Ole Lund

Summary

Affiliation: Center for Biological Sequence Analysis
Country: Denmark

Publications

  1. doi request reprint Bioinformatics identification of antigenic peptide: predicting the specificity of major MHC class I and II pathway players
    Ole Lund
    Department of Systems Biology, Center for Biological Sequence Analysis, Technical University of Denmark, Kongens Lyngby, Denmark
    Methods Mol Biol 960:247-60. 2013
  2. pmc Plasmodium falciparum population dynamics in a cohort of pregnant women in Senegal
    Juliette Guitard
    Institut de Recherche pour le Developpement, Universite Paris Descartes, France
    Malar J 9:165. 2010
  3. pmc Peptide binding predictions for HLA DR, DP and DQ molecules
    Peng Wang
    La Jolla Institute for Allergy and Immunology, La Jolla, USA
    BMC Bioinformatics 11:568. 2010
  4. pmc Coronavirus 3CLpro proteinase cleavage sites: possible relevance to SARS virus pathology
    Lars Kiemer
    Center for Biological Sequence Analysis BioCentrum DTU, Technical University of Denmark DK 2800 Lyngby
    BMC Bioinformatics 5:72. 2004
  5. ncbi request reprint Definition of supertypes for HLA molecules using clustering of specificity matrices
    Ole Lund
    Center for Biological Sequence Analysis, BioCentrum DTU, Technical University of Denmark, Building 208, 2800 Lyngby, Denmark
    Immunogenetics 55:797-810. 2004
  6. pmc Human leukocyte antigen (HLA) class I restricted epitope discovery in yellow fewer and dengue viruses: importance of HLA binding strength
    Ole Lund
    Department of Systems Biology, Center for Biological Sequence Analysis, Technical University of Denmark, Lyngby, Denmark
    PLoS ONE 6:e26494. 2011
  7. pmc NetMHCpan, a method for MHC class I binding prediction beyond humans
    Ilka Hoof
    Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, Building 208, 2800, Lyngby, Denmark
    Immunogenetics 61:1-13. 2009
  8. pmc Quantitative predictions of peptide binding to any HLA-DR molecule of known sequence: NetMHCIIpan
    Morten Nielsen
    Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, Lyngby, Denmark
    PLoS Comput Biol 4:e1000107. 2008
  9. pmc NetMHCpan, a method for quantitative predictions of peptide binding to any HLA-A and -B locus protein of known sequence
    Morten Nielsen
    Center for Biological Sequence Analysis, BioCentrum DTU, Technical University of Denmark, Lyngby, Denmark
    PLoS ONE 2:e796. 2007
  10. pmc MHC motif viewer
    Nicolas Rapin
    Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, Lyngby, Denmark
    Immunogenetics 60:759-65. 2008

Detail Information

Publications70

  1. doi request reprint Bioinformatics identification of antigenic peptide: predicting the specificity of major MHC class I and II pathway players
    Ole 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...
  2. pmc Plasmodium falciparum population dynamics in a cohort of pregnant women in Senegal
    Juliette Guitard
    Institut de Recherche pour le Developpement, Universite Paris Descartes, France
    Malar J 9:165. 2010
    ..VAR2CSA is the main candidate for a pregnancy malaria vaccine, but vaccine development may be complicated by its sequence polymorphism...
  3. pmc Peptide binding predictions for HLA DR, DP and DQ molecules
    Peng Wang
    La Jolla Institute for Allergy and Immunology, La Jolla, USA
    BMC Bioinformatics 11:568. 2010
    ..This reflects a significant gap in knowledge as HLA DP and DQ molecules are presumably equally important, and have only been studied less because they are more difficult to handle experimentally...
  4. pmc Coronavirus 3CLpro proteinase cleavage sites: possible relevance to SARS virus pathology
    Lars Kiemer
    Center for Biological Sequence Analysis BioCentrum DTU, Technical University of Denmark DK 2800 Lyngby
    BMC Bioinformatics 5:72. 2004
    ..Prompted by this, we set out to analyse and predict cleavage by the coronavirus main proteinase using computational methods...
  5. ncbi request reprint Definition of supertypes for HLA molecules using clustering of specificity matrices
    Ole 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...
