Research Topics
| Claus LundegaardSummaryAffiliation: Center for Biological Sequence Analysis Country: Denmark Publications
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Detail Information
Publications
Accurate approximation method for prediction of class I MHC affinities for peptides of length 8, 10 and 11 using prediction tools trained on 9mersClaus Lundegaard
Center for Biological Sequence Analysis CBS, Department of Systems Biology, The Technical University of Denmark DTU, Kemitorvet Build 208, 2800 Lyngby, Denmark
Bioinformatics 24:1397-8. 2008..AVAILABILITY: The algorithm has been implemented in the web-accessible servers NetMHC-3.0: http://www.cbs.dtu.dk/services/NetMHC-3.0, and NetMHCpan-1.1: http://www.cbs.dtu.dk/services/NetMHCpan-1.1..
Modeling the adaptive immune system: predictions and simulationsClaus Lundegaard
Center for Biological Sequence Analysis, CBS, Kemitorvet 208, Technical University of Denmark, DK 2800 Lyngby, Denmark
Bioinformatics 23:3265-75. 2007..Simulation systems and mathematical modeling are also now beginning to reach a level where these methods will be able to answer more complex immunological questions...- The validity of predicted T-cell epitopesClaus Lundegaard
Center for Biological Sequence Analysis, BioCentrum, Building 208, Technical University of Denmark, 2800 Lyngby, Denmark
Trends Biotechnol 24:537-8. 2006..This work underlines the importance of bioinformatics as a resource-saving tool in the field of epitope discovery. In addition, the data can be used to benchmark the performance of other new or existing CTL epitope-prediction tools... 
Major histocompatibility complex class I binding predictions as a tool in epitope discoveryClaus Lundegaard
Department of Systems Biology, Centre for Biological Sequence Analysis, Technical University of Denmark, Lyngby, Denmark
Immunology 130:309-18. 2010..We conclude that this new generation of epitope discovery systems has become a highly efficient tool for epitope discovery, and recommend that the less accurate prediction systems of the past be abandoned, as these are obsolete...- Prediction of epitopes using neural network based methodsClaus Lundegaard
Center for Biological Sequence Analysis, DTU Systems Biology, Building 208, Technical University of Denmark, DK 2800 Lyngby, Denmark
J Immunol Methods 374:26-34. 2011..Selected potential epitopes were all evaluated experimentally using ex vivo assays... - State of the art and challenges in sequence based T-cell epitope predictionClaus Lundegaard
The Technical University of Denmark DTU, Dept, of Systems Biology, Center for Biological Sequence Analysis CBS, Kemitorvet 208, DK 2800 Kgs, Lyngby, Denmark
Immunome Res 6:S3. 2010..Here, we will go through some of the history of sequence-based predictions of helper as well as cytotoxic T cell epitopes. We will focus on some of the most accurate methods and their basic background... - Quantitative predictions of peptide binding to any HLA-DR molecule of known sequence: NetMHCIIpanMorten Nielsen
Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, Lyngby, Denmark
PLoS Comput Biol 4:e1000107. 2008.... - Improved prediction of MHC class I and class II epitopes using a novel Gibbs sampling approachMorten Nielsen
Center for Biological Sequence Analysis, BioCentrum DTU, Building 208, Technical University of Denmark, DK 2800 Lyngby, Denmark
Bioinformatics 20:1388-97. 2004..The calculation demonstrates that the predictive performance of the Gibbs sampler is higher than that of ClustalW and in most cases also higher than that of the TEPITOPE method... - NetMHCpan, a method for quantitative predictions of peptide binding to any HLA-A and -B locus protein of known sequenceMorten Nielsen
Center for Biological Sequence Analysis, BioCentrum DTU, Technical University of Denmark, Lyngby, Denmark
PLoS ONE 2:e796. 2007..The human MHC class I system (HLA-I) is extremely polymorphic. The number of registered HLA-I molecules has now surpassed 1500. Characterizing the specificity of each separately would be a major undertaking... - Selecting informative data for developing peptide-MHC binding predictors using a query by committee approachJens Kaae Christensen
Center for Biological Sequence Analysis, BioCentrum DTU, Technical University of Denmark, DK 2800 Lyngby, Denmark
