaby, Robin G. (2015) Sedimentary DNA from a submerged site reveals wheat in the British Isles 8000 years ago. Science, Volume 347 (Number 6225). pp. 998-1001. doi:10.1126/science.1261278

Pallen, Mark J. (2014) Diagnostic metagenomics : potential applications to bacterial, viral and parasitic infections. Parasitology , Volume 141 (Number 14). pp. 1856-1862. doi:10.1017/S0031182014000134

Halachev, Mihail R., Chan, Jacqueline, Constantinidou, Chrystala, Cumley, Nicola, Bradley, Craig, Smith-Banks, Matthew, Oppenheim, Beryl and Pallen, Mark J. (2014) Genomic epidemiology of a protracted hospital outbreak caused by multidrug-resistant Acinetobacter baumannii in Birmingham, England. Genome Medicine, Volume 6 (Number 11). pp. 1-13. Article number 70. doi:10.1186/s13073-014-0070-x

Quick, Joshua, Cumley, Nicola, Wearn, Christopher M., Niebel, Marc, Constantinidou, Chrystala, Thomas, Christopher M., Pallen, Mark J., Moiemen, Naiem S., Bamford, Amy, Oppenheim, Beryl and 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, Volume 4 (Number 11). Article number e006278. doi:10.1136/bmjopen-2014-006278

Doughty, Emma L., Sergeant, Martin J., Ifedayo, Adetifa M. O., Antonio, Martin and 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 . Article number e585 . doi:10.7717/peerj.585

Kay, Gemma L., Sergeant, Martin J., Giuffra, Valentina, Bandiera, Pasquale, Milanese, Marco, Bramanti, Barbara, Bianucci, Raffaella and Pallen, Mark J. (2014) Recovery of a medieval Brucella melitensis genome using shotgun metagenomics. mBio, Volume 5 (Number 4). Article number e01337-14. doi:10.1128/mBio.01337-14

Quick, Joshua , Constantinidou, Chrystala, Pallen, Mark J., Oppenheim, Beryl and Loman, Nicholas J. (2014) Draft genome sequence of Elizabethkingia meningoseptica isolated from a traumatic wound. Genome Announcements, Volume 2 (Number 3). Article number e00355-14. doi:10.1128/genomeA.00355-14

Sergeant, Martin J., Constantinidou, Chrystala, Cogan, Tristan A., Bedford, Michael R., Penn, Charles W. and Pallen, Mark J. (2014) Extensive microbial and functional diversity within the chicken cecal microbiome. PLoS ONE , Volume 9 (Number 3). Article number e91941. doi:10.1371/journal.pone.0091941

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. and Pallen, Mark J. (2014) Microarray analysis of the ler regulon in enteropathogenic and enterohaemorrhagic escherichia coli strains. PLoS One, Volume 9 (Number 1). e80160. doi:10.1371/journal.pone.0080160

Snyder, L. A., Loman, Nicholas J., Faraj, L. A., Levi, K., Weinstock, G., Boswell, T. C., Pallen, Mark J. and 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, Volume 18 (Number 42). 20611.

(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. doi:10.5539/gjhs.v5n6p112

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. and Clarke, Stuart C. (2013) Clonal expansion within pneumococcal serotype 6C after use of seven-valent vaccine. PLoS One, Volume 8 (Number 5). e64731. doi:10.1371/journal.pone.0064731

Robinson, Esther R., Walker, Timothy M. and Pallen, Mark J. (2013) Genomics and outbreak investigation : from sequence to consequence. Genome Medicine, 5 (4). 36. doi:10.1186/gm440

(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, Volume 8 (Number 4). Article number e60933. doi:10.1371/journal.pone.0060933

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 and 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, Volume 309 (Number 14). pp. 1502-1510. doi:10.1001/jama.2013.3231

Loman, Nicholas J., Constantinidou, Chrystala, Chan, Jacqueline, Halachev, Mihail R., Sergeant, Martin J., Penn, Charles W., Robinson, Esther R. and 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. doi:10.1038/nrmicro2850

Constantinidou, Chrystala, Sergeant, Martin J., Cogan, Tristan, Penn, Charles W. and Pallen, Mark J. (2012) High-throughput sequencing of 16S rRNA gene amplicons : effects of extraction procedure, primer length and annealing temperature. PLoS One, Volume 7 (Number 5). Article number e38094. doi:10.1371/journal.pone.0038094

