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David Ussery

TitleProfessor
InstitutionUniversity of Arkansas for Medical Sciences
DepartmentBiomedical Informatics, College of Medicine
Address501 Jack Stephens Drive
Mail Slot # 782
Little Rock AR 72205
Phone501-603-1766
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    Other Positions
    TitleProfessor
    InstitutionUniversity of Arkansas for Medical Sciences
    DepartmentPhysiology and Biophysics, College of Medicine

    Other Roles
    Director, Arkansas Center for Ecological and Genomic Medicine (ArC-GEM)

    Collapse Overview 
    Collapse overview
    Adjunct Professor, Department of Laboratory Medicine, Children’s and Women’s Health, Faculty of Medicine, NTNU, Trondheim, Norway

    Founding Member, Genomic Standards Consortium (GSC)

    Senior Editor, Standards in Genomic Sciences (SIGS)

    Advisory Board, EcoCyc, SRI, Palo Alto, California


    Collapse Biography 
    Collapse awards and honors
    2016Arkansas Research Alliance Fellow, Dept. Biomedical Informatics, COM
    2017Helen Adams & Arkansas Research Alliance Professor & Chair, Dept. Biomedical Informatics, COM

    Collapse Bibliographic 
    Collapse additional bibliographic sources
    The links below are provided by the researcher to provide access to external online bibliographies that they keep independently from the Profiles System.
    Collapse selected publications
    Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Faculty can login to make corrections and additions.
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    1. Alkam D, Wongsurawat T, Jenjaroenpun P, Connor S, Hobbs C, Wassenaar TM, Jun SR, Nookaew I, Ussery D. Three Complete Genome Sequences of Genotype G Mumps Virus from the 2016 Outbreak in Arkansas, USA. Genome Announc. 2017 Aug 10; 5(32). PMID: 28798162.
      View in: PubMed
    2. Zhang Q, Jun SR, Leuze M, Ussery D, Nookaew I. Viral Phylogenomics Using an Alignment-Free Method: A Three-Step Approach to Determine Optimal Length of k-mer. Sci Rep. 2017 Jan 19; 7:40712. PMID: 28102365.
      View in: PubMed
    3. Wassenaar TM, Ussery DW, Ingmer H. The qacC Gene Has Recently Spread between Rolling Circle Plasmids of Staphylococcus, Indicative of a Novel Gene Transfer Mechanism. Front Microbiol. 2016; 7:1528. PMID: 27729906.
      View in: PubMed
    4. Leekitcharoenphon P, Hendriksen RS, Le Hello S, Weill FX, Baggesen DL, Jun SR, Ussery DW, Lund O, Crook DW, Wilson DJ, Aarestrup FM. Global Genomic Epidemiology of Salmonella enterica Serovar Typhimurium DT104. Appl Environ Microbiol. 2016 Apr; 82(8):2516-26. PMID: 26944846; PMCID: PMC4959494.
    5. Jun SR, Wassenaar TM, Nookaew I, Hauser L, Wanchai V, Land M, Timm CM, Lu TY, Schadt CW, Doktycz MJ, Pelletier DA, Ussery DW. Diversity of Pseudomonas Genomes, Including Populus-Associated Isolates, as Revealed by Comparative Genome Analysis. Appl Environ Microbiol. 2015 Oct 30; 82(1):375-83. PMID: 26519390; PMCID: PMC4702629.
    6. Timm CM, Campbell AG, Utturkar SM, Jun SR, Parales RE, Tan WA, Robeson MS, Lu TY, Jawdy S, Brown SD, Ussery DW, Schadt CW, Tuskan GA, Doktycz MJ, Weston DJ, Pelletier DA. Metabolic functions of Pseudomonas fluorescens strains from Populus deltoides depend on rhizosphere or endosphere isolation compartment. Front Microbiol. 2015; 6:1118. PMID: 26528266; PMCID: PMC4604316.
    7. Espinoza-Valles I, Vora GJ, Lin B, Leekitcharoenphon P, González-Castillo A, Ussery D, Høj L, Gomez-Gil B. Unique and conserved genome regions in Vibrio harveyi and related species in comparison with the shrimp pathogen Vibrio harveyi CAIM 1792. Microbiology. 2015 Sep; 161(9):1762-79. PMID: 26198743.
      View in: PubMed
    8. Jun SR, Leuze MR, Nookaew I, Uberbacher EC, Land M, Zhang Q, Wanchai V, Chai J, Nielsen M, Trolle T, Lund O, Buzard GS, Pedersen TD, Wassenaar TM, Ussery DW. Ebolavirus comparative genomics. FEMS Microbiol Rev. 2015 Sep; 39(5):764-78. PMID: 26175035; PMCID: PMC4551310.
    9. Wassenaar TM, Ussery D, Nielsen LN, Ingmer H. Review and phylogenetic analysis of qac genes that reduce susceptibility to quaternary ammonium compounds in Staphylococcus species. Eur J Microbiol Immunol (Bp). 2015 Mar; 5(1):44-61. PMID: 25883793; PMCID: PMC4397847.
