David W Ussery

Summary

Affiliation: Center for Biological Sequence Analysis
Country: Denmark

Publications

  1. ncbi request reprint Bias of purine stretches in sequenced chromosomes
    David Ussery
    Department of Biotechnology, Center for Biological Sequence Analysis, The Technical University of Denmark, Lyngby
    Comput Chem 26:531-41. 2002
  2. ncbi request reprint Genome Update: AT content in sequenced prokaryotic genomes
    David W Ussery
    Center for Biological Sequence Analysis, Department of Biotechnology, Building 208, The Technical University of Denmark, Lyngby, DK 2800, Denmark
    Microbiology 150:749-52. 2004
  3. pmc Computational genomics-proteomics and Phylogeny analysis of twenty one mycobacterial genomes (Tuberculosis & non Tuberculosis strains)
    Fathiah Zakham
    Laboratoire de Virologie et Hygiène and Microbiologie, Faculte des Sciences et Techniques, BP 146, Mohammedia, 20650, Morocco
    Microb Inform Exp 2:7. 2012
  4. pmc Analysis of evolutionary patterns of genes in Campylobacter jejuni and C. coli
    Lars Snipen
    Department of Chemistry, Biotechnology and Food Sciences, Norwegian University of Life Sciences, As, Norway
    Microb Inform Exp 2:8. 2012
  5. pmc Relative entropy differences in bacterial chromosomes, plasmids, phages and genomic islands
    Jon Bohlin
    Norwegian School of Veterinary Science, Epicentre, Department of Food Safety and Infection Biology, Ullevålsveien 72, Oslo, Norway
    BMC Genomics 13:66. 2012
  6. pmc Molecular analysis of the emergence of pandemic Vibrio parahaemolyticus
    E Fidelma Boyd
    Department of Biological Sciences, University of Delaware, Newark, DE 19716, USA
    BMC Microbiol 8:110. 2008
  7. pmc Analysis of intra-genomic GC content homogeneity within prokaryotes
    Jon Bohlin
    Norwegian School of Veterinary Science, Department of Food Safety and Infection Biology, Ullevålsveien 72, P, O, Box 8146 Dep, NO 0033 Oslo, Norway
    BMC Genomics 11:464. 2010
  8. pmc Analysis of two large functionally uncharacterized regions in the Methanopyrus kandleri AV19 genome
    Lars Juhl Jensen
    Center for Biological Sequence Analysis, BioCentrum DTU, Building 208, The Technical University of Denmark, DK 2800 Lyngby, Denmark
    BMC Genomics 4:12. 2003
  9. pmc Reliability and applications of statistical methods based on oligonucleotide frequencies in bacterial and archaeal genomes
    Jon Bohlin
    Norwegian School of Veterinary Science, P O Box 8146 Dep, N 0033 Oslo, Norway
    BMC Genomics 9:104. 2008
  10. pmc The genome of the versatile nitrogen fixer Azorhizobium caulinodans ORS571
    Kyung Bum Lee
    Laboratory of Plant Biotechnology, Biotechnology Research Center, University of Tokyo, Tokyo 113 8657, Japan
    BMC Genomics 9:271. 2008

Detail Information

Publications74

  1. ncbi request reprint Bias of purine stretches in sequenced chromosomes
    David Ussery
    Department of Biotechnology, Center for Biological Sequence Analysis, The Technical University of Denmark, Lyngby
    Comput Chem 26:531-41. 2002
    ....
  2. ncbi request reprint Genome Update: AT content in sequenced prokaryotic genomes
    David W Ussery
    Center for Biological Sequence Analysis, Department of Biotechnology, Building 208, The Technical University of Denmark, Lyngby, DK 2800, Denmark
    Microbiology 150:749-52. 2004
  3. pmc Computational genomics-proteomics and Phylogeny analysis of twenty one mycobacterial genomes (Tuberculosis & non Tuberculosis strains)
    Fathiah Zakham
    Laboratoire de Virologie et Hygiène and Microbiologie, Faculte des Sciences et Techniques, BP 146, Mohammedia, 20650, Morocco
    Microb Inform Exp 2:7. 2012
    ..abstract:..