Loman, Nicholas J., Misra, Raju V., Dallman, Timothy J., Constantinidou, Chrystala, Gharbia, Saheer E., Wain, John and Pallen, Mark J. (2012) Performance comparison of benchtop high-throughput sequencing platforms. Nature Biotechnology, Volume 30 (Number 5). pp. 434-439. doi:10.1038/nbt.2198

Islam, Md. Shahidul, Shaw, Robert K., Frankel, Gad, Pallen, Mark J. and 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. doi:10.1042/BJ20110912

Van Wyhe, John and Pallen, Mark J. (2012) The ‘Annie Hypothesis' : did the death of His daughter cause Darwin to ‘Give up Christianity’? Centaurus, Volume 54 (Number 2). pp. 105-123. doi:10.1111/j.1600-0498.2012.00256.x

Chan, Jacqueline, Halachev, Mihail R., Loman, Nicholas J., Constantinidou, Chrystala and Pallen, Mark J. (2012) Defining bacterial species in the genomic era : insights from the genus Acinetobacter. BMC Microbiology, 12 (1). 302. doi:10.1186/1471-2180-12-302

Kochar, M., Crosatti, M., Harrison, E. M., Rieck, B., Chan, J., Constantinidou, Chrystala, Pallen, Mark J., Ou, H.-Y. and 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 (Number 4). pp. 1845-1853. doi:10.1128/AAC.05334-11

Williams, Tiffany M., Loman, Nicholas J., Ebruke, Chinelo, Musher, Daniel M., Adegbola, Richard A., Pallen, Mark J., Weinstock, George M. and Antonio, Martin (2012) Genome analysis of a highly virulent serotype 1 strain of streptococcus pneumoniae from West Africa. PLoS One, Volume 7 (Number 10). Article number e26742. doi:10.1371/journal.pone.0026742

Chan, Jacqueline, Pallen, Mark J., Oppenheim, Beryl and Constantinidou, Chrystala (2012) Genome sequencing in clinical microbiology. Nature Biotechnology, Volume 30 (Number 11). pp. 1068-1071. doi:10.1038/nbt.2410

Chan, Jacqueline, Pallen, Mark J., Oppenheim, Beryl and Constantinidou, Chrystala (2012) Genome sequencing in clinical microbiology. Nature Biotechnology, Volume 30 (Number 11). pp. 1068-1071. doi:10.1038/nbt.2410

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 and Besra, Gurdyal S. (2012) Identification of novel Imidazo[1,2-a]pyridine inhibitors targeting M. tuberculosis QcrB. PLoS One, Volume 7 (Number 12). Article number e52951. doi:10.1371/journal.pone.0052951

Loman, Nicholas J., Misra, Raju V., Dallman, Timothy J, Constantinidou, Chrystala, Gharbia, Saheer E, Wain, John and Pallen, Mark J. (2012) Performance comparison of benchtop high-throughput sequencing platforms. Nature Biotechnology, 30 (6). p. 562. doi:10.1038/nbt0612-562f

Chan, Jacqueline, Halachev, Mihail R., Yates, Emma, Smith, Grace and Pallen, Mark J. (2012) Whole-genome sequence of the emerging pathogen mycobacterium abscessus strain 47J26. Journal of Bacteriology, Volume 194 (Number 2). p. 549. doi:10.1128/JB.06440-11

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. and Henderson, I. R. (2011) Complete genome sequence of the Crohn's disease-associated adherent-invasive escherichia coliStrain HM605. Journal of Bacteriology, Volume 193 (Number 17). Article number 4540. doi:10.1128/JB.05374-11

(2011) Open-source genomic analysis of shiga-toxin–producing E. coli O104:H4. New England Journal Of Medicine , 365 (8). pp. 718-724. doi:10.1056/NEJMoa1107643

Pallen, Mark J. and Loman, Nicholas J. (2011) Are diagnostic and public health bacteriology ready to become branches of genomic medicine? Genome Medicine, Volume 3 (Number 8). Article number 53. doi:10.1186/gm269

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. and 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, Volume 66 (Number 7). pp. 1499-1503. doi:10.1093/jac/dkr168

Islam, Md. Shahidul, Pallen, Mark J. and 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. doi:10.1042/BJ20110260

Shaw, Robert K., Lasa, Iñigo, García, Begoña M., Pallen, Mark J., Hinton, Jay C. D., Berger, Cedric N. and Frankel, Gad (2011) Cellulose mediates attachment of Salmonella enterica Serovar Typhimurium to tomatoes. Environmental Microbiology Reports, Volume 3 (Number 5). pp. 569-573. doi:10.1111/j.1758-2229.2011.00263.x

