Colin F Davenport
Affiliation: Hannover Medical School
- Genometa--a fast and accurate classifier for short metagenomic shotgun readsColin F Davenport
Pediatric Pneumology, Allergology and Neonatology, Hannover Medical School, Hannover, Lower Saxony, Germany
PLoS ONE 7:e41224. 2012..This method is one of the most user-friendly and resource efficient approaches and is thus feasible for rapidly analysing millions of short reads on a personal computer...
- The SeqWord Genome Browser: an online tool for the identification and visualization of atypical regions of bacterial genomes through oligonucleotide usageHamilton Ganesan
Dep of Biochemistry, Bioinformatics and Computational Biology Unit, University of Pretoria, Lynnwood Road, Hillcrest, Pretoria, 0002, South Africa
BMC Bioinformatics 9:333. 2008..The purpose of this research was to make OU statistical analysis available as a novel web-based tool for functional genomics and annotation. The tool is also available as a downloadable package...
- Visualization of Pseudomonas genomic structure by abundant 8-14mer oligonucleotidesColin F Davenport
Klinische Forschergruppe, OE 6711, Medizinische Hochschule Hannover, Hanover, Germany
Environ Microbiol 11:1092-104. 2009..In the future of next-generation ultra-high throughput DNA sequencing, the composition of bacterial metagenomes may be quantified by scanning the primary sequence reads for these 8-14mer markers...
- Abundant oligonucleotides common to most bacteriaColin F Davenport
Pediatric Pneumology and Neonatology, Hanover Medical School, Hanover, Lower Saxony, Germany
PLoS ONE 5:e9841. 2010..We surveyed overrepresented mid-length oligomers across all prokaryotes and normalised for base composition and embedded oligomers using zero and second order Markov models...
- Intraclonal diversity of the Pseudomonas aeruginosa cystic fibrosis airway isolates TBCF10839 and TBCF121838: distinct signatures of transcriptome, proteome, metabolome, adherence and pathogenicity despite an almost identical genome sequenceJens Klockgether
Klinische Forschergruppe, Zentrum Biochemie und Zentrum Kinder und Jugendmedizin, OE 6710, D 30625 Hannover, Germany
Environ Microbiol 15:191-210. 2013..Microevolution in P. aeruginosa apparently can generate novel complex traits by few or even single mutations provided that predisposing mutational events had occurred before in the clonal lineage...
- Pseudomonas putida KT2440 genome update by cDNA sequencing and microarray transcriptomicsSarah Frank
Klinische Forschergruppe, Medizinische Hochschule Hannover, Carl Neuberg Strasse 1, Hannover, Germany
Environ Microbiol 13:1309-26. 2011..The study demonstrates the power of next-generation cDNA sequencing for the quantitation of mRNA transcripts and the refinement of bacterial genome annotation...
- Intraclonal genome diversity of Pseudomonas aeruginosa clones CHA and TBOliver Ki Bezuidt
Klinische Forschergruppe, Klinik für Pädiatrische Pneumologie, Allergologie und Neonatologie, Medizinische Hochschule Hannover, Hannover D 30625, Germany
BMC Genomics 14:416. 2013..The outcome was compared with the intraclonal genome diversity between three more closely related isolates of another clonal complex...
- Microevolution of the major common Pseudomonas aeruginosa clones C and PA14 in cystic fibrosis lungsNina Cramer
Klinische Forschergruppe, Klinik für Pädiatrische Pneumologie, Allergologie und Neonatologie, OE 6710, Medizinische Hochschule Hannover, Carl Neuberg Str 1, D 30625 Hannover, Germany
Environ Microbiol 13:1690-704. 2011..Late clone C and PA14 persistors in the CF lungs were compromised in growth and cytotoxicity, but their mutation frequency was normal even in mutL mutant clades...
- Intraclonal genome diversity of the major Pseudomonas aeruginosa clones C and PA14Sebastian Fischer
Clinical Research Group Molecular Pathology of Cystic Fibrosis and Pseudomonas Genomics, OE 6710, Hannover Medical School, Hannover, Germany
Environ Microbiol Rep 8:227-34. 2016..Each strain carried a large cargo of unique genes. The two dominant worldwide distributed P. aeruginosa clones combine an almost invariant core with the flexible gain and loss of genetic elements that spread by horizontal transfer. ..
- Functional genomics of the initial phase of cold adaptation of Pseudomonas putida KT2440Sarah Frank
Clinical Research Group, Medical School Hannover, Hannover, Germany
FEMS Microbiol Lett 318:47-54. 2011..At the investigated early time point of cold adaptation, the transcriptome was reprogrammed in almost all functional categories, but the protein profile had still not adapted to the change of living conditions in the cold...
- Genome diversity of Pseudomonas aeruginosa PAO1 laboratory strainsJens Klockgether
Klinische Forschergruppe, Medizinische Hochschule Hannover, Hannover, Germany
J Bacteriol 192:1113-21. 2010..High-throughput genome resequencing will resolve more cases and could become a proper quality control for strain collections...
- Advances in computational analysis of metagenome sequencesColin F Davenport
Klinische Forschergruppe, Klinik für Pädiatrische Pneumologie, Allergologie und Neonatologie, OE 6710, Medizinische Hochschule Hannover, D 30625 Hannover, Germany
Environ Microbiol 15:1-5. 2013..In conclusion, massively parallel sequencing of metagenomic DNA allows deep insights into the composition and the genetic repertoire of polymicrobial communities...