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1. Full Text NetMHC-3.0: accurate web accessible predictions of human, mouse and monkey MHC class I affinities for peptides of length 8-11
by Lundegaard, Claus and Lamberth, Kasper and Harndahl, Mikkel and Buus, Søren and Lund, Ole and Nielsen, Morten
Nucleic Acids Research, ISSN 0305-1048, 7/2008, Volume 36, Issue suppl_2, pp. W509 - W512
NetMHC-3.0 is trained on a large number of quantitative peptide data using both affinity data from the Immune Epitope Database and Analysis Resource (IEDB) and... 
BIOCHEMISTRY & MOLECULAR BIOLOGY | Peptides - chemistry | Humans | Peptides - immunology | Histocompatibility Antigens Class I - genetics | HLA Antigens - genetics | HLA Antigens - metabolism | Histocompatibility Antigens Class I - metabolism | Animals | Alleles | Epitopes - chemistry | Mice | Software | Internet | Haplorhini - genetics
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2. Trauma and healing under state terrorism
by Agger, Inger and Jensen, Sren Buus
1996, ISBN 1856493830, vii, 246
Torture victims | Psychological aspects | Victims of state-sponsored terrorism | Human rights advocacy | Government, Resistance to | Mental health
Book
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3. Full Text Accurate pan-specific prediction of peptide-MHC class II binding affinity with improved binding core identification
by Andreatta, Massimo and Karosiene, Edita and Rasmussen, Michael and Stryhn, Anette and Buus, Søren and Nielsen, Morten
Immunogenetics, ISSN 0093-7711, 11/2015, Volume 67, Issue 11, pp. 641 - 650
A key event in the generation of a cellular response against malicious organisms through the endocytic pathway is binding of peptidic antigens by major... 
Human Genetics | Gene Function | Allergology | Biomedicine | Immunology | Peptide binding | Artificial neural networks | T cell cross-reactivity | Binding core | MHC class II | Peptide-MHC | Cell Biology | TCR | PROTEIN | RECOGNITION | T-CELL EPITOPES | IMMUNOLOGY | HLA-DR | SEQUENCE | GENETICS & HEREDITY | CROSS-REACTIVITY | GENERATION | FLANKING RESIDUES | MOLECULAR-BASIS | Amino Acid Sequence | Computational Biology - methods | Peptide Fragments - metabolism | Humans | Models, Molecular | Molecular Sequence Data | Histocompatibility Antigens Class II - chemistry | Epitopes - immunology | Sequence Homology, Amino Acid | Peptide Fragments - chemistry | Algorithms | Animals | Histocompatibility Antigens Class II - immunology | Databases, Protein | Protein Binding | Histocompatibility Antigens Class II - metabolism | Mice | Binding Sites | Cluster Analysis | Neural Networks (Computer) | Chemical properties | Peptides | T cells | Neural networks | Analysis | Antigenic determinants | Tcell cross-reactivity
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4. Full Text Automated high-throughput mapping of linear B-cell epitopes using a statistical analysis of high-density peptide microarray data
by Østerbye, Thomas and Buus, Søren
Methods in Molecular Biology, ISSN 1064-3745, 2015, Volume 1348, pp. 215 - 228
Detailed information of antibodies' specificity is often missing or inadequate even for continuous (i.e., linear) epitopes. Recent developments in peptide... 
Eta square | Antibody epitope | Linear epitopes | Peptide chip | ANOVA | High-Throughput Screening Assays | Analysis of Variance | Peptides - chemistry | Position-Specific Scoring Matrices | Epitopes, B-Lymphocyte - chemistry | Peptides - immunology | Antigens - immunology | Epitope Mapping - methods | Epitopes, B-Lymphocyte - immunology | Antigens - chemistry | Protein Array Analysis - methods
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5. Sexuality and chronic illness
: a comprehensive approach
by Schover, Leslie R and Jensen, Søren Buus
1988, ISBN 089862715X, ix, 357
Sex Disorders | Sex Behavior | Chronic Disease | Sexual disorders | Chronically ill | Sexual behavior
Book
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6. Full Text 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
by Karosiene, Edita and Rasmussen, Michael and Blicher, Thomas and Lund, Ole and Buus, Søren and Nielsen, Morten
Immunogenetics, ISSN 0093-7711, 10/2013, Volume 65, Issue 10, pp. 711 - 724
Major histocompatibility complex class II (MHCII) molecules play an important role in cell-mediated immunity. They present specific peptides derived from... 
