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.

Wordle diagram derived from recent Pallen group grant applications

• Pallen on Radio 4 show In our Time with Melvyn Bragg (see also blog entry)
• Loman kickstarts crowdsourcing analysis of E. coli O104 with an assembly of Ion Torrent Data
• Pallen wins Ion Torrent PGM, a new class of high-throughput sequencer.

• 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 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 [contact us on sequencing@contacts.bham.ac.uk]
  • World Map of High-Throughput Sequencing Facilities
  • our BLOG: Pathogens: Genes and Genomes [feed]
  • pathogenomenick (Nick Loman) on Twitter
  • mjpallen (Mark Pallen) 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 (MRC): See Acibase website
• The chicken caecal microbiome: from baseline to biology (BBSRC)
• 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]

Group Members

Current members

Professor Mark Pallen
Professor of Microbial
Genomics

Dr Nick Loman
Bioinformatician

Dr Mihail "Mike" Halachev
Bioinformatician

Dr Jacqueline Chan
Post-doctoral Research Fellow

Dr. Martin Sergeant
Post-doctoral Research Fellow

Dr Rob Shaw
Post-doctoral Reseach Fellow

Dr Chrsytala Constantinidou
Research Officer

Past members

Dr. Lewis Bingle
(now in University of Sunderland)

Rasha Younis
(now working in Genetics in the Medical School)

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)

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