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Connection

David Ussery to Genome, Bacterial

This is a "connection" page, showing publications David Ussery has written about Genome, Bacterial.

 
Connection Strength
  
 
 
13.176
  
  1. Abram K, Udaondo Z, Bleker C, Wanchai V, Wassenaar TM, Robeson MS, Ussery DW. Mash-based analyses of Escherichia coli genomes reveal 14 distinct phylogroups. Commun Biol. 2021 01 26; 4(1):117.
    View in: PubMed
    Score: 0.685
  2. Cabal A, Jun SR, Jenjaroenpun P, Wanchai V, Nookaew I, Wongsurawat T, Burgess MJ, Kothari A, Wassenaar TM, Ussery DW. Genome-Based Comparison of Clostridioides difficile: Average Amino Acid Identity Analysis of Core Genomes. Microb Ecol. 2018 Oct; 76(3):801-813.
    View in: PubMed
    Score: 0.558
  3. 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. 2016 01 01; 82(1):375-83.
    View in: PubMed
    Score: 0.476
  4. 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.
    View in: PubMed
    Score: 0.455
  5. Cook H, Ussery DW. Sigma factors in a thousand E. coli genomes. Environ Microbiol. 2013 Dec; 15(12):3121-9.
    View in: PubMed
    Score: 0.410
  6. 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.
    View in: PubMed
    Score: 0.390
  7. ?zen AI, Ussery DW. Defining the Pseudomonas genus: where do we draw the line with Azotobacter? Microb Ecol. 2012 Feb; 63(2):239-48.
    View in: PubMed
    Score: 0.355
  8. 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.
    View in: PubMed
    Score: 0.333
  9. Lukjancenko O, Wassenaar TM, Ussery DW. Comparison of 61 sequenced Escherichia coli genomes. Microb Ecol. 2010 Nov; 60(4):708-20.
    View in: PubMed
    Score: 0.330
  10. 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.
    View in: PubMed
    Score: 0.314
  11. Ussery DW, Kiil K, Lagesen K, Sicheritz-Pont?n T, Bohlin J, Wassenaar TM. The genus burkholderia: analysis of 56 genomic sequences. Genome Dyn. 2009; 6:140-157.
    View in: PubMed
    Score: 0.310
  12. 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.
    View in: PubMed
    Score: 0.281
  13. 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.
    View in: PubMed
    Score: 0.280
  14. Reva ON, Hallin PF, Willenbrock H, Sicheritz-Ponten T, T?mmler B, Ussery DW. Global features of the Alcanivorax borkumensis SK2 genome. Environ Microbiol. 2008 Mar; 10(3):614-25.
    View in: PubMed
    Score: 0.276
  15. 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.
    View in: PubMed
    Score: 0.274
  16. Willenbrock H, Ussery DW. Prediction of highly expressed genes in microbes based on chromatin accessibility. BMC Mol Biol. 2007 Feb 13; 8:11.
    View in: PubMed
    Score: 0.260
  17. Ussery DW. Leaner and meaner genomes in Escherichia coli. Genome Biol. 2006; 7(10):237.
    View in: PubMed
    Score: 0.255
  18. 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.
    View in: PubMed
    Score: 0.253
  19. 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.
    View in: PubMed
    Score: 0.247
  20. 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 (Reading). 2006 Mar; 152(Pt 3):579-583.
    View in: PubMed
    Score: 0.244
  21. Kiil K, Ferchaud JB, David C, Binnewies TT, Wu H, Sicheritz-Pont?n T, Willenbrock H, Ussery DW. Genome update: distribution of two-component transduction systems in 250 bacterial genomes. Microbiology (Reading). 2005 Nov; 151(Pt 11):3447-3452.
    View in: PubMed
    Score: 0.238
  22. Kill K, Binnewies TT, Sicheritz-Pont?n T, Willenbrock H, Hallin PF, Wassenaar TM, Ussery DW. Genome update: sigma factors in 240 bacterial genomes. Microbiology (Reading). 2005 Oct; 151(Pt 10):3147-3150.
    View in: PubMed
    Score: 0.237
  23. Bendtsen JD, Binnewies TT, Hallin PF, Ussery DW. Genome update: prediction of membrane proteins in prokaryotic genomes. Microbiology (Reading). 2005 Jul; 151(Pt 7):2119-2121.
    View in: PubMed
    Score: 0.233
  24. 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 (Reading). 2005 Apr; 151(Pt 4):1013-1016.
