Events News Research CBS CBS Publications Bioinformatics
Staff Contact About Internal CBS CBS Other

2013 (1) 2012 (15) 2011 (6) 2010 (14) 2009 (9) 2008 (10) 2007 and before (76) Books (9)

2013

    CMG-biotools, a free workbench for basic Comparative Microbial Genomics
    Vesth T, Lagesen K, Acar O, Ussery D
    PLoS ONE, in the press, 2013

2012

    Polyclonality of concurrent natural populations of Alteromonas macleodii.
    Gonzaga A, Martin-Cuadrado AB, López-Pérez M, Megumi Mizuno C, García-Heredia I, Kimes NE, Lopez-García P, Moreira D, Ussery D, Zaballos M, Ghai R, Rodriguez-Valera F
    Genome Biol Evol 4(12):1360-74 doi:10.1093/gbe/evs112, 2012
    PubMed
    Polyclonality of concurrent natural populations of Alteromonas macleodii.
    Gonzaga A, Martin-Cuadrado AB, López-Pérez M, Megumi Mizuno C, García-Heredia I, Kimes NE, Lopez-García P, Moreira D, Ussery D, Zaballos M, Ghai R, Rodriguez-Valera F
    Genome Biol Evol 4(12):1360-74 doi:10.1093/gbe/evs112, 2012
    PubMed
    Polyclonality of concurrent natural populations of Alteromonas macleodii
    Gonzaga A, Martin-Cuadrado AB, López-Pérez M, Mizuno CM, García-Heredia I, Kimes NE, Lopez-García P, Moreira D, Ussery D, Zaballos M, Ghai R, Rodriguez-Valera F
    Genome Biol Evol 4(12):1360-74 doi:10.1093/gbe/evs112, 2012
    PubMed
    Is the pan-genome also a pan-selectome?
    Rodriguez-Valera F, Ussery DW
    F1000 Research, 1:16 (doi: 10.3410/f1000research.1-16.v1), 2012
    Relevant URL
    From essential to persistent genes: A functional approach to construct synthetic life
    Acevedo-Rocha CG, Fang G, Schmidt M, Ussery DW, Danchin A
    Trends in Genetics, in the press (2012), 2012
    A domain sequence approach to pangenomics: applications to Escherichia coli
    Snipen LG, Ussery DW
    F1000 Research, 1:19 (doi: 10.3410/f1000research.1-19.v1), 2012
    Relevant URL
    Cholera in Haiti: Lack of evidence for a contribution of non-O1 Vibro cholera
    Mekalanos JJ, Robins W, Ussery DW, Davis BM, Schadt E, Waldor MK
    PNAS, in the press, September, 2012, 2012
    Computational genomics, proteomics, and phylogeny analysis of twenty one mycobacterial genomes (Tuberculosis & non Tuberculosis strains)
    Zakham F, Aouane O, Ussery D, Benjouad A, Ennaji MM
    The Journal of Microbial Informatics and Experimintaion, in the press (August, 2012), 2012
    Campylobacter fetus subspecies: Comparative genomics and prediction of potential virulence targets
    Ali A, Soares SC, Santos AR, Guimarães LC, Barbosa E, Almeida SS, Abreu VA, Carneiro AR, Ramos RT, Bakhtiar SM, Hassan SS, Ussery DW, On S, Silva A, Schneider MP, Lage AP, Miyoshi A, Azevedo V
    Gene 508(2):145-56 doi:10.1016/j.gene.2012.07.070, 2012
    PubMed
    Analysis of Co-evolving Genes in Campylobacter jejuni and and C. coli
    Snipen L, Wassenaar T, Altermann E, Olson J, Kathariou S, Lagesen K, Takamiya M, Knoechel S, Ussery DW, Meinersmann RJ
    Microbial Informatics and Experimentation, 2012
    Bayesian prediction of bacterial growth temperature range based on genome sequences
    Jensen DB, Vest TC, Hallin PF, Pedersen AG, Ussery D
    BMC Genomics, 2012
    PubMed
    Relevant URL
    Two novel methods for using genome sequences to infer taxonomy
    Ussery DW, Gordon SV
    Microbiology (Reading, Engl.) 158:1414 doi:10.1099/mic.0.059816-0, 2012
    PubMed
    LeuO is a global regulator of gene expression in Salmonella enterica serovar Typhimurium
    Dillon SC, Espinosa E, Hokamp K, Ussery DW, Casadesús J, Dorman CJ
    Mol. Microbiol. 85(6):1072-89 doi:10.1111/j.1365-2958.2012.08162.x, 2012
    PubMed
    Global transcriptional mapping, RNA polymerase distribution and the unique sRNA complement of the model pathogen Salmonella enterica serovar Typhimurium
    Kröger C, Dillon SC, Cameron ADS, Papenfort K, Sivasankaran SK, Hokamp K, Chao Y, Sittka A, Hébrard M, Händler K, Colgan A, Leekitcharoenphon P, Langridge GC, Lohan AJ, Loftus B, Lucchini S, Thompson A, Ussery DW, Sharma CM, Dorman CJ, Thomson N, Vogel J, Hinton JCD
    Proceedings of the National Academy of Science USA , 2012 (in press), 2012
    Genomic variation in Salmonella enterica core genes for epidemiological typing
    Leekitcharoenphon P, Lukjancenko O, Friis C, Aarestrup FM, Ussery DW
    BMC Genomics 2012, 13:88, 2012
    pubmed link

