Bacterial Pathogenomics

The Pallen Research Group

Our group benefits from Research-Council funding spanning bioinformatics and laboratory-based projects. Our interests focus on bacterial pathogenomics and type III secretion.

December 2009: in front of the Newcomen steam engine, Black Country Living Museum.
From Left to Right: Rob Shaw, Nick Loman, Tony Haines, Mark Pallen, Mike Halachev, Lewis Bingle, Rasha Younis, Raffaele Zarrilli (collaborator visiting from Italy)

• BBSRC Project Grant: xBASE: a bioinformatics resource for the AgriFood bacteriology community, (2007-2012); employs Nick Loman and Mike Halchev
  • xBASE latest stable Database Release
  • xBASE latest Database Release in beta-testing, now with >2000 genomes
  • xBASE bacterial genome annotation service
  • My xBASE allows you to combine the power of xBASE with your own sequences
  • publication in Nucleic Acids Research.
• High-throughput Sequencing
  • bioinformatics support for UB Genomics, our local 454 high-throughput sequencing service; employs Tony Haines [contact us on sequencing@contacts.bham.ac.uk]
  • World Map of High-Throughput Sequencing Facilities
  • our BLOG: Pathogens: Genes and Genomes [feed]
  • pathogenomenick on Twitter
• Microbial TIR domains, collaboration with DSTL [publication]
• Evolution of bacterial flagella and of type III secretion [publications]

• Genome sequencing of Acinetobacter baumannii isolates from Birmingham and Italy
• With colleagues in Birmingham, genome re-sequencing of enteric organisms (E. coli, Salmonella, Campylobacter).
• With collaborators in Nottingham, genome sequencing of hospital pathogens (Staphylococcus aureus, Pseudomonas aeruginosa, Clostridium difficile).
• Genomic epidemiology of Mycobacterium tuberculosis isolates from the Crown Hills Outbreak, with collaborators in Leicester.
• Genome sequencing of pneumococcal isolates from the Gambia, as part of an international team of collaborators from MRC Gambia and WashU
• Genome sequencing of Laribacter hongkongensis with HKU [publication]
• Genome sequencing of Helicobacter canadensis, with Brendan Wren, LSHTM [publication]

• BBSRC Project Grant: Ler, a versatile global regulator from E. coli O157 and related strains (2007-2010); supports Lewis Bingle and Rasha Younis
• Development of novel reporter system for type III secretion [Rasha Younis]
• Interactions between enteric pathogens and plants: collaboration led by Gadi Frankel; employs Rob Shaw [publications]
• BBSRC Project Grant: Discovery and characterisation of novel type III secretion effectors (2006-2009; Sophie Matthews; Rob Shaw; Rasha Younis) [publication in PNAS]

Current members

Professor Mark Pallen
Professor of Microbial
Genomics

Dr Nick Loman
Bioinformatician

Dr Mihail "Mike" Halachev
Bioinformatician

Dr Tony Haines
Bioinformatician

Dr Lewis Bingle
Post-doctoral Research Fellow

Rasha Younis
Part-time Research Assistant

Dr Rob Shaw
Post-doctoral Reseach Fellow

Past members

Lori Snyder
(now at University of Kingston)

Sally (ChuanPeng) Ren
(now in Surrey)

Chris Bailey
(now working for IWGC)

Sophie Matthews

Scott Beatson
(now in Australia)

Lihong Zhang
(now in Warwick)

Roy Chaudhuri
(now in Cambridge)

Helen Betts/Hampikian
(now in Miami)

Arshad Khan
(now in London)

Martin Antonio
(now in the Gambia)