    View in: PubMed
    Score: 0.229
  25. Hallin PF, Nielsen N, Devine KM, Binnewies TT, Willenbrock H, Ussery DW. Genome update: base skews in 200+ bacterial chromosomes. Microbiology (Reading). 2005 Mar; 151(Pt 3):633-637.
    View in: PubMed
    Score: 0.227
  26. Willenbrock H, Binnewies TT, Hallin PF, Ussery DW. Genome update: 2D clustering of bacterial genomes. Microbiology (Reading). 2005 Feb; 151(Pt 2):333-336.
    View in: PubMed
    Score: 0.226
  27. Hallin PF, Coenye T, Binnewies TT, Jarmer H, Saerfeldt HH, Ussery DW. Genome update: correlation of bacterial genomic properties. Microbiology (Reading). 2004 Dec; 150(Pt 12):3899-903.
    View in: PubMed
    Score: 0.224
  28. Ussery DW, Binnewies TT, Gouveia-Oliveira R, Jarmer H, Hallin PF. Genome update: DNA repeats in bacterial genomes. Microbiology (Reading). 2004 Nov; 150(Pt 11):3519-3521.
    View in: PubMed
    Score: 0.222
  29. Hallin PF, Binnewies TT, Ussery DW. Genome update: chromosome atlases. Microbiology (Reading). 2004 Oct; 150(Pt 10):3091-3.
    View in: PubMed
    Score: 0.221
  30. Ussery DW, Tindb?k N, Hallin PF. Genome update: promoter profiles. Microbiology (Reading). 2004 Sep; 150(Pt 9):2791-2793.
    View in: PubMed
    Score: 0.220
  31. Ussery DW, Jensen MS, Poulsen TR, Hallin PF. Genome update: alignment of bacterial chromosomes. Microbiology (Reading). 2004 Aug; 150(Pt 8):2491-2493.
    View in: PubMed
    Score: 0.218
  32. Ussery DW, Hallin PF. Genome Update: annotation quality in sequenced microbial genomes. Microbiology (Reading). 2004 Jul; 150(Pt 7):2015-2017.
    View in: PubMed
    Score: 0.217
  33. Ussery DW, Hallin PF, Lagesen K, Wassenaar TM. Genome update: tRNAs in sequenced microbial genomes. Microbiology (Reading). 2004 Jun; 150(Pt 6):1603-1606.
    View in: PubMed
    Score: 0.216
  34. Ussery DW, Hallin PF, Lagesen K, Coenye T. Genome update: rRNAs in sequenced microbial genomes. Microbiology (Reading). 2004 May; 150(Pt 5):1113-1115.
    View in: PubMed
    Score: 0.215
  35. Ussery DW, Hallin PF. Genome Update: AT content in sequenced prokaryotic genomes. Microbiology (Reading). 2004 Apr; 150(Pt 4):749-752.
    View in: PubMed
    Score: 0.213
  36. Ussery DW. Genome update: 161 prokaryotic genomes sequenced, and counting. Microbiology (Reading). 2004 Feb; 150(Pt 2):261-263.
    View in: PubMed
    Score: 0.211
  37. Wanchai V, Patumcharoenpol P, Nookaew I, Ussery D. dBBQs: dataBase of Bacterial Quality scores. BMC Bioinformatics. 2017 12 28; 18(Suppl 14):483.
    View in: PubMed
    Score: 0.138
  38. Espinoza-Valles I, Vora GJ, Lin B, Leekitcharoenphon P, Gonz?lez-Castillo A, Ussery D, H?j 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 (Reading). 2015 Sep; 161(9):1762-1779.
    View in: PubMed
    Score: 0.117
  39. 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.
    View in: PubMed
    Score: 0.113
  40. 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.
    View in: PubMed
    Score: 0.099
  41. 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.
    View in: PubMed
    Score: 0.097
  42. 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.
    View in: PubMed
    Score: 0.097
  43. 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.
    View in: PubMed
    Score: 0.096
  44. Ali A, Soares SC, Santos AR, Guimar?es 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.
    View in: PubMed
    Score: 0.095
  45. Larsen MV, Cosentino S, Rasmussen S, Friis C, Hasman H, Marvig RL, Jelsbak L, Sicheritz-Pont?n T, Ussery DW, Aarestrup FM, Lund O. Multilocus sequence typing of total-genome-sequenced bacteria. J Clin Microbiol. 2012 Apr; 50(4):1355-61.
    View in: PubMed
    Score: 0.091
  46. Gonzaga A, Martin-Cuadrado AB, L?pez-P?rez M, Megumi Mizuno C, Garc?a-Heredia I, Kimes NE, Lopez-Garc?a 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.
    View in: PubMed
    Score: 0.091