Human Genetics | Gene Function | Allergology | Biomedicine | Immunology | MHC binding specificity | Human leukocyte antigens | Artificial neural networks | T cell epitope | Peptide–MHC binding | MHC class II | Cell Biology | Peptide-MHC binding | PROTEIN | NETMHCPAN | PEPTIDE BINDING | IMMUNOLOGY | MOLECULES | DATABASE | SUPERTYPES | MATRICES | SEQUENCE | DISEASE | GENETICS & HEREDITY | Tcell epitope | EPITOPES | Protein Structure, Tertiary | Amino Acid Sequence | Computational Biology - methods | Reproducibility of Results | Protein Structure, Secondary | Histocompatibility Antigens Class II - classification | Humans | Models, Molecular | Molecular Sequence Data | HLA-DR Antigens - chemistry | HLA-DQ Antigens - immunology | HLA-DR Antigens - genetics | Sequence Homology, Amino Acid | HLA-DP Antigens - chemistry | HLA-DP Antigens - genetics | Histocompatibility Antigens Class II - immunology | HLA-DQ Antigens - genetics | HLA-DQ Antigens - chemistry | HLA-DR Antigens - immunology | Histocompatibility Antigens Class II - genetics | HLA-DP Antigens - immunology | Cluster Analysis | Histocompatibility antigens | Analysis | Methods | HLA histocompatibility antigens | Amino acid sequence
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7. Full Text MHC Class II epitope predictive algorithms
by Nielsen, Morten and Lund, Ole and Buus, Søren and Lundegaard, Claus
Immunology, ISSN 0019-2805, 07/2010, Volume 130, Issue 3, pp. 319 - 328
Major histocompatibility complex class II (MHC‐II) molecules sample peptides from the extracellular space, allowing the immune system to detect the presence of... 
epitope prediction | human leucocyte antigen | major histocompatibility complex class II | major histocompatibility complex peptide binding | T helper responses | Human leucocyte antigen | Epitope prediction | Major histocompatibility complex class II | Major histocompatibility complex peptide binding | MYCOBACTERIUM-TUBERCULOSIS | HLA-DR BINDING | TAP TRANSPORT EFFICIENCY | COMPLEX CLASS-II | T-CELL EPITOPES | ARTIFICIAL NEURAL-NETWORK | ANTIGEN PRESENTATION | IMMUNOLOGY | PEPTIDE BINDING PREDICTION | QUANTITATIVE PREDICTIONS | IN-SILICO PREDICTION | Epitopes - immunology | Computational Biology - methods | Animals | Epitopes - metabolism | Histocompatibility Antigens Class II - immunology | Humans | Histocompatibility Antigens Class II - metabolism | Epitopes - chemistry | Histocompatibility Antigens Class II - chemistry | Histocompatibility Antigens Class II - genetics | Epitopes - genetics | Protein Binding - immunology | Algorithms | Universities and colleges | Peptides | Analysis | Antigenic determinants | Methods | Review
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8. Full Text Improved methods for predicting peptide binding affinity to MHC class II molecules
by Jensen, Kamilla Kjærgaard and Andreatta, Massimo and Marcatili, Paolo and Buus, Søren and Greenbaum, Jason A and Yan, Zhen and Sette, Alessandro and Peters, Bjoern and Nielsen, Morten
Immunology, ISSN 0019-2805, 07/2018, Volume 154, Issue 3, pp. 394 - 406
Major histocompatibility complex class II ( MHC ‐ II ) molecules are expressed on the surface of professional antigen‐presenting cells where they display... 
binding specificity | peptide | affinity predictions | immunogenic peptides | MHC | binding | T‐cell epitope | peptide–MHC binding | MHC binding specificity | T-cell epitope | MYCOBACTERIUM-TUBERCULOSIS | HLA-DR BINDING | SIZE | T-CELL EPITOPES | HLA-DR1 | NETWORKS | IMMUNOLOGY | peptide-MHC binding | PAN-SPECIFIC PREDICTION | Histocompatibility antigens | Peptides | Analysis | HLA histocompatibility antigens | T cells | Methods | Antigenic determinants | Binding | Major histocompatibility complex | Immune response | Helper cells | Predictions | Affinity | Lymphocytes T | Histocompatibility antigen HLA | Epitopes | Histocompatibility | Molecular chains | Original
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9. Full Text Definition of supertypes for HLA molecules using clustering of specificity matrices
by Lund, Ole and Nielsen, Morten and Kesmir, Can and Petersen, Anders Gorm and Lundegaard, Claus and Worning, Peder and Sylvester-Hvid, Christina and Lamberth, Kasper and Røder, Gustav and Justesen, Sune and Buus, Søren and Brunak, Søren
Immunogenetics, ISSN 0093-7711, 3/2004, Volume 55, Issue 12, pp. 797 - 810
Major histocompatibility complex (MHC) proteins are encoded by extremely polymorphic genes and play a crucial role in immunity. However, not all genetically... 
