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Items: 1 to 50 of 138

1.

An assessment of Oxford Nanopore sequencing for human gut metagenome profiling: A pilot study of head and neck cancer patients.

Wongsurawat T, Nakagawa M, Atiq O, Coleman HN, Jenjaroenpun P, Allred JI, Trammel A, Puengrang P, Ussery DW, Nookaew I.

J Microbiol Methods. 2019 Nov;166:105739. doi: 10.1016/j.mimet.2019.105739. Epub 2019 Oct 15.

PMID:
31626891
2.

SMARC-B1 deficient sinonasal carcinoma metastasis to the brain with next generation sequencing data: a case report of perineural invasion progressing to leptomeningeal invasion.

Gomez-Acevedo H, Patterson JD, Sardar S, Gokden M, Das BC, Ussery DW, Rodriguez A.

BMC Cancer. 2019 Aug 22;19(1):827. doi: 10.1186/s12885-019-6043-0.

3.

In silico Selection of Amplification Targets for Rapid Polymorphism Screening in Ebola Virus Outbreaks.

Wassenaar TM, Wanchai V, Buzard GS, Ussery DW.

Front Microbiol. 2019 Apr 26;10:857. doi: 10.3389/fmicb.2019.00857. eCollection 2019.

4.

Consent insufficient for data release-Response.

Amann RI, Baichoo S, Blencowe BJ, Bork P, Borodovsky M, Brooksbank C, Chain PSG, Colwell RR, Daffonchio DG, Danchin A, de Lorenzo V, Dorrestein PC, Finn RD, Fraser CM, Gilbert JA, Hallam SJ, Hugenholtz P, Ioannidis JPA, Jansson JK, Kim JF, Klenk HP, Klotz MG, Knight R, Konstantinidis KT, Kyrpides NC, Mason CE, McHardy AC, Meyer F, Ouzounis CA, Patrinos AAN, Podar M, Pollard KS, Ravel J, Muñoz AR, Roberts RJ, Rosselló-Móra R, Sansone SA, Schloss PD, Schriml LM, Setubal JC, Sorek R, Stevens RL, Tiedje JM, Turjanski A, Tyson GW, Ussery DW, Weinstock GM, White O, Whitman WB, Xenarios I.

Science. 2019 May 3;364(6439):446. doi: 10.1126/science.aax7509. No abstract available.

PMID:
31048484
5.

Rapid Sequencing of Multiple RNA Viruses in Their Native Form.

Wongsurawat T, Jenjaroenpun P, Taylor MK, Lee J, Tolardo AL, Parvathareddy J, Kandel S, Wadley TD, Kaewnapan B, Athipanyasilp N, Skidmore A, Chung D, Chaimayo C, Whitt M, Kantakamalakul W, Sutthent R, Horthongkham N, Ussery DW, Jonsson CB, Nookaew I.

Front Microbiol. 2019 Feb 25;10:260. doi: 10.3389/fmicb.2019.00260. eCollection 2019.

6.

Complete Genome and Plasmid Sequences of Escherichia coli Type Strain ATCC 11775.

Wadley TD, Jenjaroenpun P, Wongsurawat T, Ussery DW, Nookaew I.

Microbiol Resour Announc. 2019 Feb 28;8(9). pii: e00046-19. doi: 10.1128/MRA.00046-19. eCollection 2019 Feb.

7.

Mechanisms linking preterm birth to onset of cardiovascular disease later in adulthood.

Bavineni M, Wassenaar TM, Agnihotri K, Ussery DW, Lüscher TF, Mehta JL.

Eur Heart J. 2019 Apr 7;40(14):1107-1112. doi: 10.1093/eurheartj/ehz025.

PMID:
30753448
8.

Toward unrestricted use of public genomic data.

Amann RI, Baichoo S, Blencowe BJ, Bork P, Borodovsky M, Brooksbank C, Chain PSG, Colwell RR, Daffonchio DG, Danchin A, de Lorenzo V, Dorrestein PC, Finn RD, Fraser CM, Gilbert JA, Hallam SJ, Hugenholtz P, Ioannidis JPA, Jansson JK, Kim JF, Klenk HP, Klotz MG, Knight R, Konstantinidis KT, Kyrpides NC, Mason CE, McHardy AC, Meyer F, Ouzounis CA, Patrinos AAN, Podar M, Pollard KS, Ravel J, Muñoz AR, Roberts RJ, Rosselló-Móra R, Sansone SA, Schloss PD, Schriml LM, Setubal JC, Sorek R, Stevens RL, Tiedje JM, Turjanski A, Tyson GW, Ussery DW, Weinstock GM, White O, Whitman WB, Xenarios I.

