Ole Lund
- 2013
- Published
Bioinformatics Identification of Antigenic Peptide: Predicting the Specificity of Major MHC Class I and II Pathway Players.. / Lund, Ole; Karosiene, Edita; Lundegaard, Claus; Larsen, Mette Voldby; Nielsen, Morten.
In: Antigen Processing : Methods and Protocols. 2013. p. 247-260 (Methods in Molecular Biology, Vol. 960).Publication: Research - peer-review › Book chapter – Annual report year: 2013
- Published
ChemProt-2.0: visual navigation in a disease chemical biology database. / Kjærulff, Sonny Kim; Wich, Louis; Kringelum, Jens Vindahl; Jacobsen, Ulrik Plesner; Kouskoumvekaki, Irene; Audouze, Karine Marie Laure; Lund, Ole; Brunak, Søren; Oprea, Tudor; Taboureau, Olivier .
In: Nucleic Acids Research, Vol. 41, No. D1, 2013, p. D464-D469.Publication: Research - peer-review › Journal article – Annual report year: 2013
- Published
Genotyping using whole-genome sequencing is a realistic alternative to surveillance based on phenotypic antimicrobial susceptibility testing. / Zankari, Ea; Hasman, Henrik; Kaas, Rolf Sommer; Seyfarth, Anne Mette; Agersø, Yvonne; Lund, Ole; Larsen, Mette Voldby; Aarestrup, Frank Møller.
In: Journal of Antimicrobial Chemotherapy, Vol. 68, No. 4, 2013, p. 771-777.Publication: Research - peer-review › Journal article – Annual report year: 2012
- Published
Identification of Y-Chromosomally Encoded Minor Histocompatibility Antigens Using a Reverse Immunology Approach. / Mortensen, Bo Kok; Brændstrup, Peter; Larsen, Malene Erup; Larsen, Mette Voldby; Lund, Ole; Rasmussen, Michael; Buus, Søren; Stryhn, Anette; Vindeløv, Lars.
In: Biology of Blood and Marrow Transplantation, Vol. 19, No. 2, 2013, p. S335.Publication: Research - peer-review › Conference abstract in journal – Annual report year: 2013
- Published
Structural analysis of B-cell epitopes in antibody:protein complexes. / Kringelum, Jens Vindahl; Nielsen, Morten; Padkjær, Søren Berg; Lund, Ole.
In: Molecular Immunology, Vol. 53, No. 1-2, 2013, p. 24-34.Publication: Research - peer-review › Journal article – Annual report year: 2012
- 2012
- Published
Characterization of HIV-Specific CD4+T Cell Responses against Peptides Selected with Broad Population and Pathogen Coverage. / Buggert, Marcus; Norstrom, Melissa M.; Czarnecki, Chris; Tupin, Emmanuel; Luo, Ma; Gyllensten, Katarina; Sonnerborg, Anders; Lundegaard, Claus; Lund, Ole; Nielsen, Morten; Karlsson, Annika C.
In: P L o S One, Vol. 7, No. 7, 2012.Publication: Research - peer-review › Journal article – Annual report year: 2012
- Published
Concepts in Mechanism Based Modeling. / Lund, Ole; Laugesen, Jakob Lund; Mosekilde, Erik.
In: Biosimulation in Biomedical Research, Health Care and Drug Development. Springer-Verlag/Wien, 2012. p. 19-41.Publication: Research - peer-review › Book chapter – Annual report year: 2012
- Published
Identification of acquired antimicrobial resistance genes. / Zankari, Ea; Hasman, Henrik; Cosentino, Salvatore; Vestergaard, Martin; Rasmussen, Simon; Lund, Ole; Aarestrup, Frank Møller; Larsen, Mette Voldby.
In: Journal of Antimicrobial Chemotherapy, Vol. 67, No. 11, 2012, p. 2640-2644.Publication: Research - peer-review › Journal article – Annual report year: 2012
- Published
Identification of a Novel UTY‐Encoded Minor Histocompatibility Antigen. / Mortensen, B. K.; Rasmussen, A. H.; Larsen, Malene Erup; Larsen, Mette Voldby; Lund, Ole; Braendstrup, P.; Harndahl, Mikkel Nors; Rasmussen, M.; Buus, S.; Stryhn, A.; Vindeløv, Lars.
In: Scandinavian Journal of Immunology, Vol. 76, No. 2, 2012, p. 141-150.Publication: Research - peer-review › Journal article – Annual report year: 2012
- Published
Immune epitope database analysis resource. / Kim, Yohan; Ponomarenko, Julia; Zhu, Zhanyang; Tamang, Dorjee; Wang, Peng; Greenbaum, Jason; Lundegaard, Claus; Sette, Alessandro; Lund, Ole; Bourne, Philip E.; Nielsen, Morten; Peters, Bjoern.
In: Nucleic Acids Research, Vol. 40, No. W1, 2012, p. W525-W530.Publication: Research - peer-review › Journal article – Annual report year: 2012
- Published
Multilocus Sequence Typing of Total-Genome-Sequenced Bacteria. / Larsen, Mette Voldby; Cosentino, Salvatore; Rasmussen, Simon; Rundsten, Carsten Friis; Hasman, Henrik; Marvig, Rasmus Lykke; Jelsbak, Lars; Sicheritz-Pontén, Thomas; Ussery, David W.; Aarestrup, Frank M.; Lund, Ole.
In: Journal of Clinical Microbiology, Vol. 50, No. 4, 2012, p. 1355-1361.Publication: Research - peer-review › Journal article – Annual report year: 2012
- Published
Mycobacterium leprae virulence-associated peptides are indicators of exposure to M. leprae in Brazil, Ethiopia and Nepal. / Bobosha, Kidist; Tang, Sheila Tuyet; van der Ploeg-van Schip, Jolien J.; Bekele, Yonas; Martins, Marcia V. S. B.; Lund, Ole; Franken, Kees L. M. C.; Khadge, Saraswoti; de Andrade Pontes, Maria Araci; Goncalves, Heitor de Sa; Hussien, Jemal; Thapa, Pratibha; Kunwar, Chhatra B.; Hagge, Deanna A.; Aseffa, Abraham; Vidal Pessolani, Maria Cristina; Pereira, Geraldo M. B.; Ottenhoff, Tom H. M.; Geluk, Annemieke.
