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Items: 1 to 50 of 174

1.

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.

2.

Genomic characterization of mumps viruses from a large-scale mumps outbreak in Arkansas, 2016.

Alkam D, Jenjaroenpun P, Wongsurawat T, Udaondo Z, Patumcharoenpol P, Robeson M, Haselow D, Mason W, Nookaew I, Ussery D, Jun SR.

Infect Genet Evol. 2019 Jul 15;75:103965. doi: 10.1016/j.meegid.2019.103965. [Epub ahead of print]

PMID:
31319177
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.

Decaffeinated Green Tea Extract Does Not Elicit Hepatotoxic Effects and Modulates the Gut Microbiome in Lean B6C3F₁ Mice.

Gurley BJ, Miousse IR, Nookaew I, Ewing LE, Skinner CM, Jenjaroenpun P, Wongsurawat T, Kennon-McGill S, Avula B, Bae JY, McGill MR, Ussery D, Khan IA, Koturbash I.

Nutrients. 2019 Apr 3;11(4). pii: E776. doi: 10.3390/nu11040776.

6.

Draft Genome Sequences of 48 Vancomycin-Resistant Enterococcus faecium Strains Isolated from Inpatients with Bacteremia and Urinary Tract Infection.

Udaondo Z, Wongsurawat T, Jenjaroenpun P, Anderson C, Lopez J, Mohan M, Tytarenko R, Walker B, Nookaew I, Ussery D, Kothari A, Jun SR.

Microbiol Resour Announc. 2019 Apr 11;8(15). pii: e00222-19. doi: 10.1128/MRA.00222-19.

7.

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.

8.

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.

9.

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
10.

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.

11.

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.

12.

PARP1 Is Up-Regulated in Non-small Cell Lung Cancer Tissues in the Presence of the Cyanobacterial Toxin Microcystin.

Apopa PL, Alley L, Penney RB, Arnaoutakis K, Steliga MA, Jeffus S, Bircan E, Gopalan B, Jin J, Patumcharoenpol P, Jenjaroenpun P, Wongsurawat T, Shah N, Boysen G, Ussery D, Nookaew I, Fagan P, Bebek G, Orloff MS.

Front Microbiol. 2018 Aug 6;9:1757. doi: 10.3389/fmicb.2018.01757. eCollection 2018.

13.

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.

14.

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.

15.

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.

16.

dBBQs: dataBase of Bacterial Quality scores.

Wanchai V, Patumcharoenpol P, Nookaew I, Ussery D.

BMC Bioinformatics. 2017 Dec 28;18(Suppl 14):483. doi: 10.1186/s12859-017-1900-9.

17.

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.

18.

Three Complete Genome Sequences of Genotype G Mumps Virus from the 2016 Outbreak in Arkansas, USA.

Alkam D, Wongsurawat T, Jenjaroenpun P, Connor S, Hobbs C, Wassenaar TM, Jun SR, Nookaew I, Ussery D.

Genome Announc. 2017 Aug 10;5(32). pii: e00555-17. doi: 10.1128/genomeA.00555-17.

19.

Viral Phylogenomics Using an Alignment-Free Method: A Three-Step Approach to Determine Optimal Length of k-mer.

Zhang Q, Jun SR, Leuze M, Ussery D, Nookaew I.

Sci Rep. 2017 Jan 19;7:40712. doi: 10.1038/srep40712.

20.

Integrated omics analyses reveal the details of metabolic adaptation of Clostridium thermocellum to lignocellulose-derived growth inhibitors released during the deconstruction of switchgrass.

Poudel S, Giannone RJ, Rodriguez M Jr, Raman B, Martin MZ, Engle NL, Mielenz JR, Nookaew I, Brown SD, Tschaplinski TJ, Ussery D, Hettich RL.

Biotechnol Biofuels. 2017 Jan 10;10:14. doi: 10.1186/s13068-016-0697-5. eCollection 2017.

21.
22.

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.

23.

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.

24.

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.

25.

Unique and conserved genome regions in Vibrio harveyi and related species in comparison with the shrimp pathogen Vibrio harveyi CAIM 1792.

Espinoza-Valles I, Vora GJ, Lin B, Leekitcharoenphon P, González-Castillo A, Ussery D, Høj L, Gomez-Gil B.

Microbiology. 2015 Sep;161(9):1762-79. doi: 10.1099/mic.0.000141. Epub 2015 Jul 21.

PMID:
26198743
26.

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.

27.

The continuing antenatal management program (CAMP): Outpatient monitoring of high-risk pregnancies. Keeps patients safe, costs low and care nearby.

Hughes DS, Ussery DJ, Woodruff DL, Sandlin AT, Kinder SR, Magann EF.

Sex Reprod Healthc. 2015 Jun;6(2):108-9. doi: 10.1016/j.srhc.2015.01.001. Epub 2015 Jan 7.

PMID:
25998879
28.

Review and phylogenetic analysis of qac genes that reduce susceptibility to quaternary ammonium compounds in Staphylococcus species.

Wassenaar TM, Ussery D, Nielsen LN, Ingmer H.

Eur J Microbiol Immunol (Bp). 2015 Mar;5(1):44-61. doi: 10.1556/EUJMI-D-14-00038. Epub 2015 Mar 26. Review.

29.

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.

30.

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.

31.

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.

32.

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
33.

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.

34.

Genomic standards consortium projects.

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.

Stand Genomic Sci. 2014 Feb 15;9(3):599-601. doi: 10.4056/sigs.5559680. eCollection 2014 Jun 15.

35.

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
36.

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.

37.

Vibrio chromosome-specific families.

Lukjancenko O, Ussery DW.

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

38.

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.

39.

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.

40.

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
41.

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.

42.

CMG-biotools, a free workbench for basic comparative microbial genomics.

Vesth T, Lagesen K, Acar Ö, Ussery D.

PLoS One. 2013;8(4):e60120. doi: 10.1371/journal.pone.0060120. Epub 2013 Apr 5.

43.

Genome sequencing identifies two nearly unchanged strains of persistent Listeria monocytogenes isolated at two different fish processing plants sampled 6 years apart.

Holch A, Webb K, Lukjancenko O, Ussery D, Rosenthal BM, Gram L.

Appl Environ Microbiol. 2013 May;79(9):2944-51. doi: 10.1128/AEM.03715-12. Epub 2013 Feb 22.

44.

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.

45.

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.

46.

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.

47.

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;4(12):1360-74. doi: 10.1093/gbe/evs112.

48.

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.

49.

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.

50.

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.

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