  6. pmc Human leukocyte antigen (HLA) class I restricted epitope discovery in yellow fewer and dengue viruses: importance of HLA binding strength
    Ole 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...
  7. pmc NetMHCpan, a method for MHC class I binding prediction beyond humans
    Ilka Hoof
    Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, Building 208, 2800, Lyngby, Denmark
    Immunogenetics 61:1-13. 2009
    ..The high performance of NetMHCpan-2.0 for non-human primates documents the method's ability to provide broad allelic coverage also beyond human MHC molecules. The method is available at http://www.cbs.dtu.dk/services/NetMHCpan...
  8. pmc Quantitative predictions of peptide binding to any HLA-DR molecule of known sequence: NetMHCIIpan
    Morten Nielsen
    Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, Lyngby, Denmark
    PLoS Comput Biol 4:e1000107. 2008
    ....
  9. pmc NetMHCpan, a method for quantitative predictions of peptide binding to any HLA-A and -B locus protein of known sequence
    Morten 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...
  10. pmc MHC motif viewer
    Nicolas Rapin
    Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, Lyngby, Denmark
    Immunogenetics 60:759-65. 2008
    ..The MHC motif viewer is available at http://www.cbs.dtu.dk/biotools/MHCMotifViewer/ ...
  11. ncbi request reprint An integrative approach to CTL epitope prediction: a combined algorithm integrating MHC class I binding, TAP transport efficiency, and proteasomal cleavage predictions
    Mette 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...
  12. doi request reprint NetMHCcons: a consensus method for the major histocompatibility complex class I predictions
    Edita 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...
  13. ncbi request reprint Selecting informative data for developing peptide-MHC binding predictors using a query by committee approach
    Jens 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...
  14. ncbi request reprint Improved prediction of MHC class I and class II epitopes using a novel Gibbs sampling approach
    Morten Nielsen
    Center for Biological Sequence Analysis, BioCentrum DTU, Building 208, Technical University of Denmark, DK 2800 Lyngby, Denmark
    Bioinformatics 20:1388-97. 2004
    ..Subsequently, the weight-matrix can be applied to identifying effectively potential MHC binding peptides and to guiding the process of rational vaccine design...
  15. pmc MHCcluster, a method for functional clustering of MHC molecules
    Martin Thomsen
    Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, Building 208, Kemitorvet, Lyngby 2800, Denmark
    Immunogenetics 65:655-65. 2013
    ..Also, we use MHCcluster to show that chimpanzee MHC class I molecules have a reduced functional diversity compared to that of HLA class I molecules. MHCcluster is available at www.cbs.dtu.dk/services/MHCcluster-2.0...
  16. pmc NetMHC-3.0: accurate web accessible predictions of human, mouse and monkey MHC class I affinities for peptides of length 8-11
    Claus 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...
  17. pmc Prediction of MHC class II binding affinity using SMM-align, a novel stabilization matrix alignment method
    Morten 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...
  18. pmc NN-align. An artificial neural network-based alignment algorithm for MHC class II peptide binding prediction
    Morten Nielsen
    Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, DK 2800 Lyngby, Denmark
    BMC Bioinformatics 10:296. 2009
    ....
  19. pmc Limitations of Ab initio predictions of peptide binding to MHC class II molecules
    Hao Zhang
    Center for Biological Sequence Analysis, Department for Systems Biology, Technical University of Denmark, Lyngby, Denmark
    PLoS ONE 5:e9272. 2010
    ....
  20. doi request reprint Simultaneous alignment and clustering of peptide data using a Gibbs sampling approach
    Massimo Andreatta
    Center for Biological Sequence Analysis, Technical University of Denmark, DK 2800 Lyngby, Denmark
    Bioinformatics 29:8-14. 2013
    ..Interpretation of such large peptide datasets, however, is a complex task, especially when the data contain multiple receptor binding motifs, and/or the motifs are found at different locations within distinct peptides...
  21. pmc Large-scale validation of methods for cytotoxic T-lymphocyte epitope prediction
    Mette 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...
  22. doi request reprint Interdisciplinary analysis of HIV-specific CD8+ T cell responses against variant epitopes reveals restricted TCR promiscuity
    Ilka Hoof
    Department of Systems Biology, Center for Biological Sequence Analysis, Technical University of Denmark, Lyngby, Denmark
    J Immunol 184:5383-91. 2010
    ....
