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Results: 1 to 20 of 358

1.

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.

2.

Automated benchmarking of peptide-MHC class I binding predictions.

Trolle T, Metushi IG, Greenbaum JA, Kim Y, Sidney J, Lund O, Sette A, Peters B, Nielsen M.

Bioinformatics. 2015 Feb 25. pii: btv123. [Epub ahead of print]

PMID:
25717196
3.

Novel variation and de novo mutation rates in population-wide de novo assembled Danish trios.

Besenbacher S, Liu S, Izarzugaza JM, Grove J, Belling K, Bork-Jensen J, Huang S, Als TD, Li S, Yadav R, Rubio-García A, Lescai F, Demontis D, Rao J, Ye W, Mailund T, Friborg RM, Pedersen CN, Xu R, Sun J, Liu H, Wang O, Cheng X, Flores D, Rydza E, Rapacki K, Damm Sørensen J, Chmura P, Westergaard D, Dworzynski P, Sørensen TI, Lund O, Hansen T, Xu X, Li N, Bolund L, Pedersen O, Eiberg H, Krogh A, Børglum AD, Brunak S, Kristiansen K, Schierup MH, Wang J, Gupta R, Villesen P, Rasmussen S.

Nat Commun. 2015 Jan 19;6:5969. doi: 10.1038/ncomms6969.

4.

Solving the problem of comparing whole bacterial genomes across different sequencing platforms.

Kaas RS, Leekitcharoenphon P, Aarestrup FM, Lund O.

PLoS One. 2014 Aug 11;9(8):e104984. doi: 10.1371/journal.pone.0104984. eCollection 2014.

5.

Two euAGAMOUS genes control C-function in Medicago truncatula.

Serwatowska J, Roque E, Gómez-Mena C, Constantin GD, Wen J, Mysore KS, Lund OS, Johansen E, Beltrán JP, Cañas LA.

PLoS One. 2014 Aug 8;9(8):e103770. doi: 10.1371/journal.pone.0103770. eCollection 2014.

6.

MR1-restricted MAIT cells display ligand discrimination and pathogen selectivity through distinct T cell receptor usage.

Gold MC, McLaren JE, Reistetter JA, Smyk-Pearson S, Ladell K, Swarbrick GM, Yu YY, Hansen TH, Lund O, Nielsen M, Gerritsen B, Kesmir C, Miles JJ, Lewinsohn DA, Price DA, Lewinsohn DM.

J Exp Med. 2014 Jul 28;211(8):1601-10. doi: 10.1084/jem.20140507. Epub 2014 Jul 21.

7.

NetFCM: a semi-automated web-based method for flow cytometry data analysis.

Frederiksen J, Buggert M, Karlsson AC, Lund O.

Cytometry A. 2014 Nov;85(11):969-77. doi: 10.1002/cyto.a.22510. Epub 2014 Jul 18.

PMID:
25044796
8.

T-bet and Eomes are differentially linked to the exhausted phenotype of CD8+ T cells in HIV infection.

Buggert M, Tauriainen J, Yamamoto T, Frederiksen J, Ivarsson MA, Michaëlsson J, Lund O, Hejdeman B, Jansson M, Sönnerborg A, Koup RA, Betts MR, Karlsson AC.

PLoS Pathog. 2014 Jul 17;10(7):e1004251. doi: 10.1371/journal.ppat.1004251. eCollection 2014 Jul.

9.

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
10.

In silico detection and typing of plasmids using PlasmidFinder and plasmid multilocus sequence typing.

Carattoli A, Zankari E, García-Fernández A, Voldby Larsen M, Lund O, Villa L, Møller Aarestrup F, Hasman H.

Antimicrob Agents Chemother. 2014 Jul;58(7):3895-903. doi: 10.1128/AAC.02412-14. Epub 2014 Apr 28.

11.

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.

12.

Real-time whole-genome sequencing for routine typing, surveillance, and outbreak detection of verotoxigenic Escherichia coli.

Joensen KG, Scheutz F, Lund O, Hasman H, Kaas RS, Nielsen EM, Aarestrup FM.

J Clin Microbiol. 2014 May;52(5):1501-10. doi: 10.1128/JCM.03617-13. Epub 2014 Feb 26.

13.

Evaluation of whole genome sequencing for outbreak detection of Salmonella enterica.

Leekitcharoenphon P, Nielsen EM, Kaas RS, Lund O, Aarestrup FM.

PLoS One. 2014 Feb 4;9(2):e87991. doi: 10.1371/journal.pone.0087991. eCollection 2014.

14.

Multiparametric bioinformatics distinguish the CD4/CD8 ratio as a suitable laboratory predictor of combined T cell pathogenesis in HIV infection.

Buggert M, Frederiksen J, Noyan K, Svärd J, Barqasho B, Sönnerborg A, Lund O, Nowak P, Karlsson AC.

J Immunol. 2014 Mar 1;192(5):2099-108. doi: 10.4049/jimmunol.1302596. Epub 2014 Feb 3.

15.

Evaluation of peptide selection approaches for epitope-based vaccine design.

Schubert B, Lund O, Nielsen M.

Tissue Antigens. 2013 Oct;82(4):243-51. doi: 10.1111/tan.12199.

PMID:
24461003
16.

Low-bandwidth and non-compute intensive remote identification of microbes from raw sequencing reads.

Gautier L, Lund O.

PLoS One. 2013 Dec 31;8(12):e83784. doi: 10.1371/journal.pone.0083784. eCollection 2013.

17.

PathogenFinder--distinguishing friend from foe using bacterial whole genome sequence data.

Cosentino S, Voldby Larsen M, Møller Aarestrup F, Lund O.

PLoS One. 2013 Oct 28;8(10):e77302. doi: 10.1371/journal.pone.0077302. eCollection 2013. Erratum in: PLoS One. 2013;8(12). doi:10.1371/annotation/b84e1af7-c127-45c3-be22-76abd977600f.

18.

Rapid whole-genome sequencing for detection and characterization of microorganisms directly from clinical samples.

Hasman H, Saputra D, Sicheritz-Ponten T, Lund O, Svendsen CA, Frimodt-Møller N, Aarestrup FM.

J Clin Microbiol. 2014 Jan;52(1):139-46. doi: 10.1128/JCM.02452-13. Epub 2013 Oct 30. Erratum in: J Clin Microbiol. 2014 Aug;52(8):3136.

19.

NetMHCIIpan-3.0, a common pan-specific MHC class II prediction method including all three human MHC class II isotypes, HLA-DR, HLA-DP and HLA-DQ.

Karosiene E, Rasmussen M, Blicher T, Lund O, Buus S, Nielsen M.

Immunogenetics. 2013 Oct;65(10):711-24. doi: 10.1007/s00251-013-0720-y. Epub 2013 Jul 31.

20.

MHCcluster, a method for functional clustering of MHC molecules.

Thomsen M, Lundegaard C, Buus S, Lund O, Nielsen M.

Immunogenetics. 2013 Sep;65(9):655-65. doi: 10.1007/s00251-013-0714-9. Epub 2013 Jun 18.

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