BUPA Foundation

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

Biotechnology and Biological Sciences Research Council (Great Britain) (BBSRC)

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

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

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

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

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

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

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

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

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

Commonwealth Fund

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

Engineering and Physical Sciences Research Council (EPSRC)

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

European Regional Development Fund (ERDF)

(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

European Research Council (ERC)

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

Global Alliance for TB Drug Development

(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

Medical Research Council (Great Britain) (MRC)

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

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

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

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

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

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

National Center for Research Resources (U.S.) (NCRR)

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

National Human Genome Research Institute (U.S.) (NHGRI)

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

National Institute for Health Research (Great Britain) (NIHR)

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

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

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

National Institutes of Health (U.S.) (NIH)

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

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

Research Councils UK (RCUK)

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

Royal Society (Great Britain)

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

Royal Society (Great Britain). Wolfson Research Merit Award (RSWRMA)

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

Sardinia (Italy)

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

Seventh Framework Programme (European Commission) (FP7)

(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

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

Spain. Ministerio de Economía y Competitividad [Ministry of Economy and Competitiveness] (MINECO)

(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

University of Warwick. Institute of Advanced Study (IAS)

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

Warwick Medical School

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

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

Wellcome Trust

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

Wellcome Trust (London, England)

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

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