Colin F Davenport

Summary

Affiliation: Hannover Medical School
Country: Germany

Publications

  1. pmc Genometa--a fast and accurate classifier for short metagenomic shotgun reads
    Colin F Davenport
    Pediatric Pneumology, Allergology and Neonatology, Hannover Medical School, Hannover, Lower Saxony, Germany
    PLoS ONE 7:e41224. 2012
  2. pmc The SeqWord Genome Browser: an online tool for the identification and visualization of atypical regions of bacterial genomes through oligonucleotide usage
    Hamilton Ganesan
    Dep of Biochemistry, Bioinformatics and Computational Biology Unit, University of Pretoria, Lynnwood Road, Hillcrest, Pretoria, 0002, South Africa
    BMC Bioinformatics 9:333. 2008
  3. doi Visualization of Pseudomonas genomic structure by abundant 8-14mer oligonucleotides
    Colin F Davenport
    Klinische Forschergruppe, OE 6711, Medizinische Hochschule Hannover, Hanover, Germany
    Environ Microbiol 11:1092-104. 2009
  4. pmc Abundant oligonucleotides common to most bacteria
    Colin F Davenport
    Pediatric Pneumology and Neonatology, Hanover Medical School, Hanover, Lower Saxony, Germany
    PLoS ONE 5:e9841. 2010
  5. doi 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 sequence
    Jens Klockgether
    Klinische Forschergruppe, Zentrum Biochemie und Zentrum Kinder und Jugendmedizin, OE 6710, D 30625 Hannover, Germany
    Environ Microbiol 15:191-210. 2013
  6. doi Pseudomonas putida KT2440 genome update by cDNA sequencing and microarray transcriptomics
    Sarah Frank
    Klinische Forschergruppe, Medizinische Hochschule Hannover, Carl Neuberg Strasse 1, Hannover, Germany
    Environ Microbiol 13:1309-26. 2011
  7. pmc Intraclonal genome diversity of Pseudomonas aeruginosa clones CHA and TB
    Oliver Ki Bezuidt
    Klinische Forschergruppe, Klinik für Pädiatrische Pneumologie, Allergologie und Neonatologie, Medizinische Hochschule Hannover, Hannover D 30625, Germany
    BMC Genomics 14:416. 2013
  8. doi Microevolution of the major common Pseudomonas aeruginosa clones C and PA14 in cystic fibrosis lungs
    Nina 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
  9. doi Functional genomics of the initial phase of cold adaptation of Pseudomonas putida KT2440
    Sarah Frank
    Clinical Research Group, Medical School Hannover, Hannover, Germany
    FEMS Microbiol Lett 318:47-54. 2011
  10. pmc Genome diversity of Pseudomonas aeruginosa PAO1 laboratory strains
    Jens Klockgether
    Klinische Forschergruppe, Medizinische Hochschule Hannover, Hannover, Germany
    J Bacteriol 192:1113-21. 2010

Collaborators

Detail Information

Publications11

  1. pmc Genometa--a fast and accurate classifier for short metagenomic shotgun reads
    Colin F Davenport
    Pediatric Pneumology, Allergology and Neonatology, Hannover Medical School, Hannover, Lower Saxony, Germany
    PLoS ONE 7:e41224. 2012
    ..mh-hannover.de/genometa/ and on http://code.google.com/p/genometa/. This program has been tested on Ubuntu Linux and Windows XP/7...
  2. pmc The SeqWord Genome Browser: an online tool for the identification and visualization of atypical regions of bacterial genomes through oligonucleotide usage
    Hamilton 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...
  3. doi Visualization of Pseudomonas genomic structure by abundant 8-14mer oligonucleotides
    Colin 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...
  4. pmc Abundant oligonucleotides common to most bacteria
    Colin 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...
  5. doi 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 sequence
    Jens 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...
  6. doi Pseudomonas putida KT2440 genome update by cDNA sequencing and microarray transcriptomics
    Sarah 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...
  7. pmc Intraclonal genome diversity of Pseudomonas aeruginosa clones CHA and TB
    Oliver 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...
  8. doi Microevolution of the major common Pseudomonas aeruginosa clones C and PA14 in cystic fibrosis lungs
    Nina 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...
  9. doi Functional genomics of the initial phase of cold adaptation of Pseudomonas putida KT2440
    Sarah 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...
  10. pmc Genome diversity of Pseudomonas aeruginosa PAO1 laboratory strains
    Jens 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...
  11. doi Advances in computational analysis of metagenome sequences
    Colin 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...