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2012 (1) 2010 (3) 2009 (2) 2008 (2) 2007 (3) 2006 (3) 2005 and before (20) Books (1)

2012

    Bayesian prediction of bacterial optimum temperature based on genome sequences
    Jensen DB, Vest TC, Hallin PF, Pedersen AG, Ussery D
    BMC Genomics, 2012

2010

    Genomic Characterization of Campylobacter jejuni strain M1
    Friis C, Wassenaar T, Javed M, Snipen L, Lagesen K, Hallin P, Newell D, Toszeghy M, RIdley A, Manning G, Ussery D
    PLoS ONE, 2010
    PubMed
    Parallel Genetic and Phenotypic Evolution of DNA Superhelicity in Experimental Populations of Escherichia coli
    Crozat E, Winkworth C, Gaffé J, Hallin PF, Riley MA, Lenski RE, Schneider D
    Mol. Biol. Evol doi:10.1093/molbev/msq099, 2010
    PubMed
    On the Origins of a Vibrio species
    Vesth T, Wassenaar TM, Hallin PF, Snipen L, Lagesen K, , Ussery DW
    Microbial Ecology, 59:1-13, 2010

2009

    Computational tools and Interoperability in Comparative Genomics
    Hallin PF
    Ph.D. thesis, 2009
    GeneWiz browser: An Interactive Tool for Visualizing Sequenced Chromosomes
    Hallin PF, Stærfeldt HH, Rotenberg E, Binnewies TT, Benham CJ, , Ussery DW
    Standards in Genomic Sciences, 1:204-215, 2009
    Relevant URL

2008

    Global features of the Alcanivorax borkumensis SK2 genome
    Reva ON, Hallin PF, Willenbrock H, Sicheritz-Ponten T, Tummler B, Ussery DW
    Environ Microbiol. 2008 Mar;10(3):614-25 and Mol Genet Genomics, 279:523-534, (2008), 2008
    PubMed
    The genome BLASTatlas-a GeneWiz extension for visualization ofwhole-genome homology
    Hallin PF, Binnewies TT, Ussery DW
    Mol Biosyst 4:363-71 (2008), 2008
    PubMed

2007

    The Complete Genome Sequence and Analysis of the EpsilonproteobacteriumArcobacter butzleri
    Miller WG, Parker CT, Rubenfield M, Mendz GL, Wosten MM, Ussery DW, Stolz JF, Binnewies TT, Hallin PF, Wang G, Malek JA, Rogosin A, Stanker LH, Mandrell RE
    PLoS ONE. 2007 Dec 26;2(12):e1358., 2007
    PubMed
    Characterization of probiotic Escherichia coli isolates with a novel pan-genome microarray
    Willenbrock H, Hallin PF, Wassenaar TM, Ussery DW
    Genome Biol 8:R267 (2007), 2007
    PubMed
    RNAmmer: consistent and rapid annotation of ribosomal RNA genes
    Lagesen K, Hallin P, Rødland EA, Stærfeldt HH, Rognes T, Ussery DW
    Nucleic Acids Research 35:3100-3108,(2007)., 2007
    PubMed

2006

    Structural features of fungal genomes
    Wanchanthuek P, Hallin PF, Gouveia-Oliveira R, Ussery DW
    Topics in Current Genetics, 15, 47-77, 2006
    Ten years of bacterial genome sequencing: comparative-genomics-based discoveries
    Binnewies TT, Motro Y, Hallin PF, Lund O, Dunn D, La T, Hampson DJ, Bellgard M, Wassenaar TM, Ussery DW
    Functional and Integrative Genomics, 6, [Epub ahead of print], 2006
    PubMed
    Origin of Replication in Circular Prokaryotic Chromosomes
    Worning P, Jensen LJ, Hallin PF, Stærfeldt HH, Ussery DW
    Environ Microbiol, 8, 353-61, 2006
    PubMed