Science. 2019 Jan 25;363(6425):350-352. doi: 10.1126/science.aaw1280. No abstract available.

9.

Genome Sequences of Zika Virus Strains Recovered from Amniotic Fluid, Placenta, and Fetal Brain of a Microcephaly Patient in Thailand, 2017.

Wongsurawat T, Jenjaroenpun P, Athipanyasilp N, Kaewnapan B, Leelahakorn N, Angkasekwinai N, Kantakamalakul W, Sutthent R, Ussery DW, Horthongkham N, Nookaew I.

Microbiol Resour Announc. 2018 Sep 20;7(11). pii: e01020-18. doi: 10.1128/MRA.01020-18. eCollection 2018 Sep.

10.

Case of Microcephaly after Congenital Infection with Asian Lineage Zika Virus, Thailand.

Wongsurawat T, Athipanyasilp N, Jenjaroenpun P, Jun SR, Kaewnapan B, Wassenaar TM, Leelahakorn N, Angkasekwinai N, Kantakamalakul W, Ussery DW, Sutthent R, Nookaew I, Horthongkham N.

Emerg Infect Dis. 2018 Sep;24(9). doi: 10.3201/eid2409.180416. Epub 2018 Sep 17.

11.

Genome-Based Comparison of Clostridioides difficile: Average Amino Acid Identity Analysis of Core Genomes.

Cabal A, Jun SR, Jenjaroenpun P, Wanchai V, Nookaew I, Wongsurawat T, Burgess MJ, Kothari A, Wassenaar TM, Ussery DW.

Microb Ecol. 2018 Oct;76(3):801-813. doi: 10.1007/s00248-018-1155-7. Epub 2018 Feb 14.

12.

Complete genomic and transcriptional landscape analysis using third-generation sequencing: a case study of Saccharomyces cerevisiae CEN.PK113-7D.

Jenjaroenpun P, Wongsurawat T, Pereira R, Patumcharoenpol P, Ussery DW, Nielsen J, Nookaew I.

Nucleic Acids Res. 2018 Apr 20;46(7):e38. doi: 10.1093/nar/gky014.

13.

Suggested mechanisms for Zika virus causing microcephaly: what do the genomes tell us?

Jun SR, Wassenaar TM, Wanchai V, Patumcharoenpol P, Nookaew I, Ussery DW.

BMC Bioinformatics. 2017 Dec 28;18(Suppl 14):471. doi: 10.1186/s12859-017-1894-3.

14.
15.

Global Genomic Epidemiology of Salmonella enterica Serovar Typhimurium DT104.

Leekitcharoenphon P, Hendriksen RS, Le Hello S, Weill FX, Baggesen DL, Jun SR, Ussery DW, Lund O, Crook DW, Wilson DJ, Aarestrup FM.

Appl Environ Microbiol. 2016 Apr 4;82(8):2516-26. doi: 10.1128/AEM.03821-15. Print 2016 Apr.

16.

Metabolic functions of Pseudomonas fluorescens strains from Populus deltoides depend on rhizosphere or endosphere isolation compartment.

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.

Front Microbiol. 2015 Oct 14;6:1118. doi: 10.3389/fmicb.2015.01118. eCollection 2015.

17.

Diversity of Pseudomonas Genomes, Including Populus-Associated Isolates, as Revealed by Comparative Genome Analysis.

Jun SR, Wassenaar TM, Nookaew I, Hauser L, Wanchai V, Land M, Timm CM, Lu TY, Schadt CW, Doktycz MJ, Pelletier DA, Ussery DW.

Appl Environ Microbiol. 2015 Oct 30;82(1):375-83. doi: 10.1128/AEM.02612-15. Print 2016 Jan 1.

18.

Ebolavirus comparative genomics.

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.

FEMS Microbiol Rev. 2015 Sep;39(5):764-78. doi: 10.1093/femsre/fuv031. Epub 2015 Jul 14. Review.

19.

Insights from 20 years of bacterial genome sequencing.

Land M, Hauser L, Jun SR, Nookaew I, Leuze MR, Ahn TH, Karpinets T, Lund O, Kora G, Wassenaar T, Poudel S, Ussery DW.

Funct Integr Genomics. 2015 Mar;15(2):141-61. doi: 10.1007/s10142-015-0433-4. Epub 2015 Feb 27. Review.

20.

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.

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.

Biomed Res Int. 2015;2015:139580. doi: 10.1155/2015/139580. Epub 2015 Jan 29.

21.

Molecular analysis of asymptomatic bacteriuria Escherichia coli strain VR50 reveals adaptation to the urinary tract by gene acquisition.

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.

