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Connection

David Ussery to Sequence Analysis, DNA

This is a "connection" page, showing publications David Ussery has written about Sequence Analysis, DNA.

 
Connection Strength
  
 
 
3.130
  
  1. Bohlin J, Skjerve E, Ussery DW. Investigations of oligonucleotide usage variance within and between prokaryotes. PLoS Comput Biol. 2008 Apr 18; 4(4):e1000057.
    View in: PubMed
    Score: 0.297
  2. 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.
    View in: PubMed
    Score: 0.241
  3. 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: 0.239
  4. Ussery DW, Tindb?k N, Hallin PF. Genome update: promoter profiles. Microbiology (Reading). 2004 Sep; 150(Pt 9):2791-2793.
    View in: PubMed
    Score: 0.231
  5. 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.
    View in: PubMed
    Score: 0.229
  6. 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: 0.227
  7. 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: 0.180
  8. 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: 0.125
  9. 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: 0.120
  10. 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: 0.087
  11. 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: 0.083
  12. 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: 0.082
  13. 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: 0.082
  14. 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: 0.074
  15. 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: 0.073
  16. 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, W?sten 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.
    View in: PubMed
    Score: 0.068
  17. 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: 0.065
  18. Bendtsen JD, Binnewies TT, Hallin PF, Sicheritz-Pont?n T, Ussery DW. Genome update: prediction of secreted proteins in 225 bacterial proteomes. Microbiology (Reading). 2005 Jun; 151(Pt 6):1725-1727.
    View in: PubMed
    Score: 0.061
  19. 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: 0.059
  20. 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: 0.059
  21. 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: 0.057
  22. 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: 0.056
  23. Jenjaroenpun P, Wongsurawat T, Wadley TD, Wassenaar TM, Liu J, Dai Q, Wanchai V, Akel NS, Jamshidi-Parsian A, Franco AT, Boysen G, Jennings ML, Ussery DW, He C, Nookaew I. Decoding the epitranscriptional landscape from native RNA sequences. Nucleic Acids Res. 2021 01 25; 49(2):e7.
    View in: PubMed
    Score: 0.045
  24. Wongsurawat T, Nakagawa M, Atiq O, Coleman HN, Jenjaroenpun P, Allred JI, Trammel A, Puengrang P, Ussery DW, Nookaew I. An assessment of Oxford Nanopore sequencing for human gut metagenome profiling: A pilot study of head and neck cancer patients. J Microbiol Methods. 2019 11; 166:105739.
    View in: PubMed
    Score: 0.041
  25. Jenjaroenpun P, Wongsurawat T, Pereira R, Patumcharoenpol P, Ussery DW, Nielsen J, Nookaew I. Complete genomic and transcriptional landscape analysis using third-generation sequencing: a case study of Saccharomyces cerevisiae CEN.PK113-7D. Nucleic Acids Res. 2018 04 20; 46(7):e38.
    View in: PubMed
    Score: 0.037
  26. 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: 0.032
  27. 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: 0.030
  28. 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: 0.026
  29. 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: 0.025
  30. 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: 0.025
  31. 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: 0.023
  32. 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: 0.021
  33. Stanke F, Becker T, Cuppens H, Kumar V, Cassiman JJ, Jansen S, Radojkovic D, Siebert B, Yarden J, Ussery DW, Wienker TF, T?mmler 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.
    View in: PubMed
    Score: 0.016
  34. 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.
    View in: PubMed
    Score: 0.013
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.