    10. Land M, Hauser L, Jun SR, Nookaew I, Leuze MR, Ahn TH, Karpinets T, Lund O, Kora G, Wassenaar T, Poudel S, Ussery DW. Insights from 20 years of bacterial genome sequencing. Funct Integr Genomics. 2015 Mar; 15(2):141-61. PMID: 25722247; PMCID: PMC4361730.
    11. Beatson SA, Ben Zakour NL, Totsika M, Forde BM, Watts RE, Mabbett AN, Szubert JM, Sarkar S, Phan MD, Peters KM, Petty NK, Alikhan NF, Sullivan MJ, Gawthorne JA, Stanton-Cook M, Nhu NT, Chong TM, Yin WF, Chan KG, Hancock V, Ussery DW, Ulett GC, Schembri MA. Molecular analysis of asymptomatic bacteriuria Escherichia coli strain VR50 reveals adaptation to the urinary tract by gene acquisition. Infect Immun. 2015 May; 83(5):1749-64. PMID: 25667270; PMCID: PMC4399054.
    12. Ali A, Naz A, Soares SC, Bakhtiar M, Tiwari S, Hassan SS, Hanan F, Ramos R, Pereira U, Barh D, Figueiredo HC, Ussery DW, Miyoshi A, Silva A, Azevedo V. Pan-genome analysis of human gastric pathogen H. pylori: comparative genomics and pathogenomics approaches to identify regions associated with pathogenicity and prediction of potential core therapeutic targets. Biomed Res Int. 2015; 2015:139580. PMID: 25705648; PMCID: PMC4325212.
    13. Thompson CC, Amaral GR, Campeão M, Edwards RA, Polz MF, Dutilh BE, Ussery DW, Sawabe T, Swings J, Thompson FL. Microbial taxonomy in the post-genomic era: rebuilding from scratch? Arch Microbiol. 2015 Apr; 197(3):359-70. PMID: 25533848.
      View in: PubMed
    14. Land ML, Hyatt D, Jun SR, Kora GH, Hauser LJ, Lukjancenko O, Ussery DW. Quality scores for 32,000 genomes. Stand Genomic Sci. 2014; 9:20. PMID: 25780509; PMCID: PMC4334873.
    15. Haugum K, Johansen J, Gabrielsen C, Brandal LT, Bergh K, Ussery DW, Drabløs F, Afset JE. Comparative genomics to delineate pathogenic potential in non-O157 Shiga toxin-producing Escherichia coli (STEC) from patients with and without haemolytic uremic syndrome (HUS) in Norway. PLoS One. 2014; 9(10):e111788. PMID: 25360710; PMCID: PMC4216125.
    16. Nielsen HB, Almeida M, Juncker AS, Rasmussen S, Li J, Sunagawa S, Plichta DR, Gautier L, Pedersen AG, Le Chatelier E, Pelletier E, Bonde I, Nielsen T, Manichanh C, Arumugam M, Batto JM, Quintanilha Dos Santos MB, Blom N, Borruel N, Burgdorf KS, Boumezbeur F, Casellas F, Doré J, Dworzynski P, Guarner F, Hansen T, Hildebrand F, Kaas RS, Kennedy S, Kristiansen K, Kultima JR, Léonard P, Levenez F, Lund O, Moumen B, Le Paslier D, Pons N, Pedersen O, Prifti E, Qin J, Raes J, Sørensen S, Tap J, Tims S, Ussery DW, Yamada T. Identification and assembly of genomes and genetic elements in complex metagenomic samples without using reference genomes. Nat Biotechnol. 2014 Aug; 32(8):822-8. PMID: 24997787.
      View in: PubMed
    17. Lukjancenko O, Ussery DW. Vibrio chromosome-specific families. Front Microbiol. 2014; 5:73. PMID: 24672511; PMCID: PMC3957060.
    18. Larsen MV, Cosentino S, Lukjancenko O, Saputra D, Rasmussen S, Hasman H, Sicheritz-Pontén T, Aarestrup FM, Ussery DW, Lund O. Benchmarking of methods for genomic taxonomy. J Clin Microbiol. 2014 May; 52(5):1529-39. PMID: 24574292; PMCID: PMC3993634.
    19. Field D, Sterk P, Kottmann R, De Smet JW, Amaral-Zettler L, Cochrane G, Cole JR, Davies N, Dawyndt P, Garrity GM, Gilbert JA, Glöckner FO, Hirschman L, Klenk HP, Knight R, Kyrpides N, Meyer F, Karsch-Mizrachi I, Morrison N, Robbins R, San Gil I, Sansone S, Schriml L, Tatusova T, Ussery D, Yilmaz P, White O, Wooley J, Caporaso G. Genomic standards consortium projects. Stand Genomic Sci. 2014 Jun 15; 9(3):599-601. PMID: 25197446; PMCID: PMC4148985.