Zarrilli, R., Giannouli, M., Rocco, F., Loman, Nicholas J., Haines, A. S., Constantinidou, Chrystala, Pallen, Mark J., Triassi, M. and 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, Volume 193 (Number 9). pp. 2359-2360. doi:10.1128/JB.00245-11

Pallen, Mark J. (2011) Time to recognise that mitochondria are bacteria? Trends in Microbiology, Volume 19 (Number 2). pp. 58-64. doi:10.1016/j.tim.2010.11.001

Halachev, Mihail R., Loman, Nicholas J. and Pallen, Mark J. (2011) Calculating orthologs in bacteria and archaea : a divide and conquer approach. PLoS One, Volume 6 (Number 12). Article number e28388. doi:10.1371/journal.pone.0028388

Ricci, V., Loman, Nicholas J., Pallen, Mark J., Ivens, Alasdair, Fookes, M., Langridge, G. C., Wain, J. and Piddock, Laura J. V. (2011) The TCA cycle is not required for selection or survival of multidrug-resistant Salmonella. Journal of Antimicrobial Chemotherapy, Volume 67 (Number 3). pp. 589-599. doi:10.1093/jac/dkr515

Islam, Md. Shahidul, Pallen, Mark J. and Busby, Stephen J. W. (2011) A cryptic promoter in theLEE1regulatory region of enterohaemorrhagicEscherichia coli: promoter specificity in AT-rich gene regulatory regions. Biochemical Journal, Volume 436 (Number 3). pp. 681-686. doi:10.1042/BJ20110260

(2010) A commensal gone bad : complete genome sequence of the prototypical enterotoxigenic escherichia coli strain H10407. Journal of Bacteriology, Volume 192 (Number 21). pp. 5822-5831. doi:10.1128/JB.00710-10

Shukla, Anshuman, Pallen, Mark J., Anthony, Mark and White, Scott A. (2010) The homodimeric GBS1074 fromStreptococcus agalactiae. Acta Crystallographica Section F Structural Biology and Crystallization Communications, Volume 66 (Number 11). pp. 1421-1425. doi:10.1107/S1744309110036286

Shaw, Robert K., Berger, Cedric N., Pallen, Mark J., Sjöling, Åsa and Frankel, Gad (2010) Flagella mediate attachment of enterotoxigenic Escherichia coli to fresh salad leaves. Environmental Microbiology Reports, Volume 3 (Number 1). pp. 112-117. doi:10.1111/j.1758-2229.2010.00195.x

(2010) Complete genome sequence and comparative metabolic profiling of the prototypical enteroaggregative escherichia coli strain 042. PLoS One, 5 (1). e8801. doi:10.1371/journal.pone.0008801

Loman, Nicholas J. and Pallen, Mark J. (2010) EntrezAJAX : direct web browser access to the Entrez Programming Utilities. Source Code for Biology and Medicine, volume 5 (Number 1). Article number 6. doi:10.1186/1751-0473-5-6

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 . S1. doi:10.1016/S0195-6701(10)00376-2

Pallen, Mark J., Loman, Nicholas J. and Penn, Charles W. (2010) High-throughput sequencing and clinical microbiology : progress, opportunities and challenges. Current Opinion in Microbiology, Volume 13 (Number 5). pp. 625-631. doi:10.1016/j.mib.2010.08.003

Lewis, T., Loman, Nicholas J., Bingle, L., Jumaa, P., Weinstock, G. M., Mortiboy, D. and 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, Volume 75 (Number 1). pp. 37-41. doi:10.1016/j.jhin.2010.01.012

Islam, Md. Shahidul, Bingle, Lewis E. H., Pallen, Mark J. and Busby, Stephen J. W. (2010) Organization of the LEE1 operon regulatory region of enterohaemorrhagic Escherichia coli O157:H7 and activation by GrlA. Molecular Microbiology, 79 (2). pp. 468-483. doi:10.1111/j.1365-2958.2010.07460.x

Younis, R., Bingle, L. E. H., Rollauer, S., Munera, D., Busby, S. J., Johnson, S., Deane, J. E., Lea, S. M., Frankel, G. and 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, Volume 192 (Number 22). pp. 6093-6098. doi:10.1128/JB.00760-10

Snyder, Lori A. S., Loman, Nicholas J., Linton, James D., Langdon, Rebecca R., Weinstock, George M., Wren, Brendan and Pallen, Mark J. (2010) Simple sequence repeats in Helicobacter canadensis and their role in phase variable expression and C-terminal sequence switching. BMC Genomics, Volume 11 (Number 1). Article number 67. doi:10.1186/1471-2164-11-67