In: Instituto Oswaldo Cruz, Rio de Janeiro. Memorias, Vol. 107, 2012, p. 112-123.Publication: Research - peer-review › Journal article – Annual report year: 2013
- Published
NetMHCcons: a consensus method for the major histocompatibility complex class I predictions. / Karosiene, Edita; Lundegaard, Claus; Lund, Ole; Nielsen, Morten.
In: Immunogenetics, Vol. 64, No. 3, 2012, p. 177-186.Publication: Research - peer-review › Journal article – Annual report year: 2012
- Published
Predictions versus high-throughput experiments in T-cell epitope discovery: competition or synergy?. / Lundegaard, Claus; Lund, Ole; Nielsen, Morten.
In: Expert Review of Vaccines, Vol. 11, No. 1, 2012, p. 43.Publication: Research - peer-review › Journal article – Annual report year: 2012
- Published
Reliable B cell epitope predictions: impacts of method development and improved benchmarking.. / Kringelum, Jens Vindahl; Lundegaard, Claus; Lund, Ole; Nielsen, Morten.
In: P L o S Computational Biology, Vol. 8, No. 12, 2012, p. e1002829.Publication: Research - peer-review › Journal article – Annual report year: 2012
- Published
Targeting of conserved Gag-epitopes in early HIV infection is associated with lower plasma viral load and slower CD4+ T cell depletion. / Pérez, Carina L, Dr.; Milush, Jeffrey M, Dr.; Buggert, Marcus, Dr.; Eriksson, Emily, Dr.; Larsen, Mette Voldby; Liegler, Teri; Hartogensis, Wendy, Dr.; Bacchetti, Peter, Dr.; Lund, Ole; Hecht, Frederick, Dr.; Nixon, Douglas, Dr.; Karlsson, Annika C, Dr.
In: AIDS Research and Human Retroviruses, No. ja, 2012, p. 1-38.Publication: Research - peer-review › Journal article – Annual report year: 2012
- Published
The Cancer Exome Generated by Alternative mRNA Splicing Dilutes Predicted HLA Class I Epitope Density. / Stranzl, Thomas; Larsen, Mette Voldby; Lund, Ole; Nielsen, Morten; Brunak, Søren.
In: P L o S One, Vol. 7, No. 9, 2012, p. e38670.Publication: Research - peer-review › Journal article – Annual report year: 2012
- 2011
- Published
An Aboriginal Australian Genome Reveals Separate Human Dispersals into Asia. / Rasmussen, Morten; Guo, Xiaosen; Wang, Yong; Lohmueller, Kirk E.; Rasmussen, Simon; Albrechtsen, Anders; Skotte, Line; Lindgreen, Stinus; Metspalu, Mait; Jombart, Thibaut; Kivisild, Toomas; Zhai, Weiwei; Eriksson, Anders; Manica, Andrea; Orlando, Ludovic; De La Vega, Francisco M.; Tridico, Silvana; Metspalu, Ene; Nielsen, Kasper; Ávila-Arcos, María C.; Moreno-Mayar, J. Víctor; Muller, Craig; Dortch, Joe; Gilbert, M. Thomas P.; Lund, Ole; Wesolowska, Agata; Karmin, Monika; Weinert, Lucy A.; Wang, Bo; Li, Jun; Tai, Shuaishuai; Xiao, Fei; Hanihara, Tsunehiko; van Driem, George; Jha, Aashish R.; Ricaut, François-Xavier; de Knijff, Peter; Migliano, Andrea B; Gallego Romero, Irene; Kristiansen, Karsten; Lambert, David M.; Brunak, Søren; Forster, Peter; Brinkmann, Bernd; Nehlich, Olaf; Bunce, Michael; Richards, Michael; Gupta, Ramneek; Bustamante, Carlos D.; Krogh, Anders; Foley, Robert A.; Lahr, Marta M.; Balloux, Francois; Sicheritz-Pontén, Thomas; Villems, Richard; Nielsen, Rasmus; Wang, Jun; Willerslev, Eske.
In: Science, Vol. 334, No. 6052, 2011, p. 94-98.Publication: Research - peer-review › Journal article – Annual report year: 2011
- Published
Bistability in autoimmune diseases. / Rapin, Nicolas; Mosekilde, Erik; Lund, Ole.
In: Autoimmunity, Vol. 44, No. 4, 2011, p. 256-260.Publication: Research - peer-review › Journal article – Annual report year: 2011
- Published
Genome-Based In Silico Identification of New Mycobacterium tuberculosis Antigens Activating Polyfunctional CD8+ T Cells in Human Tuberculosis. / Tang, Sheila Tuyet; van Meijgaarden, Krista E.; Caccamo, Nadia; Guggino, Giuliana; Klein, Michel R.; van Weeren, Pascale; Kazi, Fatima; Stryhn, Anette; Zaigler, Alexander; Sahin, Ugur; Buus, Søren; Dieli, Francesco; Lund, Ole; Ottenhoff, Tom H. M.
In: Journal of Immunology, Vol. 186, No. 2, 2011, p. 1068-1080.Publication: Research - peer-review › Journal article – Annual report year: 2011
- Published
Human Leukocyte Antigen (HLA) Class I Restricted Epitope Discovery in Yellow Fewer and Dengue Viruses: Importance of HLA Binding Strength.. / Lund, Ole; Nascimento, Eduardo J. M.; Maciel, Milton, Jr; Nielsen, Morten; Larsen, Mette Voldby; Lundegaard, Claus; Harndahl, Mikkel; Lamberth, Kasper; Buus, Søren; Salmon, Jérôme; August, Thomas J.; Marques, Ernesto T A, Jr.
In: P L o S One, Vol. 6, No. 10, 2011, p. e26494.Publication: Research - peer-review › Journal article – Annual report year: 2011
- Published
Identification of MHC class II restricted T‐cell‐mediated reactivity against MHC class I binding Mycobacterium tuberculosis peptides. / Wang, Mingjun; Tang, Sheila Tuyet; Stryhn, Anette; Justesen, Sune; Larsen, Mette Voldby; Dziegiel, Morten H.; Lewinsohn, David M.; Buus, Søren; Lund, Ole; Claesson, Mogens H.