  4. pmc Analysis of evolutionary patterns of genes in Campylobacter jejuni and C. coli
    Lars Snipen
    Department of Chemistry, Biotechnology and Food Sciences, Norwegian University of Life Sciences, As, Norway
    Microb Inform Exp 2:8. 2012
    ..abstract:..
  5. pmc Relative entropy differences in bacterial chromosomes, plasmids, phages and genomic islands
    Jon Bohlin
    Norwegian School of Veterinary Science, Epicentre, Department of Food Safety and Infection Biology, Ullevålsveien 72, Oslo, Norway
    BMC Genomics 13:66. 2012
    ..We analyzed the differences in information capacity between prokaryotic chromosomes, genomic islands (GI), phages, and plasmids. Relative entropy was estimated using the Kullback-Leibler measure...
  6. pmc Molecular analysis of the emergence of pandemic Vibrio parahaemolyticus
    E Fidelma Boyd
    Department of Biological Sciences, University of Delaware, Newark, DE 19716, USA
    BMC Microbiol 8:110. 2008
    ..This new highly virulent strain is now globally disseminated...
  7. pmc Analysis of intra-genomic GC content homogeneity within prokaryotes
    Jon Bohlin
    Norwegian School of Veterinary Science, Department of Food Safety and Infection Biology, Ullevålsveien 72, P, O, Box 8146 Dep, NO 0033 Oslo, Norway
    BMC Genomics 11:464. 2010
    ..We utilize a new quantity GCVAR, the intra-genomic GC content variability with respect to the average GC content of the total genome. A low GCVAR indicates intra-genomic GC homogeneity and high GCVAR heterogeneity...
  8. pmc Analysis of two large functionally uncharacterized regions in the Methanopyrus kandleri AV19 genome
    Lars Juhl Jensen
    Center for Biological Sequence Analysis, BioCentrum DTU, Building 208, The Technical University of Denmark, DK 2800 Lyngby, Denmark
    BMC Genomics 4:12. 2003
    ..These hypothetical genes are typically short and randomly scattered throughout the genome. This trend is seen for most of the bacterial and archaeal genomes published to date...
  9. pmc Reliability and applications of statistical methods based on oligonucleotide frequencies in bacterial and archaeal genomes
    Jon Bohlin
    Norwegian School of Veterinary Science, P O Box 8146 Dep, N 0033 Oslo, Norway
    BMC Genomics 9:104. 2008
    ..Additionally, the reliability of the methods was tested by comparing both real and random genomic DNA...
  10. pmc The genome of the versatile nitrogen fixer Azorhizobium caulinodans ORS571
    Kyung Bum Lee
    Laboratory of Plant Biotechnology, Biotechnology Research Center, University of Tokyo, Tokyo 113 8657, Japan
    BMC Genomics 9:271. 2008
    ..The host is a fast-growing, submergence-tolerant tropical legume on which A. caulinodans can efficiently induce nodule formation on the root system and on adventitious rootlets located on the stem...
  11. pmc Stretches of alternating pyrimidine/purines and purines are respectively linked with pathogenicity and growth temperature in prokaryotes
    Jon Bohlin
    Norwegian School of Veterinary Science, Oslo, Norway
    BMC Genomics 10:346. 2009
    ....
  12. pmc Comparison of protein coding gene contents of the fungal phyla Pezizomycotina and Saccharomycotina
    Mikko Arvas
    VTT, Tietotie 2, Espoo, P, O, Box 1500, 02044 VTT, Finland
    BMC Genomics 8:325. 2007
    ..We have carried out a computational genome wide comparison of protein coding gene content of Saccharomycotina and Pezizomycotina, which include industrially important yeasts and filamentous fungi, respectively...