2011

    Defining the Pseudomonas Genus: Where Do We Draw the Line with Azotobacter?
    Özen AI, Ussery DW
    Springer, July 13, 2011
    Relevant URL
    The Genomic Standards Consortium
    Field D, Amaral-Zettler, L, Cochrane G, Cole JR, Dawyndt P, Garrity G, Gilbert J, Glöckner F, Hirschman L, Karsch-Mizrachi I, Klenk H, Knight R, Kottmann R, Kyrpides N, Meyer F, San Gil I, Sansone S, Schriml L, Sterk P, Tatusova T, Ussery D, White O, Wooley J
    PLoS Biology, 2011
    The Salmonella enterica Pan-genome
    Jacobsen A, Hendriksen RS, Aaresturp FM, Ussery DW, Friis C
    Microb. Ecol. 62(3):487-504 doi:10.1007/s00248-011-9880-1, 2011
    PubMed
    Mycobacterial species as case-study of comparative genome analysis
    Zakham F, Belayachi L, Ussery D, Akrim M, Benjouad A, El Aouad R, Ennaji MM
    Cell. Mol. Biol. (Noisy-le-grand):OL1462-9, 2011
    PubMed
    Genome Sequence of the Campylobacter jejuni strain 327, a turkey strain isolated from a slaughterhouse
    Takamiya M, Ozen A, Rasmussen M, Alter T, Gilbert T, Ussery D, Knøchel S
    Standards in Genomic Sciences, May 12, 2011
    Relevant URL
    A Closer Look at Bacteroides: Phylogenetic Relationship and Genomic Implications of a Life in the Human Gut
    Karlsson FH, Ussery DW, Nielsen J, Nookaew I
    Microb. Ecol. 61(3):473-85 doi:10.1007/s00248-010-9796-1, 2011
    PubMed

2010

    An Inordinate Fondness of Bacteria - a review of Signature in the Cell by Stephen Meyer
    Ussery DW
    NCSE Reports, 2010
    One Small Step for Bacteria, or One Giant Leap for Mankind?
    Ussery DW
    Journal of Cosmology, 2010
    Read article
    Design of an Enterobacteriaceae Pan-genome Microarray Chip
    Lukjancenko O, Ussery DW
    CSBio 2010 Proceedings, 115: 174-189, 2010
    The Genome Atlas Resource
    Qureshi M, Rotenberg E, Staerfeldt HH, Hansson L, Ussery DW
    CSBio 2010 Proceedings, 115: 149-158, 2010
    Genomic comparisons of Brucella spp. and closely related bacteria using base compositional and proteome based methods
    Bohlin J, Snipen L, Cloeckaert A, Lagesen K, Ussery D, Kristoffersen AB, Godfroid J
    BMC Evol. Biol. 10:249 doi:10.1186/1471-2148-10-249, 2010
    PubMed
    Read article
    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 5(8):e12253 doi:10.1371/journal.pone.0012253, 2010
    PubMed
    Analysis of intra-genomic GC content homogeneity within prokaryotes
    Bohlin J, Snipen L, Hardy SP, Kristoffersen AB, Lagesen K, Donsvik T, Skjerve E, Ussery DW
    BMC Genomics 11:464 doi:10.1186/1471-2164-11-464, 2010
    PubMed
    Comparison of 61 Sequenced Escherichia coli Genomes Microbial Ecology
    Lukjancenko O, Wassenaar TM, Ussery DW
    Microb. Ecol. 60(4):708-20 doi:10.1007/s00248-010-9717-3, 2010
    PubMed
    Standard operating procedure for computing pangenome trees
    Snipen L, Ussery DW
    Standards in Genomic Sciences, 2010
    Read abstract
    The Thousandth Genome – A Cautionary Tale
    Lagesen K, Ussery DW, Wassenaar TM
    Microbiology 156:603-609, 2010
    Genomic Analysis of Two-Component Signal Transduction Proteins in Basidiomycetes
    Lavín JL, Ramírez L, Ussery DW, Pisabarro AG, Oguiza JA
    J. Mol. Microbiol. Biotechnol. 18(2):63-73 doi:10.1159/000277654, 2010
    PubMed
    Differences in two-component signal transduction proteins among the genus Brucella: implications for host preference and pathogenesis
    Lavín JL, Binnewies TT, Pisabarro AG, Ussery DW, García-Lobo JM, Oguiza JA
    Veterinary Microbiology, in the press, 2010
    Comparative Genomics of Green Sulfur Bacteria
    Davenport C, Ussery DW, Tümmler B
    Photosyn. Res. 104:137-52 doi:10.1007/s11120-009-9515-2, 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