2005

    Genome Update: Protein secretion systems in 225 bacterial genomes
    Binnewies TT, Bendtsen JD, Hallin PF, Nielsen N, Wassenaar TM, Pedersen MB, Klemm P, Ussery DW
    Microbiology., 151(Pt 4):1013-6, 2005
    PubMed
    Genome opdate: Protein secretion systems in 225 bacterial genomes
    Bennewies TT, Bendtsen JD, Hallin PF, Nielsen N, Wassenaar TM, Pedersen MB, Klemm P, Ussery DW
    Microbiology, 151, 1013-1016, 2005
    PubMed
    Genome update: Prediction of secreted proteins in 225 bacterial proteomes
    Bendtsen JD, Binnewies TT, Hallin PF, Sicheritz-Pontén T, Ussery DW
    Microbiology, 151, 1725-1727, 2005
    PubMed
    Genome update: Prediction of membrane proteins in prokaryotic genomes
    Bendtsen JD, Binnewies TT, Hallin PF, Ussery DW
    Microbiology, 151, 2119-2121, 2005
    PubMed
    Genome update: Sigma factors in 240 bacterial genomes
    Kiil K, Binnewies TT, Sicheritz-Pontén T, Willenbrock H, Hallin PF, Wassenaart TM, Ussery DW
    Microbiology-SGM, 151, 3147-3150, 2005
    PubMed
    Genome Update: proteome comparisons
    Binnewies TT, Hallin PF, Staerfeldt HH, Ussery DW
    Microbiology, 151, 1-4, 2005
    PubMed
    Genome update: 2D clustering of bacterial genomes
    Willenbrock H, Binnewies TT, Hallin PF, Ussery DW
    Microbiology, 151, 333-6, 2005
    PubMed
    Genome update: base skews in 200+ bacterial chromosomes
    Hallin PF, Nielsen N, Devine KM, Binnewies TT, Willenbrock H, Ussery DW
    Microbiology, 151, 633-7, 2005
    PubMed

2004

    Genome update: correlation of bacterial genomic properties
    Hallin PF, Coenye T, Binnewies TT, Jarmer H, Staerfeldt HH, Ussery DW
    Microbiology, 150, 3899-903, 2004
    PubMed
    Genome Update: DNA repeats in bacterial genomes
    Ussery DW, Binnewies TT, Gouveia-Oliveira R, Jarmer H, Hallin PF
    Microbiology 150, 3519-21, 2004
    PubMed
    Genome Update: alignment
    Ussery DW, Jensen MS, Poulsen TR, Hallin PF
    Microbiology 150, 2491-3, 2004
    PubMed
    Genome update: chromosome atlases
    Hallin PF, Binnewies TT, Ussery DW
    Microbiology, 150, 3091-3, 2004
    PubMed
    Genome update: promoter profiles
    Ussery DW, Tindbaek N, Hallin PF
    Microbiology, 150, 2791-3, 2004
    PubMed
    Genome update: alignment of bacterial chromosomes
    Ussery DW, Jensen MS, Poulsen TR, Hallin PF
    Microbiology, 150, 2491-3, 2004
    PubMed
    Genome Update: annotation quality in sequenced microbial genomes
    Ussery DW, Hallin PF
    Microbiology, 150, 2015-7, 2004
    PubMed
    CBS genome atlas database: a dynamic storage for bioinformatic results and sequence data
    Hallin PF, Ussery DW
    Bioinformatics, 12;20, 3682-6, 2004
    PubMed
    Genome Update: tRNAs in sequenced microbial genomes
    Ussery DW, Hallin PF, Lagesen K, Wassenaar TM
    Microbiology, 150, 1603-6, 2004
    PubMed
    Genome update: rRNAs in sequenced microbial genomes
    Ussery DW, Hallin PF, Lagesen K, Coenye T
    Microbiology, 150, 1113-5, 2004
    PubMed
    Genome Update: AT content in sequenced prokaryotic genomes
    Ussery DW, Hallin PF
    Microbiology, 150, 749-52, 2004
    PubMed
    Genome Update: length distributions of sequenced prokaryotic genomes
    Ussery DW, Hallin PF
    Microbiology, 150, 513-16, 2004
    PubMed


Books

    Tools for comparison of bacterial genomes
    Wassenaar TM, Binnewies TT, Hallin PF, Ussery DW
    Microbiology of Hydrocarbons, Oils, Lipids, and Derived Compounds, (Springer-Verlag, Heidelberg, Germany), 2009

2012 (1) 2010 (3) 2009 (2) 2008 (2) 2007 (3) 2006 (3) 2005 and before (20) Books (1)