  13. pmc Analysis of genomic signatures in prokaryotes using multinomial regression and hierarchical clustering
    Jon Bohlin
    Norwegian School of Veterinary Science, Oslo, Norway
    BMC Genomics 10:487. 2009
    ..The regression model included the cluster groups as the response variable with AT content, phyla, growth temperature, selective pressure, habitat, sequence size, oxygen requirement and pathogenicity as predictors...
  14. pmc Comparative genomic analysis of two-component regulatory proteins in Pseudomonas syringae
    José L Lavín
    Departamento de Producción Agraria, Universidad Publica de Navarra, 31006 Pamplona, Spain
    BMC Genomics 8:397. 2007
    ..P. syringae requires a complex array of TCS proteins to cope with diverse plant hosts, host responses, and environmental conditions...
  15. pmc Microbial comparative pan-genomics using binomial mixture models
    Lars Snipen
    Biostatistics, Department of Chemistry, Biotechnology and Food Sciences, Norwegian University of Life Sciences, As, Norway
    BMC Genomics 10:385. 2009
    ..Attempts to estimate these quantities have been made, using regression methods or mixture models. We extend the latter approach by using statistical ideas developed for capture-recapture problems in ecology and epidemiology...
  16. pmc Genomic taxonomy of Vibrios
    Cristiane C Thompson
    Laboratory of Molecular Genetics of Microrganims, Oswaldo Cruz Institute, FIOCRUZ, Rio de Janeiro, Brazil
    BMC Evol Biol 9:258. 2009
    ..Our aim is to analyse the usefulness of these tools for species identification in vibrios...
  17. pmc Genomic comparisons of Brucella spp. and closely related bacteria using base compositional and proteome based methods
    Jon Bohlin
    Norwegian School of Veterinary Science, Department of Food Safety and Infection Biology, EpiCenter, Ullevålsveien 72, PO Box 8146 Dep, NO 0033 Oslo, Norway
    BMC Evol Biol 10:249. 2010
    ....
  18. ncbi request reprint Genome update: DNA repeats in bacterial genomes
    David W Ussery
    Center for Biological Sequence Analysis, Department of Biotechnology, Building 208, The Technical University of Denmark, DK 2800 Kgs Lyngby, Denmark
    Microbiology 150:3519-21. 2004
  19. pmc Leaner and meaner genomes in Escherichia coli
    David W Ussery
    Center for Biological Sequence Analysis, BioCentrum DTU, Technical University of Denmark, DK 2800 Kgs, Lyngby, Denmark
    Genome Biol 7:237. 2006
    ..Comparison with related bacterial genomes that have undergone a natural reduction in size suggests that there is plenty of scope for yet more deletions...
  20. ncbi request reprint Environmental influences on DNA curvature
    D W Ussery
    Centre for Biological Sequence Analysis, Department of Biotechnology, The Technical University of Denmark, Lyngby
    J Biomol Struct Dyn 16:811-23. 1999
    ..The data have implications for models for DNA curvature and for environmentally-sensitive DNA conformations in the regulation of gene expression...
  21. ncbi request reprint Genome Update: annotation quality in sequenced microbial genomes
    David W Ussery
    Center for Biological Sequence Analysis, Department of Biotechnology, Building 208, The Technical University of Denmark, DK 2800 Kgs Lyngby, Denmark
    Microbiology 150:2015-7. 2004
  22. ncbi request reprint Genome update: alignment of bacterial chromosomes
    David W Ussery
    Center for Biological Sequence Analysis, Department of Biotechnology, Building 208, The Technical University of Denmark, DK 2800 Kgs Lyngby, Denmark
    Microbiology 150:2491-3. 2004
  23. ncbi request reprint Genome organisation and chromatin structure in Escherichia coli
    D Ussery
    Center for Biological Sequence Analysis, Department of Biotechnology, Building 208, The Technical University of Denmark, 2800 Kgs Lyngby, Denmark
    Biochimie 83:201-12. 2001
    ..We also show that the regions upstream of genes regulated by H-NS are more curved and have a higher AT content than regions upstream of other genes. These regions in general would also be localised near the replication terminus...