    Studies on Monitoring and Tracking Genetic Resources
    Garrity GM, Thompson LM, Ussery DW, Paskin N, Baker D, Desmeth P, Schindel DE, Ong PS
    Convention on Biological Diversity (21 January, 2009)[UNEP/CBD/ABS/GTLE/2/INF/4], 2009
    The 2008 update of the Aspergillus nidulans genome annotation: a community effort
    Wortman JR, Gilsenan JM, Joardar V, Deegan J, Clutterbuck J, Andersen MR, Archer D, Bencina M, Braus G, Coutinho P, von Döhren H, Doonan J, Driessen AJ, Durek P, Espeso E, Fekete E, Flipphi M, Estrada CG, Geysens S, Goldman G, de Groot PW, Hansen K, Harris SD, Heinekamp T, Helmstaedt K, Henrissat B, Hofmann G, Homan T, Horio T, Horiuchi H, James S, Jones M, Karaffa L, Karányi Z, Kato M, Keller N, Kelly DE, Kiel JA, Kim JM, van der Klei IJ, Klis FM, Kovalchuk A, Krasevec N, Kubicek CP, Liu B, Maccabe A, Meyer V, Mirabito P, Miskei M, Mos M, Mullins J, Nelson DR, Nielsen J, Oakley BR, Osmani SA, Pakula T, Paszewski A, Paulsen I, Pilsyk S, Pócsi I, Punt PJ, Ram AF, Ren Q, Robellet X, Robson G, Seiboth B, van Solingen P, Specht T, Sun J, Taheri-Talesh N, Takeshita N, Ussery D, vanKuyk PA, Visser H, van de Vondervoort PJ, de Vries RP, Walton J, Xiang X, Xiong Y, Zeng AP, Brandt BW, Cornell MJ, van den Hondel CA, Visser J, Oliver SG, Turner G
    Fungal Genetics and Biology, 45:S2-S13,, 2009
    Studies on Monitoring and Tracking Genetic Resources: An Executive Summary
    Garrity GM, Thompson LM, Ussery DW, Paskin N, Baker D, Desmeth P, Schindel DE, Ong PS
    Standards in Genomic Sciences, 1:78-86, 2009
    Stretches of alternating pyrimidine/ purines and purines are respectively linked with pathogenicity and growth temperature in prokaryotes
    Bohlin J, Hardy SP, Ussery DW
    BMC Genomics 10:346 doi:10.1186/1471-2164-10-346, 2009
    PubMed
    Read article
    Genomic taxonomy of vibrios
    Thompson CC, Vicente AC, Souza RC, Vasconcelos AT, Vesth T, Alves N Jr, Ussery DW, Iida T, Thompson FL
    BMC Evol. Biol. 9:258 doi:10.1186/1471-2148-9-258, 2009
    PubMed
    Read abstract
    Analysis of genomic signatures in prokaryotes using multinomial regression and hierarchical clustering
    Bohlin J, Skjerve E, Ussery DW
    BMC Genomics, 10:487, 2009
    Read article
    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
    Microbial comparative pan-genomics using binomial mixture models
    Snipen L, Almøy T, Ussery DW
    BMC Genomics 10:385 doi:10.1186/1471-2164-10-385, 2009
    PubMed
    Analysis and prediction of gene splice sites in four Aspergillus genomes
    Wang K, Ussery DW, Brunak S
    Fungal Genet. Biol.:S14-8 doi:10.1016/j.fgb.2008.09.010, 2009
    PubMed