Neural Comput 15:2931-42. 2003..Finally, it should be noted that data selection strategies similar to those used here might be of use in other settings in which generation of more data is a costly process... - NetMHCcons: a consensus method for the major histocompatibility complex class I predictionsEdita Karosiene
Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, Building 208, Kemitorvet, Lyngby, 2800, Denmark
Immunogenetics 64:177-86. 2012..The final method, NetMHCcons, is publicly available at www.cbs.dtu.dk/services/NetMHCcons , and allows the user in an automatic manner to obtain the most accurate predictions for any given MHC molecule... - Prediction of MHC class II binding affinity using SMM-align, a novel stabilization matrix alignment methodMorten Nielsen
Center for Biological Sequence Analysis, BioCentrum DTU, Technical University of Denmark, Lyngby, Denmark
BMC Bioinformatics 8:238. 2007..The predictive performance of the method is validated on a large MHC class II benchmark data set covering 14 HLA-DR (human MHC) and three mouse H2-IA alleles... - NetMHC-3.0: accurate web accessible predictions of human, mouse and monkey MHC class I affinities for peptides of length 8-11Claus Lundegaard
CBS, Department of Systems Biology, Technical University of Denmark DTU, Kemitorvet Build 208, 2800 Lyngby, Denmark
Nucleic Acids Res 36:W509-12. 2008..Here, the performance is further validated and benchmarked using a large set of newly published affinity data, non-redundant to the training set. The server is free of use and available at: http://www.cbs.dtu.dk/services/NetMHC... - Large-scale validation of methods for cytotoxic T-lymphocyte epitope predictionMette V Larsen
Center for Biological Sequence Analysis, BioCentrum DTU, Building 208, Technical University of Denmark, DK 2800 Lyngby, Denmark
BMC Bioinformatics 8:424. 2007..Here, we develop such large-scale benchmark and corresponding performance measures and report the performance of an updated version 1.2 of NetCTL in comparison with the four other methods... - An integrative approach to CTL epitope prediction: a combined algorithm integrating MHC class I binding, TAP transport efficiency, and proteasomal cleavage predictionsMette Voldby Larsen
Center for Biological Sequence Analysis, BioCentrum-DTU, Technical University of Denmark, Lyngby, Denmark
Eur J Immunol 35:2295-303. 2005..The method is available at http://www.cbs.dtu.dk/services/NetCTL. Supplementary material is available at http://www.cbs.dtu.dk/suppl/immunology/CTL.php... - Pan-specific MHC class I predictors: a benchmark of HLA class I pan-specific prediction methodsHao Zhang
Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, Lyngby 2800, Denmark
Bioinformatics 25:83-9. 2009..These pan-specific human lymphocyte antigen (HLA) predictors have not previously been compared using independent evaluation sets... - Human leukocyte antigen (HLA) class I restricted epitope discovery in yellow fewer and dengue viruses: importance of HLA binding strengthOle Lund
Department of Systems Biology, Center for Biological Sequence Analysis, Technical University of Denmark, Lyngby, Denmark
PLoS ONE 6:e26494. 2011..All three peptides that elicited responses had an HLA binding affinity of 2 nM or less. The results indicate the importance of the strength of HLA binding in shaping the immune response... - Definition of supertypes for HLA molecules using clustering of specificity matricesOle Lund
Center for Biological Sequence Analysis, BioCentrum DTU, Technical University of Denmark, Building 208, 2800 Lyngby, Denmark
Immunogenetics 55:797-810. 2004..Supplementary material is available at http://www.cbs.dtu.dk/researchgroups/immunology/supertypes.html... - Predictions versus high-throughput experiments in T-cell epitope discovery: competition or synergy?Claus Lundegaard
Technical University of Denmark DTU, Center for Biological Sequence Analysis, Department of Systems Biology, Kemitorvet 208, DK 2800, Kgs Lyngby, Denmark
Expert Rev Vaccines 11:43-54. 2012..We expect prediction methods as well as experimental validation methods to continue to develop and that we will soon see clinical trials of products whose development has been guided by prediction methods... - CPHmodels-3.0--remote homology modeling using structure-guided sequence profilesMorten Nielsen
Center for Biological Sequence Analysis, Department of Systems Biology, The Technical University of Denmark, Denmark