    20. Vesth T, Ozen A, Andersen SC, Kaas RS, Lukjancenko O, Bohlin J, Nookaew I, Wassenaar TM, Ussery DW. Veillonella, Firmicutes: Microbes disguised as Gram negatives. Stand Genomic Sci. 2013 Dec 20; 9(2):431-48. PMID: 24976898; PMCID: PMC4062629.
    21. Jensen DB, Ussery DW. Bayesian prediction of microbial oxygen requirement. F1000Res. 2013; 2:184. PMID: 26913185; PMCID: PMC4743139.
    22. Cook H, Ussery DW. Sigma factors in a thousand E. coli genomes. Environ Microbiol. 2013 Dec; 15(12):3121-9. PMID: 23992563.
      View in: PubMed
    23. Bohlin J, Brynildsrud O, Vesth T, Skjerve E, Ussery DW. Amino acid usage is asymmetrically biased in AT- and GC-rich microbial genomes. PLoS One. 2013; 8(7):e69878. PMID: 23922837; PMCID: PMC3724673.
    24. Vesth T, Lagesen K, Acar Ö, Ussery D. CMG-biotools, a free workbench for basic comparative microbial genomics. PLoS One. 2013; 8(4):e60120. PMID: 23577086; PMCID: PMC3618517.
    25. Holch A, Webb K, Lukjancenko O, Ussery D, Rosenthal BM, Gram L. Genome sequencing identifies two nearly unchanged strains of persistent Listeria monocytogenes isolated at two different fish processing plants sampled 6 years apart. Appl Environ Microbiol. 2013 May; 79(9):2944-51. PMID: 23435887; PMCID: PMC3623136.
    26. Jensen DB, Vesth TC, Hallin PF, Pedersen AG, Ussery DW. Bayesian prediction of bacterial growth temperature range based on genome sequences. BMC Genomics. 2012; 13 Suppl 7:S3. PMID: 23282160; PMCID: PMC3521210.
    27. Acevedo-Rocha CG, Fang G, Schmidt M, Ussery DW, Danchin A. From essential to persistent genes: a functional approach to constructing synthetic life. Trends Genet. 2013 May; 29(5):273-9. PMID: 23219343; PMCID: PMC3642372.
    28. Kaas RS, Friis C, Ussery DW, Aarestrup FM. Estimating variation within the genes and inferring the phylogeny of 186 sequenced diverse Escherichia coli genomes. BMC Genomics. 2012 Oct 31; 13:577. PMID: 23114024; PMCID: PMC3575317.
    29. Mekalanos JJ, Robins W, Ussery DW, Davis BM, Schadt E, Waldor MK. Non-O1 Vibrio cholerae unlinked to cholera in Haiti. Proc Natl Acad Sci U S A. 2012 Nov 20; 109(47):E3206; author reply E3207. PMID: 23035253; PMCID: PMC3511112.
    30. Snipen LG, Ussery DW. A domain sequence approach to pangenomics: applications to Escherichia coli. F1000Res. 2012; 1:19. PMID: 24555018; PMCID: PMC3901455.1.
    31. Rodriguez-Valera F, Ussery DW. Is the pan-genome also a pan-selectome? F1000Res. 2012; 1:16. PMID: 24358823; PMCID: PMC3782348.
    32. Zakham F, Aouane O, Ussery D, Benjouad A, Ennaji MM. Computational genomics-proteomics and Phylogeny analysis of twenty one mycobacterial genomes (Tuberculosis & non Tuberculosis strains). Microb Inform Exp. 2012 Aug 28; 2(1):7. PMID: 22929624; PMCID: PMC3504576.
    33. Snipen L, Wassenaar TM, Altermann E, Olson J, Kathariou S, Lagesen K, Takamiya M, Knøchel S, Ussery DW, Meinersmann RJ. Analysis of evolutionary patterns of genes in Campylobacter jejuni and C. coli. Microb Inform Exp. 2012 Aug 28; 2(1):8. PMID: 22929701; PMCID: PMC3502170.
    34. 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. Campylobacter fetus subspecies: comparative genomics and prediction of potential virulence targets. Gene. 2012 Oct 25; 508(2):145-56. PMID: 22890137.
      View in: PubMed
    35. Dillon SC, Espinosa E, Hokamp K, Ussery DW, Casadesús J, Dorman CJ. LeuO is a global regulator of gene expression in Salmonella enterica serovar Typhimurium. Mol Microbiol. 2012 Sep; 85(6):1072-89. PMID: 22804842.
      View in: PubMed
    36. Kröger C, Dillon SC, Cameron AD, 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, Ussery DW, Dorman CJ, Thomson NR, Vogel J, Hinton JC. The transcriptional landscape and small RNAs of Salmonella enterica serovar Typhimurium. Proc Natl Acad Sci U S A. 2012 May 15; 109(20):E1277-86. PMID: 22538806; PMCID: PMC3356629.
    37. Ussery DW, Gordon SV. Two novel methods for using genome sequences to infer taxonomy. Microbiology. 2012 Jun; 158(Pt 6):1414. PMID: 22504434.