2008

    The minimum information about a genome sequence (MIGS) specification
    Field D, Garrity G, Gray T, Morrison N, Selengut J, Sterk P, Tatusova T, Thomson N, Allen MJ, Angiuoli SV, Ashburner M, Axelrod N, Baldauf S, Ballard S, Boore J, Cochrane G, Cole J, Dawyndt P, De Vos P, DePamphilis C, Edwards R, Faruque N, Feldman R, Gilbert J, Gilna P, Glöckner FO, Goldstein P, Guralnick R, Haft D, Hancock D, Hermjakob H, Hertz-Fowler C, Hugenholtz P, Joint I, Kagan L, Kane M, Kennedy J, Kowalchuk G, Kottmann R, Kolker E, Kravitz S, Kyrpides N, Leebens-Mack J, Lewis SE, Li K, Lister AL, Lord P, Maltsev N, Markowitz V, Martiny J, Methe B, Mizrachi I, Moxon R, Nelson K, Parkhill J, Proctor L, White O, Sansone SA, Spiers A, Stevens R, Swift P, Taylor C, Tateno Y, Tett A, Turner S, Ussery D, Vaughan B, Ward N, Whetzel T, San Gil I, Wilson G, Wipat A
    Nat. Biotechnol. 26(5):541-7 doi:10.1038/nbt1360, 2008
    PubMed
    Towards a richer description of our complete collection of genomes and metagenomes: the ’Minimum Information about a Genome Sequence’ (MIGS) specification
    Field D, Garrity G, Gray T, Morrison N, Selengut J, Sterk P, Tatusova T, Thomson N, Allen MJ, Angiuolii SV, Ashburner M, Axelrod N, Baldauf S, Boore SBJ, Cochrane G, Cole J, Dawyndt P, Vos PD, dePamphilis C, Edwards R, Faruque N, Feldman R, Gilbert J, Gilna P, Glöckner FO, Goldstein P, Guralnick R, Haft D, Hancock D, Hermjakob H, Hertz-Fowler C, Hugenholtz P, Joint I, Kagan L, Kane M, Kennedy J, Kowalchuk G, Kottmann R, Kolker E, Kravitz S, Kyrpides N, Leebens-Mack J, Lewis SE, Li K, Lister A, Lord P, Maltsev N, Markowitz V, Martiny J, Methe B, Moxon R, Nelson K, Parkhill J, Proctor L, Sansone SA, Spiers A, Stevens R, Swift P, Taylor C, Tateno Y, Tett A, Turner S, Ussery DW, Vaughan B, Ward N, Whetzel T, Wilson G, Wipat A
    Nat. Biotechnol. 26(5):541-7 doi:10.1038/nbt1360, 2008
    PubMed
    Reliability and applications of statistical methods based on oligonucleotide frequencies in bacterial and archaeal genomes
    Bohlin J, Skjerve E, Ussery DW
    BMC Genomics 9:104 doi:10.1186/1471-2164-9-104, 2008
    PubMed
    BMC Genomics link
    Transcriptomics and adaptive genomics of the asymptomatic bacteria Escherichia coli strain 83972
    Hancock V, Seshasayee AS, Ussery DW, Luscombe NM, Klemm P
    Mol. Genet. Genomics 279(5):523-34 doi:10.1007/s00438-008-0330-9, 2008
    PubMed
    Investigations of oligonucleotide usage variance within and between prokaryotes
    Bohlin J, Skjerve E, Ussery D
    PLoS Comput. Biol. 4(4):e1000057 doi:10.1371/journal.pcbi.1000057, 2008
    PubMed
    PLoS Computational Biology link
    Toward a Standards-Compliant Genomic and Metagenomic Publication Record
    Garrity GM, Field D, Kyrpides N, Hirschman L, Sansone SA, Angiuoli S, Cole JR, Glöckner FO, Kolker E, Kowalchuk G, Moran MA, Ussery D, White O
    OMICS 12(2):157-60 doi:10.1089/omi.2008.A2B2, 2008
    PubMed
    Molecular analysis of the emergence of pandemic Vibrio parahaemolyticus
    Boyd EF, Cohen AL, Naughton LM, Ussery DW, Binnewies TT, Stine OC, Parent MA
    BMC Microbiol. 8:110 doi:10.1186/1471-2180-8-110, 2008
    PubMed
    The genome of the versatile nitrogen fixer Azorhizobium caulinodans ORS571
    Lee KB, De Backer P, Aono T, Liu CT, Suzuki S, Suzuki T, Kaneko T, Yamada M, Tabata S, Kupfer DM, Najar FZ, Wiley GB, Roe B, Binnewies TT, Ussery DW, D’Haeze WD, Herder JD, Gevers D, Vereecke D, Holsters M, Oyaizu H
    BMC Genomics 9:271 doi:10.1186/1471-2164-9-271, 2008
    PubMed
    Global features of the Alcanivorax borkumensis SK2 genome
    Reva ON, Hallin PF, Willenbrock H, Sicheritz-Ponten T, Tummler B, Ussery DW
    Environ. Microbiol. 10(3):614-25, 2008
    PubMed
    The genome BLASTatlas-a GeneWiz extension for visualization ofwhole-genome homology
    Hallin PF, Binnewies TT, Ussery DW
    Mol Biosyst 4(5):363-71 doi:10.1039/b717118h, 2008
    PubMed