  23. pmc Systematic characterisation of cellular localisation and expression profiles of proteins containing MHC ligands
    Agnieszka S Juncker
    Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, Lyngby, Denmark
    PLoS ONE 4:e7448. 2009
    ..Presentation of peptides on Major Histocompatibility Complex (MHC) molecules is the cornerstone in immune system activation and increased knowledge of the characteristics of MHC ligands and their source proteins is highly desirable...
  24. pmc The PickPocket method for predicting binding specificities for receptors based on receptor pocket similarities: application to MHC-peptide binding
    Hao Zhang
    Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, Lyngby 2800, Denmark
    Bioinformatics 25:1293-9. 2009
    ..Here, we present a method that can extrapolate from variants with known binding specificity to those where no experimental data are available...
  25. doi request reprint Accurate approximation method for prediction of class I MHC affinities for peptides of length 8, 10 and 11 using prediction tools trained on 9mers
    Claus 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
    ..In this validation, the approximation method has an accuracy that is comparable to or better than methods trained on a peptide length identical to the predicted peptides...
  26. pmc The cancer exome generated by alternative mRNA splicing dilutes predicted HLA class I epitope density
    Thomas Stranzl
    Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, Lyngby, Denmark
    PLoS ONE 7:e38670. 2012
    ..This variation contributes to the observed significant lower likelihood of cancer-specific peptides to be predicted epitopes compared to peptides found in normal tissue...
  27. pmc Prediction of epitopes using neural network based methods
    Claus 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...
  28. pmc Benchmarking of methods for genomic taxonomy
    Mette V Larsen
    Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, Kongens Lyngby, Denmark
    J Clin Microbiol 52:1529-39. 2014
    ..The KmerFinder method had the overall highest accuracy and correctly identified from 93% to 97% of the isolates in the evaluations sets...
  29. pmc 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
    Edita Karosiene
    Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, Building 208, Kemitorvet, 2800, Lyngby, Denmark
    Immunogenetics 65:711-24. 2013
    ..0 method is the first pan-specific predictor covering all HLA class II molecules with known sequences including HLA-DR, HLA-DP, and HLA-DQ. The NetMHCpan-3.0 method is available at http://www.cbs.dtu.dk/services/NetMHCIIpan-3.0 . ..
  30. pmc 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...
  31. pmc Major histocompatibility complex class I binding predictions as a tool in epitope discovery
    Claus 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...
  32. pmc MHC class II epitope predictive algorithms
    Morten 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...
  33. pmc Identification of CD8+ T cell epitopes in the West Nile virus polyprotein by reverse-immunology using NetCTL
    Mette Voldby Larsen
    Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, Lyngby, Denmark
    PLoS ONE 5:e12697. 2010
    ..West Nile virus (WNV) is a growing threat to public health and a greater understanding of the immune response raised against WNV is important for the development of prophylactic and therapeutic strategies...
  34. pmc SigniSite: Identification of residue-level genotype-phenotype correlations in protein multiple sequence alignments
    Leon Eyrich Jessen
    Department of Systems Biology, Center for Biological Sequence Analysis, Technical University of Denmark, Kemitorvet, Building 208, DK 2800 Lyngby, Denmark
    Nucleic Acids Res 41:W286-91. 2013
    ..For both data sets, SigniSite was found to outperform SPEER. SigniSite is available at: http://www.cbs.dtu.dk/services/SigniSite/. ..
  35. doi request reprint Genotyping using whole-genome sequencing is a realistic alternative to surveillance based on phenotypic antimicrobial susceptibility testing
    Ea Zankari
    National Food Institute, Technical University of Denmark, 2800 Kgs Lyngby, Denmark
    J Antimicrob Chemother 68:771-7. 2013
    ..The aim of this study was to evaluate WGS as a routine tool for surveillance of antimicrobial resistance compared with current phenotypic procedures...
  36. ncbi request reprint The role of the proteasome in generating cytotoxic T-cell epitopes: insights obtained from improved predictions of proteasomal cleavage
    Morten 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...
