Ole Lund

  1. 2015
  2. Published

    Bioinformatics prediction of swine MHC class I epitopes from Porcine Reproductive and Respiratory Syndrome Virus. / Welner, Simon; Nielsen, Morten; Lund, Ole; Jungersen, Gregers; Larsen, Lars Erik.

    2015. Abstract from Keystone Symposia on Molecular and Cellular Biology: Accelerating life science discovery, Keystone, United States.

    Publication: Research - peer-reviewConference abstract for conference – Annual report year: 2015

  3. 2014
  4. Published
  5. Published
  6. Published

    Characterisation of the Ara h 1-specific IgE repertoire in peanut allergic patients using phage display technology and next generation sequencing. / Christiansen, Anders; Bøgh, Katrine Lindholm; Kringelum, Jens Vindahl; Hansen, Christian Skjødt; Rigby, N. M.; Eiwegger, T.; Szepfalusi, Z.; Lund, Ole; Dufva, Martin.

    In: ALLERGY, Vol. 69, No. Supplement, 297, 2014, p. 140-140.

    Publication: Research - peer-reviewConference abstract in journal – Annual report year: 2014

  7. Published

    Database-driven primary analysis of raw sequencing data. / Gautier, Laurent (Inventor); Lund, Ole (Inventor).

    IPC No.: G06F19/22. Patent No.: WO2014060305. Apr 24, 2014.

    Publication: ResearchPatent – Annual report year: 2014

  8. Published

    Evaluation of whole genome sequencing for outbreak detection of Salmonella enterica. / Leekitcharoenphon, Pimlapas; Nielsen, Eva M.; Kaas, Rolf Sommer; Lund, Ole; Aarestrup, Frank Møller.

    In: P L o S One, Vol. 9, No. 2, e87991, 2014.

    Publication: Research - peer-reviewJournal article – Annual report year: 2014

  9. Published

    Identification and assembly of genomes and genetic elements in complex metagenomic samples without using reference genomes. / Nielsen, Henrik Bjørn; Almeida, Mathieu; Juncker, Agnieszka; Rasmussen, Simon; Li, Junhua; Sunagawa, Shinichi; Plichta, Damian Rafal; Gautier, Laurent; Pedersen, Anders Gorm; Emmanuelle, Le Chatelier; Pelletier, Eric; Bonde, Ida; Nielsen, Trine; Manichanh, Chaysavanh; Arumugam, Manimozhiyan; Batto, Jean-Michel; dos Santos, Marcelo Bertalan Quintanilha; Blom, Nikolaj; Borruel, Natalia; Burgdorf, Kristoffer S.; Boumezbeur, Fouad; Casellas, Francesc; Doré, Joël; Dworzynski, Piotr; Guarner, Francisco; Hansen, Torben; Hildebrand, Falk; Kaas, Rolf Sommer; Kennedy, Sean; Kristiansen, Karsten; Kultima, Jens Roat; Léonard, Pierre; Levenez, Florence; Lund, Ole; Moumen, Bouziane; Denis, Le Paslier; Pons, Nicolas; Pedersen, Oluf; Prifti, Edi; Qin, Junjie; Raes, Jeroen; Sørensen, Søren; Tap, Julien; Tims, Sebastian; Ussery, David; Yamada, Takuji; Renault, Pierre; Sicheritz-Pontén, Thomas; Bork, Peer; Wang, Jun; Brunak, Søren; Ehrlich, S. Dusko.

    In: Nature Biotechnology, Vol. 32, No. 8, 2014, p. 822-828.

    Publication: Research - peer-reviewJournal article – Annual report year: 2014

  10. Published

    Immunoinformatics of Placental Malaria Vaccine Development. / Jessen, Leon Eyrich; Lund, Ole (Main supervisor); Hviid, Lars (Supervisor); Nielsen, Morten (Supervisor).

    Technical University of Denmark, 2014. 239 p.

    Publication: ResearchPh.D. thesis – Annual report year: 2014

  11. E-pub ahead of print

    In Silico Detection and Typing of Plasmids using PlasmidFinder and Plasmid Multilocus Sequence Typing. / Carattoli, Alessandra; Zankari, Ea; García-Fernández, Aurora; Larsen, Mette Voldby; Lund, Ole; Villa, Laura; Aarestrup, Frank Møller; Hasman, Henrik.

    In: Antimicrobial Agents and Chemotherapy, Vol. 58, No. 7, 2014, p. 3895-3903.

    Publication: Research - peer-reviewJournal article – Annual report year: 2014

  12. Published

    MR1-restricted MAIT cells display ligand discrimination and pathogen selectivity through distinct T cell receptor usage.. / Gold, Marielle C.; McLaren, James E.; Reistetter, Joseph A.; Smyk-Pearson, Sue; Ladell, Kristin; Swarbrick, Gwendolyn M.; Yu, Yik Y. L.; Hansen, Ted H.; Lund, Ole; Nielsen, Morten; Gerritsen, Bram; Kesmir, Can; Miles, John J.; Lewinsohn, Deborah A.; Price, David A.; Lewinsohn, David M.