2007

    Identification of putative noncoding RNA genes in the Burkholderia cenocepacia J2315 genome
    Coenye T, Drevinek P, Mahenthiralingam E, Shah SA, Gill RT, Vandamme P, Ussery DW
    FEMS Microbiol. Lett. 276(1):83-92, 2007
    PubMed
    Comparative genomic analysis of two-component regulatory proteins in Pseudomonas syringae
    Lavin JL, Kiil K, Resano O, Ussery DW, Oguiza JA
    BMC Genomics 8:397, 2007
    PubMed
    Link to article
    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 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(12):R267, 2007
    PubMed
    Comparison of protein coding gene contents of the fungal phyla Pezizomycotina and Saccharomycotina
    Arvas MM, Kivioja T, Mitchell A, Saloheimo M, Ussery DW, Penttila M, Oliver S
    BMC Genomics 8:325, 2007
    PubMed
    Genome sequencing and analysis of the versatile cell factory Aspergillus niger CBS 513.88
    Pel HJ, de Winde JH, Archer DB, Dyer PS, Hofmann G, Schaap PJ, Turner G, de Vries RP, Albang R, Albermann K, Andersen MR, Bendtsen JD, Benen JA, van den Berg M, Breestraat S, Caddick MX, Contreras R, Cornell M, Coutinho PM, Danchin EG, Debets AJ, Dekker P, van Dijck PW, van Dijk A, Dijkhuizen L, Driessen AJ, d\'Enfert C, Geysens S, Goosen C, Groot GS, de Groot PW, Guillemette T, Henrissat B, Herweijer M, van den Hombergh JP, van den Hondel CA, van der Heijden RT, van der Kaaij RM, Klis FM, Kools HJ, Kubicek CP, van Kuyk PA, Lauber J, Lu X, van der Maarel MJ, Meulenberg R, Menke H, Mortimer MA, Nielsen J, Oliver SG, Olsthoorn M, Pal K, van Peij NN, Ram AF, Rinas U, Roubos JA, Sagt CM, Schmoll M, Sun J, Ussery D, Varga J, Vervecken W, van de Vondervoort PJ, Wedler H, Wosten HA, Zeng AP, van Ooyen AJ, Visser J, Stam H
    Nat. Biotechnol. 25(2):221-31, 2007
    PubMed
    Prediction of highly expressed genes in microbes based on chromatin accessibility
    Willenbrock H, Ussery DW
    BMC Mol. Biol. 8:11, 2007
    PubMed
    Link to BMC Molecular Biology file
    The importance of virulence prediction and gene networks in microbial risk assessment
    Wassenaar GM, Gamieldien J, Shatkin JA, Luber P, Moyer N, Carpenter T, Ussery DW
    Human and Ecological Risk Assessment, 13, 1-15, 2007
    RNAmmer: consistent and rapid annotation of ribosomal RNA genes
    Lagesen K, Hallin P, Rødland EA, Stærfeldt HH, Rognes T, Ussery DW
    Nucleic Acids Res. 35(9):3100-8, 2007
    PubMed

2006

    Opening the pan-genomics box
    Read T, Ussery DW
    Current Opinion in Microbiology, 9:496-498, 2006
    Design of a 7 Genomes Escherichia coli Microarray for Comparative Genomic Profiling
    Willenbrock H, Petersen A, Sekse C, Kiil K, Wasteson Y, Ussery DW
    J. Bacteriol. 188(22):7713-21, 2006
    PubMed
    Leaner and Meaner Genomes in Escherichia coli
    Ussery DW
    Genome Biol. 7(10):237, 2006
    PubMed
    An environmental signature for 323 microbial genomes based on codon adaptation indices
    Willenbrock H, Friis C, Juncker AS, Ussery DW
    Genome Biol. 7(12):R114, 2006
    PubMed
    The genomic code: inferring Vibrionaceae niche specialization
    Reen FJ, Almagro-Moreno S, Ussery D et al
    Nat. Rev. Microbiol. 4(9):697-704, 2006
    PubMed
    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
    The TNFalpha receptor TNFRSF1A and genes encoding the amiloride-sensitive sodium channel ENaC as modulators in cystic fibrosis
    Stanke F, Becker T, Cuppens H, Kumar V, Cassiman JJ, Jansen S, Radojkovic D, Siebert B, Yarden J, Ussery DW, Wienker TF, Tummler B
    Hum. Genet. 119(3):331-43, 2006
    PubMed
    Genome update: purine strand bias in 280 bacterial genomes
    Champ PC, Binnewies TT, Nielsen N, Zinman G, Kiil K, Wu H, Bohlin J, Ussery DW
    Microbiology (Reading, Engl.) 152:579-83, 2006
    PubMed
    Origin of Replication in Circular Prokaryotic Chromosomes
    Worning P, Jensen LJ, Hallin PF, Stærfeldt HH, Ussery DW
    Environ. Microbiol. 8(2):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 (Reading, Engl.) 151:1013-6, 2005
    PubMed
    Extracytoplasmic function sigma factors in Pseudomona syringae
    Oguiza JA, Kiil K, Ussery DW
    Trends Microbiol. 13(12):565-8, 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 (Reading, Engl.) 151:1013-6, 2005
    PubMed
    Genome update: Prediction of secreted proteins in 225 bacterial proteomes
    Bendtsen JD, Binnewies TT, Hallin PF, Sicheritz-Pontén T, Ussery DW
    Microbiology (Reading, Engl.) 151:1725-7, 2005
    PubMed
    Genome update: Prediction of membrane proteins in prokaryotic genomes
    Bendtsen JD, Binnewies TT, Hallin PF, Ussery DW
    Microbiology (Reading, Engl.) 151:2119-21, 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 (Reading, Engl.) 151:3147-50, 2005
    PubMed
    Genome update: Distribution of two.component trensduction systems in 250 bacterial genomes
    Kiil K, Ferchaud JB, David C, Binnewies T, Wu H, Sicheritz-Pontén T, Willenbrock H, Ussery DW
    Microbiology (Reading, Engl.) 151:3447-52, 2005
    PubMed
    Crystal ball. Systems biology: in the broadest sense of the word
    Ussery DW, de Lichtenberg U, Jensen LJ
    Environ. Microbiol. 7(4):482-3, 2005
    PubMed
    Genome Update: proteome comparisons
    Binnewies TT, Hallin PF, Staerfeldt HH, Ussery DW
    Microbiology (Reading, Engl.) 151:1-4, 2005
    PubMed
    Genome update: 2D clustering of bacterial genomes
    Willenbrock H, Binnewies TT, Hallin PF, Ussery DW
    Microbiology (Reading, Engl.) 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 (Reading, Engl.) 151:633-7, 2005
    PubMed