  24. ncbi request reprint Genome update: 161 prokaryotic genomes sequenced, and counting
    David W Ussery
    Center for Biological Sequence Analysis, Department of Biotechnology, Building 208, The Technical University of Denmark, Lyngby, DK 2800, Denmark
    Microbiology 150:261-3. 2004
  25. ncbi request reprint Genome update: Length distributions of sequenced prokaryotic genomes
    David W Ussery
    Center for Biological Sequence Analysis, Department of Biotechnology, Building 208, The Technical University of Denmark, Lyngby, DK 2800, Denmark
    Microbiology 150:513-6. 2004
  26. ncbi request reprint Genome update: tRNAs in sequenced microbial genomes
    David W Ussery
    Center for Biological Sequence Analysis, Department of Biotechnology, Building 208, The Technical University of Denmark, DK 2800 Kgs Lyngby, Denmark
    Microbiology 150:1603-6. 2004
  27. ncbi request reprint Genome update: sigma factors in 240 bacterial genomes
    Kristoffer Kill
    Center for Biological Sequence Analysis, BioCentrum DTU, Building 208, The Technical University of Denmark, DK 2800 Kgs Lyngby, Denmark
    Microbiology 151:3147-50. 2005
  28. pmc Estimating variation within the genes and inferring the phylogeny of 186 sequenced diverse Escherichia coli genomes
    Rolf S Kaas
    DTU Food, The Technical University of Denmark, Kgs Lyngby, Denmark
    BMC Genomics 13:577. 2012
    ..This knowledge will be useful for creating better phylogenies, for determination of molecular clocks and for improved typing techniques...
  29. ncbi request reprint Ten years of bacterial genome sequencing: comparative-genomics-based discoveries
    Tim T Binnewies
    Center for Biological Sequence Analysis, Technical University of Denmark, 2800, Lyngby, Denmark
    Funct Integr Genomics 6:165-85. 2006
    ..The newly proposed Minimal Information about a Genome Sequence standard has been developed to obtain this information...
  30. pmc Genomic variation in Salmonella enterica core genes for epidemiological typing
    Pimlapas Leekitcharoenphon
    National Food Institute, Building 204, The Technical University of Denmark, 2800 Kgs Lyngby, Denmark
    BMC Genomics 13:88. 2012
    ..The core genes--the genes that are conserved in all (or most) members of a genus or species--are potentially good candidates for investigating genomic variation in phylogeny and epidemiology...
  31. ncbi request reprint Genome update: prediction of secreted proteins in 225 bacterial proteomes
    Jannick D Bendtsen
    Center for Biological Sequence Analysis, BioCentrum DTU, The Technical University of Denmark, DK 2800 Kgs, Lyngby, Denmark
    Microbiology 151:1725-7. 2005
  32. pmc Transcriptomics and adaptive genomics of the asymptomatic bacteriuria Escherichia coli strain 83972
    Viktoria Hancock
    Microbial Adhesion Group, Risø DTU, Technical University of Denmark, Building 301, 2800 Kgs Lyngby, Denmark
    Mol Genet Genomics 279:523-34. 2008
    ..Genes expressed in CFT073 but not in 83972 were identified and can be considered as virulence factor candidates. Strain 83972 is a deconstructed pathogen rather than a commensal strain that has acquired fitness properties...