  47. Lukjancenko O, Ussery DW, Wassenaar TM. Comparative genomics of Bifidobacterium, Lactobacillus and related probiotic genera. Microb Ecol. 2012 Apr; 63(3):651-73.
    View in: PubMed
    Score: 0.090
  48. Takamiya M, Ozen A, Rasmussen M, Alter T, Gilbert T, Ussery DW, Kn?chel S. Genome sequences of two stress-tolerant Campylobacter jejuni poultry strains, 305 and DFVF1099. J Bacteriol. 2011 Oct; 193(19):5546-7.
    View in: PubMed
    Score: 0.090
  49. Jacobsen A, Hendriksen RS, Aaresturp FM, Ussery DW, Friis C. The Salmonella enterica pan-genome. Microb Ecol. 2011 Oct; 62(3):487-504.
    View in: PubMed
    Score: 0.088
  50. 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.
    View in: PubMed
    Score: 0.086
  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.
    View in: PubMed
    Score: 0.083
  52. Lagesen K, Ussery DW, Wassenaar TM. Genome update: the 1000th genome--a cautionary tale. Microbiology (Reading). 2010 Mar; 156(Pt 3):603-608.
    View in: PubMed
    Score: 0.080
  53. 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.
    View in: PubMed
    Score: 0.080
  54. 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.
    View in: PubMed
    Score: 0.079
  55. Snipen L, Alm?y T, Ussery DW. Microbial comparative pan-genomics using binomial mixture models. BMC Genomics. 2009 Aug 19; 10:385.
    View in: PubMed
    Score: 0.077
  56. 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.
    View in: PubMed
    Score: 0.072
  57. 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.
    View in: PubMed
    Score: 0.071
  58. Miller WG, Parker CT, Rubenfield M, Mendz GL, W?sten 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.
    View in: PubMed
    Score: 0.069
  59. Lav?n 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.
    View in: PubMed
    Score: 0.068
  60. Lagesen K, Hallin P, R?dland EA, Staerfeldt HH, Rognes T, Ussery DW. RNAmmer: consistent and rapid annotation of ribosomal RNA genes. Nucleic Acids Res. 2007; 35(9):3100-8.
    View in: PubMed
    Score: 0.066
  61. 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.
    View in: PubMed
    Score: 0.065
  62. 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.
    View in: PubMed
    Score: 0.063
  63. Oguiza JA, Kiil K, Ussery DW. Extracytoplasmic function sigma factors in Pseudomonas syringae. Trends Microbiol. 2005 Dec; 13(12):565-8.
    View in: PubMed
    Score: 0.060
  64. Binnewies TT, Hallin PF, St?rfeldt HH, Ussery DW. Genome Update: proteome comparisons. Microbiology (Reading). 2005 Jan; 151(Pt 1):1-4.
    View in: PubMed
    Score: 0.056
  65. Ussery DW, Hallin PF. Genome update: Length distributions of sequenced prokaryotic genomes. Microbiology (Reading). 2004 Mar; 150(Pt 3):513-516.
    View in: PubMed
    Score: 0.053
  66. M?lbak L, Tett A, Ussery DW, Wall K, Turner S, Bailey M, Field D. The plasmid genome database. Microbiology (Reading). 2003 Nov; 149(Pt 11):3043-3045.
    View in: PubMed
    Score: 0.052
  67. 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.
    View in: PubMed
    Score: 0.031
  68. 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.
    View in: PubMed
    Score: 0.028
  69. Dillon SC, Espinosa E, Hokamp K, Ussery DW, Casades?s J, Dorman CJ. LeuO is a global regulator of gene expression in Salmonella enterica serovar Typhimurium. Mol Microbiol. 2012 Sep; 85(6):1072-89.
    View in: PubMed
    Score: 0.024
  70. 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.
    View in: PubMed
    Score: 0.021
  71. Lav?n JL, Binnewies TT, Pisabarro AG, Ussery DW, Garc?a-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.
    View in: PubMed
    Score: 0.020
  72. 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.
    View in: PubMed
    Score: 0.018
Connection Strength

The connection strength for concepts is the sum of the scores for each matching publication.

Publication scores are based on many factors, including how long ago they were written and whether the person is a first or senior author.