In: Immunology, Vol. 132, No. 4, 2011, p. 482-491.Publication: Research - peer-review › Journal article – Annual report year: 2011
- Published
Immune system simulation online. / Rapin, Nicolas; Lund, Ole; Castiglione, Filippo.
In: Bioinformatics, Vol. 27, No. 14, 2011, p. 2013-2014.Publication: Research - peer-review › Journal article – Annual report year: 2011
- Published
Interdisciplinary Evaluation of Broadly-Reactive HLA Class II Restricted Epitopes Eliciting HIV-Specific CD4+T Cell Responses : Abstract of poster presentation. / Buggert, M.; Norström, M.; Lundegaard, Claus; Lund, Ole; Nielsen, Morten; Karlsson, A. C.
In: AIDS RESEARCH AND HUMAN RETROVIRUSES, Vol. 27, No. 10, 2011, p. A88-A88.Publication: Research - peer-review › Conference article – Annual report year: 2011
- Published
Machine learning competition in immunology – Prediction of HLA class I binding peptides. / Zhang, Guang Lan; Ansari, Hifzur Rahman; Bradley, Phil; Cawley, Gavin C.; Hertz, Tomer; Hu, Xihao; Jojic, Nebojsa; Kim, Yohan; Kohlbacher, Oliver; Lund, Ole; Lundegaard, Claus; Magaret, Craig A.; Nielsen, Morten; Papadopoulos, Harris; Raghava, G.P.S.; Tal, Vider-Shalit; Xue, Li C.; Yanover, Chen; Zhu, Shanfeng; Rock, Michael T.; Crowe, James E.; Panayiotou, Christos; Polycarpou, Marios M.; Duch, Włodzisław; Brusic, Vladimir.
In: Journal of Immunological Methods, Vol. 374, No. 1-2, 2011, p. 1-4.Publication: Research - peer-review › Journal article – Annual report year: 2012
- Published
MULTIPRED2: A computational system for large-scale identification of peptides predicted to bind to HLA supertypes and alleles. / Zhang, Guang Lan; DeLuca, David S.; Keskin, Derin B.; Chitkushev, Lou; Zlateva, Tanya; Lund, Ole; Reinherz, Ellis L.; Brusic, Vladimir.
In: Journal of Immunological Methods, Vol. 374, No. 1-2, 2011, p. 53-61.Publication: Research - peer-review › Journal article – Annual report year: 2011
- Published
NNAlign: A Web-Based Prediction Method Allowing Non-Expert End-User Discovery of Sequence Motifs in Quantitative Peptide Data. / Andreatta, Massimo; Schafer-Nielsen, Claus; Lund, Ole; Buus, Søren; Nielsen, Morten.
In: P L o S One, Vol. 6, No. 11, 2011, p. e26781.Publication: Research - peer-review › Journal article – Annual report year: 2011
- Published
Porcine major histocompatibility complex (MHC) class I molecules and analysis of their peptide-binding specificities. / Pedersen, Lasse Eggers; Harndahl, Mikkel; Rasmussen, Michael; Lamberth, Kasper; Golde, William T.; Lund, Ole; Nielsen, Morten; Buus, Soren.
In: Immunogenetics, Vol. 63, No. 12, 2011, p. 821-834.Publication: Research - peer-review › Journal article – Annual report year: 2011
- Published
Prediction of epitopes using neural network based methods. / Lundegaard, Claus; Lund, Ole; Nielsen, Morten.
In: Journal of Immunological Methods, Vol. 374, No. 1-2, 2011, p. 26-34.Publication: Research - peer-review › Journal article – Annual report year: 2010
- 2010
- Published
Computational Immunology Meets Bioinformatics: The Use of Prediction Tools for Molecular Binding in the Simulation of the Immune System. / Rapin, N.; Lund, Ole; Bernaschi, M.; Castiglione, F.
In: P L o S One, Vol. 5, No. 4, 2010.Publication: Research - peer-review › Journal article – Annual report year: 2010
- Published
CPHmodels-3.0--remote homology modeling using structure-guided sequence profiles. / Nielsen, Morten; Lundegaard, Claus; Lund, Ole; Petersen, Thomas Nordahl.
In: Nucleic Acids Research, Vol. 38, 2010, p. W576-W581.Publication: Research - peer-review › Journal article – Annual report year: 2010
- Published
Degree of Predicted Minor Histocompatibility Antigen Mismatch Correlates with Poorer Clinical Outcomes of Nonmyeloablative Allogeneic Hematopoietic Cell Transplantation. / Larsen, Malene Erup; Kornblit, B; Larsen, Mette Voldby; Masmas, TN; Nielsen, Morten; Thiim, Martin Hansen; Garred, P; Stryhn, A; Lund, Ole; Buus, S; Vindelov, L.
In: Blood & Marrow Transplant Newsletter, Vol. 16, No. 10, 2010.Publication: Research - peer-review › Journal article – Annual report year: 2010
- Published
HLA Class I Binding 9mer Peptides from Influenza A Virus Induce CD4(+) T Cell Responses. / Wang, M. J.; Larsen, Mette Voldby; Nielsen, Morten; Harndahl, M.; Justesen, S.; Dziegiel, M.H.; Buus, S.; Tang, Sheila Tuyet; Lund, Ole; Claesson, M.H.
In: P L o S One, Vol. 5, No. 5, 2010, p. e10533.Publication: Research - peer-review › Journal article – Annual report year: 2010
- Published
Identification of CD8(+) T Cell Epitopes in the West Nile Virus Polyprotein by Reverse-Immunology Using NetCTL. / Larsen, Mette Voldby; Lelic, A.; Parsons, R.; Nielsen, Morten; Hoof, I.; Lamberth, K.; Loeb, M.B.; Buus, S.; Bramson, J.; Lund, Ole.
In: P L o S One, Vol. 5, No. 9, 2010.Publication: Research - peer-review › Journal article – Annual report year: 2010
- Published
ImmunoGrid: towards agent-based simulations of the human immune system at a natural scale. / Halling-Brown, M.; Pappalardo, F.; Rapin, Nicolas; Zhang, P.; Alemani, D.; Emerson, A.; Castiglione, F.; Duroux, P.; Pennisi, M.; Miotto, O.; Churchill, D.; Rossi, E.; Moss, D.S.; Sansom, C.E.; Bernaschi, M.; Lefranc, M.P.; Brunak, Søren; Lund, Ole; Motta, S.; Lollini, P.L.; Murgo, A.; Palladini, A.; Basford, K.E.; Brusic, V.; Shepherd, A.J.
