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Items: 1 to 20 of 181

1.

Large scale automated phylogenomic analysis of bacterial isolates and the Evergreen Online platform.

Szarvas J, Ahrenfeldt J, Cisneros JLB, Thomsen MCF, Aarestrup FM, Lund O.

Commun Biol. 2020 Mar 20;3(1):137. doi: 10.1038/s42003-020-0869-5.

2.

Metaphylogenetic analysis of global sewage reveals that bacterial strains associated with human disease show less degree of geographic clustering.

Ahrenfeldt J, Waisi M, Loft IC, Clausen PTLC, Allesøe R, Szarvas J, Hendriksen RS, Aarestrup FM, Lund O.

Sci Rep. 2020 Feb 20;10(1):3033. doi: 10.1038/s41598-020-59292-w.

3.

The COMPARE Data Hubs.

Amid C, Pakseresht N, Silvester N, Jayathilaka S, Lund O, Dynovski LD, Pataki BÁ, Visontai D, Xavier BB, Alako BTF, Belka A, Cisneros JLB, Cotten M, Haringhuizen GB, Harrison PW, Höper D, Holt S, Hundahl C, Hussein A, Kaas RS, Liu X, Leinonen R, Malhotra-Kumar S, Nieuwenhuijse DF, Rahman N, Dos S Ribeiro C, Skiby JE, Schmitz D, Stéger J, Szalai-Gindl JM, Thomsen MCF, Cacciò SM, Csabai I, Kroneman A, Koopmans M, Aarestrup F, Cochrane G.

Database (Oxford). 2019 Jan 1;2019. pii: baz136. doi: 10.1093/database/baz136.

4.

Improved Resistance Prediction in Mycobacterium tuberculosis by Better Handling of Insertions and Deletions, Premature Stop Codons, and Filtering of Non-informative Sites.

Johnsen CH, Clausen PTLC, Aarestrup FM, Lund O.

Front Microbiol. 2019 Oct 31;10:2464. doi: 10.3389/fmicb.2019.02464. eCollection 2019.

5.

Specific gut microbiome members are associated with distinct immune markers in pediatric allogeneic hematopoietic stem cell transplantation.

Ingham AC, Kielsen K, Cilieborg MS, Lund O, Holmes S, Aarestrup FM, Müller KG, Pamp SJ.

Microbiome. 2019 Sep 13;7(1):131. doi: 10.1186/s40168-019-0745-z.

6.

Root-Associated Microbial Communities of Abies nordmanniana: Insights Into Interactions of Microbial Communities With Antioxidative Enzymes and Plant Growth.

Garcia-Lemos AM, Großkinsky DK, Stokholm MS, Lund OS, Nicolaisen MH, Roitsch TG, Veierskov B, Nybroe O.

Front Microbiol. 2019 Aug 22;10:1937. doi: 10.3389/fmicb.2019.01937. eCollection 2019.

7.

Ceftriaxone use in a tertiary care hospital in Kilimanjaro, Tanzania: A need for a hospital antibiotic stewardship programme.

Sonda TB, Horumpende PG, Kumburu HH, van Zwetselaar M, Mshana SE, Alifrangis M, Lund O, Aarestrup FM, Chilongola JO, Mmbaga BT, Kibiki GS.

PLoS One. 2019 Aug 5;14(8):e0220261. doi: 10.1371/journal.pone.0220261. eCollection 2019.

8.

Proof of concept: used malaria rapid diagnostic tests applied for parallel sequencing for surveillance of molecular markers of anti-malarial resistance in Bissau, Guinea-Bissau during 2014-2017.

Nag S, Ursing J, Rodrigues A, Crespo M, Krogsgaard C, Lund O, Aarestrup FM, Alifrangis M, Kofoed PE.

Malar J. 2019 Jul 26;18(1):252. doi: 10.1186/s12936-019-2894-8.

9.

High-Throughput Sequencing-Based Investigation of Viruses in Human Cancers by Multienrichment Approach.

Mollerup S, Asplund M, Friis-Nielsen J, Kjartansdóttir KR, Fridholm H, Hansen TA, Herrera JAR, Barnes CJ, Jensen RH, Richter SR, Nielsen IB, Pietroni C, Alquezar-Planas DE, Rey-Iglesia A, Olsen PVS, Rajpert-De Meyts E, Groth-Pedersen L, von Buchwald C, Jensen DH, Gniadecki R, Høgdall E, Langhoff JL, Pete I, Vereczkey I, Baranyai Z, Dybkaer K, Johnsen HE, Steiniche T, Hokland P, Rosenberg J, Baandrup U, Sicheritz-Pontén T, Willerslev E, Brunak S, Lund O, Mourier T, Vinner L, Izarzugaza JMG, Nielsen LP, Hansen AJ.

J Infect Dis. 2019 Sep 13;220(8):1312-1324. doi: 10.1093/infdis/jiz318.

10.

LRE-Finder, a Web tool for detection of the 23S rRNA mutations and the optrA, cfr, cfr(B) and poxtA genes encoding linezolid resistance in enterococci from whole-genome sequences.

Hasman H, Clausen PTLC, Kaya H, Hansen F, Knudsen JD, Wang M, Holzknecht BJ, Samulioniené J, Røder BL, Frimodt-Møller N, Lund O, Hammerum AM.