Infect Immun. 2015 May;83(5):1749-64. doi: 10.1128/IAI.02810-14. Epub 2015 Feb 9.

22.

Microbial taxonomy in the post-genomic era: rebuilding from scratch?

Thompson CC, Amaral GR, Campeão M, Edwards RA, Polz MF, Dutilh BE, Ussery DW, Sawabe T, Swings J, Thompson FL.

Arch Microbiol. 2015 Apr;197(3):359-70. doi: 10.1007/s00203-014-1071-2. Epub 2014 Dec 23.

PMID:
25533848
23.

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.

Haugum K, Johansen J, Gabrielsen C, Brandal LT, Bergh K, Ussery DW, Drabløs F, Afset JE.

PLoS One. 2014 Oct 31;9(10):e111788. doi: 10.1371/journal.pone.0111788. eCollection 2014.

24.

Identification and assembly of genomes and genetic elements in complex metagenomic samples without using reference genomes.

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; MetaHIT Consortium, Renault P, Sicheritz-Ponten T, Bork P, Wang J, Brunak S, Ehrlich SD; MetaHIT Consortium.

Nat Biotechnol. 2014 Aug;32(8):822-8. doi: 10.1038/nbt.2939. Epub 2014 Jul 6.

PMID:
24997787
25.

Veillonella, Firmicutes: Microbes disguised as Gram negatives.

Vesth T, Ozen A, Andersen SC, Kaas RS, Lukjancenko O, Bohlin J, Nookaew I, Wassenaar TM, Ussery DW.

Stand Genomic Sci. 2013 Dec 15;9(2):431-48. doi: 10.4056/sigs.2981345. eCollection 2013 Dec 20.

26.

Vibrio chromosome-specific families.

Lukjancenko O, Ussery DW.

Front Microbiol. 2014 Mar 18;5:73. doi: 10.3389/fmicb.2014.00073. eCollection 2014.

27.

Benchmarking of methods for genomic taxonomy.

Larsen MV, Cosentino S, Lukjancenko O, Saputra D, Rasmussen S, Hasman H, Sicheritz-Pontén T, Aarestrup FM, Ussery DW, Lund O.

J Clin Microbiol. 2014 May;52(5):1529-39. doi: 10.1128/JCM.02981-13. Epub 2014 Feb 26.

28.

Quality scores for 32,000 genomes.

Land ML, Hyatt D, Jun SR, Kora GH, Hauser LJ, Lukjancenko O, Ussery DW.

Stand Genomic Sci. 2014 Dec 8;9:20. doi: 10.1186/1944-3277-9-20. eCollection 2014.

29.

Sigma factors in a thousand E. coli genomes.

Cook H, Ussery DW.

Environ Microbiol. 2013 Dec;15(12):3121-9. doi: 10.1111/1462-2920.12236. Epub 2013 Aug 29.

PMID:
23992563
30.

Amino acid usage is asymmetrically biased in AT- and GC-rich microbial genomes.

Bohlin J, Brynildsrud O, Vesth T, Skjerve E, Ussery DW.

PLoS One. 2013 Jul 26;8(7):e69878. doi: 10.1371/journal.pone.0069878. Print 2013.

31.

Bayesian prediction of bacterial growth temperature range based on genome sequences.

Jensen DB, Vesth TC, Hallin PF, Pedersen AG, Ussery DW.

BMC Genomics. 2012;13 Suppl 7:S3. doi: 10.1186/1471-2164-13-S7-S3. Epub 2012 Dec 13.

32.

Bayesian prediction of microbial oxygen requirement.

Jensen DB, Ussery DW.

F1000Res. 2013 Sep 13;2:184. doi: 10.12688/f1000research.2-184.v1. eCollection 2013.

33.

From essential to persistent genes: a functional approach to constructing synthetic life.

Acevedo-Rocha CG, Fang G, Schmidt M, Ussery DW, Danchin A.

Trends Genet. 2013 May;29(5):273-9. doi: 10.1016/j.tig.2012.11.001. Epub 2012 Dec 6.

34.

Estimating variation within the genes and inferring the phylogeny of 186 sequenced diverse Escherichia coli genomes.

Kaas RS, Friis C, Ussery DW, Aarestrup FM.

BMC Genomics. 2012 Oct 31;13:577. doi: 10.1186/1471-2164-13-577.

35.

Non-O1 Vibrio cholerae unlinked to cholera in Haiti.

Mekalanos JJ, Robins W, Ussery DW, Davis BM, Schadt E, Waldor MK.

Proc Natl Acad Sci U S A. 2012 Nov 20;109(47):E3206; author reply E3207. doi: 10.1073/pnas.1212443109. Epub 2012 Oct 3. No abstract available.

36.