  37. pmc NNAlign: a web-based prediction method allowing non-expert end-user discovery of sequence motifs in quantitative peptide data
    Massimo Andreatta
    Center for Biological Sequence Analysis, Technical University of Denmark, Kongens Lyngby, Denmark
    PLoS ONE 6:e26781. 2011
    ..We have successfully applied this method to several different data sets including peptide microarray-derived sets containing more than 100,000 data points. NNAlign is available online at http://www.cbs.dtu.dk/services/NNAlign...
  38. pmc CPHmodels-3.0--remote homology modeling using structure-guided sequence profiles
    Morten 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/...
  39. ncbi request reprint The validity of predicted T-cell epitopes
    Claus 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...
  40. pmc Reliable prediction of T-cell epitopes using neural networks with novel sequence representations
    Morten 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...
  41. pmc Reliable B cell epitope predictions: impacts of method development and improved benchmarking
    Jens 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...
  42. ncbi request reprint Modeling the adaptive immune system: predictions and simulations
    Claus Lundegaard
    Center for Biological Sequence Analysis, CBS, Kemitorvet 208, Technical University of Denmark, DK 2800 Lyngby, Denmark
    Bioinformatics 23:3265-75. 2007
    ..The specifics of how and where they might be implemented have recently been reviewed in the literature. However, the background and concerns for selecting between the different available methods have so far not been adequately covered...
  43. pmc Amino acid similarity accounts for T cell cross-reactivity and for "holes" in the T cell repertoire
    Sune Frankild
    Center for Biological Sequence Analysis, Technical University of Denmark, Lyngby, Denmark
    PLoS ONE 3:e1831. 2008
    ..Several studies suggest that CTL clones can recognize highly diverse peptides, some sharing no obvious sequence identity. The emerging realization in the field is that T cell receptors (TcR) recognize multiple distinct ligands...
  44. pmc Real-time whole-genome sequencing for routine typing, surveillance, and outbreak detection of verotoxigenic Escherichia coli
    Katrine Grimstrup Joensen
    National Food Institute, Division for Epidemiology and Microbial Genomics, Technical University of Denmark, Kongens Lyngby, Denmark
    J Clin Microbiol 52:1501-10. 2014
    ..Therefore, WGS typing is a superior alternative to conventional typing strategies. This approach may also be applied to typing and surveillance of other pathogens. ..
  45. pmc ChemProt-2.0: visual navigation in a disease chemical biology database
    Sonny Kim Kjærulff
    Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, 2800 Lyngby, Denmark
    Nucleic Acids Res 41:D464-9. 2013
    ..Filtering options were included in order to facilitate and to guide dynamic search of specific queries...
  46. pmc NetMHCIIpan-2.0 - Improved pan-specific HLA-DR predictions using a novel concurrent alignment and weight optimization training procedure
    Morten 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...
  47. doi request reprint Humans with chimpanzee-like major histocompatibility complex-specificities control HIV-1 infection
    Ilka Hoof
    Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, Lyngby, Denmark
    AIDS 22:1299-303. 2008
    ..Chimpanzees control HIV-1 viral replication and develop a chronic infection without progressing to AIDS. A similar course of disease is observed in human long-term non-progressors...
  48. doi request reprint Degree of predicted minor histocompatibility antigen mismatch correlates with poorer clinical outcomes in nonmyeloablative allogeneic hematopoietic cell transplantation
    Malene Erup Larsen
    Center for Biological Sequence Analysis, DTU Systems Biology, Technical University of Denmark, DK 2800 Lyngby, Denmark
    Biol Blood Marrow Transplant 16:1370-81. 2010
    ..Furthermore, our data suggest a possible role for in silico based miHA predictions in donor selection as well as in selecting candidate miHAs for further evaluation in in vitro and in vivo experiments...
  49. pmc Structural insight into epitopes in the pregnancy-associated malaria protein VAR2CSA
    Pernille Andersen
    Center for Biological Sequence Analysis, BioCentrum DTU, Denmark
    PLoS Pathog 4:e42. 2008
    ..These results comprise an important step towards understanding the structure of VAR2CSA on the surface of CSA-binding infected erythrocytes...