2004

    DNA bendability and Nucleosome positioning in transcriptional regulation
    Dlakic M, Brunak S, Ussery DW
    DNA Conformation in Transcription, chapter 14, 2004
    Distribution and characterization of staphylococcal interspersed repeat units (SIRUs) and potential use for strain differentiation
    Hardy KJ, Ussery DW, Oppenheim BA, Hawkey PM
    Microbiology (Reading, Engl.) 150:4045-52, 2004
    PubMed
    Genome update: correlation of bacterial genomic properties
    Hallin PF, Coenye T, Binnewies TT, Jarmer H, Staerfeldt HH, Ussery DW
    Microbiology (Reading, Engl.) 150:3899-903, 2004
    PubMed
    Genome Update: DNA repeats in bacterial genomes
    Ussery DW, Binnewies TT, Gouveia-Oliveira R, Jarmer H, Hallin PF
    Microbiology (Reading, Engl.) 150:3519-21, 2004
    PubMed
    Genome Update: alignment
    Ussery DW, Jensen MS, Poulsen TR, Hallin PF
    Microbiology (Reading, Engl.) 150:2491-3, 2004
    PubMed
    Chromatin architecture and gene expression in Escherichia coli
    Willenbrock H, Ussery DW
    Genome Biol. 5(12):252, 2004
    PubMed
    Genome update: chromosome atlases
    Hallin PF, Binnewies TT, Ussery DW
    Microbiology (Reading, Engl.) 150:3091-3, 2004
    PubMed
    Complete DNA sequence of the linear mitochondrial genome of the pathogenic yeast Candida parapsilosis
    Nosek J, Novotna M, Hlavatovicova Z, Ussery DW, Fajkus J, Tomaska L
    Mol. Genet. Genomics 272(2):173-80, 2004
    PubMed
    Genome update: promoter profiles
    Ussery DW, Tindbaek N, Hallin PF
    Microbiology (Reading, Engl.) 150:2791-3, 2004
    PubMed
    Genome update: alignment of bacterial chromosomes
    Ussery DW, Jensen MS, Poulsen TR, Hallin PF
    Microbiology (Reading, Engl.) 150:2491-3, 2004
    PubMed
    Genome Update: annotation quality in sequenced microbial genomes
    Ussery DW, Hallin PF
    Microbiology (Reading, Engl.) 150:2015-7, 2004
    PubMed
    CBS genome atlas database: a dynamic storage for bioinformatic results and sequence data
    Hallin PF, Ussery DW
    Bioinformatics 20(18):3682-6, 2004
    PubMed
    Genome Update: tRNAs in sequenced microbial genomes
    Ussery DW, Hallin PF, Lagesen K, Wassenaar TM
    Microbiology (Reading, Engl.) 150:1603-6, 2004
    PubMed
    Genome update: rRNAs in sequenced microbial genomes
    Ussery DW, Hallin PF, Lagesen K, Coenye T
    Microbiology (Reading, Engl.) 150:1113-5, 2004
    PubMed
    Genome Update: AT content in sequenced prokaryotic genomes
    Ussery DW, Hallin PF
    Microbiology (Reading, Engl.) 150:749-52, 2004
    PubMed
    Genome Update: length distributions of sequenced prokaryotic genomes
    Ussery DW, Hallin PF
    Microbiology (Reading, Engl.) 150:513-6, 2004
    PubMed
    Genome Update: 161 prokaryotic genomes sequenced, and counting
    Ussery DW
    Microbiology (Reading, Engl.) 150:261-3, 2004
    PubMed
    Global regulation of virulence and the stress response by CsrA in the highly adapted human gastric pathogen Helicobacter pylori
    Barnard FM, Loughlin MF, Fainberg HP, Messenger MP, Ussery DW, Williams P, Jenks PJ
    Mol. Microbiol. 51(1):15-32, 2004
    PubMed