      View in: PubMed
    38. Leekitcharoenphon P, Lukjancenko O, Friis C, Aarestrup FM, Ussery DW. Genomic variation in Salmonella enterica core genes for epidemiological typing. BMC Genomics. 2012 Mar 12; 13:88. PMID: 22409488; PMCID: PMC3359268.
    39. Bohlin J, van Passel MW, Snipen L, Kristoffersen AB, Ussery D, Hardy SP. Relative entropy differences in bacterial chromosomes, plasmids, phages and genomic islands. BMC Genomics. 2012 Feb 10; 13:66. PMID: 22325062; PMCID: PMC3305612.
    40. Larsen MV, Cosentino S, Rasmussen S, Friis C, Hasman H, Marvig RL, Jelsbak L, Sicheritz-Pontén T, Ussery DW, Aarestrup FM, Lund O. Multilocus sequence typing of total-genome-sequenced bacteria. J Clin Microbiol. 2012 Apr; 50(4):1355-61. PMID: 22238442; PMCID: PMC3318499.
    41. 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. Polyclonality of concurrent natural populations of Alteromonas macleodii. Genome Biol Evol. 2012; 4(12):1360-74. PMID: 23212172; PMCID: PMC3542563.
    42. Lukjancenko O, Ussery DW, Wassenaar TM. Comparative genomics of Bifidobacterium, Lactobacillus and related probiotic genera. Microb Ecol. 2012 Apr; 63(3):651-73. PMID: 22031452; PMCID: PMC3324989.
    43. Takamiya M, Ozen A, Rasmussen M, Alter T, Gilbert T, Ussery DW, Knøchel S. Genome sequences of two stress-tolerant Campylobacter jejuni poultry strains, 305 and DFVF1099. J Bacteriol. 2011 Oct; 193(19):5546-7. PMID: 21914871; PMCID: PMC3187440.
    44. Özen AI, Ussery DW. Defining the Pseudomonas genus: where do we draw the line with Azotobacter? Microb Ecol. 2012 Feb; 63(2):239-48. PMID: 21811795; PMCID: PMC3275731.
    45. Field D, Amaral-Zettler L, Cochrane G, Cole JR, Dawyndt P, Garrity GM, Gilbert J, Glöckner FO, Hirschman L, Karsch-Mizrachi I, Klenk HP, Knight R, Kottmann R, Kyrpides N, Meyer F, San Gil I, Sansone SA, Schriml LM, Sterk P, Tatusova T, Ussery DW, White O, Wooley J. The Genomic Standards Consortium. PLoS Biol. 2011 Jun; 9(6):e1001088. PMID: 21713030; PMCID: PMC3119656.
    46. Jacobsen A, Hendriksen RS, Aaresturp FM, Ussery DW, Friis C. The Salmonella enterica pan-genome. Microb Ecol. 2011 Oct; 62(3):487-504. PMID: 21643699; PMCID: PMC3175032.
    47. Takamiya M, Ozen A, Rasmussen M, Alter T, Gilbert T, Ussery DW, Knøchel S. Genome Sequence of Campylobacter jejuni strain 327, a strain isolated from a turkey slaughterhouse. Stand Genomic Sci. 2011 Apr 29; 4(2):113-22. PMID: 21677848; PMCID: PMC3111999.
    48. Brede DA, Snipen LG, Ussery DW, Nederbragt AJ, Nes IF. Complete genome sequence of the commensal Enterococcus faecalis 62, isolated from a healthy Norwegian infant. J Bacteriol. 2011 May; 193(9):2377-8. PMID: 21398545; PMCID: PMC3133060.
    49. Karlsson FH, Ussery DW, Nielsen J, Nookaew I. A closer look at bacteroides: phylogenetic relationship and genomic implications of a life in the human gut. Microb Ecol. 2011 Apr; 61(3):473-85. PMID: 21222211.
      View in: PubMed
    50. Friis C, Wassenaar TM, Javed MA, Snipen L, Lagesen K, Hallin PF, Newell DG, Toszeghy M, Ridley A, Manning G, Ussery DW. Genomic characterization of Campylobacter jejuni strain M1. PLoS One. 2010 Aug 26; 5(8):e12253. PMID: 20865039; PMCID: PMC2928727.
    51. Bohlin J, Snipen L, Cloeckaert A, Lagesen K, Ussery D, Kristoffersen AB, Godfroid J. Genomic comparisons of Brucella spp. and closely related bacteria using base compositional and proteome based methods. BMC Evol Biol. 2010 Aug 13; 10:249. PMID: 20707916; PMCID: PMC2928237.
    52. Bohlin J, Snipen L, Hardy SP, Kristoffersen AB, Lagesen K, Dønsvik T, Skjerve E, Ussery DW. Analysis of intra-genomic GC content homogeneity within prokaryotes. BMC Genomics. 2010 Aug 06; 11:464. PMID: 20691090; PMCID: PMC3091660.