  50. pmc Identification of acquired antimicrobial resistance genes
    Ea Zankari
    National Food Institute, Technical University of Denmark, 2800 Kgs Lyngby, Denmark
    J Antimicrob Chemother 67:2640-4. 2012
    ..Thus, the current challenge is to extract the relevant information from the large amount of generated data...
  51. pmc State of the art and challenges in sequence based T-cell epitope prediction
    Claus 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...
  52. pmc Rapid whole-genome sequencing for detection and characterization of microorganisms directly from clinical samples
    Henrik Hasman
    National Food Institute, Technical University of Denmark, Lyngby, Denmark
    J Clin Microbiol 52:139-46. 2014
    ..This may prove very useful, but the need for data analysis is still a hurdle to clinical implementation. To overcome this problem, a publicly available bioinformatic tool was developed in this study. ..
  53. pmc PathogenFinder--distinguishing friend from foe using bacterial whole genome sequence data
    Salvatore Cosentino
    Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, Kgs Lyngby, Denmark
    PLoS ONE 8:e77302. 2013
    ..Furthermore the pathogenicity prediction web-server could be used to isolate the potential pathogenic features of both known and unknown strains. ..
  54. pmc Structural analysis of B-cell epitopes in antibody:protein complexes
    Jens Vindahl Kringelum
    Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, Kemitorvet, Building 208, DK 2800 Lyngby, Denmark
    Mol Immunol 53:24-34. 2013
    ..Our results, in combination with previously findings, give a detailed picture of the B-cell epitope that may be used in development of improved B-cell prediction methods...
  55. doi request reprint Genome-based in silico identification of new Mycobacterium tuberculosis antigens activating polyfunctional CD8+ T cells in human tuberculosis
    Sheila T Tang
    Center for Biological Sequence Analysis, Technical University of Denmark, 2800 Lyngby, Denmark
    J Immunol 186:1068-80. 2011
    ..tuberculosis Ags are recognized by (poly)functional CD8(+) T cells during control of infection. These results impact on TB-vaccine design and biomarker identification...
  56. pmc Evaluation of whole genome sequencing for outbreak detection of Salmonella enterica
    Pimlapas Leekitcharoenphon
    Division for Epidemiology and Microbial Genomics, National Food Institute, Technical University of Denmark, Kgs Lyngby, Denmark Department of System Biology, Center for Biological Sequence Analysis, Technical University of Denmark, Kgs Lyngby, Denmark
    PLoS ONE 9:e87991. 2014
    ..Our study also indicates that WGS alone is insufficient to determine whether strains are related or un-related to outbreaks. This still requires the combination of epidemiological data and whole genome sequencing results...
  57. pmc Integrating genome-based informatics to modernize global disease monitoring, information sharing, and response
    Frank M Aarestrup
    Technical University of Denmark, Lyngby, Denmark
    Emerg Infect Dis 18:e1. 2012
    ....
  58. pmc In silico prediction of human pathogenicity in the γ-proteobacteria
    Massimo Andreatta
    Center for Biological Sequence Analysis, Technical University of Denmark, Kongens Lyngby, Denmark
    PLoS ONE 5:e13680. 2010
    ..Bioinformatics-based methods are therefore strongly needed to mine the fast growing number of genome sequences and assess in a rapid and reliable way the pathogenicity of novel bacteria...
  59. pmc Prediction of residues in discontinuous B-cell epitopes using protein 3D structures
    Pernille Haste Andersen
    Center for Biological Sequence Analysis, BioCentrum, Technical University of Denmark, DK 2800 Lyngby, Denmark
    Protein Sci 15:2558-67. 2006
    ..Predictions by the DiscoTope method can guide experimental epitope mapping in both rational vaccine design and development of diagnostic tools, and may lead to more efficient epitope identification...
  60. ncbi request reprint Ten years of bacterial genome sequencing: comparative-genomics-based discoveries
    Tim T Binnewies
    Center for Biological Sequence Analysis, Technical University of Denmark, 2800, Lyngby, Denmark
    Funct Integr Genomics 6:165-85. 2006
    ..The newly proposed Minimal Information about a Genome Sequence standard has been developed to obtain this information...
