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Results: 1 to 20 of 47

1.

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]
2.

In silico peptide-binding predictions of passerine MHC class I reveal similarities across distantly related species, suggesting convergence on the level of protein function.

Follin E, Karlsson M, Lundegaard C, Nielsen M, Wallin S, Paulsson K, Westerdahl H.

Immunogenetics. 2013 Apr;65(4):299-311. doi: 10.1007/s00251-012-0676-3. Epub 2013 Jan 29.

PMID:
23358931
[PubMed - indexed for MEDLINE]
3.

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]
4.

Reliable B cell epitope predictions: impacts of method development and improved benchmarking.

Kringelum JV, Lundegaard C, Lund O, Nielsen M.

PLoS Comput Biol. 2012;8(12):e1002829. doi: 10.1371/journal.pcbi.1002829. Epub 2012 Dec 27.

PMID:
23300419
[PubMed - indexed for MEDLINE]
Free PMC Article
5.

Characterization of HIV-specific CD4+ T cell responses against peptides selected with broad population and pathogen coverage.

Buggert M, Norström MM, Czarnecki C, Tupin E, Luo M, Gyllensten K, Sönnerborg A, Lundegaard C, Lund O, Nielsen M, Karlsson AC.

PLoS One. 2012;7(7):e39874. doi: 10.1371/journal.pone.0039874. Epub 2012 Jul 5.

PMID:
22792193
[PubMed - indexed for MEDLINE]
Free PMC Article
6.

Immune epitope database analysis resource.

Kim Y, Ponomarenko J, Zhu Z, Tamang D, Wang P, Greenbaum J, Lundegaard C, Sette A, Lund O, Bourne PE, Nielsen M, Peters B.

Nucleic Acids Res. 2012 Jul;40(Web Server issue):W525-30. doi: 10.1093/nar/gks438. Epub 2012 May 18.

PMID:
22610854
[PubMed - indexed for MEDLINE]
Free PMC Article
7.

Predictions versus high-throughput experiments in T-cell epitope discovery: competition or synergy?

Lundegaard C, Lund O, Nielsen M.

Expert Rev Vaccines. 2012 Jan;11(1):43-54. doi: 10.1586/erv.11.160.

PMID:
22149708
[PubMed - indexed for MEDLINE]
Free PMC Article
8.

Human leukocyte antigen (HLA) class I restricted epitope discovery in yellow fewer and dengue viruses: importance of HLA binding strength.

Lund O, Nascimento EJ, Maciel M Jr, Nielsen M, Larsen MV, Lundegaard C, Harndahl M, Lamberth K, Buus S, Salmon J, August TJ, Marques ET Jr.

PLoS One. 2011;6(10):e26494. doi: 10.1371/journal.pone.0026494. Epub 2011 Oct 19. Erratum in: PLoS One. 2011;6(11). doi:10.1371/annotation/254c9f39-1c6b-4f48-a947-b4ed931642e7.

PMID:
22039500
[PubMed - indexed for MEDLINE]
Free PMC Article
9.

NetMHCcons: a consensus method for the major histocompatibility complex class I predictions.

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

Immunogenetics. 2012 Mar;64(3):177-86. doi: 10.1007/s00251-011-0579-8. Epub 2011 Oct 20.

PMID:
22009319
[PubMed - indexed for MEDLINE]
10.

Machine learning competition in immunology - Prediction of HLA class I binding peptides.

Zhang GL, Ansari HR, Bradley P, Cawley GC, Hertz T, Hu X, Jojic N, Kim Y, Kohlbacher O, Lund O, Lundegaard C, Magaret CA, Nielsen M, Papadopoulos H, Raghava GP, Tal VS, Xue LC, Yanover C, Zhu S, Rock MT, Crowe JE, Panayiotou C, Polycarpou MM, Duch W, Brusic V.

J Immunol Methods. 2011 Nov 30;374(1-2):1-4. doi: 10.1016/j.jim.2011.09.010. Epub 2011 Sep 29. No abstract available.

PMID:
21986107
[PubMed - indexed for MEDLINE]
11.

NetTurnP--neural network prediction of beta-turns by use of evolutionary information and predicted protein sequence features.

Petersen B, Lundegaard C, Petersen TN.

PLoS One. 2010 Nov 30;5(11):e15079. doi: 10.1371/journal.pone.0015079.

PMID:
21152409
[PubMed - indexed for MEDLINE]
Free PMC Article
12.

NetMHCIIpan-2.0 - Improved pan-specific HLA-DR predictions using a novel concurrent alignment and weight optimization training procedure.

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

Immunome Res. 2010 Nov 13;6:9. doi: 10.1186/1745-7580-6-9.

PMID:
21073747
[PubMed]
Free PMC Article
13.

State of the art and challenges in sequence based T-cell epitope prediction.

Lundegaard C, Hoof I, Lund O, Nielsen M.

Immunome Res. 2010 Nov 3;6 Suppl 2:S3. doi: 10.1186/1745-7580-6-S2-S3.

PMID:
21067545
[PubMed]
Free PMC Article
14.

Prediction of epitopes using neural network based methods.

Lundegaard C, Lund O, Nielsen M.

J Immunol Methods. 2011 Nov 30;374(1-2):26-34. doi: 10.1016/j.jim.2010.10.011. Epub 2010 Oct 31.

PMID:
21047511
[PubMed - indexed for MEDLINE]
Free PMC Article
15.

Mice, men and MHC supertypes.

Lundegaard C.

Expert Rev Vaccines. 2010 Jul;9(7):713-8. doi: 10.1586/erv.10.76.

PMID:
20624044
[PubMed]
16.

CPHmodels-3.0--remote homology modeling using structure-guided sequence profiles.

Nielsen M, Lundegaard C, Lund O, Petersen TN.

Nucleic Acids Res. 2010 Jul;38(Web Server issue):W576-81. doi: 10.1093/nar/gkq535. Epub 2010 Jun 11.

PMID:
20542909
[PubMed - indexed for MEDLINE]
Free PMC Article
17.

Major histocompatibility complex class I binding predictions as a tool in epitope discovery.

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

Immunology. 2010 Jul;130(3):309-18. doi: 10.1111/j.1365-2567.2010.03300.x. Epub 2010 May 26. Review.

PMID:
20518827
[PubMed - indexed for MEDLINE]
Free PMC Article
18.

MHC class II epitope predictive algorithms.

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

Immunology. 2010 Jul;130(3):319-28. doi: 10.1111/j.1365-2567.2010.03268.x. Epub 2010 Apr 12. Review.

PMID:
20408898
[PubMed - indexed for MEDLINE]
Free PMC Article
19.

NetCTLpan: pan-specific MHC class I pathway epitope predictions.

Stranzl T, Larsen MV, Lundegaard C, Nielsen M.

Immunogenetics. 2010 Jun;62(6):357-68. doi: 10.1007/s00251-010-0441-4. Epub 2010 Apr 9.

PMID:
20379710
[PubMed - indexed for MEDLINE]
Free PMC Article
20.

A generic method for assignment of reliability scores applied to solvent accessibility predictions.

Petersen B, Petersen TN, Andersen P, Nielsen M, Lundegaard C.

BMC Struct Biol. 2009 Jul 31;9:51. doi: 10.1186/1472-6807-9-51.

PMID:
19646261
[PubMed - indexed for MEDLINE]
Free PMC Article

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