In: Royal Society of London. Philosophical Transactions. Mathematical, Physical and Engineering Sciences, Vol. 368, No. 1920, 2010, p. 2799-2815.Publication: Research - peer-review › Journal article – Annual report year: 2010
- Published
Insight into Antigenic Diversity of VAR2CSA-DBL5 epsilon Domain from Multiple Plasmodium falciparum Placental Isolates. / Gnidehou, Sedami; Jessen, Leon Ivar; Gangnard, Stephane; Ermont, Caroline; Triqui, CHoukri; Quiviger, Mickael; Guitard, Juliette; Lund, Ole; Deloron, Philippe; Ndam, Nicaise Tuikue.
In: P L o S One, Vol. 5, No. 10, 2010, p. e13105.Publication: Research - peer-review › Journal article – Annual report year: 2010
- Published
In Silico Prediction of Human Pathogenicity in the gamma-Proteobacteria. / Andreatta, Massimo; Nielsen, Morten; Aarestrup, Frank Møller; Lund, Ole.
In: P L o S One, Vol. 5, No. 10, 2010.Publication: Research - peer-review › Journal article – Annual report year: 2010
- Published
Interdisciplinary Analysis of HIV-Specific CD8(+) T Cell Responses against Variant Epitopes Reveals Restricted TCR Promiscuity. / Hoof, Ilka; Perez, C.L.; Buggert, M.; Gustafsson, R.K.L.; Nielsen, Morten; Lund, Ole; Karlsson, A.C.
In: Journal of Immunology, Vol. 184, No. 9, 2010, p. 5383-5391.Publication: Research - peer-review › Journal article – Annual report year: 2010
- Published
Limitations of Ab Initio Predictions of Peptide Binding to MHC Class II Molecules. / Zhang, Hao; Lund, Ole; Nielsen, Morten; Wang, P; Papangelopoulos, N; Xu, Y; Sette, A; Bourne, PE; Ponomarenko, J; Peters, B.
In: P L o S One, Vol. 5, No. 2, 2010, p. e9272.Publication: Research - peer-review › Journal article – Annual report year: 2010
- Published
Major histocompatibility complex class I binding predictions as a tool in epitope discovery. / Lundegaard, Claus; Lund, Ole; Buus, Søren; Nielsen, Morten.
In: Immunology, Vol. 130, No. 3, 2010, p. 309-318.Publication: Research - peer-review › Journal article – Annual report year: 2010
- Published
MHC Class II epitope predictive algorithms. / Nielsen, Morten; Lund, Ole; Buus, S; Lundegaard, Claus.
In: Immunology, Vol. 130, No. 3, 2010, p. 319-328.Publication: Research - peer-review › Journal article – Annual report year: 2010
- Published
NetMHCIIpan-2.0 - Improved pan-specific HLA-DR predictions using a novel concurrent alignment and weight optimization training procedure. / Nielsen, Morten; Justesen, Sune Frederik Lamdahl; Lund, Ole; Lundegaard, Claus; Buus, S.
In: Immunome Research, 2010, p. 21073747.Publication: Research - peer-review › Journal article – Annual report year: 2010
- Published
Peptide binding predictions for HLA DR, DP and DQ molecules. / Wang, P.; Sidney, J.; Kim, Y.; Sette, A.; Lund, Ole; Nielsen, Morten; Peters, B.
In: B M C Bioinformatics, Vol. 568, No. 11, 2010.Publication: Research - peer-review › Journal article – Annual report year: 2010
- Published
Plasmodium falciparum population dynamics in a cohort of pregnant women in Senegal. / Guitard, Juliette; Andersen, Pernille; Ermont, Caroline; Gnidehou, Sedami; Fievet, Nadine; Lund, Ole; Deloron, Philippe; Ndam, Nicaise Tuikue.
In: Malaria Journal, Vol. 9, No. 165, 2010.Publication: Research - peer-review › Journal article – Annual report year: 2010
- Published
State of the art and challenges in sequence based T-cell epitope prediction. / Lundegaard, Claus; Hoof, Ilka; Lund, Ole; Nielsen, Morten.
In: Immunome Research, Vol. 3, No. 6, 2010, p. 21067545.Publication: Research - peer-review › Journal article – Annual report year: 2010
- Published
The MHC motif viewer: a visualization tool for MHC binding motifs. / Rapin, Nicolas; Hoof, Ilka; Lund, Ole; Nielsen, Morten.
In: Current Protocols in Immunology, 2010.Publication: Research - peer-review › Journal article – Annual report year: 2010
- 2009
- Published
Degenerate Peptide Specificity of MHC Molecules and T cell Receptors in Immunodominance and Tolerance. / Pletscher-Frankild, Sune; Lundegaard, Claus (Supervisor); Lund, Ole (Supervisor).
Kgs. Lyngby, Denmark : Technical University of Denmark (DTU), 2009.Publication: Research › Ph.d. thesis – Annual report year: 2009
- Published
Bioinformatics and simulation of the immune system. / Rapin, Nicolas; Brunak, Søren (Supervisor); Lund, Ole (Supervisor).
Kgs. Lyngby, Denmark : Technical University of Denmark (DTU), 2009.Publication: Research › Ph.d. thesis – Annual report year: 2009
- Published
Prediction and analysis of MHC class I binding specificities beyond humans. / Hoof, Ilka; Lund, Ole (Supervisor).
Kgs. Lyngby, Denmark : Technical University of Denmark (DTU), 2009.Publication: Research › Ph.d. thesis – Annual report year: 2009
- Published
Genome - and HLA-Wide Scanning and Validation of Cytotoxic CD8+ T Cell Responses in Bacterial and Viral Pathogens. / Tang, Sheila Tuyet; Lundegaard, Claus (Supervisor); Lund, Ole (Supervisor).