2003

    The sigma54 regulon (sigmulon) of Pseudomonas putida
    Cases I, Ussery DW, de Lorenzo V
    Environ. Microbiol. 5(12):1281-93, 2003
    PubMed
    The Plasmid Genome Database
    Molbak L, Tett A, Ussery DW, Wall K, Turner S, Bailey M, Field D
    Microbiology (Reading, Engl.) 149:3043-5, 2003
    PubMed
    Functionality of System Components: Conservation of Protein Function in Protein Feature Space
    Jensen LJ, Ussery DW, Brunak S
    Genome Res. 13(11):2444-9, 2003
    PubMed
    Genomic characteristics of the Campylobacter fetus sap island
    Zheng-Chao Tu, Ussery DW, Pride DT, Blaser MJ
    Genome Letters, 2, 34-40, 2003
    Genome Letters website
    Sequence analysis of three mitochondrial DNA molecules reveals interesting differences among Saccharomyces yeasts
    Langkjær RB, Casaregola S, Ussery DW, Gaillardin C, Piskur J
    Nucleic Acids Res. 31(12):3081-91, 2003
    PubMed
    Strand misalignments lead to quasipalindrome correction
    van Noort V, Worning P, Ussery DW, Rosche WA, Sinden RR
    Trends Genet. 19(7):365-9, 2003
    PubMed
    RpoD promoters in Campylobacter jejuni exhibit a strong periodic signal instead of a -35 box
    Petersen L, Larsen TS, Ussery DW, On SL, Krogh A
    J. Mol. Biol. 326(5):1361-72, 2003
    PubMed
    Analysis of two large functionally uncharacterized regions in the Methanopyrus kandleri AV19 genome
    Jensen LJ, Skovgaard M, Sicheritz-Ponten T, Jørgensen MK, Lundegaard C, Pedersen CC, Petersen N, Ussery D
    BMC Genomics 4(1):12, 2003
    PubMed

2002

    Comparative Genomics of Pseudomonas aeruginosa PAO1 and Pseudomonas putida KT2440: Orthologs, Codon Usage, REP Elements and Oligonucleotide Motif Signatures
    Weinel C, Ussery DW, Ohlsson H, Sicheritz-Ponten T, Kiewitz C, Tümmler B
    Genome Letters, 1, 175-187, 2002
    Genome Letters website
    Hyperstructures, genome analysis and I-cells
    Amar P, Ballet P, Barlovatz-Meimon G, Benecke A, Bernot G, Bouligand Y, Bourguine P, Delaplace F, Delosme JM, Demarty M, Fishov I, Fourmentin-Guilbert J, Fralick J, Giavitto JL, Gleyse B, Godin C, Incitti R, Kepes F, Lange C, Le Sceller L, Loutellier C, Michel O, Molina F, Monnier C, Natowicz R, Norris V, Orange N, Pollard H, Raine D, Ripoll P, Rouviere-Yaniv J, Saier M Jr, Soler P, Tambourin P, Thellier M, Tracqui P, Ussery D, Vincent JC, Vannier JP, Wiggins P, Zemirline A
    Acta Biotheor. 50(4):357-73, 2002
    PubMed
    DNA Microarray analysis of fim mutations in Escherichia coli
    Schembri MA, Ussery D, Workman C, Hasman H, Klemm P
    Mol. Genet. Genomics 267(6):721-9, 2002
    PubMed
    The Atlas Visualisation of Genome-wide Information
    Skovgaard M, Jensen LJ, Friis C, Stærfeldt H-H, Worning P, Brunak S, Ussery D
    Methods in Microbiology, 33, 49-63, 2002
    Bias of purine stretches in sequenced chromosomes
    Ussery D, Soumpasis DM, Brunak S, Stærfeldt HH, Worning P, Krogh A
    Comput. Chem. 26(5):531-41, 2002
    PubMed
    Inheritance and organisation of the mitochondiral genome differ between two Saccharomyces
    Petersen RF, Langkjær RB, Hvidfeldt J, Gartner J, Palmen W, Ussery DW, Piskur J
    Indian J. Biochem. Biophys. 12(1):21-3, 2002
    PubMed
    Visualisation and Significance of DNA Structural Motifs in the Campylobacter jejuni genome
    Petersen L, On SLW, Ussery D
    Genome Letters, 1, 16-25, 2002
    Relevant URL
    The genome sequence of Schizosaccharomyces pombe
    Wood V, Gwilliam R, Rajandream M-A, Lyne M, Lyne R, Stewart A, Sgouros J, Peat N, Hayles J, Baker S, Basham D, Bowman S, Brooks K, Brown D, Brown S, Chillingworth T, Churcher C, Collins M, Connor R, Cronin A, Davis P, Feltwell T, Fraser A, Gentles S, Goble A, Hamlin N, Harris D, Hidalgo J, Hodgson G, Holroyd S, Hornsby T, Howarth S, Huckle EJ, Hunt S, Jagels K, James K, Jones L, Jones M, Leather S, McDonald S, McLean J, Moule S, Mungall K, Murphy L, Niblett D, Odell C, Oliver K, O'Neil S, Pearson D, Quail MA, Rabbinowitsch E, Rutherford K, Rutter S, Saunders D, Seeger K, Sharp S, Skelton J, Simmonds M, Squares R, Squares S, Stevens K, Taylor K, Taylor RG, Walsh S, Warren T, Whitehead S, Woodward J, Volckaert G, Aert R, Robben J, Grymonprez B, Weltjens I, Vanstreels E, Rieger M, Schäfer M, Muller-Auer S, Gabel C, Fuchs M, Fritzc C, Holzer E, Moestl D, Hilbert H, Borzym K, Langer I, Beck A, Lehrach H, Reinhardt R, Pohl TM, Eger P, Zimmermann W, Wedler H, Wambutt R, Purnelle B, Goffeau A, Cadieu E, Dréano S, Gloux S, Lelaure V, Mottier S, Galibert F, Aves SJ, Xiang Z, Hunt C, Moore K, Hurst SM, Lucas M, Rochet M, Gaillardin C, Tallada VA, Garzon A, Thode G, Daga RR, Cruzado L, Jimenez J, Sanchez M, del Rey F, Dominguez A, Revuelta JL, Moreno S, Armstrong J, Forsburg S, Cerrutti L, Lowe T, McCombie WR, Paulsen I, Potashkin J, Shpakovski GV, Ussery D, Barrell BG, Nurse P
    Nature 415(6874):871-80, 2002
    PubMed
    Evaluation of potential regulatory elements identified as DNase I hypersensitive sites in the CFTR gene
    Phylactides M, Rowntree R, Nuthall H, Ussery D, Wheeler A, Harris A
    Eur. J. Biochem. 269(2):553-9, 2002
    PubMed

