Ole Lund

40 papers A 1Journal 33Unranked 5
YearRankTypeTitle / Venue / Authors
2021 J jnl
Automated download and clean-up of family-specific databases for kmer-based virus identification.
Bioinform.
Rosa L. Allesøe, Camilla K. Lemvigh, My V. T. Phan, Philip T. L. C. Clausen, Alfred F. Florensa, Marion Koopmans, Ole Lund, Matthew Cotten
2019 J jnl
The COMPARE Data Hubs.
Database J. Biol. Databases Curation
Clara Amid, Nima Pakseresht, Nicole Silvester, Suran Jayathilaka, Ole Lund, Lukasz D. Dynovski, Bálint Á Pataki, Dávid Visontai, Basil Britto Xavier, Blaise T. F. Alako, Ariane Belka, Jose L. B. Cisneros, Matthew Cotten, George B. Haringhuizen, Peter W. Harrison, Dirk Höper, Sam Holt, Camilla Hundahl, Abdulrahman Hussein, Rolf S. Kaas, Xin Liu, Rasko Leinonen, Surbhi Malhotra-Kumar, David F. Nieuwenhuijse, Nadim Rahman, Carolina dos S. Ribeiro, Jeffrey E. Skiby, Dennis Schmitz, József Stéger, János M. Szalai-Gindl, Martin Christen Frølund Thomsen, Simone M. Cacciò, István Csabai, Annelies Kroneman, Marion Koopmans, Frank Aarestrup, Guy Cochrane
2018 J jnl
Benchmarking the HLA typing performance of Polysolver and Optitype in 50 Danish parental trios.
BMC Bioinform.
Maria Luisa Matey-Hernandez, Lasse Maretty, Jacob Malte Jensen, Bent Petersen, Jonas Andreas Sibbesen, Siyang Liu, Palle Villesen, Laurits Skov, Kirstine Belling, Christian Theil Have, José M. G. Izarzugaza, Marie Grosjean, Jette Bork-Jensen, Jakob Grove, Thomas D. Als, Shujia Huang, Yuqi Chang, Ruiqi Xu, Weijian Ye, Junhua Rao, Xiaosen Guo, Jihua Sun, Hongzhi Cao, Chen Ye, John van Beusekom, Thomas Espeseth, Esben N. Flindt, Rune M. Friborg, Anders E. Halager, Stephanie Le Hellard, Christina M. Hultman, Francesco Lescai, Shengting Li, Ole Lund, Peter Løngreen, Thomas Mailund, Ole Mors, Christian N. S. Pedersen, Thomas Sicheritz-Pontén, Patrick F. Sullivan, Ali Syed, David Westergaard, Rachita Yadav, Ning Li, Xun Xu, Torben Hansen, Anders Krogh, Lars Bolund, Thorkild I. A. Sørensen, Oluf Pedersen, Ramneek Gupta, Simon Rasmussen, Søren Besenbacher, Anders D. Børglum, Jun Wang, Hans Eiberg, Karsten Kristiansen, Mikkel Heide Schierup, Søren Brunak
2018 J jnl
Rapid and precise alignment of raw reads against redundant databases with KMA.
BMC Bioinform.
Philip T. L. C. Clausen, Frank Aarestrup, Ole Lund
2017 J jnl
RUCS: rapid identification of PCR primers for unique core sequences.
Bioinform.
Martin Christen Frølund Thomsen, Henrik Hasman, Henrik Westh, Hülya Kaya, Ole Lund
2017 J jnl
Sequencing and
Nat.
Lasse Maretty, Jacob Malte Jensen, Bent Petersen, Jonas Andreas Sibbesen, Siyang Liu, Palle Villesen, Laurits Skov, Kirstine Belling, Christian Theil Have, José M. G. Izarzugaza, Marie Grosjean, Jette Bork-Jensen, Jakob Grove, Thomas D. Als, Shujia Huang, Yuqi Chang, Ruiqi Xu, Weijian Ye, Junhua Rao, Xiaosen Guo, Jihua Sun, Hongzhi Cao, Chen Ye, John van Beusekom, Thomas Espeseth, Esben N. Flindt, Rune M. Friborg, Anders E. Halager, Stephanie Le Hellard, Christina M. Hultman, Francesco Lescai, Shengting Li, Ole Lund, Peter Løngreen, Thomas Mailund, Maria Luisa Matey-Hernandez, Ole Mors, Christian N. S. Pedersen, Thomas Sicheritz-Pontén, Patrick F. Sullivan, Ali Syed, David Westergaard, Rachita Yadav, Ning Li, Xun Xu, Torben Hansen, Anders Krogh, Lars Bolund, Thorkild I. A. Sørensen, Oluf Pedersen, Ramneek Gupta, Simon Rasmussen, Søren Besenbacher, Anders D. Børglum, Jun Wang, Hans Eiberg, Karsten Kristiansen, Søren Brunak, Mikkel Heide Schierup
2016 J jnl
ChemProt-3.0: a global chemical biology diseases mapping.
Database J. Biol. Databases Curation
Jens Kringelum, Sonny Kim Kjærulff, Søren Brunak, Ole Lund, Tudor I. Oprea, Olivier Taboureau
2015 J jnl
Automated benchmarking of peptide-MHC class I binding predictions.