Kgs. Lyngby, Denmark : Technical University of Denmark (DTU), 2009.Publication: Research › Ph.d. thesis – Annual report year: 2009
- Published
Full genome sequence of a Danish isolate of Mycobacterium avium subspecies paratuberculosis, strain Ejlskov2007. / Afzal, Mamuna; Abidi, Soad; Mikkelsen, Heidi; Tang, Sheila Tuyet; Lund, Ole; Nielsen, Morten; Lundegaard, Claus; Jungersen, Gregers; Ussery, David.
2009. Poster session presented at 10th International Colloquium on Paratuberculosis, Minneapolis, MN, United States.Publication: Research › Poster – Annual report year: 2009
- Published
High-affinity human leucocyte antigen class I binding variola-derived peptides induce CD4(+) T cell responses more than 30 years post-vaccinia virus vaccination. / Wang, M.; Tang, Sheila Tuyet; Lund, Ole; Dziegiel, M. H.; Buus, S.; Claesson, M. H.
In: Clinical and Experimental Immunology, Vol. 155, No. 3, 2009, p. 441-446.Publication: Research - peer-review › Journal article – Annual report year: 2009
- Published
In-Silico identification of peptides for the diagnostics of paratuberculosis.. / Tang, Sheila Tuyet; Lund, Ole; Jungersen, Gregers; Nielsen, Morten; Mikkelsen, Heidi; Lundegaard, Claus.
2009. Poster session presented at 10th International Colloquium on Paratuberculosis, Minneapolis, MN, United States.Publication: Research › Poster – Annual report year: 2009
- Published
NetMHCpan, a method for MHC class I binding prediction beyond humans.. / Hoof, Ilka; Peters, B; Sidney, J; Pedersen, Lasse Eggers; Sette, A; Lund, Ole; Buus, Søren; Nielsen, Morten.
In: Immunogenetics, Vol. 61, No. 1, 2009, p. 1-13.Publication: Research - peer-review › Journal article – Annual report year: 2009
- Published
New-generation vaccines : Combining immunology with oganic chemistry and bioinformatics in engineering challanges. / Heegaard, Peter M. H.; Lund, Ole.
In: Engineering challenges: energy, climate change & health. Kgs.Lyngby : Technical University of Denmark, 2009. p. 210-221 (DTU research series).Publication: Research › Book chapter – Annual report year: 2009
- Published
NN-align. An artificial neural network-based alignment algorithm for MHC class II peptide binding prediction. / Nielsen, Morten; Lund, Ole.
In: B M C Bioinformatics, Vol. 10, 2009, p. 296.Publication: Research - peer-review › Journal article – Annual report year: 2009
- Published
Systematic Characterisation of Cellular Localisation and Expression Profiles of Proteins Containing MHC Ligands. / Juncker, Agnieszka; Larsen, Mette Voldby; Weinhold, Nils; Nielsen, Morten; Brunak, Søren; Lund, Ole.
In: P L o S One, Vol. 4, No. 10, 2009.Publication: Research - peer-review › Journal article – Annual report year: 2009
- Published
The PickPocket method for predicting binding specificities for receptors based on receptor pocket similarities: application to MHC-peptide binding. / Zhang, H.; Lund, Ole; Nielsen, M.
In: Bioinformatics, Vol. 25, No. 10, 2009, p. 1293-1299.Publication: Research - peer-review › Journal article – Annual report year: 2009
- 2008
- Published
Accurate approximation method for prediction of class I MHC affinities for peptides of length 8, 10 and 11 using prediction tools trained on 9mers. / Lundegaard, Claus; Lund, Ole; Nielsen, Morten.
In: Bioinformatics, Vol. 24, No. 11, 2008, p. 1397-1398.Publication: Research - peer-review › Journal article – Annual report year: 2008
- Published
Amino acid similarity accounts for T cell cross-reactivity and for "holes" in the T cell repertoire. / Pletscher-Frankild, Sune; de Boer, Rob J.; Lund, Ole; Nielsen, Morten; Kesmir, Can.
In: PLoS ONE, Vol. 3, No. 3, 2008, p. e1831.Publication: Research - peer-review › Journal article – Annual report year: 2008
- Published
Broadly Immunogenic HLA Class I Supertype-Restricted Elite CTL Epitopes Recognized in a Diverse Population Infected with Different HIV-1 Subtypes. / Pérez, Carina L; Larsen, Mette Voldby; Gustafsson, Rasmus; Norström, Melissa M; Atlas, Ann; Nixon, Douglas F; Nielsen, Morten; Lund, Ole; Karlsson, Annika C.
In: Journal of Immunology, Vol. 180, No. 7, 2008, p. 5092-5100.Publication: Research - peer-review › Journal article – Annual report year: 2008
- Published
Epitope mapping and analysis of sequence variation in VAR2CSA DBL3X involved in P-falciparum placental sequestration. / Rask, Thomas Salhøj; Dahlback, Madeleine; Andersen, Pernille H.; Nielsen, Morten A.; Ndam, Nicaise T.; Resende, Mafalda; Turner, Louise; Deloron, Philippe; Hviid, Lars; Lund, Ole; Pedersen, Anders Gorm; Theander, Thor G.; Salanti, Ali.
In: Infection Genetics and Evolution, Vol. 8, No. 4, 2008, p. S17-S18.Publication: Research - peer-review › Conference abstract in journal – Annual report year: 2008
- Published
Humans with chimpanzee-like major histocompatibility complex-specificities control HIV-1 infection. / Hoof, Ilka; Kesmir, Can; Lund, Ole; Nielsen, Morten.
In: AIDS, Vol. 22, No. 11, 2008, p. 1299-303.Publication: Research - peer-review › Journal article – Annual report year: 2008
- Published
Immune epitope database analysis resource (IEDB-AR). / Zhang, Qing; Wang, Peng; Kim, Yohan; Andersen, Pernille; Beaver, John; Bourne, Philip; Bui, Huynh-Hoa; Buus, Søren; Pletscher-Frankild, Sune; Greenbaum, Jason; Lund, Ole; Lundegaard, Claus; Nielsen, Morten; Ponomarenko, Julia; Sette, Alessandro; Zhu, Zhanyang; Peters, Bjoern.
