- Reagent and laboratory contamination can critically impact sequence-based microbiome analyses
Susannah J Salter
Pathogen Genomics Group, Wellcome Trust Sanger Institute, Hinxton, UK
BMC Biol 12:87. 2014
..One potential confounder of these sequence-based approaches is the presence of contamination in DNA extraction kits and other laboratory reagents...
- Are diagnostic and public health bacteriology ready to become branches of genomic medicine?
Mark J Pallen
Centre for Systems Biology, School of Biosciences, University of Birmingham, Birmingham, B15 2TT, UK
Genome Med 3:53. 2011
..mean we are on the brink of a revolution in diagnostic and public health microbiology, in which high-throughput sequencing usurps the traditional 'M, C & S', or will the discipline's innate conservatism stand firm for decades to come?..
- Defining bacterial species in the genomic era: insights from the genus Acinetobacter
Jacqueline Z M Chan
Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Edgbaston B15 2TT, UK
BMC Microbiol 12:302. 2012
..Here, drawing on the genus Acinetobacter as a test case, we examine whether bacterial taxonomy could abandon phenotypic approaches and DNA-DNA hybridization and, instead, rely exclusively on analyses of genome sequence data...
- Simple sequence repeats in Helicobacter canadensis and their role in phase variable expression and C-terminal sequence switching
Lori A S Snyder
Centre for Systems Biology, School of Biosciences, University of Birmingham, Edgbaston, Birmingham B152TT, UK
BMC Genomics 11:67. 2010
..Helicobacter canadensis is an emerging human pathogen and zoonotic agent. The genome of H. canadensis was sequenced previously and determined to contain 29 annotated coding regions associated with homopolymeric tracts...
- EntrezAJAX: direct web browser access to the Entrez Programming Utilities
Nicholas J Loman
Centre for Systems Biology, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
Source Code Biol Med 5:6. 2010
..For the purposes of speed, reliability and scalability, EntrezAJAX has been deployed on Google App Engine, a freely available cloud service. The EntrezAJAX webpage is located at http://entrezajax.appspot.com/..
- High-throughput sequencing and clinical microbiology: progress, opportunities and challenges
Mark J Pallen
School of Biosciences, University of Birmingham, Birmingham, B15 2TT, United Kingdom
Curr Opin Microbiol 13:625-31. 2010
..We should prepare for the coming 'technological singularity' in sequencing, when this technology becomes so fast and so cheap that it threatens to out-compete existing diagnostic and typing methods in microbiology...
- xBASE2: a comprehensive resource for comparative bacterial genomics
Roy R Chaudhuri
Centre for Systems Biology, University of Birmingham, Birmingham B15 2TT, UK
Nucleic Acids Res 36:D543-6. 2008
..bham.ac.uk), now provides comprehensive coverage of all bacterial genomes and features an updated modularized backend and an improved user interface, which includes a taxonomy browser and a powerful full-text search facility...