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Items: 1 to 20 of 47


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.


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.


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.


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.


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.


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.


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.


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.


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.


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.


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.


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.


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.


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.


Mice, men and MHC supertypes.

Lundegaard C.

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


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.


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.


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.


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.


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.

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