  33. ncbi request reprint Genome update: correlation of bacterial genomic properties
    Peter F Hallin
    Center for Biological Sequence Analysis, Department of Biotechnology, Building 208, The Technical University of Denmark, DK 2800 Kgs Lyngby, Denmark
    Microbiology 150:3899-903. 2004
  34. pmc Design of a seven-genome Escherichia coli microarray for comparative genomic profiling
    Hanni Willenbrock
    Center for Biological Sequence Analysis, Technical University of Denmark, Building 301, DK 2800 Kgs Lyngby, Denmark
    J Bacteriol 188:7713-21. 2006
    ..8 and 97.7% of queried chromosomal genes for the two control strains. Finally, we demonstrate that use of spatial information, in terms of the physical chromosomal locations of probes, improves the analysis...
  35. pmc Genomic characterization of Campylobacter jejuni strain M1
    Carsten Friis
    Department of Systems Biology, The Technical University of Denmark, Lyngby, Denmark
    PLoS ONE 5:e12253. 2010
    ..Trees based on 16S rRNA sequences and on the total gene families in each genome are presented. The findings are discussed in the background of the proven virulence potential of M1...
  36. ncbi request reprint Genome Update: Protein secretion systems in 225 bacterial genomes
    Tim T Binnewies
    Center for Biological Sequence Analysis, BioCentrum DTU, Building 208, The Technical University of Denmark, DK 2800 Kgs Lyngby, Denmark
    Microbiology 151:1013-6. 2005
  37. ncbi request reprint Genome update: purine strand bias in 280 bacterial genomes
    P Christoph Champ
    Center for Biological Sequence Analysis, BioCentrum DTU, Building 208, The Technical University of Denmark, DK 2800 Kgs, Lyngby, Denmark
    Microbiology 152:579-83. 2006
  38. ncbi request reprint Genome update: base skews in 200+ bacterial chromosomes
    Peter F Hallin
    Center for Biological Sequence Analysis, Department of Biotechnology, Building 208, The Technical University of Denmark, DK 2800 Kgs Lyngby, Denmark
    Microbiology 151:633-7. 2005
  39. pmc Characterization of probiotic Escherichia coli isolates with a novel pan-genome microarray
    Hanni Willenbrock
    Center for Biological Sequence Analysis, Technical University of Denmark, 2800 Lyngby, Denmark
    Genome Biol 8:R267. 2007
    ....
  40. pmc Prediction of highly expressed genes in microbes based on chromatin accessibility
    Hanni Willenbrock
    Center for Biological Sequence Analysis, BioCentrum, Technical University of Denmark, DK 2800 Kgs, Lyngby, Denmark
    BMC Mol Biol 8:11. 2007
    ..Moreover, position preference is examined further in 328 sequenced microbial genomes...
  41. ncbi request reprint Genome update: distribution of two-component transduction systems in 250 bacterial genomes
    Kristoffer Kiil
    Center for Biological Sequence Analysis, BioCentrum DTU, Building 208, The Technical University of Denmark, DK 2800 Kgs, Lyngby, Denmark
    Microbiology 151:3447-52. 2005
  42. ncbi request reprint Genome Update: proteome comparisons
    Tim T Binnewies
    Center for Biological Sequence Analysis, Department of Biotechnology, Building 208, The Technical University of Denmark, DK 2800 Kgs Lyngby, Denmark
    Microbiology 151:1-4. 2005
  43. ncbi request reprint Genome update: rRNAs in sequenced microbial genomes
    David W Ussery
    Center for Biological Sequence Analysis, Department of Biotechnology, Building 208, The Technical University of Denmark, Lyngby, DK 2800, Denmark
    Microbiology 150:1113-5. 2004
  44. pmc Comparative genomics of Bifidobacterium, Lactobacillus and related probiotic genera
    Oksana Lukjancenko
    Center for Biological Sequence Analysis, Department of Systems Biology, The Technical University of Denmark, Building 208, 2800 Kgs, Lyngby, Denmark
    Microb Ecol 63:651-73. 2012
    ..This study illustrates how over 80 genomes can be broadly compared using simple bioinformatic tools, leading to both confirmation of known information as well as novel observations...
