| Reliable prediction of T‐cell epitopes using neural networks with novel sequence representations M Nielsen, C Lundegaard, P Worning, SL Lauemøller, K Lamberth, ... Protein Science 12 (5), 1007-1017, 2003 | 1327 | 2003 |
| NetMHC-3.0: accurate web accessible predictions of human, mouse and monkey MHC class I affinities for peptides of length 8–11 C Lundegaard, K Lamberth, M Harndahl, S Buus, O Lund, M Nielsen Nucleic acids research 36 (suppl_2), W509-W512, 2008 | 927 | 2008 |
| Large-scale validation of methods for cytotoxic T-lymphocyte epitope prediction MV Larsen, C Lundegaard, K Lamberth, S Buus, O Lund, M Nielsen BMC bioinformatics 8, 1-12, 2007 | 926 | 2007 |
| A generic method for assignment of reliability scores applied to solvent accessibility predictions B Petersen, TN Petersen, P Andersen, M Nielsen, C Lundegaard BMC structural biology 9, 1-10, 2009 | 743 | 2009 |
| Reliable B cell epitope predictions: impacts of method development and improved benchmarking JV Kringelum, C Lundegaard, O Lund, M Nielsen PLoS computational biology 8 (12), e1002829, 2012 | 714 | 2012 |
| NetMHCpan, a method for quantitative predictions of peptide binding to any HLA-A and-B locus protein of known sequence M Nielsen, C Lundegaard, T Blicher, K Lamberth, M Harndahl, S Justesen, ... PloS one 2 (8), e796, 2007 | 686 | 2007 |
| Prediction of MHC class II binding affinity using SMM-align, a novel stabilization matrix alignment method M Nielsen, C Lundegaard, O Lund BMC bioinformatics 8, 1-12, 2007 | 666 | 2007 |
| The role of the proteasome in generating cytotoxic T-cell epitopes: insights obtained from improved predictions of proteasomal cleavage M Nielsen, C Lundegaard, O Lund, C Keşmir Immunogenetics 57, 33-41, 2005 | 604 | 2005 |
| Immune epitope database analysis resource Y Kim, J Ponomarenko, Z Zhu, D Tamang, P Wang, J Greenbaum, ... Nucleic acids research 40 (W1), W525-W530, 2012 | 542 | 2012 |
| CPHmodels-3.0—remote homology modeling using structure-guided sequence profiles M Nielsen, C Lundegaard, O Lund, TN Petersen Nucleic acids research 38 (suppl_2), W576-W581, 2010 | 444 | 2010 |
| An integrative approach to CTL epitope prediction: a combined algorithm integrating MHC class I binding, TAP transport efficiency, and proteasomal cleavage predictions MV Larsen, C Lundegaard, K Lamberth, S Buus, S Brunak, O Lund, ... European journal of immunology 35 (8), 2295-2303, 2005 | 425 | 2005 |
| Immune epitope database analysis resource (IEDB-AR) Q Zhang, P Wang, Y Kim, P Haste-Andersen, J Beaver, PE Bourne, ... Nucleic acids research 36 (suppl_2), W513-W518, 2008 | 419 | 2008 |
| NetMHCcons: a consensus method for the major histocompatibility complex class I predictions E Karosiene, C Lundegaard, O Lund, M Nielsen Immunogenetics 64, 177-186, 2012 | 399 | 2012 |
| NetCTLpan: pan-specific MHC class I pathway epitope predictions T Stranzl, MV Larsen, C Lundegaard, M Nielsen Immunogenetics 62, 357-368, 2010 | 393 | 2010 |
| A community resource benchmarking predictions of peptide binding to MHC-I molecules B Peters, HH Bui, S Frankild, M Nielsen, C Lundegaard, E Kostem, ... PLoS computational biology 2 (6), e65, 2006 | 356 | 2006 |
| Definition of supertypes for HLA molecules using clustering of specificity matrices O Lund, M Nielsen, C Kesmir, AG Petersen, C Lundegaard, P Worning, ... Immunogenetics 55, 797-810, 2004 | 356 | 2004 |
| Improved prediction of MHC class I and class II epitopes using a novel Gibbs sampling approach M Nielsen, C Lundegaard, P Worning, CS Hvid, K Lamberth, S Buus, ... Bioinformatics 20 (9), 1388-1397, 2004 | 346 | 2004 |
| Quantitative predictions of peptide binding to any HLA-DR molecule of known sequence: NetMHCIIpan M Nielsen, C Lundegaard, T Blicher, B Peters, A Sette, S Justesen, ... PLoS computational biology 4 (7), e1000107, 2008 | 334 | 2008 |
| MHC class II epitope predictive algorithms M Nielsen, O Lund, S Buus, C Lundegaard Immunology 130 (3), 319-328, 2010 | 295 | 2010 |
| Accurate approximation method for prediction of class I MHC affinities for peptides of length 8, 10 and 11 using prediction tools trained on 9mers C Lundegaard, O Lund, M Nielsen Bioinformatics 24 (11), 1397-1398, 2008 | 288 | 2008 |