    53. Lukjancenko O, Wassenaar TM, Ussery DW. Comparison of 61 sequenced Escherichia coli genomes. Microb Ecol. 2010 Nov; 60(4):708-20. PMID: 20623278; PMCID: PMC2974192.
    54. Lavín JL, Binnewies TT, Pisabarro AG, Ussery DW, García-Lobo JM, Oguiza JA. Differences in two-component signal transduction proteins among the genus Brucella: implications for host preference and pathogenesis. Vet Microbiol. 2010 Aug 26; 144(3-4):478-83. PMID: 20153589.
      View in: PubMed
    55. Snipen L, Ussery DW. Standard operating procedure for computing pangenome trees. Stand Genomic Sci. 2010 Jan 28; 2(1):135-41. PMID: 21304685; PMCID: PMC3035256.
    56. Davenport C, Ussery DW, Tümmler B. Comparative genomics of green sulfur bacteria. Photosynth Res. 2010 Jun; 104(2-3):137-52. PMID: 20099081.
      View in: PubMed
    57. Lavín JL, Ramírez L, Ussery DW, Pisabarro AG, Oguiza JA. Genomic analysis of two-component signal transduction proteins in basidiomycetes. J Mol Microbiol Biotechnol. 2010; 18(2):63-73. PMID: 20110730.
      View in: PubMed
    58. Lagesen K, Ussery DW, Wassenaar TM. Genome update: the 1000th genome--a cautionary tale. Microbiology. 2010 Mar; 156(Pt 3):603-8. PMID: 20093288.
      View in: PubMed
    59. Vesth T, Wassenaar TM, Hallin PF, Snipen L, Lagesen K, Ussery DW. On the origins of a Vibrio species. Microb Ecol. 2010 Jan; 59(1):1-13. PMID: 19830476; PMCID: PMC2807590.
    60. Thompson CC, Vicente AC, Souza RC, Vasconcelos AT, Vesth T, Alves N, Ussery DW, Iida T, Thompson FL. Genomic taxonomy of Vibrios. BMC Evol Biol. 2009 Oct 27; 9:258. PMID: 19860885; PMCID: PMC2777879.
    61. Bohlin J, Skjerve E, Ussery DW. Analysis of genomic signatures in prokaryotes using multinomial regression and hierarchical clustering. BMC Genomics. 2009 Oct 21; 10:487. PMID: 19845945; PMCID: PMC2770534.
    62. Hallin PF, Stærfeldt HH, Rotenberg E, Binnewies TT, Benham CJ, Ussery DW. GeneWiz browser: An Interactive Tool for Visualizing Sequenced Chromosomes. Stand Genomic Sci. 2009 Sep 25; 1(2):204-15. PMID: 21304658; PMCID: PMC3035224.
    63. Snipen L, Almøy T, Ussery DW. Microbial comparative pan-genomics using binomial mixture models. BMC Genomics. 2009 Aug 19; 10:385. PMID: 19691844; PMCID: PMC2907702.
    64. Wassenaar TM, Bohlin J, Binnewies TT, Ussery DW. Genome comparison of bacterial pathogens. Genome Dyn. 2009; 6:1-20. PMID: 19696490.
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    65. Ussery DW, Kiil K, Lagesen K, Sicheritz-Pontén T, Bohlin J, Wassenaar TM. The genus burkholderia: analysis of 56 genomic sequences. Genome Dyn. 2009; 6:140-57. PMID: 19696499.
      View in: PubMed
    66. Bohlin J, Hardy SP, Ussery DW. Stretches of alternating pyrimidine/purines and purines are respectively linked with pathogenicity and growth temperature in prokaryotes. BMC Genomics. 2009 Jul 31; 10:346. PMID: 19646265; PMCID: PMC2728739.
    67. Garrity GM, Thompson LM, Ussery DW, Paskin N, Baker D, Desmeth P, Schindel DE, Ong PS. Studies on monitoring and tracking genetic resources: an executive summary. Stand Genomic Sci. 2009 Jul 20; 1(1):78-86. PMID: 21304641; PMCID: PMC3035216.
    68. 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. The 2008 update of the Aspergillus nidulans genome annotation: a community effort. Fungal Genet Biol. 2009 Mar; 46 Suppl 1:S2-13. PMID: 19146970; PMCID: PMC2826280.
    69. Wang K, Ussery DW, Brunak S. Analysis and prediction of gene splice sites in four Aspergillus genomes. Fungal Genet Biol. 2009 Mar; 46 Suppl 1:S14-8. PMID: 18948220.
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    70. Boyd EF, Cohen AL, Naughton LM, Ussery DW, Binnewies TT, Stine OC, Parent MA. Molecular analysis of the emergence of pandemic Vibrio parahaemolyticus. BMC Microbiol. 2008 Jun 30; 8:110. PMID: 18590559; PMCID: PMC2491623.
