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Results: 1 to 20 of 355

1.

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.

PMID:
25110940
[PubMed - in process]
Free PMC Article
2.

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.

PMID:
25105497
[PubMed - in process]
Free PMC Article
3.

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.

PMID:
25049333
[PubMed - in process]
4.

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

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

Cytometry A. 2014 Jul 18. doi: 10.1002/cyto.a.22510. [Epub ahead of print]

PMID:
25044796
[PubMed - as supplied by publisher]
5.

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.

PMID:
25032686
[PubMed - in process]
Free PMC Article
6.

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
[PubMed - in process]
7.

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.

PMID:
24777092
[PubMed - in process]
Free PMC Article
8.

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.

PMID:
24574292
[PubMed - in process]
Free PMC Article
9.

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.

PMID:
24574290
[PubMed - in process]
Free PMC Article
10.

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.

PMID:
24505344
[PubMed - in process]
Free PMC Article
11.

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.

PMID:
24493822
[PubMed - indexed for MEDLINE]
12.

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
[PubMed - in process]
13.

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.

PMID:
24391826
[PubMed - in process]
Free PMC Article
14.

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.

PMID:
24204795
[PubMed - indexed for MEDLINE]
Free PMC Article
15.

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.

PMID:
24172157
[PubMed - indexed for MEDLINE]
Free PMC Article
16.

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.

PMID:
23900783
[PubMed - indexed for MEDLINE]
17.

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.

PMID:
23775223
[PubMed - indexed for MEDLINE]
18.

SigniSite: Identification of residue-level genotype-phenotype correlations in protein multiple sequence alignments.

Jessen LE, Hoof I, Lund O, Nielsen M.

Nucleic Acids Res. 2013 Jul;41(Web Server issue):W286-91. doi: 10.1093/nar/gkt497. Epub 2013 Jun 12.

PMID:
23761454
[PubMed - indexed for MEDLINE]
Free PMC Article
19.

Bioinformatics identification of antigenic peptide: predicting the specificity of major MHC class I and II pathway players.

Lund O, Karosiene E, Lundegaard C, Larsen MV, Nielsen M.

Methods Mol Biol. 2013;960:247-60. doi: 10.1007/978-1-62703-218-6_19.

PMID:
23329492
[PubMed - indexed for MEDLINE]
20.

Mycobacterium leprae virulence-associated peptides are indicators of exposure to M. leprae in Brazil, Ethiopia and Nepal.

Bobosha K, Tang ST, van der Ploeg-van Schip JJ, Bekele Y, Martins MV, Lund O, Franken KL, Khadge S, Pontes MA, Gonçalves Hde S, Hussien J, Thapa P, Kunwar CB, Hagge DA, Aseffa A, Pessolani MC, Pereira GM, Ottenhoff TH, Geluk A.

Mem Inst Oswaldo Cruz. 2012 Dec;107 Suppl 1:112-23.

PMID:
23283462
[PubMed - indexed for MEDLINE]
Free Article

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