In: Nucleic Acids Research, Vol. W36, 2008, p. W513-W518.Publication: Research - peer-review › Journal article – Annual report year: 2008
- Published
MHC-I-restricted epitopes conserved among variola and other related orthopoxviruses are recognized by T cells 30 years after vaccination. / Tang, Sheila Tuyet; Wang, M.; Lamberth, K.; Harndahl, M.; Dziegiel, M.H.; Claesson, M.H.; Buus, Søren; Lund, Ole.
In: Archives of Virology, Vol. 153, No. 10, 2008, p. 1833-1844.Publication: Research - peer-review › Journal article – Annual report year: 2008
- Published
MHC motif viewer. / Rapin, Nicolas Philippe Jean-Pierre; Hoof, Ilka; Lund, Ole; Nielsen, Morten.
In: Immunogenetics, Vol. 60, No. 12, 2008, p. 759-765.Publication: Research - peer-review › Journal article – Annual report year: 2008
- Published
NetMHC-3.0: accurate web accessible predictions of human, mouse and monkey MHC class I affinities for peptides of length 8-11. / Lundegaard, Claus; Lamberth, K; Harndahl, M; Buus, Søren; Lund, Ole; Nielsen, Morten.
In: Nucleic Acids Research, Vol. 36, 2008, p. W509-W512.Publication: Research - peer-review › Journal article – Annual report year: 2008
- Published
Quantitative predictions of peptide binding to any HLA-DR molecule of known sequence: NetMHCIIpan. / Nielsen, Morten; Lundegaard, Claus; Blicher, Thomas; Peters, B; Sette, A; Justesen, S; Buus, S; Lund, Ole.
In: PloS Computational Biology, Vol. 4, No. 7, 2008, p. e1000107.Publication: Research - peer-review › Journal article – Annual report year: 2008
- Published
Structural Insight into Epitopes in the Pregnancy-Associated Malaria Protein VAR2CSA. / Andersen, P; Nielsen, MA; Resende, M; Rask, Thomas Salhøj; Dahlbäck, M; Theander, T; Lund, Ole; Salanti, A.
In: P L o S Pathogens, Vol. 4, No. 2, 2008, p. 42.Publication: Research - peer-review › Journal article – Annual report year: 2008
- Published
The peptide-binding specificity of HLA-A*3001 demonstrates membership of the HLA-A3 supertype. / Lamberth, K; Røder, G; Harndahl, M; Nielsen, Morten; Lundegaard, Claus; Schafer-Nielsen, C; Lund, Ole; Buus, Søren.
In: Immunogenetics, Vol. 60, No. 11, 2008, p. 633-643.Publication: Research - peer-review › Journal article – Annual report year: 2008
- 2007
- Published
Prediction and identification of B-cell epitopes using protein structure information. / Andersen, Pernille; Lund, Ole (Supervisor).
Kgs. Lyngby, Denmark : Technical University of Denmark (DTU), 2007.Publication: Research › Ph.d. thesis – Annual report year: 2007
- Published
DNA Microarrays in Comparative Genomics and Transcriptomics. / Willenbrock, Hanni; Wassenaar, Gertrude Maria (Supervisor); Ussery, David (Supervisor); Lund, Ole (Supervisor).
2007. 133 p.Publication: Research › Ph.d. thesis – Annual report year: 2007
- Published
Prediction of T-cell Epitopes for Therapeutic and Prophylactic Vaccines. / Larsen, Mette Voldby; Brunak, Søren (Supervisor); Lund, Ole (Supervisor).
2007. 164 p.Publication: Research › Ph.d. thesis – Annual report year: 2007
- Published
CTL epitopes for influenza A including the H5N1 bird flu; genome-, pathogen-, and HLA-wide screening. / Wang, M.J.; Lamberth, K.; Harndahl, M.; Roder, G.; Stryhn, A.; Larsen, Mette Voldby; Nielsen, Morten; Lundegaard, Claus; Tang, Sheila Tuyet; Dziegiel, M.H.; Rosenkvist, J.; Pedersen, A.E.; Buus, Søren; Claesson, M.H.; Lund, Ole.
In: Vaccine, Vol. 25, No. 15, 2007, p. 2823-2831.Publication: Research - peer-review › Journal article – Annual report year: 2007
- Published
Large-scale validation of methods for cytotoxic T-lymphocyte epitope prediction. / Larsen, Mette Voldby; Lundegaard, Claus; Lamberth, K.; Buus, S.; Lund, Ole; Nielsen, Morten.
In: BMC Bioinformatics, Vol. 8, 2007, p. 424.Publication: Research - peer-review › Journal article – Annual report year: 2007
- Published
Modeling the adaptive immune system: predictions and simulations. Bioinformatics.. / Lundegaard, Claus; Lund, Ole; Kesmir, Can; Brunak, Søren; Nielsen, Morten.
In: Bioinformatics, No. 23, 2007, p. 3265-75.Publication: Research - peer-review › Journal article – Annual report year: 2007
- Published
NetMHCpan, a method for quantitative predictions of peptide binding to any HLA-A and -B locus protein of known sequence. / Nielsen, Morten; Lundegaard, Claus; Blicher, Thomas; Lamberth, K.; Harndahl, M.; Justesen, S.; Roder, G.; Peters, B.; Sette, A.; Lund, Ole; Buus, S.
In: PLoS ONE, No. 8, 2007, p. e796.Publication: Research - peer-review › Journal article – Annual report year: 2007
- Published
Prediction of MHC class II binding affinity using SMM-align, a novel stabilization matrix alignment method. / Nielsen, Morten; Lundegaard, Claus; Lund, Ole.
In: BMC Bioinformatics, Vol. 8, 2007, p. 238.Publication: Research - peer-review › Journal article – Annual report year: 2007
- Published
Towards a consensus on datasets and evaluation metrics for developing B-cell epitope prediction tools. / Greenbaum, Jason A.; Andersen, Pernille; Blythe, Martin; Bui, Huynh-Hoa; Cachau, Raul E.; Crowe, James; Davies, Matthew; Kolaskar, A. S.; Lund, Ole; Morrison, Sherrie; Mumey, Brendan; Ofran, Yanay; Pellequer, Jean-Luc; Pinilla, Clemencia; Ponomarenko, Julia V.; Raghava, G. P. S.; van Regenmortel, Marc H.; Roggen, Erwin L.; Sette, Alessandro; Schlessinger, Avner; Sollner, Johannes; Zand, Martin; Peters, Bjoern.