    71. 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 W, Herder JD, Gevers D, Vereecke D, Holsters M, Oyaizu H. The genome of the versatile nitrogen fixer Azorhizobium caulinodans ORS571. BMC Genomics. 2008 Jun 04; 9:271. PMID: 18522759; PMCID: PMC2443382.
    72. 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. Toward a standards-compliant genomic and metagenomic publication record. OMICS. 2008 Jun; 12(2):157-60. PMID: 18564916.
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    73. 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. The minimum information about a genome sequence (MIGS) specification. Nat Biotechnol. 2008 May; 26(5):541-7. PMID: 18464787; PMCID: PMC2409278.
    74. Hancock V, Seshasayee AS, Ussery DW, Luscombe NM, Klemm P. Transcriptomics and adaptive genomics of the asymptomatic bacteriuria Escherichia coli strain 83972. Mol Genet Genomics. 2008 May; 279(5):523-34. PMID: 18317809; PMCID: PMC2329726.
    75. Bohlin J, Skjerve E, Ussery DW. Investigations of oligonucleotide usage variance within and between prokaryotes. PLoS Comput Biol. 2008 Apr 18; 4(4):e1000057. PMID: 18421372; PMCID: PMC2289840.
    76. Hallin PF, Binnewies TT, Ussery DW. The genome BLASTatlas-a GeneWiz extension for visualization of whole-genome homology. Mol Biosyst. 2008 May; 4(5):363-71. PMID: 18414733.
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    77. Bohlin J, Skjerve E, Ussery DW. Reliability and applications of statistical methods based on oligonucleotide frequencies in bacterial and archaeal genomes. BMC Genomics. 2008 Feb 28; 9:104. PMID: 18307761; PMCID: PMC2289816.
    78. Miller WG, Parker CT, Rubenfield M, Mendz GL, Wösten MM, Ussery DW, Stolz JF, Binnewies TT, Hallin PF, Wang G, Malek JA, Rogosin A, Stanker LH, Mandrell RE. The complete genome sequence and analysis of the epsilonproteobacterium Arcobacter butzleri. PLoS One. 2007 Dec 26; 2(12):e1358. PMID: 18159241; PMCID: PMC2147049.
    79. Reva ON, Hallin PF, Willenbrock H, Sicheritz-Ponten T, Tümmler B, Ussery DW. Global features of the Alcanivorax borkumensis SK2 genome. Environ Microbiol. 2008 Mar; 10(3):614-25. PMID: 18081853.
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    80. Coenye T, Drevinek P, Mahenthiralingam E, Shah SA, Gill RT, Vandamme P, Ussery DW. Identification of putative noncoding RNA genes in the Burkholderia cenocepacia J2315 genome. FEMS Microbiol Lett. 2007 Nov; 276(1):83-92. PMID: 17937666.
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    81. Lavín JL, Kiil K, Resano O, Ussery DW, Oguiza JA. Comparative genomic analysis of two-component regulatory proteins in Pseudomonas syringae. BMC Genomics. 2007 Oct 31; 8:397. PMID: 17971244; PMCID: PMC2222644.
    82. Arvas M, Kivioja T, Mitchell A, Saloheimo M, Ussery D, Penttila M, Oliver S. Comparison of protein coding gene contents of the fungal phyla Pezizomycotina and Saccharomycotina. BMC Genomics. 2007 Sep 17; 8:325. PMID: 17868481; PMCID: PMC2045113.
    83. Lagesen K, Hallin P, Rødland EA, Staerfeldt HH, Rognes T, Ussery DW. RNAmmer: consistent and rapid annotation of ribosomal RNA genes. Nucleic Acids Res. 2007; 35(9):3100-8. PMID: 17452365; PMCID: PMC1888812.
    84. Willenbrock H, Ussery DW. Prediction of highly expressed genes in microbes based on chromatin accessibility. BMC Mol Biol. 2007 Feb 13; 8:11. PMID: 17295928; PMCID: PMC1805505.
    85. 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, Wösten HA, Zeng AP, van Ooyen AJ, Visser J, Stam H. Genome sequencing and analysis of the versatile cell factory Aspergillus niger CBS 513.88. Nat Biotechnol. 2007 Feb; 25(2):221-31. PMID: 17259976.
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    86. Willenbrock H, Hallin PF, Wassenaar TM, Ussery DW. Characterization of probiotic Escherichia coli isolates with a novel pan-genome microarray. Genome Biol. 2007; 8(12):R267. PMID: 18088402; PMCID: PMC2246269.
    87. Ussery DW. Leaner and meaner genomes in Escherichia coli. Genome Biol. 2006; 7(10):237. PMID: 17076878; PMCID: PMC1794563.
    88. Willenbrock H, Petersen A, Sekse C, Kiil K, Wasteson Y, Ussery DW. Design of a seven-genome Escherichia coli microarray for comparative genomic profiling. J Bacteriol. 2006 Nov; 188(22):7713-21. PMID: 16963574; PMCID: PMC1636325.