  45. ncbi request reprint RpoD promoters in Campylobacter jejuni exhibit a strong periodic signal instead of a -35 box
    Lise Petersen
    Center for Biological Sequence Analysis, Technical University of Denmark, DK 2800 Lyngby, Denmark
    J Mol Biol 326:1361-72. 2003
    ....
  46. ncbi request reprint Genome update: 2D clustering of bacterial genomes
    Hanni Willenbrock
    Center for Biological Sequence Analysis, Department of Biotechnology, Building 208, The Technical University of Denmark, DK 2800 Kgs Lyngby, Denmark
    Microbiology 151:333-6. 2005
  47. doi request reprint The genome BLASTatlas-a GeneWiz extension for visualization of whole-genome homology
    Peter F Hallin
    Center for Biological Sequence Analysis, Department of Systems Biology, The Technical University of Denmark, Lyngby, Denmark
    Mol Biosyst 4:363-71. 2008
    ..This tool can be relevant in many pangenomic as well as in metagenomic studies, by giving a quick overview of clusters of insertion sites, genomic islands and overall homology between a reference sequence and a data set...
  48. pmc An environmental signature for 323 microbial genomes based on codon adaptation indices
    Hanni Willenbrock
    Center for Biological Sequence Analysis, BioCentrum DTU, The Technical University of Denmark, DK 2800 Lyngby, Denmark
    Genome Biol 7:R114. 2006
    ..Here, we evaluate and compare two very different methods for estimating CAI values, one corresponding to translational codon usage bias and the second obtained mathematically by searching for the most dominant codon bias...
  49. pmc Bayesian prediction of bacterial growth temperature range based on genome sequences
    Dan B Jensen
    Technical University of Denmark, Center for Systems Biology, Denmark
    BMC Genomics 13:S3. 2012
    ..Being able to accurately predict this based on a genomic sequence, would thus allow for an efficient and targeted search for production organisms, reducing the need for culturing experiments...
  50. pmc On the origins of a Vibrio species
    Tammi Vesth
    Center for Biological Sequence Analysis, Department of Systems Biology, The Technical University of Denmark, Kgs Lyngby, Denmark
    Microb Ecol 59:1-13. 2010
    ..We are able to identify a number of genes that are conserved in, and unique to, V. cholerae. Some of these genes may be crucial to the niche adaptation of this species...
  51. pmc The Salmonella enterica pan-genome
    Annika Jacobsen
    Department of Systems Biology, Center for Biological Sequence Analysis, Technical University of Denmark, Building 208, 2800 Kongens Lyngby, Denmark
    Microb Ecol 62:487-504. 2011
    ..These include the SPIs but also encompass phage insertion sites and transposable elements. The islands were typically well conserved in several, but not all, isolates--a difference which may have implications in, e.g., host specificity...
  52. ncbi request reprint Genome update: promoter profiles
    David W Ussery
    Center for Biological Sequence Analysis, Department of Biotechnology, Building 208, The Technical University of Denmark, DK 2800 Kgs Lyngby, Denmark
    Microbiology 150:2791-3. 2004
  53. pmc Comparison of 61 sequenced Escherichia coli genomes
    Oksana Lukjancenko
    Center for Biological Sequence Analysis, Department of Systems Biology, The Technical University of Denmark, Lyngby, Denmark
    Microb Ecol 60:708-20. 2010
    ..The diversity within the species E. coli, and the overlap in gene content between this and related species, suggests a continuum rather than sharp species borders in this group of Enterobacteriaceae...
