 |
|
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. 2012 Jan;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. 2012 Jan;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. 2012 Dec 3, 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, Guimarăes 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. 2012 Aug 6. [Epub ahead of print], 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 optimum temperature based on genome sequences
Jensen DB, Vest TC, Hallin PF, Pedersen AG, Ussery D
BMC Genomics, 2012 |
|
Two novel methods for using genome sequences to infer taxonomy
Ussery DW, Gordon SV
Microbiology. 2012 Jun;158(Pt 6):1414. Epub 2012 Apr 13, 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. 2012 Jul 16. 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, June 4, 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) Feb, 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, Knřchel 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
Microbial Ecology, January 11, 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., 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, 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, 2010 |
PubMed
|
Comparison of 61 Sequenced Escherichia coli Genomes Microbial Ecology
Lukjancenko O, Wassenaar TM, Ussery DW
Microb. Ecol., 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
Journal of Molecular Microbiology and Biotechnology, 18:63-73 in the press, 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
Photosynthesis Research, 103: in the press, 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, 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, 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, Stćrfeldt 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, Almřy T, Ussery DW
BMC Genomics. ;10:385, 2009 |
PubMed
|
Analysis and prediction of gene splice sites in four Aspergillus genomes
Wang K, Ussery DW, Brunak S
Fungal Genetics and Biology, Volume 46, Issue 1, Supplement , March 2009, Pages S14-S18, Thematic Issue: Aspergillus Genomics and Beyond., 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
Nature Biotechnology, 2008 May;26(5):541-7, 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
Nature Biotechnology, 26:541-547, (2008), 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, 49:104 (2008). doi:10.1371/journal.pcbi.1000057, 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, 279:523-534, (2008)., 2008 |
PubMed
|
Investigations of oligonucleotide usage variance within and between prokaryotes
Bohlin J, Skjerve E, Ussery D
PLoS Computational Biology, 4:e1000057 (2008), 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 - A Journal of Integrative Biology, 12:157-160, (2008), 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. 2008 Jun 30;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. 2008 Jun 4;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. 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
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 276:83-92,(2007)., 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 (Sept. 2007), 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. 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
|
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 3:325, 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
|
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, Rřdland EA, Stćrfeldt HH, Rognes T, Ussery DW
Nucleic Acids Research 35:3100-3108,(2007)., 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
Journal of Bacteriology, 188:7713-7721, 2006 |
PubMed
|
Leaner and Meaner Genomes in Escherichia coli
Ussery DW
GenomeBiology, 7:237, 2006 |
PubMed
|
An environmental signature for 323 microbial genomes based on codon adaptation indices
Willenbrock H, Friis C, Juncker AS, Ussery DW
Genome Biology, 7, R114, 2006 |
PubMed
|
The genomic code: inferring Vibrionaceae niche specialization
Reen FJ, Almagro-Moreno S, Ussery D et al
Nature Reviews Microbiology 4, 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, 152(Pt 3): 579-83, 2006 |
PubMed
|
Origin of Replication in Circular Prokaryotic Chromosomes
Worning P, Jensen LJ, Hallin PF, Stćrfeldt 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
|
Extracytoplasmic function sigma factors in Pseudomona syringae
Oguiza JA, Kiil K, Ussery DW
Trends Microbiology, 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, 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: 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, 151, 3447-3452, 2005 |
PubMed
|
Crystal ball. Systems biology: in the broadest sense of the word
Ussery DW, de Lichtenberg U, Jensen LJ
Environmental Microbiology, 7, 482-83, 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
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, 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, 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
|
Chromatin architecture and gene expression in Escherichia coli
Willenbrock H, Ussery DW
Genome Biology, 5, 252, 2004 |
PubMed
|
Genome update: chromosome atlases
Hallin PF, Binnewies TT, Ussery DW
Microbiology, 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
Molecular Genetics Genomics, 272, 173-80, 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
|
Genome Update: 161 prokaryotic genomes sequenced, and counting
Ussery DW
Microbiology, 150, 261-263, 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
Molecular Microbiology, 51,15-32, 2004 |
PubMed
|
2003
The sigma54 regulon (sigmulon) of Pseudomonas putida
Cases I, Ussery DW, de Lorenzo V
Environmental Microbiology, 5, 1281-93, 2003 |
PubMed
|
The Plasmid Genome Database
Molbak L, Tett A, Ussery DW, Wall K, Turner S, Bailey M, Field D
Microbiology, 149, 3043-3045, 2003 |
PubMed
|
Functionality of System Components: Conservation of Protein Function in Protein Feature Space
Jensen LJ, Ussery DW, Brunak S
Genome Res., 13, 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
Langkjćr RB, Casaregola S, Ussery DW, Gaillardin C, Piskur J
Nucleic Acids Res, 31, 3081-91, 2003 |
PubMed
|
Strand misalignments lead to quasipalindrome correction
van Noort V, Worning P, Ussery DW, Rosche WA, Sinden RR
Trends Genet, 19, 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, 1361-72, 2003 |
PubMed
|
Analysis of two large functionally uncharacterized regions in the Methanopyrus kandleri AV19 genome
Jensen LJ, Skovgaard M, Sicheritz-Ponten T, Jřrgensen MK, Lundegaard C, Pedersen CC, Petersen N, Ussery D
BMC Genomics, 4, 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
vActa Biotheor, 50, 357-73, 2002 |
PubMed
|
DNA Microarray analysis of fim mutations in Escherichia coli
Schembri MA, Ussery D, Workman C, Hasman H, Klemm P
Molecular Genetics and Genomics, 267, 721-729, 2002 |
PubMed
|
The Atlas Visualisation of Genome-wide Information
Skovgaard M, Jensen LJ, Friis C, Stćrfeldt 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, Stćrfeldt HH, Worning P, Krogh A
Computers and Chemistry, 26, 531-541, 2002 |
PubMed
|
Inheritance and organisation of the mitochondiral genome differ between two Saccharomyces
Petersen RF, Langkjćr RB, Hvidfeldt J, Gartner J, Palmen W, Ussery DW, Piskur J
J. Mol. Biol., 318, 627-636, 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, 871-880, 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, 553-559, 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, 202-212 (cover illustration), 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, 425-428, 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, 47-51, 2000 |
PubMed
|
A DNA structural atlas for Escherichia coli
Pedersen AG, Jensen LJ, Stćrfeldt H, Brunak S, Ussery DW
J. Mol.Biol., 299, 907-930, 2000 |
PubMed
Publication download
|
A Classification of Possible Routes of Darwinian Evolution
Thornhill RH, Ussery DW
J. Theor. Biol., 203, 111-116, 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, 706-709, 2000 |
PubMed
|
1999
Three views of microbial genomes
Jensen LJ, Friis C, Ussery DW
Res. Microbiol., 150, 773-777, 1999 |
PubMed
|
Environmental Influences on DNA Curvature
Ussery DW, Higgins CF, Bolshoy A
J. Biomol. Struct. Dyn., 16, 811-824, 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
Microbial Pathogenomics,Karger AG publishers, Basel, 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 |
|
|
|
This file was last modified Friday 3rd of September 2010 09:03:29 GMT |
|
|
|