    89. Reen FJ, Almagro-Moreno S, Ussery D, Boyd EF. The genomic code: inferring Vibrionaceae niche specialization. Nat Rev Microbiol. 2006 09; 4(9):697-704. PMID: 16894340.
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    90. Binnewies TT, Motro Y, Hallin PF, Lund O, Dunn D, La T, Hampson DJ, Bellgard M, Wassenaar TM, Ussery DW. Ten years of bacterial genome sequencing: comparative-genomics-based discoveries. Funct Integr Genomics. 2006 Jul; 6(3):165-85. PMID: 16773396.
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    91. Champ PC, Binnewies TT, Nielsen N, Zinman G, Kiil K, Wu H, Bohlin J, Ussery DW. Genome update: purine strand bias in 280 bacterial genomes. Microbiology. 2006 Mar; 152(Pt 3):579-83. PMID: 16514138.
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    92. Stanke F, Becker T, Cuppens H, Kumar V, Cassiman JJ, Jansen S, Radojkovic D, Siebert B, Yarden J, Ussery DW, Wienker TF, Tümmler B. The TNFalpha receptor TNFRSF1A and genes encoding the amiloride-sensitive sodium channel ENaC as modulators in cystic fibrosis. Hum Genet. 2006 Apr; 119(3):331-43. PMID: 16463024.
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    93. Worning P, Jensen LJ, Hallin PF, Staerfeldt HH, Ussery DW. Origin of replication in circular prokaryotic chromosomes. Environ Microbiol. 2006 Feb; 8(2):353-61. PMID: 16423021.
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    94. Willenbrock H, Friis C, Juncker AS, Ussery DW. An environmental signature for 323 microbial genomes based on codon adaptation indices. Genome Biol. 2006; 7(12):R114. PMID: 17156429; PMCID: PMC1794427.
    95. Kiil K, Ferchaud JB, David C, Binnewies TT, Wu H, Sicheritz-Pontén T, Willenbrock H, Ussery DW. Genome update: distribution of two-component transduction systems in 250 bacterial genomes. Microbiology. 2005 Nov; 151(Pt 11):3447-52. PMID: 16272367.
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    96. Oguiza JA, Kiil K, Ussery DW. Extracytoplasmic function sigma factors in Pseudomonas syringae. Trends Microbiol. 2005 Dec; 13(12):565-8. PMID: 16257528.
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    97. Kill K, Binnewies TT, Sicheritz-Pontén T, Willenbrock H, Hallin PF, Wassenaar TM, Ussery DW. Genome update: sigma factors in 240 bacterial genomes. Microbiology. 2005 Oct; 151(Pt 10):3147-50. PMID: 16207898.
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    98. Bendtsen JD, Binnewies TT, Hallin PF, Ussery DW. Genome update: prediction of membrane proteins in prokaryotic genomes. Microbiology. 2005 Jul; 151(Pt 7):2119-21. PMID: 16000701.
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    99. Bendtsen JD, Binnewies TT, Hallin PF, Sicheritz-Pontén T, Ussery DW. Genome update: prediction of secreted proteins in 225 bacterial proteomes. Microbiology. 2005 Jun; 151(Pt 6):1725-7. PMID: 15941981.
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    100. Ussery DW, de Lichtenberg U, Jensen LJ. Crystal ball. Systems biology: in the broadest sense of the word. Environ Microbiol. 2005 Apr; 7(4):482-3. PMID: 15816924.
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    101. Binnewies TT, Bendtsen JD, Hallin PF, Nielsen N, Wassenaar TM, Pedersen MB, Klemm P, Ussery DW. Genome Update: Protein secretion systems in 225 bacterial genomes. Microbiology. 2005 Apr; 151(Pt 4):1013-6. PMID: 15817770.
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    102. Hallin PF, Nielsen N, Devine KM, Binnewies TT, Willenbrock H, Ussery DW. Genome update: base skews in 200+ bacterial chromosomes. Microbiology. 2005 Mar; 151(Pt 3):633-7. PMID: 15758208.
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    103. Willenbrock H, Binnewies TT, Hallin PF, Ussery DW. Genome update: 2D clustering of bacterial genomes. Microbiology. 2005 Feb; 151(Pt 2):333-6. PMID: 15699184.
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    104. Binnewies TT, Hallin PF, Staerfeldt HH, Ussery DW. Genome Update: proteome comparisons. Microbiology. 2005 Jan; 151(Pt 1):1-4. PMID: 15632419.
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    105. Willenbrock H, Ussery DW. Chromatin architecture and gene expression in Escherichia coli. Genome Biol. 2004; 5(12):252. PMID: 15575978; PMCID: PMC545790.
    106. Hallin PF, Coenye T, Binnewies TT, Jarmer H, Saerfeldt HH, Ussery DW. Genome update: correlation of bacterial genomic properties. Microbiology. 2004 Dec; 150(Pt 12):3899-903. PMID: 15583141.
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    107. Ussery DW, Binnewies TT, Gouveia-Oliveira R, Jarmer H, Hallin PF. Genome update: DNA repeats in bacterial genomes. Microbiology. 2004 Nov; 150(Pt 11):3519-21. PMID: 15528640.