  54. ncbi request reprint Genome update: prediction of membrane proteins in prokaryotic genomes
    Jannick D Bendtsen
    Center for Biological Sequence Analysis, BioCentrum DTU, Building 208, The Technical University of Denmark, DK 2800 Kgs, Lyngby, Denmark
    Microbiology 151:2119-21. 2005
  55. ncbi request reprint Genome update: chromosome atlases
    Peter F Hallin
    Center for Biological Sequence Analysis, Department of Biotechnology, Building 208, The Technical University of Denmark, DK 2800 Kgs Lyngby, Denmark
    Microbiology 150:3091-3. 2004
  56. ncbi request reprint CBS Genome Atlas Database: a dynamic storage for bioinformatic results and sequence data
    Peter F Hallin
    Center for Biological Sequence Analysis CBS, BioCentrum DTU, Building 208, The Technical University of Denmark, DK 2800 Lyngby, Denmark
    Bioinformatics 20:3682-6. 2004
    ..cbs.dtu.dk/services/GenomeAtlas/. SUPPLEMENTARY INFORMATION: This paper has a supplemental information page which links to the examples presented: www.cbs.dtu.dk/services/GenomeAtlas/suppl/bioinfdatabase...
  57. pmc Multilocus sequence typing of total-genome-sequenced bacteria
    Mette V Larsen
    Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, Lyngby, Denmark
    J Clin Microbiol 50:1355-61. 2012
    ..The method presented here enables investigators to determine the sequence types of their isolates on the basis of WGS data. This method is publicly available at www.cbs.dtu.dk/services/MLST...
  58. pmc Chromatin architecture and gene expression in Escherichia coli
    Hanni Willenbrock
    Center for Biological Sequence Analysis, Department of Biotechnology, Building 208, Technical University of Denmark, DK 28OO Kgs, Lyngby, Denmark
    Genome Biol 5:252. 2004
    ..Two recent genome-scale analyses underscore the importance of DNA topology and chromatin structure in regulating transcription in Escherichia coli...
  59. ncbi request reprint Crystal ball. Systems biology: in the broadest sense of the word
    David W Ussery
    Ulrik de Lichtenberg, Center for Biological Sequence Analysis, Technical University of Denmark
    Environ Microbiol 7:482-3. 2005
  60. pmc Functionality of system components: conservation of protein function in protein feature space
    Lars Juhl Jensen
    Center for Biological Sequence Analysis, BioCentrum DTU, The Technical University of Denmark, DK 2800 Lyngby, Denmark
    Genome Res 13:2444-9. 2003
    ..From this analysis, we conclude that for the posttranslational modifications studied, both the cellular use and the sequence motifs are conserved within Eukarya...
  61. pmc Defining the Pseudomonas genus: where do we draw the line with Azotobacter?
    Asli I Ozen
    Center for Biological Sequence Analysis, Department of Systems Biology, The Technical University of Denmark, Lyngby, Denmark
    Microb Ecol 63:239-48. 2012
    ..The results of these different methods point to a high similarity between A. vinelandii and the Pseudomonas genus, suggesting that Azotobacter might actually be a Pseudomonas...
  62. ncbi request reprint Inheritance and organisation of the mitochondrial genome differ between two Saccharomyces yeasts
    Randi F Petersen
    BioCentrum DTU, Technical University of Denmark, Building 301, DK 2800 Kgl Lyngby, Denmark
    J Mol Biol 318:627-36. 2002
    ..cerevisiae. The structure of one suppressive S. castellii mutant, CA38, was also determined. Apparently, a short direct intergenic repeat was involved in the generation of this petite mtDNA molecule...
  63. pmc RNAmmer: consistent and rapid annotation of ribosomal RNA genes
    Karin Lagesen
    Centre for Molecular Biology and Neuroscience and Institute of Medical Microbiology, University of Oslo, NO 0027 Oslo, Norway
    Nucleic Acids Res 35:3100-8. 2007
    ..Novel, unannotated rRNAs are also predicted in many genomes. The software as well as the genome analysis results are available at the CBS web server...
  64. ncbi request reprint Global features of the Alcanivorax borkumensis SK2 genome
    Oleg N Reva
    Klinische Forschergruppe, OE6711, Medizinische Hochschule Hannover, Carl Neuberg Strasse 1, D 30625 Hannover, Germany
    Environ Microbiol 10:614-25. 2008
    ....