Nucleic Acids Res 38:W576-81. 2010..Beside its accuracy, one of the important features of the method is its speed. For most queries, the response time of the server is <20 min. The web server is available at http://www.cbs.dtu.dk/services/CPHmodels/... - MHC class II epitope predictive algorithmsMorten Nielsen
Department of Systems Biology, Technical University of Denmark, Centre for Biological Sequence Analysis, Lyngby, Denmark
Immunology 130:319-28. 2010..Furthermore, the pan-specific methods have been used to make a graphical atlas such as the MHCMotifviewer, which allows for visual comparison of specificities of different alleles... - NetCTLpan: pan-specific MHC class I pathway epitope predictionsThomas Stranzl
Department of Systems Biology DTU, Building 208, Center for Biological Sequence Analysis, Technical University of Denmark, Lyngby, 2800, Denmark
Immunogenetics 62:357-68. 2010..The method and benchmark datasets are available at http://www.cbs.dtu.dk/services/NetCTLpan/... - Reliable prediction of T-cell epitopes using neural networks with novel sequence representationsMorten Nielsen
Center for Biological Sequence Analysis, BioCentrum DTU, Technical University of Denmark, DK 2800 Lyngby, Denmark
Protein Sci 12:1007-17. 2003..Finally, we use the method to predict T-cell epitopes for the genome of hepatitis C virus and discuss possible applications of the prediction method to guide the process of rational vaccine design... - NetTurnP--neural network prediction of beta-turns by use of evolutionary information and predicted protein sequence featuresBent Petersen
Department of Systems Biology, Center for Biological Sequence Analysis CBS, Technical University of Denmark, Lyngby, Denmark
PLoS ONE 5:e15079. 2010..CONCLUSION: The NetTurnP method has been implemented as a webserver, which is freely available at http://www.cbs.dtu.dk/services/NetTurnP/. NetTurnP is the only available webserver that allows submission of multiple sequences... - The role of the proteasome in generating cytotoxic T-cell epitopes: insights obtained from improved predictions of proteasomal cleavageMorten Nielsen
Center for Biological Sequence Analysis, Technical University of Denmark, BioCentrum DTU, Building 208, 2800, Lyngby, Denmark
Immunogenetics 57:33-41. 2005..e., the specificity of TAP has evolved to fit the specificity of the proteasome. This evolutionary relationship allows for a more efficient antigen presentation... - Bioinformatics Identification of Antigenic Peptide: Predicting the Specificity of Major MHC Class I and II Pathway PlayersOle Lund
Department of Systems Biology, Center for Biological Sequence Analysis, Technical University of Denmark, Kongens Lyngby, Denmark
Methods Mol Biol 960:247-60. 2013..This wide usage has led to the confusion of defining which of the many methods to use for what problems. In this chapter, an overview is given focusing on the suite of tools developed at the Technical University of Denmark... - NetMHCIIpan-2.0 - Improved pan-specific HLA-DR predictions using a novel concurrent alignment and weight optimization training procedureMorten Nielsen
Center A for Biological Sequence Analysis, BioCentrum DTU, Building 208, Technical University of Denmark, DK 2800 Lyngby, Denmark
Immunome Res 6:9. 2010..Characterizing each MHC-II molecule using peptide-screening binding assays is hence not a viable option... - A generic method for assignment of reliability scores applied to solvent accessibility predictionsBent Petersen
Center for Biological Sequence Analysis CBS, Department of Systems Biology, Kemitorvet 208, Technical University of Denmark DTU, Lyngby, Denmark
BMC Struct Biol 9:51. 2009..As a solution to this challenge, we have implemented a method that predicts the relative surface accessibility of an amino acid and simultaneously predicts the reliability for each prediction, in the form of a Z-score... - Reliable B cell epitope predictions: impacts of method development and improved benchmarkingJens Vindahl Kringelum
Center for Biological Sequence Analysis, Technical University of Denmark, Lyngby, Denmark
PLoS Comput Biol 8:e1002829. 2012..The updated version of DiscoTope is available at www.cbs.dtu.dk/services/DiscoTope-2.0... - Immune epitope database analysis resourceYohan Kim
La Jolla Institute for Allergy and Immunology, 9420 Athena Circle, La Jolla, CA 92037, USA
Nucleic Acids Res 40:W525-30. 2012..Specifically, the predictive tools can be programmatically accessed using a web interface and can also be downloaded as software packages...