In: Journal of molecular recognition, No. 2, 2007, p. 75-82.Publication: Research - peer-review › Journal article – Annual report year: 2007
- 2006
- Published
A community resource benchmarking predictions of peptide binding to MHC-I molecules. / Peters, B; Bui, HH; Pletscher-Frankild, Sune; Nielsen, Morten; Lundegaard, Claus; Kostem, E; Basch, D; Lamberth, K; Harndahl, M; Fleri, W; Wilson, SS; Sidney, J; Lund, Ole; Buus, S; Sette, Alessandro.
In: PloS Computational Biology, Vol. 2, No. 6, 2006, p. 574-584.Publication: Research - peer-review › Journal article – Annual report year: 2006
- Published
Epitope mapping and topographic analysis of VAR2CSA DBL3X involved in P-falciparum placental sequestration. / Dahlback, Madeleine; Rask, Thomas Salhøj; Andersen, Pernille; Nielsen, Morten A; Ndam, Nicaise T.; Resende, Mafalda; Turner, Louise; Deloron, Philippe; Hviid, Lars; Lund, Ole; Pedersen, Anders Gorm; Theander, Thor G.; Salanti, Ali.
In: PLoS Pathogens, Vol. 2, No. 11, 2006, p. 1069-1082.Publication: Research - peer-review › Journal article – Annual report year: 2006
- Published
Improved method for predicting linear B-cell epitopes. / Larsen, Jens Erik Pontoppidan; Lund, Ole; Nielsen, Morten.
In: Immunome Research, Vol. 2, 2006, p. 2.Publication: Research › Journal article – Annual report year: 2006
- Published
Modelling the human immune system by combining bioinformatics and systems biology approaches. / Rapin, Nicolas Philippe Jean-Pierre; Kesmir, Can; Frankild, Sune; Nielsen, Morten; Lundegaard, Claus; Brunak, Søren; Lund, Ole.
In: Journal of Biological Physics, Vol. 32, No. 3-4, 2006, p. 335-353.Publication: Research - peer-review › Journal article – Annual report year: 2006
- Published
Prediction of residues in discontinuous B-cell epitopes using protein 3D structures. / Andersen, P.H.; Nielsen, Morten; Lund, Ole.
In: Protein Science, Vol. 15, No. 11, 2006, p. 2558-2567.Publication: Research - peer-review › Journal article – Annual report year: 2006
- Published
TAP-independent MHC class I presentation.. / Larsen, Mette Voldby; Nielsen, Morten; Weinzierl, A; Lund, Ole.
In: Current Immunology Reviews, Vol. 2, No. 3, 2006, p. 233-245.Publication: Research - peer-review › Journal article – Annual report year: 2006
- Published
The validity of predicted T-cell epitopes. / Lundegaard, Claus; Nielsen, Morten; Lund, Ole.
In: Trends in Biotechnology, Vol. 24, No. 12, 2006, p. 537-538.Publication: Research - peer-review › Journal article – Annual report year: 2006
- 2005
- Published
An integrative approach to CTL epitope prediction: A combined algorithm integrating MHC class I binding, TAP transport efficiency, and proteasomal cleavage predictions. / Larsen, M V; Lundegaard, Claus; Lamberth, K; Buus, S; Brunak, Søren; Lund, Ole; Nielsen, Morten.
In: European Journal of Immunology, Vol. 35, No. 8, 2005, p. 2295-2303.Publication: Research - peer-review › Journal article – Annual report year: 2005
- Published
The design and implementation of the immune epitope database and analysis resource. / Peters, B.; Sidney, J.; Bourne, P.; Bui, H.H.; Buus, S.; Doh, G.; Fleri, W.; Kronenberg, M.; Kubo, R.; Lund, Ole; Nemazee, D.; Ponomarenko, J.V.; Sathiamurthy, M.; Schoenberger, S.P.; Stewart, S.; Surko, P.; Way, S.; Wilson, S.; Sette, A.
In: Immunogenetics, Vol. 57, No. 5, 2005, p. 326-336.Publication: Research - peer-review › Journal article – Annual report year: 2005
- Published
The Immune Epitope Database and Analysis Resource: From Vision to Blueprint. / Peters, B.; Sidney, J.; Bourne, P.; Bui, H. H.; Buus, S.; Doh, G.; Fleri, W.; Kronenberg, M.; Kubo, R.; Lund, Ole; Nemazee, D.; Ponomarenko, J. V.; Sathiamurthy, M.; Schoenberger, S.; Stewart, S.; Surko, P.; Way, S.; Wilson, S.; Sette, A.
In: PLoS - Biology, Vol. 3, No. 3, 2005, p. 379-381.Publication: Research - peer-review › Journal article – Annual report year: 2005
- Published
The role of the proteasome in generating cytotoxic T-cell epitopes: insights obtained from improved predictions of proteasomal cleavage. / Nielsen, Morten; Lundegaard, Claus; Lund, Ole; Kesmir, Can.
In: Immunogenetics, Vol. 57, No. 1-2, 2005, p. 33-41.Publication: Research - peer-review › Journal article – Annual report year: 2005
- 2004
- Published
Coronavirus 3CL(pro) proteinase cleavage sites: Possible relevance to SARS virus pathology. / Kiemer, Lars; Lund, Ole; Brunak, Søren; Blom, Nikolaj.
In: BMC Bioinformatics, Vol. 5, 2004, p. 72.Publication: Research - peer-review › Journal article – Annual report year: 2004
- Published
Definition of supertypes for HLA molecules using clustering of specificity matrices. / Lund, Ole; Nielsen, Morten; Kesmir, Can; Petersen, A.G.; Lundegaard, Claus; Worning, Peder; Sylvester-Hvid, C.; Lamberth, K.; Roder, G.; Justesen, S.; Buus, S.; Brunak, Søren.
In: Immunogenetics, Vol. 55, No. 12, 2004, p. 797-810.Publication: Research - peer-review › Journal article – Annual report year: 2004
- Published
Improved prediction of MHC class I and class II epitopes using a novel Gibbs sampling approach. / Nielsen, Morten; Lundegaard, Claus; Worning, Peder; Hvid, C.S.; Lamberth, K.; Buus, S.; Brunak, Søren; Lund, Ole.