    In: Journal of Experimental Medicine, Vol. 211, No. 8, 2014, p. 1601-1610.

    Publication: Research - peer-reviewJournal article – Annual report year: 2014

  13. Published

    Multiparametric Bioinformatics Distinguish the CD4/CD8 Ratio as a Suitable Laboratory Predictor of Combined T Cell Pathogenesis in HIV Infection. / Buggert, Marcus; Frederiksen, Juliet Wairimu; Noyan, Kajsa; Svärd, Jenny; Barqasho, Babilonia; Sönnerborg, Anders; Lund, Ole; Nowak, Piotr; Karlsson, Annika C.

    In: Journal of Immunology, Vol. 192, No. 5, 2014, p. 2099-2108.

    Publication: Research - peer-reviewJournal article – Annual report year: 2014

  14. Published

    NetFCM: A Semi-Automated Web-Based Method for Flow Cytometry Data Analysis. / Frederiksen, Juliet Wairimu; Buggert, Marcus; Karlsson, Annika C.; Lund, Ole.

    In: Cytometry. Part A, Vol. 85, No. 11, 2014, p. 969-977.

    Publication: Research - peer-reviewJournal article – Annual report year: 2014

  15. Published
  16. Published
  17. Published
  18. Published

    Solving the Problem of Comparing Whole Bacterial Genomes across Different Sequencing Platforms. / Kaas, Rolf Sommer; Leekitcharoenphon, Pimlapas; Aarestrup, Frank Møller; Lund, Ole.

    In: PLOS ONE, Vol. 9, No. 8, e104984, 2014.

    Publication: Research - peer-reviewJournal article – Annual report year: 2014

  19. Published

    T-bet and Eomes Are Differentially Linked to the Exhausted Phenotype of CD8+T Cells in HIV Infection. / Buggert, Marcus; Tauriainen, Johanna; Yamamoto, Takuya; Frederiksen, Juliet Wairimu; Ivarsson, Martin A.; Michaelsson, Jakob; Lund, Ole; Hejdeman, Bo; Jansson, Marianne; Sonnerborg, Anders; Koup, Richard A.; Betts, Michael R.; Karlsson, Annika C.

    In: P L o S Pathogens, Vol. 10, No. 7, e1004251, 2014.

    Publication: Research - peer-reviewJournal article – Annual report year: 2014

  20. Published

    Whole Genome Epidemiological Typing of Salmonella. / Leekitcharoenphon, Pimlapas; Aarestrup, Frank Møller (Main supervisor); Lund, Ole (Supervisor); Ussery, David (Supervisor).

    National Food Institute, 2014. 112 p.

    Publication: ResearchPh.D. thesis – Annual report year: 2014

  21. 2013
  22. 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.

    Antigen Processing : Methods and Protocols. 2013. p. 247-260 (Methods in Molecular Biology, Vol. 960).

    Publication: Research - peer-reviewBook chapter – Annual report year: 2013

  23. Published
  24. Published

    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. / Karosiene, Edita; Rasmussen, Michael; Blicher, Thomas; Lund, Ole; Buus, S.; Nielsen, Morten Munch.

    In: Immunogenetics, Vol. 65, No. 10, 2013, p. 711-724.

    Publication: Research - peer-reviewJournal article – Annual report year: 2013

  25. Published

    Epitope prediction methods. / Karosiene, Edita; Nielsen, Morten (Main supervisor); Lund, Ole (Supervisor).

    Kgs. Lyngby : Technical University of Denmark, 2013. 127 p.

    Publication: ResearchPh.D. thesis – Annual report year: 2013

  26. Published

    Evaluation of peptide selection approaches for epitope‐based vaccine design. / Schubert, B.; Lund, Ole; Nielsen, Morten.

    In: Tissue Antigens, Vol. 82, No. 4, 2013, p. 243–251.

    Publication: Research - peer-reviewJournal article – Annual report year: 2013

  27. Published
  28. 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-reviewConference abstract in journal – Annual report year: 2013

  29. 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: Scandinavian Journal of Immunology, Vol. 77, No. 4, 2013, p. 317-318.

    Publication: Research - peer-reviewConference abstract in journal – Annual report year: 2013

  30. Published

    Low-Bandwidth and Non-Compute Intensive Remote Identification of Microbes from Raw Sequencing Reads. / Gautier, Laurent; Lund, Ole.

    In: P L o S One, Vol. 8, No. 12, e83784, 2013.

    Publication: Research - peer-reviewJournal article – Annual report year: 2014

  31. Published

    MHCcluster, a method for functional clustering of MHC molecules. / Thomsen, Martin Christen Frølund; Lundegaard, Claus; Buus, Søren; Lund, Ole; Nielsen, Morten.