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 and 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). e1000416. doi:10.1371/journal.pgen.1000416

Snyder, Lori A. S., Loman, Nicholas J., Pallen, Mark J. and Penn, C. W. (2009) Next-generation sequencing—the promise and perils of charting the great microbial unknown. Microbial Ecology, 57 (1). pp. 1-3. doi:10.1007/s00248-008-9465-9

Snyder, Lori A.S., Loman, Nicholas J., Fütterer, Klaus and Pallen, Mark J. (2009) Bacterial flagellar diversity and evolution : seek simplicity and distrust it? Trends in Microbiology, 17 (1). pp. 1-5. doi:10.1016/j.tim.2008.10.002

Snyder, Lori A. S., Cole, Jeff A and 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). p. 70. doi:10.1186/1471-2164-10-70

Pallen, Mark J. (2009) Darwin : from the origin of species to the origin of infection. Microbiology Today, 36 . p. 76.

Lee, David J., Bingle, Lewis E. H., Heurlier, Karin, Pallen, Mark J., Penn, Charles W., Busby, Stephen J. W. and Hobman, Jon L. (2009) Gene doctoring : a method for recombineering in laboratory and pathogenic Escherichia coli strains. BMC Microbiology, 9 (1). p. 252. doi:10.1186/1471-2180-9-252

Loman, Nicholas J., Snyder, Lori A. S., Linton, James D., Langdon, Rebecca R., Lawson, A. J., Weinstock, G. M., Wren, B. W. and Pallen, Mark J. (2009) Genome sequence of the emerging pathogen helicobacter canadensis. Journal of Bacteriology, 191 (17). pp. 5566-5567. doi:10.1128/JB.00729-09

Berger, Cedric N., Shaw, Robert K., Ruiz-Perez, Fernando, Nataro, James P., Henderson, Ian R., Pallen, Mark J. and Frankel, Gad (2009) Interaction of enteroaggregative escherichia coli with salad leaves. Environmental Microbiology Reports, 1 (4). pp. 234-239. doi:10.1111/j.1758-2229.2009.00037.x

Berger, Cedric N., Shaw, Robert K., Brown, Derek, Mather, H., Clare, Simon, Dougan, G., Pallen, Mark J. and Frankel, Gad (2009) Interaction of salmonella enterica with basil and other salad leaves. The ISME Journal, 3 (2). pp. 261-265. doi:10.1038/ismej.2008.95

Spear, Abigail M., Loman, Nicholas J., Atkins, Helen S. and Pallen, Mark J. (2009) Microbial TIR domains : not necessarily agents of subversion? Trends in Microbiology, 17 (9). pp. 393-398. doi:10.1016/j.tim.2009.06.005

Chaudhuri, R. R., Loman, Nicholas J., Snyder, L. A.S., Bailey, C. M., Stekel, D. J. and Pallen, Mark J. (2008) xBASE2 : a comprehensive resource for comparative bacterial genomics. Nucleic Acids Research, 36 (Suppl. 1). D543-D546. doi:10.1093/nar/gkm928

Shaw, Robert K., Berger, C. N., Feys, B., Knutton, S., Pallen, Mark J. and Frankel, Gad (2008) Enterohemorrhagic escherichia coli exploits EspA filaments for attachment to salad leaves. Applied and Environmental Microbiology, 74 (9). pp. 2908-2914. doi:10.1128/AEM.02704-07

Singh, M. P., Shaw, Robert K., Knutton, S., Pallen, Mark J., Crepin, Valerie F. and 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. doi:10.1128/JB.01753-07

Arbeloa, Ana, Bulgin, Richard R., MacKenzie, Georgina, Shaw, Robert K., Pallen, Mark J., Crepin, Valerie F., Berger, Cedric N. and Frankel, Gad (2008) Subversion of actin dynamics by EspM effectors of attaching and effacing bacterial pathogens. Cellular Microbiology, 10 (7). pp. 1429-1441. doi:10.1111/j.1462-5822.2008.01136.x

Bingle, Lewis E. H., Bailey, Christopher M. and Pallen, Mark J. (2008) Type VI secretion : a beginner's guide. Current Opinion in Microbiology, 11 (1). pp. 3-8. doi:10.1016/j.mib.2008.01.006

Loman, Nicholas J. and Pallen, Mark J. (2008) XDR-TB genome sequencing : a glimpse of the microbiology of the future. Future Microbiology, 3 (2). pp. 111-113. doi:10.2217/17460913.3.2.111