Analysis of evolutionary patterns of genes in Campylobacter jejuni and C. coli.

Snipen L, Wassenaar TM, Altermann E, Olson J, Kathariou S, Lagesen K, Takamiya M, Knøchel S, Ussery DW, Meinersmann RJ.

Microb Inform Exp. 2012 Aug 28;2(1):8. doi: 10.1186/2042-5783-2-8.

37.

Campylobacter fetus subspecies: comparative genomics and prediction of potential virulence targets.

Ali A, Soares SC, Santos AR, Guimarães LC, Barbosa E, Almeida SS, Abreu VA, Carneiro AR, Ramos RT, Bakhtiar SM, Hassan SS, Ussery DW, On S, Silva A, Schneider MP, Lage AP, Miyoshi A, Azevedo V.

Gene. 2012 Oct 25;508(2):145-56. doi: 10.1016/j.gene.2012.07.070. Epub 2012 Aug 6.

38.

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 Sep;85(6):1072-89. doi: 10.1111/j.1365-2958.2012.08162.x. Epub 2012 Jul 23.

39.

The transcriptional landscape and small RNAs of Salmonella enterica serovar Typhimurium.

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.

Proc Natl Acad Sci U S A. 2012 May 15;109(20):E1277-86. doi: 10.1073/pnas.1201061109. Epub 2012 Apr 25.

40.

Two novel methods for using genome sequences to infer taxonomy.

Ussery DW, Gordon SV.

Microbiology. 2012 Jun;158(Pt 6):1414. doi: 10.1099/mic.0.059816-0. Epub 2012 Apr 13. No abstract available.

PMID:
22504434
41.

Genomic variation in Salmonella enterica core genes for epidemiological typing.

Leekitcharoenphon P, Lukjancenko O, Friis C, Aarestrup FM, Ussery DW.

BMC Genomics. 2012 Mar 12;13:88. doi: 10.1186/1471-2164-13-88.

42.

Multilocus sequence typing of total-genome-sequenced bacteria.

Larsen MV, Cosentino S, Rasmussen S, Friis C, Hasman H, Marvig RL, Jelsbak L, Sicheritz-Pontén T, Ussery DW, Aarestrup FM, Lund O.

J Clin Microbiol. 2012 Apr;50(4):1355-61. doi: 10.1128/JCM.06094-11. Epub 2012 Jan 11.

43.

A domain sequence approach to pangenomics: applications to Escherichia coli.

Snipen LG, Ussery DW.

Version 2. F1000Res. 2012 Oct 1 [revised 2013 Jan 1];1:19. doi: 10.12688/f1000research.1-19.v2. eCollection 2012.

44.

Is the pan-genome also a pan-selectome?

Rodriguez-Valera F, Ussery DW.

F1000Res. 2012 Sep 21;1:16. doi: 10.12688/f1000research.1-16.v1. eCollection 2012.

45.

Comparative genomics of Bifidobacterium, Lactobacillus and related probiotic genera.

Lukjancenko O, Ussery DW, Wassenaar TM.

Microb Ecol. 2012 Apr;63(3):651-73. doi: 10.1007/s00248-011-9948-y. Epub 2011 Oct 27. Review.

46.

Genome sequences of two stress-tolerant Campylobacter jejuni poultry strains, 305 and DFVF1099.

Takamiya M, Ozen A, Rasmussen M, Alter T, Gilbert T, Ussery DW, Knøchel S.

J Bacteriol. 2011 Oct;193(19):5546-7. doi: 10.1128/JB.05753-11.

47.

Defining the Pseudomonas genus: where do we draw the line with Azotobacter?

Özen AI, Ussery DW.

Microb Ecol. 2012 Feb;63(2):239-48. doi: 10.1007/s00248-011-9914-8. Epub 2011 Aug 3.

48.

The Genomic Standards Consortium.

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.

PLoS Biol. 2011 Jun;9(6):e1001088. doi: 10.1371/journal.pbio.1001088. Epub 2011 Jun 21.

49.

Genome Sequence of Campylobacter jejuni strain 327, a strain isolated from a turkey slaughterhouse.

Takamiya M, Ozen A, Rasmussen M, Alter T, Gilbert T, Ussery DW, Knøchel S.

Stand Genomic Sci. 2011 Apr 29;4(2):113-22. doi: 10.4056/sigs.1313504. Epub 2011 Apr 25.

50.

The Salmonella enterica pan-genome.

Jacobsen A, Hendriksen RS, Aaresturp FM, Ussery DW, Friis C.

Microb Ecol. 2011 Oct;62(3):487-504. doi: 10.1007/s00248-011-9880-1. Epub 2011 Jun 4. Review.

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