ANN:

Lundegaard C, Lamberth K, Harndahl M, Buus S, Lund O, and Nielsen M. 2008. NetMHC-3.0: Accurate web accessible predictions of Human, Mouse, and Monkey MHC class I affinities for peptides of length 8-11. NAR 36:W509-512.
PMID: 18463140

Lundegaard C, Nielsen M, Lund O. 2006. The validity of predicted T-cell epitopes. Trends Biotechnol 24:537-538.
PMID: 17045685

Lundegaard C, Lund O, and Nielsen M. 2008. Accurate approximation method for prediction of class I MHC affinities for peptides of length 8, 10 and 11 using prediction tools trained on 9mers. Bioinformatics 24:1397-1398.
PMID: 18413329

Nielsen M, Lundegaard C, Worning P, Lauemøller SL, Lamberth K, Buus S, Brunak S, Lund O. 2003. Reliable prediction of T-cell epitopes using neural networks with novel sequence representations. Protein Sci 12:1007-1017.
PMID: 12717023

Buus S, Lauemøller SL, Worning P, Kesmir C, Frimurer T, Corbet S, Fomsgaard A, Hilden J, Holm A, Brunak S. 2003. Sensitive quantitative predictions of peptide-MHC binding by a 'Query by Committee' artificial neural network approach. Tissue Antigens 62:378-384.
PMID: 14617044

SMM:

Peters B, Sette A. 2005. Generating quantitative models describing the sequence specificity of biological processes with the stabilized matrix method. BMC Bioinformatics 6:132.
PMID: 15927070

SMMPMBEC:

Kim Y, Sidney J, Pinilla C, Sette A, Peters B. 2009. Derivation of an amino acid similarity matrix for peptide:MHC binding and its application as a Bayesian prior. BMC Bioinformatics 10:394.
PMID: 19948066

CombLib:

Sidney J, Assarsson E, Moore C, Ngo S, Pinilla C, Sette A, Peters B. 2008. Quantitative peptide binding motifs for 19 human and mouse MHC class I molecules derived using positional scanning combinatorial peptide libraries. Immunome Res 4:2.
PMID: 18221540

Consensus:

Moutaftsi M, Peters B, Pasquetto V, Tscharke DC, Sidney J, Bui HH, Grey H, Sette A. 2006. A consensus epitope prediction approach identifies the breadth of murine T(CD8+)-cell responses to vaccinia virus. Nat Biotechnol 24:817-819.
PMID: 16767078

NetMHCpan:

Hoof I, Peters B, Sidney J, Pedersen LE, Sette A, Lund O, Buus S, Nielsen M. 2009. NetMHCpan, a method for MHC class I binding prediction beyond humans. Immunogenetics 61:1-13.
PMID: 19002680

Nielsen M, Lundegaard C, Blicher T, Lamberth K, Harndahl M, Justesen S, Roder G, Peters B, Sette A, Lund O, Buus S. 2007. NetMHCpan, a method for quantitative predictions of peptide binding to any HLA-A and -B locus protein of known sequence. PLoS ONE 2:e796.
PMID: 17726526

Manuscript detailing allele specific binding affinity threshold identification:

Paul S, Weiskopf D, Angelo MA, Sidney J, Peters B, Sette A. 2013. HLA class I alleles are associated with peptide-binding repertoires of different size, affinity, and immunogenicity. The Journal of Immunology 191(12): 5831-5839.
PMID: 24190657

Consensus:

Wang P, Sidney J, Kim Y, Sette A, Lund O, Nielsen M, Peters B. 2010. Peptide binding predictions for HLA DR, DP and DQ molecules. BMC Bioinformatics. 11:568.
PMID: 21092157

Wang P, Sidney J, Dow C, Mothé B, Sette A, Peters B. 2008. A systematic assessment of MHC class II peptide binding predictions and evaluation of a consensus approach. PLoS Comput Biol. 4(4):e1000048.
PMID: 18389056

NN-align:

Nielsen M, Lund O. 2009. NN-align. An artificial neural network-based alignment algorithm for MHC class II peptide binding prediction. BMC Bioinformatics. 10:296.
PMID: 19765293

SMM-align:

Nielsen M, Lundegaard C, Lund O. 2007. Prediction of MHC class II binding affinity using SMM-align, a novel stabilization matrix alignment method. BMC Bioinformatics. 8:238.
PMID: 17608956

Sturniolo:

Sturniolo T, Bono E, Ding J, Raddrizzani L, Tuereci O, Sahin U, Braxenthaler M, Gallazzi F, Protti MP, Sinigaglia F, Hammer J. 1999. Generation of tissue-specific and promiscuous HLA ligand databases using DNA microarrays and virtual HLA class II matrices. Nat Biotechnol. 17(6):555-561.
PMID: 10385319

NetMHCIIpan:

Karosiene E1, Rasmussen M, Blicher T, Lund O, Buus S, Nielsen M. 2013. 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. Immunogenetics65(10)711.
PMID: 23900783

Nielsen M, Lundegaard C, Blicher T, Peters B, Sette A, Justesen S, Buus S, and Lund O. 2008. Quantitative predictions of peptide binding to any HLA-DR molecule of known sequence: NetMHCIIpan. PLoS Comput Biol.4(7)e1000107.
PMID: 18604266

7-allele method:

Paul S, Arlehamn CSL, Scriba TJ, Dillon MB, Oseroff C, Hinz D, McKinney DM, Pro SC, Sidney J, Peters B, Sette A. 2015. Development and validation of a broad scheme for prediction of HLA class II restricted T cell epitopes. Journal of immunological methods. 422: 28-34.
PMID: 25862607