  65. ncbi request reprint Identification of putative noncoding RNA genes in the Burkholderia cenocepacia J2315 genome
    Tom Coenye
    Laboratorium voor Microbiologie, Universiteit Gent, Gent, Belgium
    FEMS Microbiol Lett 276:83-92. 2007
    ..The presence of a large number of ncRNA genes in this organism may help to explain its complexity, phenotypic variability and ability to survive in a remarkably wide range of environments...
  66. ncbi request reprint The sigma54 regulon (sigmulon) of Pseudomonas putida
    Ildefonso Cases
    Centro Nacional de Biotecnologia, CSIC Campus de Cantoblanco, 28049 Madrid, Spain
    Environ Microbiol 5:1281-93. 2003
    ..putida with high confidence. Our analysis has revealed new functions for sigma54 and, by means of comparative analysis with the previous studies, we have drawn a potential mechanism for the evolution of this regulatory system...
  67. ncbi request reprint Origin of replication in circular prokaryotic chromosomes
    Peder Worning
    Biological Sciences, AstraZeneca R and D Lund, Sweden
    Environ Microbiol 8:353-61. 2006
    ..The program and results for all publicly available genomes are available from http://www.cbs.dtu.dk/services/GenomeAtlas/suppl/origin...
  68. ncbi request reprint Strand misalignments lead to quasipalindrome correction
    Vera van Noort
    Nijmegen Center for Molecular Life Sciences, P A Center for Molecular and Biomolecular Informatics, Nijmegen, The Netherlands
    Trends Genet 19:365-9. 2003
  69. ncbi request reprint The plasmid genome database
    Lars Mølbak
    Danish Veterinary Institute, Bulowsvej 27, DK 1790 Copenhagen V, Denmark
    Microbiology 149:3043-5. 2003
  70. pmc Investigations of oligonucleotide usage variance within and between prokaryotes
    Jon Bohlin
    Norwegian School of Veterinary Science, Oslo, Norway
    PLoS Comput Biol 4:e1000057. 2008
    ....
  71. pmc The complete genome sequence and analysis of the epsilonproteobacterium Arcobacter butzleri
    William G Miller
    Produce Safety and Microbiology Research Unit, Agricultural Research Service, US Department of Agriculture, Albany, California, United States of America
    PLoS ONE 2:e1358. 2007
    ..Here we present the complete genome sequence of the human clinical isolate, A. butzleri strain RM4018...
  72. ncbi request reprint Extracytoplasmic function sigma factors in Pseudomonas syringae
    José A Oguiza
    Departamento de Producción Agraria, Universidad Publica de Navarra, 31006 Pamplona, Spain
    Trends Microbiol 13:565-8. 2005
    ..We highlight the presence of a P. syringae-specific ECF sigma factor that is an interesting target for future studies because of its potential role in the adaptation of P. syringae to its specialized phytopathogenic lifestyle...
  73. ncbi request reprint Global regulation of virulence and the stress response by CsrA in the highly adapted human gastric pathogen Helicobacter pylori
    Faye M Barnard
    Institute of Infections, Immunity and Inflammation, University of Nottingham, Nottingham, United Kingdom
    Mol Microbiol 51:15-32. 2004
    ..Furthermore, CsrA appears to mediate its effects in H. pylori at the post-transcriptional level by influencing the processing and translation of target transcripts, with minimal effect on the stability of the target mRNAs...
  74. ncbi request reprint The TNFalpha receptor TNFRSF1A and genes encoding the amiloride-sensitive sodium channel ENaC as modulators in cystic fibrosis
    Frauke Stanke
    Department of Pediatrics, OE6711, Hannover Medical School, Carl Neuberg Str 1, 30625, Hannover, Germany
    Hum Genet 119:331-43. 2006
    ....