Class I | Class II | LifeSciences | HLA | Supertype | Classification | Class I | Class II | class I | PEPTIDE-BINDING REPERTOIRES | MOTIFS | supertype | IMMUNOLOGY | classification | class II | PREDICTION | DATABASE | LIGANDS | GENETICS & HEREDITY | GENERATION | VACCINES | Markov Chains | Histocompatibility Antigens Class II - classification | Humans | Histocompatibility Antigens Class I - classification | Amino Acid Motifs | Cluster Analysis
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10. Full Text NetMHCpan, a method for MHC class I binding prediction beyond humans
by Hoof, Ilka and Peters, Bjoern and Sidney, John and Pedersen, Lasse Eggers and Sette, Alessandro and Lund, Ole and Buus, Søren and Nielsen, Morten
Immunogenetics, ISSN 0093-7711, 1/2009, Volume 61, Issue 1, pp. 1 - 13
Binding of peptides to major histocompatibility complex (MHC) molecules is the single most selective step in the recognition of pathogens by the cellular... 
Allergology | Gene Function | Human Genetics | CTL epitopes | Biomedicine | Immunology | Binding specificity | Artificial neural networks | MHC class I | Non-human primates | Cell Biology | SPECIFICITY | PEPTIDE-BINDING | MAJOR HISTOCOMPATIBILITY COMPLEX | IMMUNOLOGY | IDENTIFICATION | HLA-G | MOLECULES | RESPONSES | DATABASE | SEQUENCE | GENETICS & HEREDITY | Species Specificity | Humans | Macaca mulatta - immunology | HLA Antigens - genetics | Pan troglodytes - immunology | Histocompatibility Antigens Class I - metabolism | Sus scrofa - genetics | Gorilla gorilla - genetics | Computer Simulation | Protein Interaction Domains and Motifs | Epitopes, T-Lymphocyte - immunology | Gorilla gorilla - immunology | Neural Networks (Computer) | Amino Acid Sequence | Oligopeptides - immunology | Histocompatibility Antigens Class I - immunology | Pan troglodytes - genetics | HLA Antigens - immunology | Oligopeptides - metabolism | HLA Antigens - metabolism | Protein Interaction Mapping | Epitopes, T-Lymphocyte - chemistry | Algorithms | Animals | Models, Biological | Macaca mulatta - genetics | Protein Binding | Genes, MHC Class I | Mice | Immunity, Cellular | Sus scrofa - immunology | Epitopes, T-Lymphocyte - metabolism | Histocompatibility antigens | Peptides | Neural networks | Analysis | HLA histocompatibility antigens | Gorillas | Chemical properties | Universities and colleges | T cells | Methods | Medical research | Immune system
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11. Full Text Peptide-MHC class I stability is a better predictor than peptide affinity of CTL immunogenicity
by Harndahl, Mikkel and Rasmussen, Michael and Roder, Gustav and Dalgaard Pedersen, Ida and Sørensen, Mikael and Nielsen, Morten and Buus, Søren
European Journal of Immunology, ISSN 0014-2980, 06/2012, Volume 42, Issue 6, pp. 1405 - 1416
Efficient presentation of peptide-MHC class I (pMHC-I) complexes to immune T cells should benefit from a stable peptide-MHC-I interaction. However, it has been... 