2001

    Genome Organisation and Chromatin Structure in Escherichia coli
    Ussery D, Larsen TS, Wilkes KT, Friis C, Worning P, Krogh A, Brunak S
    Biochimie 83(2):201-12, 2001
    PubMed
    On the total number of genes and their length distribution in complete microbial genomes
    Skovgaard M, Jensen LJ, Brunak S, Ussery D, Krogh A
    Trends Genet. 17(8):425-8, 2001
    PubMed
    The Stealth Creationists
    Ussery DW
    Skeptic, 8, 72-74, 2001

2000

    Visualization of pathogenicity regions in bacteria
    Friis C, Jensen LJ, Ussery DW
    Genetica 108(1):47-51, 2000
    PubMed
    A DNA structural atlas for Escherichia coli
    Pedersen AG, Jensen LJ, Stærfeldt H, Brunak S, Ussery DW
    J. Mol. Biol. 299(4):907-30, 2000
    PubMed
    Publication download
    A Classification of Possible Routes of Darwinian Evolution
    Thornhill RH, Ussery DW
    J. Theor. Biol. 203(2):111-6, 2000
    PubMed
    Structural analysis of DNA sequence: evidence for lateral gene transfer in Thermotoga maritima
    Worning P, Jensen LJ, Nielson KE, Brunak S, Ussery DW
    Nucleic Acids Res. 28(3):706-9, 2000
    PubMed

1999

    Three views of microbial genomes
    Jensen LJ, Friis C, Ussery DW
    Res. Microbiol. 150:773-7, 1999
    PubMed
    Environmental Influences on DNA Curvature
    Ussery DW, Higgins CF, Bolshoy A
    J. Biomol. Struct. Dyn. 16(4):811-23, 1999
    PubMed
    A Biochemist's Response to the Biochemical Challenge to Evolution
    Ussery DW
    Bios, 70, 40-45, 1999

1998

    DNA: Structure and Function
    Sinden RR, Pearson CE, Potaman VN, Ussery DW
    in R.D. Verma (ed.), ``Advances in Genome Biology'', 5, 1-141, 1998


Books

    Genome comparison of bacterial pathogens
    Wassenaar TM, Bohlin J, Binnewies TT, Ussery DW
    chapter 1 in Genome Dynamics, volume 6 - Microbial Pathogenomics, (Karger AG publishers, Basel), 2009
    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
    The genus Burkholderia: analysis of 56 genomic sequences
    Ussery DW, Kiil K, Lagesen K, Sicheritz-Ponten T, Bohlin J, Wassenaar TM
    Genome Dyn 6:140-57 doi:10.1159/000235768, 2009
    PubMed
    COMPUTING FOR COMPARATIVE GENOMICS: Bioinformatics for Microbiologists
    Ussery DW, Borini S, Wassenaar TM
    Springer, Series: Computational Biology , Vol. 8, 2008
    Springer, to be published in autumn 2008
    Genome Diversity of Pseudomonas aeruginosa
    Klockgether J, Würdemann D, Wiehlmann L, Binnewies TT, Ussery DW, Tümmler B
    Chapter 2 in Pseudomonas: Genomics and Molecular Biology, (Edited by: Pierre Cornelis, Caister Academic Press, 2008), 2008
    Link to publisher
    Comparative Genomics of Pseudomonas
    Kiil K, Binnewies TT, Willenbrock H, Hansen SK, Yang L, Jelsbak L, Ussery DW, Friis C
    Chapter 1 in Pseudomonas: Model Organism, Pathogen, Cell Factory, (Edited by: B. H. A. Rehm, Wiley-VCH, 2008), 2008
    Link to publisher
    DNA Structure: A-, B-, and Z-DNA Families
    Ussery D
    The Encyclopedia of Life Sciences, (Macmillan Publishers, London), 2002
    Genome Sequence Databases
    Ussery DW, Brunak S
    Encyclopedia of Genetics, S. Brenner and J.H. Miller (eds.), Academic Press, 2001
    DNA Denaturation
    Ussery DW
    Encyclopedia of Genetics, S. Brenner and J.H. Miller (eds.), Academic Press, 2001

2013 (1) 2012 (15) 2011 (6) 2010 (14) 2009 (9) 2008 (10) 2007 and before (76) Books (9)