In: Bioinformatics, Vol. 20, 2004, p. 1388-1397.Publication: Research - peer-review › Journal article – Annual report year: 2004
- Published
MHC class I epitope binding prediction trained on small data sets. / Lundegaard, Claus; Nielsen, Morten; Lamberth, K.; Worning, Peder; Sylvester-Hvid, C.; Buus, S.; Brunak, Søren; Lund, Ole.
In: Artificial Immune Systems. Third International Conference, ICARIS 2004. Proceedings (Lecture Notes in Comput. Sci. Vol.3239), Vol. 3239, 2004, p. 217-225.Publication: Research - peer-review › Journal article – Annual report year: 2004
- Published
SARS CTL vaccine candidates; HLA supertype-, genome-wide scanning and biochemical validation. / Sylvester-Hvid, C.; Nielsen, Morten; Lamberth, K.; Roder, G.; Lundegaard, Claus; Worning, Peder; Thomadsen, H.; Lund, Ole; Brunak, Søren; Buus, S.
In: Tissue Antigens, Vol. 63, No. 5, 2004, p. 295-400.Publication: Research - peer-review › Journal article – Annual report year: 2004
- 2003
- Published
Reliable prediction of T-cell epitopes using neural networks with novel sequence representations. / Nielsen, Morten; Lundegaard, Claus; Worning, Peder; Lauemoller, S.L.; Lamberth, K.; Buus, S.; Brunak, Søren; Lund, Ole.
In: Protein Science, Vol. 12, No. 5, 2003, p. 1007-1017.Publication: Research - peer-review › Journal article – Annual report year: 2003
- Published
Selecting informative data for developing peptide-MHC binding predictors using a query by committee approach. / Christensen, J.K.; Lamberth, K.; Nielsen, Morten; Lundegaard, Claus; Worning, Peder; Lauemoller, S.L.; Buus, S.; Brunak, Søren; Lund, Ole.
In: Neural Computation, Vol. 15, No. 12, 2003, p. 2931-2942.Publication: Research - peer-review › Journal article – Annual report year: 2003
- 2002
- Published
Web-based Tools for Vaccine Design. / Lund, Ole; Nielsen, Morten; Kesmir, Can; Christensen, Jens K.; Lundegaard, Claus; Worning, Peder; Brunak, Søren.
In: HIV molecular immunology 2002. Theoretical Biology & Biophysics, 2002. p. 45-51.Publication: Research - peer-review › Book chapter – Annual report year: 2002
- 2000
- Published
Prediction of protein secondary structure at 80% accuracy. / Petersen, T. N.; Lundegaard, C.; Nielsen, M.; Bohr, Henrik; Bohr, Jakob; Brunak, Søren; Gippert, G. P.; Lund, Ole.
In: Proteins - Structure Function and Bioinformatics, Vol. 41, No. 1, 2000, p. 17-20.Publication: Research - peer-review › Journal article – Annual report year: 2000
- 1998
- Published
O-GLYCBASE version 3.0: a revised database of O-glycosylated proteins. / Hansen, Jan; Lund, Ole; Nilsson, Jette; Rapacki, Kristoffer; Brunak, Søren.
In: Nucleic Acids Research, Vol. 26, No. 1, 1998, p. 387-389.Publication: Research - peer-review › Journal article – Annual report year: 1998
- 1997
- Published
O-GLYCBASE version 2.0: a revised database of O-glycosylated proteins. / Hansen, Jan; Lund, Ole; Rapacki, Kristoffer; Brunak, Søren.
In: Nucleic Acids Research, Vol. 25, No. 1, 1997, p. 278-282.Publication: Research - peer-review › Journal article – Annual report year: 1997
- Published
Protein distance constraints predicted by neural networks and probability density functions. / Lund, Ole; Frimand, Kenneth; Gorodkin, Jan; Bohr, Henrik; Bohr, Jakob; Hansen, Jan; Brunak, Søren.
In: Protein Engineering, Vol. 10, No. 11, 1997, p. 1242-1248.Publication: Research - peer-review › Journal article – Annual report year: 1997
- 1996
- Published
Distance distributions in proteins: a six parameter representation. / Reese, M.G.; Lund, Ole; Bohr, Jakob; Bohr, Henrik; Hansen, Jan; Brunak, Søren.
In: Protein Engineering, Vol. 9, No. 9, 1996, p. 733-740.Publication: Research - peer-review › Journal article – Annual report year: 1996
- Published
O-GLYCBASE: a revised database of O-glycosylated proteins. / Hansen, Jan; Lund, Ole; Nielsen, Jens O.; Hansen, John-E. S.; Brunak, Søren.
In: Nucleic Acids Research, Vol. 24, No. 1, 1996, p. 248-252.Publication: Research - peer-review › Journal article – Annual report year: 1996
- Published
Prediction of the Secondary Structure of HIV-1 gp120. / Hansen, Jan; Lund, Ole; Nielsen, Jens O.; Brunak, Søren; Hansen, John-E.S.
In: Proteins: Structure, Function, and Bioinformatics, Vol. 25, No. 1, 1996, p. 1-11.Publication: Research - peer-review › Journal article – Annual report year: 1996
- Published
Relationship between protein structure and geometrical constrains. / Lund, Ole; Hansen, Jan; Brunak, Søren; Bohr, Jakob.
In: Protein Science, Vol. 5, 1996, p. 2217-2225.Publication: Research - peer-review › Journal article – Annual report year: 1996
- Published
Relationship between protein structure and geometrical constraints. / Lund, Ole; Hansen, Jan; Brunak, Søren; Bohr, Jakob.
In: Protein Science, Vol. 5, No. 11, 1996, p. 2217-2225.Publication: Research - peer-review › Journal article – Annual report year: 1996
- 1994
- Published
Glycosylation and protein conformation : Protein structure by distance analysis. / Hansen, Jan E.; Lund, Ole; Rapacki, Khristoffer; Mosekilde, Erik; Nielsen, Jens O.; Hansen, John-Erik S.
In: Protein Structure by Distance Analysis. IOS PressVan Diemenstraat 94, 1013 CN Amsterdam, Netherlands, 1994. p. 247-254.Publication: Research - peer-review › Book chapter – Annual report year: 1994