MHC | Stability | Dissociation | Immunogenicity | Peptide | IMMUNODOMINANCE | FLUORESCENCE POLARIZATION | T-CELL EPITOPES | IMMUNOLOGY | MOLECULES | COMPLEX STABILITY | GENOME-WIDE | SURFACE-PLASMON RESONANCE | QUANTITATIVE PREDICTIONS | KINETIC STABILITY | REAL-TIME | T-Lymphocytes, Cytotoxic - immunology | Antigen Presentation | Peptides - chemistry | Humans | Computational Biology | Histocompatibility Antigens Class I - immunology | Protein Stability | Histocompatibility Antigens Class I - chemistry | Peptides | Antigen presentation
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12. Full Text Major histocompatibility complex class I binding predictions as a tool in epitope discovery
by Lundegaard, Claus and Lund, Ole and Buus, Søren and Nielsen, Morten
Immunology, ISSN 0019-2805, 07/2010, Volume 130, Issue 3, pp. 309 - 318
Over the last decade, in silico models of the major histocompatibility complex (MHC) class I pathway have developed significantly. Before, peptide binding... 
epitope prediction | major histocompatibility complex–peptide binding | human leucocyte antigen | cytotoxic T lymphocytes | major histocompatibility complex class I | Major histocompatibility complex class I | Major histocompatibility complex-peptide binding | Human leucocyte antigen | Epitope prediction | Cytotoxic T lymphocytes | DENDRITIC CELLS | TAP TRANSPORT EFFICIENCY | T-CELL EPITOPES | IMMUNOLOGY | SPECIFICITY MATRICES | major histocompatibility complex-peptide binding | MHC CLASS-I | PROTEASOMAL CLEAVAGE | IMMUNOGENIC PEPTIDES | CTL EPITOPES | PEPTIDE-LOADING COMPLEX | QUANTITATIVE PREDICTIONS | Epitopes, T-Lymphocyte - chemistry | Histocompatibility Antigens Class I - metabolism | Computational Biology - methods | Animals | Humans | Histocompatibility Antigens Class I - immunology | Epitopes, T-Lymphocyte - immunology | Histocompatibility Antigens Class I - chemistry | Protein Binding - immunology | Epitopes, T-Lymphocyte - metabolism | Major histocompatibility complex | Peptides | Primates | Chemical properties | Universities and colleges | T cells | Antigenic determinants | Protein binding | Review
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13. Full Text Reliable prediction of T‐cell epitopes using neural networks with novel sequence representations
by Nielsen, Morten and Lundegaard, Claus and Worning, Peder and Lauemøller, Sanne Lise and Lamberth, Kasper and Buus, Søren and Brunak, Søren and Lund, Ole
Protein Science, ISSN 0961-8368, 05/2003, Volume 12, Issue 5, pp. 1007 - 1017
In this paper we describe an improved neural network method to predict T‐cell class I epitopes. A novel input representation has been developed consisting of a... 
artificial neural network | sequence encoding | mutual information | hidden Markov model | HLA‐A2 | T‐cell class I epitope | Hidden Markov model | Artificial neural network | HLA-A2 | T-cell class I epitope | Sequence encoding | Mutual information | MOTIFS | SPECIFICITY | BIOCHEMISTRY & MOLECULAR BIOLOGY | ALGORITHMS | HIDDEN MARKOV-MODELS | LIGANDS | DATABASE | MATRICES | CLASS-I MOLECULES | MHC MOLECULES | BINDING PEPTIDES
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14. Full Text NetMHCstab – predicting stability of peptide–MHC‐I complexes; impacts for cytotoxic T lymphocyte epitope discovery
by Jørgensen, Kasper W and Rasmussen, Michael and Buus, Søren and Nielsen, Morten
Immunology, ISSN 0019-2805, 01/2014, Volume 141, Issue 1, pp. 18 - 26
Major histocompatibility complex class I ( MHC ‐I) molecules play an essential role in the cellular immune response, presenting peptides to cytotoxic T... 
lymphocyte epitopes | MHC | immunoinformatics | peptide stability | peptide immunogenicity | cytotoxic | Cytotoxic T lymphocyte epitopes | MHC-peptide stability | Peptide immunogenicity | Immunoinformatics | IMMUNODOMINANCE | MOTIFS | SPECIFICITY | RESTRICTION | IMMUNOLOGY | cytotoxic T lymphocyte epitopes | DATABASE | SUPERTYPES | AFFINITY | DIVERSITY | BINDING | TOOL | Models, Immunological | Humans | Peptides - immunology | Histocompatibility Antigens Class I - immunology | Peptides - genetics | Histocompatibility Antigens Class I - genetics | Epitopes, T-Lymphocyte - immunology | Internet | CD8-Positive T-Lymphocytes - immunology | Neural Networks (Computer) | Proteins | Histocompatibility antigens | T cells | Neural networks | HLA histocompatibility antigens | Antigenic determinants | Cytotoxicity | Ligands | Peptides | MHC–peptide stability | Original
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