  61. ncbi request reprint Broadly immunogenic HLA class I supertype-restricted elite CTL epitopes recognized in a diverse population infected with different HIV-1 subtypes
    Carina L Pérez
    Department of Microbiology, Cell Biology, and Tumor Biology, Karolinska Institutet, and The Swedish Institute of Infectious Disease Control, Stockholm, Sweden
    J Immunol 180:5092-100. 2008
    ..Our results have important implications for the validation of potent CTL responses and show that the goal for a vaccine candidate in inducing broadly reactive CTL immune responses is attainable...
  62. ncbi request reprint Selection of proteins for human MHC class II presentation
    Li Jiang
    Department of Immunology, Wuhan University School of Medicine, Hubei, China
    Cell Mol Immunol 2:49-56. 2005
    ..These results can lead to better understanding the autoimmunity and the response to infections...
  63. pmc Immune epitope database analysis resource (IEDB-AR)
    Qing Zhang
    Immune Epitope Database and Analysis Resource IEDB AR, La Jolla Institute for Allergy and Immunology, La Jolla, CA, USA
    Nucleic Acids Res 36:W513-8. 2008
    ..New functionalities have been added to most of the previously implemented tools, and a total of eight new tools were added, including two B-cell epitope prediction tools, four T-cell epitope prediction tools and two analysis tools...
  64. ncbi request reprint CTL epitopes for influenza A including the H5N1 bird flu; genome-, pathogen-, and HLA-wide screening
    Mingjun Wang
    Laboratory of Cellular Immunology, Department of Medical Anatomy, The Panum Institute, University of Copenhagen, Blegdamsvej 3, 2200 Copenhagen N, Denmark
    Vaccine 25:2823-31. 2007
    ..To exploit this new potential, a coordinated international effort to analyze the precious source of information represented by rare patients, such as the current victims of bird flu, would be essential...
  65. ncbi request reprint Towards a consensus on datasets and evaluation metrics for developing B-cell epitope prediction tools
    Jason A Greenbaum
    Immune Epitope Database and Analysis Resource IEDB, La Jolla Institute for Allergy and Immunology, La Jolla, California, USA
    J Mol Recognit 20:75-82. 2007
    ..By developing common datasets, standardized data formats, and the means with which to consolidate information, we hope to greatly enhance the development of B-cell epitope prediction tools...
  66. pmc A community resource benchmarking predictions of peptide binding to MHC-I molecules
    Bjoern Peters
    La Jolla Institute for Allergy and Immunology, San Diego, California, USA
    PLoS Comput Biol 2:e65. 2006
    ....
  67. ncbi request reprint The design and implementation of the immune epitope database and analysis resource
    Bjoern Peters
    La Jolla Institute of Allergy and Immunology, 3030 Bunker Hill Street, Suite 326, San Diego, CA 92109, USA
    Immunogenetics 57:326-36. 2005
    ..We describe how we plan to capture, structure, and store this information, what query interfaces we will make available to the public, and what additional predictive and analytical tools we will provide...
  68. ncbi request reprint Hemodynamic function of the standard St. Jude bileaflet disc valve has no clinical impact 10 years after aortic valve replacement
    Ole Lund
    Department of Cardiothoracic Surgery, Aarhus University Hospital in Skejby, Aarhus, Denmark
    Scand Cardiovasc J 39:237-43. 2005
    ..Jude bileaflet disc valve early after aortic valve replacement (AVR). We aimed to analyse St. Jude valve hemodynamic function and its clinical impact in the survivors of a prospective series 10 years after AVR for aortic stenosis...
  69. pmc Epitope mapping and topographic analysis of VAR2CSA DBL3X involved in P. falciparum placental sequestration
    Madeleine Dahlbäck
    Centre for Medical Parasitology, University of Copenhagen and Copenhagen University Hospital Rigshospitalet, Copenhagen, Denmark
    PLoS Pathog 2:e124. 2006
    ..These findings strengthen the vaccine candidacy of VAR2CSA and will be important for choosing epitopes and variants of DBL3X to be included in a vaccine protecting women against pregnancy-associated malaria...
  70. pmc The immune epitope database and analysis resource: from vision to blueprint
    Bjoern Peters
    La Jolla Institute of Allergy and Immunology, San Diego, California, USA
    PLoS Biol 3:e91. 2005