Chaudhuri, R. R., Loman, Nicholas J., Snyder, Lori A. S., Bailey, C. M., Stekel, D. J. and Pallen, Mark J. (2008) xBASE2 : a comprehensive resource for comparative bacterial genomics. Nucleic Acids Research, 36 (Database). D543-D546. doi:10.1093/nar/gkm928

Book Item

Pallen, Mark J. and Pearn, Alison (2013) Darwin and religion. In: Ruse, Alison, (ed.) The Cambridge Encyclopedia of Darwin and Evolutionary Thought. Cambridge: Cambridge University Press. ISBN 9780521195317

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. ISBN 9781441970886

Conference Item

Sagar, Nidhi M., Kay, Gemma L., O’Connell, N., Nwokolo, Chuka U., Bardhan, Karna Dev, Quince, Christopher, Pallen, Mark J. and Arasaradnam, Ramesh P. (2016) PWE-061 Dysbiosis in patients with bile acid diarrhoea (BAD) demonstrated using 16S RNA gene sequencing. In: British Society of Gastroenterology, Annual General Meeting, 20–23 Jun 2016. Published in: Gut, 65 (Supplement 1). A168-A168. ISSN 0017-5749. doi:10.1136/gutjnl-2016-312388.307

Jones, J., Bianucci, Raffaella, Higham, T. F .G., Kay, G. L., Pallen, Mark J., Oldfield, R. and Buckley, S. A. (2015) The prehistoric ‘mummy’ from Turin’s Egyptian Museum : preliminary scientific investigations. In: 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.) and Nash, E. F. (2014) 148 Use of whole-genome sequencing to identify transmission of Pseudomonas aeruginosa between cystic fibrosis patients. In: 37th European Cystic Fibrosis Conference, 11-14 Jun 2014. Published in: Journal of Cystic Fibrosis, Volume 13 ISSN 1569-1993. doi:10.1016/S1569-1993(14)60284-8

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. and Hirschfield, Gideon (2014) Probing the microbiota in PSC : the gut adherent microbiota of PSC-IBD is distinct to that of IBD and controls. In: The 65th Annual Meeting of the American Association for the Study of Liver Diseases: The Liver Meeting 2014, Nov 2014. Published in: Hepatology, 60 (S1). 264A-267A. ISSN 0270-9139. doi:10.1002/hep.27470

Tacke, D., Gillis, M., Higgins, P. G., Millard, Andrew D., Chan, J. Z. M., Pallen, Mark J., Faetkenheuer, G., Cornely, O. A., Seifert, H. and Vehreschild, M. J. G. T. (2014) Use of whole-genome sequencing to investigate the epidemiology of vancomycin-resistant enterococci on an intensive care unit. In: 24th European Society of Clinical Microbiology and Infectious Diseases (ECCMID) Conference 2014, Barcelona, Spain, 10-14 May 2014

Attwood, N., Whitehead, R., Shukla, A., Parikh, R., Pallen, Mark J. and Anthony, M. (2007) The WXG100 protein secretion system of streptococcus agalactiae. In: Neonatal Society 2007 Summer Meeting, Portsmouth, 28-29 Jun 2007. Published in: Neonatal Society Abstracts, Summer 2007

Book

Pallen, Mark J. (2009) The rough guide to evolution. Rough Guides; Dorling Kindersley Ltd . London: Rough Guides [2009]. ISBN 9781858289465

Journal Item

Chan, Jacqueline, Sergeant, Martin J., Lee, Oona Y.-C., Minnikin, David E., Besra, Gurdyal S., Pap, Ilidkó, Spigelman, Mark, Donoghue, Helen D. and Pallen, Mark J. (2013) Metagenomic analysis of tuberculosis in a mummy. New England Journal Of Medicine , Volume 369 (Number3). pp. 289-290. doi:10.1056/NEJMc1302295

Pallen, Mark J. (2013) Reply to Updating benchtop sequencing performance comparison. Nature Biotechnology, Volume 31 (Number 4). p. 296. doi:10.1038/nbt.2531

Patent

US7968100 B2; CA2450939A1 (2011) Surface proteins from coagulase-negative staphylococci and Staphylococcus aureus that generate cross-reactive monoclonal and polyclonal antibodies. [Online]. Available at: http://www.google.com/patents/US7968100.

2320233; CA 2450939 A1 (2011) Cross-reactive monoclonal and polyclonal antibodies which recognize surface proteins from coagulase-negative staphylococci and staphylococcus aureus. [Online]. Available at: http://www.google.com.na/patents/CA2450939A1?cl=en.