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    108. Hallin PF, Binnewies TT, Ussery DW. Genome update: chromosome atlases. Microbiology. 2004 Oct; 150(Pt 10):3091-3. PMID: 15470087.
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    109. Ussery DW, Tindbaek N, Hallin PF. Genome update: promoter profiles. Microbiology. 2004 Sep; 150(Pt 9):2791-3. PMID: 15347738.
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    110. Ussery DW, Jensen MS, Poulsen TR, Hallin PF. Genome update: alignment of bacterial chromosomes. Microbiology. 2004 Aug; 150(Pt 8):2491-3. PMID: 15289544.
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    111. Hallin PF, Ussery DW. CBS Genome Atlas Database: a dynamic storage for bioinformatic results and sequence data. Bioinformatics. 2004 Dec 12; 20(18):3682-6. PMID: 15256401.
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    112. Ussery DW, Hallin PF. Genome Update: annotation quality in sequenced microbial genomes. Microbiology. 2004 Jul; 150(Pt 7):2015-7. PMID: 15256543.
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    113. Ussery DW, Hallin PF, Lagesen K, Wassenaar TM. Genome update: tRNAs in sequenced microbial genomes. Microbiology. 2004 Jun; 150(Pt 6):1603-6. PMID: 15184546.
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    114. Ussery DW, Hallin PF, Lagesen K, Coenye T. Genome update: rRNAs in sequenced microbial genomes. Microbiology. 2004 May; 150(Pt 5):1113-5. PMID: 15133066.
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    115. Ussery DW, Hallin PF. Genome Update: AT content in sequenced prokaryotic genomes. Microbiology. 2004 Apr; 150(Pt 4):749-52. PMID: 15073284.
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    116. Ussery DW, Hallin PF. Genome update: Length distributions of sequenced prokaryotic genomes. Microbiology. 2004 Mar; 150(Pt 3):513-6. PMID: 14993295.
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    117. Ussery DW. Genome update: 161 prokaryotic genomes sequenced, and counting. Microbiology. 2004 Feb; 150(Pt 2):261-3. PMID: 14766901.
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    118. Barnard FM, Loughlin MF, Fainberg HP, Messenger MP, Ussery DW, Williams P, Jenks PJ. Global regulation of virulence and the stress response by CsrA in the highly adapted human gastric pathogen Helicobacter pylori. Mol Microbiol. 2004 Jan; 51(1):15-32. PMID: 14651608.
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    119. Cases I, Ussery DW, de Lorenzo V. The sigma54 regulon (sigmulon) of Pseudomonas putida. Environ Microbiol. 2003 Dec; 5(12):1281-93. PMID: 14641574.
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    120. Mølbak L, Tett A, Ussery DW, Wall K, Turner S, Bailey M, Field D. The plasmid genome database. Microbiology. 2003 Nov; 149(Pt 11):3043-5. PMID: 14600215.
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    121. Jensen LJ, Ussery DW, Brunak S. Functionality of system components: conservation of protein function in protein feature space. Genome Res. 2003 Nov; 13(11):2444-9. PMID: 14559779; PMCID: PMC403763.
    122. van Noort V, Worning P, Ussery DW, Rosche WA, Sinden RR. Strand misalignments lead to quasipalindrome correction. Trends Genet. 2003 Jul; 19(7):365-9. PMID: 12850440.
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    123. Jensen LJ, Skovgaard M, Sicheritz-Pontén T, Jørgensen MK, Lundegaard C, Pedersen CC, Petersen N, Ussery D. Analysis of two large functionally uncharacterized regions in the Methanopyrus kandleri AV19 genome. BMC Genomics. 2003 Apr 02; 4(1):12. PMID: 12697059; PMCID: PMC156604.
    124. Petersen L, Larsen TS, Ussery DW, On SL, Krogh A. RpoD promoters in Campylobacter jejuni exhibit a strong periodic signal instead of a -35 box. J Mol Biol. 2003 Mar 07; 326(5):1361-72. PMID: 12595250.
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    125. Ussery D, Soumpasis DM, Brunak S, Staerfeldt HH, Worning P, Krogh A. Bias of purine stretches in sequenced chromosomes. Comput Chem. 2002 Jul; 26(5):531-41. PMID: 12144181.
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    126. Petersen RF, Langkjaer RB, Hvidtfeldt J, Gartner J, Palmen W, Ussery DW, Piskur J. Inheritance and organisation of the mitochondrial genome differ between two Saccharomyces yeasts. J Mol Biol. 2002 May 03; 318(3):627-36. PMID: 12054811.
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    127. Phylactides M, Rowntree R, Nuthall H, Ussery D, Wheeler A, Harris A. Evaluation of potential regulatory elements identified as DNase I hypersensitive sites in the CFTR gene. Eur J Biochem. 2002 Jan; 269(2):553-9. PMID: 11856314.
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