J Antimicrob Chemother. 2019 Jun 1;74(6):1473-1476. doi: 10.1093/jac/dkz092.

PMID:
30863844
11.

Global monitoring of antimicrobial resistance based on metagenomics analyses of urban sewage.

Hendriksen RS, Munk P, Njage P, van Bunnik B, McNally L, Lukjancenko O, Röder T, Nieuwenhuijse D, Pedersen SK, Kjeldgaard J, Kaas RS, Clausen PTLC, Vogt JK, Leekitcharoenphon P, van de Schans MGM, Zuidema T, de Roda Husman AM, Rasmussen S, Petersen B; Global Sewage Surveillance project consortium, Amid C, Cochrane G, Sicheritz-Ponten T, Schmitt H, Alvarez JRM, Aidara-Kane A, Pamp SJ, Lund O, Hald T, Woolhouse M, Koopmans MP, Vigre H, Petersen TN, Aarestrup FM.

Nat Commun. 2019 Mar 8;10(1):1124. doi: 10.1038/s41467-019-08853-3.

12.

Using WGS to identify antibiotic resistance genes and predict antimicrobial resistance phenotypes in MDR Acinetobacter baumannii in Tanzania.

Kumburu HH, Sonda T, van Zwetselaar M, Leekitcharoenphon P, Lukjancenko O, Mmbaga BT, Alifrangis M, Lund O, Aarestrup FM, Kibiki GS.

J Antimicrob Chemother. 2019 Jun 1;74(6):1484-1493. doi: 10.1093/jac/dkz055.

13.

Antibody Cross-Reactivity in Antivenom Research.

Ledsgaard L, Jenkins TP, Davidsen K, Krause KE, Martos-Esteban A, Engmark M, Rørdam Andersen M, Lund O, Laustsen AH.

Toxins (Basel). 2018 Sep 27;10(10). pii: E393. doi: 10.3390/toxins10100393. Review.

14.

Rapid and precise alignment of raw reads against redundant databases with KMA.

Clausen PTLC, Aarestrup FM, Lund O.

BMC Bioinformatics. 2018 Aug 29;19(1):307. doi: 10.1186/s12859-018-2336-6.

15.

Author Correction: Abundance and diversity of the faecal resistome in slaughter pigs and broilers in nine European countries.

Munk P, Knudsen BE, Lukjancenko O, Duarte ASR, Van Gompel L, Luiken REC, Smit LAM, Schmitt H, Garcia AD, Hansen RB, Petersen TN, Bossers A, Ruppé E, Lund O, Hald T, Pamp SJ, Vigre H, Heederik D, Wagenaar JA, Mevius D, Aarestrup FM; EFFORT Group.

Nat Microbiol. 2018 Oct;3(10):1186. doi: 10.1038/s41564-018-0241-4.

PMID:
30131524
16.

Transient Posttranscriptional Gene Silencing in Medicago truncatula: Virus-Induced Gene Silencing (VIGS).

Serwatowska J, Lund OS, Johansen IE.

Methods Mol Biol. 2018;1822:115-122. doi: 10.1007/978-1-4939-8633-0_8.

PMID:
30043300
17.

Abundance and diversity of the faecal resistome in slaughter pigs and broilers in nine European countries.

Munk P, Knudsen BE, Lukjancenko O, Duarte ASR, Van Gompel L, Luiken REC, Smit LAM, Schmitt H, Garcia AD, Hansen RB, Petersen TN, Bossers A, Ruppé E; EFFORT Group, Lund O, Hald T, Pamp SJ, Vigre H, Heederik D, Wagenaar JA, Mevius D, Aarestrup FM.

Nat Microbiol. 2018 Aug;3(8):898-908. doi: 10.1038/s41564-018-0192-9. Epub 2018 Jul 23. Erratum in: Nat Microbiol. 2018 Oct;3(10):1186.

PMID:
30038308
18.

Molecular epidemiology of virulence and antimicrobial resistance determinants in Klebsiella pneumoniae from hospitalised patients in Kilimanjaro, Tanzania.

Sonda T, Kumburu H, van Zwetselaar M, Alifrangis M, Mmbaga BT, Lund O, Kibiki GS, Aarestrup FM.

Eur J Clin Microbiol Infect Dis. 2018 Oct;37(10):1901-1914. doi: 10.1007/s10096-018-3324-5. Epub 2018 Jul 20.

PMID:
30030694
19.

Whole genome sequencing reveals high clonal diversity of Escherichia coli isolated from patients in a tertiary care hospital in Moshi, Tanzania.

Sonda T, Kumburu H, van Zwetselaar M, Alifrangis M, Mmbaga BT, Aarestrup FM, Kibiki G, Lund O.

Antimicrob Resist Infect Control. 2018 Jun 8;7:72. doi: 10.1186/s13756-018-0361-x. eCollection 2018.

20.

Benchmarking the HLA typing performance of Polysolver and Optitype in 50 Danish parental trios.

Matey-Hernandez ML; Danish Pan Genome Consortium, Brunak S, Izarzugaza JMG.

BMC Bioinformatics. 2018 Jun 25;19(1):239. doi: 10.1186/s12859-018-2239-6.

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