    In: Immunogenetics, Vol. 65, No. 9, 2013, p. 655-665.

    Publication: Research - peer-reviewJournal article – Annual report year: 2013

  32. Published

    NetFCM: A Tool for Automated Flow Cytometric Data Analysis. / Frederiksen, Juliet Wairimu; Lund, Ole; Buggert, M.; Karlsson, A.

    In: Scandinavian Journal of Immunology, Vol. 77, No. 44, 2013, p. 325.

    Publication: Research - peer-reviewConference abstract in journal – Annual report year: 2013

  33. Published

    PathogenFinder - Distinguishing Friend from Foe Using Bacterial Whole Genome Sequence Data.. / Cosentino, Salvatore; Larsen, Mette Voldby; Aarestrup, Frank Møller; Lund, Ole.

    In: PloS one., Vol. 8, No. 10, 2013, p. e77302.

    Publication: Research - peer-reviewJournal article – Annual report year: 2013

  34. Published

    Real-Time WGS-based Typing of VTEC Isolates for Surveillance and Outbreak Detection. / Joensen, Katrine Grimstrup; Hasman, Henrik; Scheutz, F.; Nielsen, E. M.; Lund, Ole; Aarestrup, Frank Møller.

    10th International Meeting on Microbial Epidemiological Markers (IMMEM-10) - Abstract Book. Paris, France, 2013. p. 209.

    Publication: Research - peer-reviewConference abstract in proceedings – Annual report year: 2013

  35. Published

    SigniSite: Identification of residue-level genotype-phenotype correlations in protein multiple sequence alignments. / Jessen, Leon Ivar; Hoof, Ilka; Lund, Ole; Nielsen, Morten.

    In: Nucleic Acids Research, Vol. 41, No. W1, 2013, p. 20W286-W291.

    Publication: Research - peer-reviewJournal article – Annual report year: 2013

  36. Published

    Simultaneous alignment and clustering of peptide data using a Gibbs sampling approach. / Andreatta, Massimo; Lund, Ole; Nielsen, Morten.

    In: Bioinformatics, Vol. 29, No. 1, 2013, p. 8-14.

    Publication: Research - peer-reviewJournal article – Annual report year: 2013

  37. 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-reviewJournal article – Annual report year: 2012

  38. Published

    Targeting of conserved gag-epitopes in early HIV infection is associated with lower plasma viral load and slower CD4+ T cell depletion.. / Perez, Carina L. ; Milush, Jeffrey M. ; Buggert, Marcus; Eriksson, Emily M. ; Larsen, Mette Voldby; Liegler, Teri; Hartogensis, Wendy; Bacchetti, Peter; Lund, Ole; Hecht, Frederick M. ; Nixon, Douglas F. ; Karlsson, Annika C. .

    In: AIDS Research and Human Retroviruses, Vol. 29, No. 3, 2013, p. 602-612.

    Publication: Research - peer-reviewJournal article – Annual report year: 2012

  39. Published

    VAR2CSA Epitope Identification - Finding All the Needles in All the Haystacks. / Jessen, L. E.; Ditlev, S. B.; Schafer-Nielsen, C.; Buus, S.; Salanti, A.; Lund, Ole.

    In: Scandinavian Journal of Immunology, Vol. 77, No. 4, 2013, p. 318-319.

    Publication: Research - peer-reviewConference abstract in journal – Annual report year: 2013

  40. 2012
  41. 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-reviewJournal article – Annual report year: 2012

  42. Published

    Concepts in Mechanism Based Modeling. / Lund, Ole; Laugesen, Jakob Lund; Mosekilde, Erik.

    Biosimulation in Biomedical Research, Health Care and Drug Development. Springer, 2012. p. 19-41.

    Publication: Research - peer-reviewBook chapter – Annual report year: 2012

  43. Published

    Discovering sequence motifs in quantitative and qualitative pepetide data. / Andreatta, Massimo; Nielsen, Morten (Supervisor); Lund, Ole (Main supervisor).

    Kgs. Lyngby : Technical University of Denmark, 2012. 105 p.

    Publication: ResearchPh.D. thesis – Annual report year: 2012

  44. Published
  45. 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-reviewJournal article – Annual report year: 2012

  46. 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-reviewJournal article – Annual report year: 2012

  47. Published
  48. 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-reviewJournal article – Annual report year: 2013

  49. 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-reviewJournal article – Annual report year: 2012

  50. 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-reviewJournal article – Annual report year: 2012

  51. 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-reviewJournal article – Annual report year: 2012

  52. Published
  53. 2011
  54. 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-reviewJournal article – Annual report year: 2011

  55. Published

    Bistability in autoimmune diseases. / Rapin, Nicolas; Mosekilde, Erik; Lund, Ole.

    In: Autoimmunity, Vol. 44, No. 4, 2011, p. 256-260.

    Publication: Research - peer-reviewJournal article – Annual report year: 2011

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