Bioinform.
Thomas Trolle, Imir G. Metushi, Jason A. Greenbaum, Yohan Kim, John Sidney, Ole Lund, Alessandro Sette, Bjoern Peters, Morten Nielsen
2015 J jnl
Reads2Type: a web application for rapid microbial taxonomy identification.
BMC Bioinform.
Dhany Saputra, Simon Rasmussen, Mette V. Larsen, Nizar Haddad, Maria Sperotto, Frank Aarestrup, Ole Lund, Thomas Sicheritz-Pontén
2013 J jnl
ChemProt-2.0: visual navigation in a disease chemical biology database.
Nucleic Acids Res.
Sonny Kim Kjærulff, Louis Wich, Jens Kringelum, Ulrik Plesner Jacobsen, Irene Kouskoumvekaki, Karine Audouze, Ole Lund, Søren Brunak, Tudor I. Oprea, Olivier Taboureau
2013 J jnl
Simultaneous alignment and clustering of peptide data using a Gibbs sampling approach.
Bioinform.
Massimo Andreatta, Ole Lund, Morten Nielsen
2012 J jnl
Immune epitope database analysis resource.
Nucleic Acids Res.
Yohan Kim, Julia V. Ponomarenko, Zhanyang Zhu, Dorjee Tamang, Peng Wang, Jason Greenbaum, Claus Lundegaard, Alessandro Sette, Ole Lund, Philip E. Bourne, Morten Nielsen, Bjoern Peters
2012 J jnl
Reliable B Cell Epitope Predictions: Impacts of Method Development and Improved Benchmarking.
PLoS Comput. Biol.
Jens Vindahl Kringelum, Claus Lundegaard, Ole Lund, Morten Nielsen
2011 J jnl
Immune system simulation online.
Bioinform.
Nicolas Rapin, Ole Lund, Filippo Castiglione
2010 J jnl
CPHmodels-3.0 - remote homology modeling using structure-guided sequence profiles.
Nucleic Acids Res.
Morten Nielsen, Claus Lundegaard, Ole Lund, Thomas Nordahl Petersen
2010 J jnl
Peptide binding predictions for HLA DR, DP and DQ molecules.
BMC Bioinform.
Peng Wang, John Sidney, Yohan Kim, Alessandro Sette, Ole Lund, Morten Nielsen, Björn Peters
2010 — conf
PopCover: a method for selecting of peptides with optimal population and pathogen coverage.
BCB
Claus Lundegaard, M. Buggert, A. C. Karlsson, Ole Lund, Carina Perez, Morten Nielsen
2009 J jnl
The PickPocket method for predicting binding specificities for receptors based on receptor pocket similarities: application to MHC-peptide binding.
Bioinform.
Hao Zhang, Ole Lund, Morten Nielsen
2008 J jnl
Accurate approximation method for prediction of class I MHC affinities for peptides of length 8, 10 and 11 using prediction tools trained on 9mers.
Bioinform.
Claus Lundegaard, Ole Lund, Morten Nielsen
2008 J jnl
Immune epitope database analysis resource (IEDB-AR).
Nucleic Acids Res.
Qing Zhang, Peng Wang, Yohan Kim, Pernille Haste-Andersen, John E. Beaver, Philip E. Bourne, Huynh-Hoa Bui, Søren Buus, Sune Frankild, Jason Greenbaum, Ole Lund, Claus Lundegaard, Morten Nielsen, Julia V. Ponomarenko, Alessandro Sette, Zhanyang Zhu, Björn Peters
2008 J jnl
NetMHC-3.0: accurate web accessible predictions of human, mouse and monkey MHC class I affinities for peptides of length 8-11.
Nucleic Acids Res.
Claus Lundegaard, Kasper Lamberth, Mikkel Harndahl, Søren Buus, Ole Lund, Morten Nielsen
2008 J jnl
Quantitative Predictions of Peptide Binding to Any HLA-DR Molecule of Known Sequence: NetMHCIIpan.
PLoS Comput. Biol.
Morten Nielsen, Claus Lundegaard, Thomas Blicher, Bjoern Peters, Alessandro Sette, Sune Justesen, Søren Buus, Ole Lund
2007 J jnl
Large-scale validation of methods for cytotoxic T-lymphocyte epitope prediction.
BMC Bioinform.
Mette V. Larsen, Claus Lundegaard, Kasper Lamberth, Søren Buus, Ole Lund, Morten Nielsen
2007 J jnl
Modeling the adaptive immune system: predictions and simulations.
Bioinform.
Claus Lundegaard, Ole Lund, Can Kesmir, Søren Brunak, Morten Nielsen
2007 J jnl
Prediction of MHC class II binding affinity using SMM-align, a novel stabilization matrix alignment method.
BMC Bioinform.
Morten Nielsen, Claus Lundegaard, Ole Lund
2006 J jnl
A Community Resource Benchmarking Predictions of Peptide Binding to MHC-I Molecules.
PLoS Comput. Biol.
Bjoern Peters, Huynh-Hoa Bui, Sune Frankild, Morten Nielsen, Claus Lundegaard, Emrah Kostem, Derek Basch, Kasper Lamberth, Mikkel Harndahl, Ward Fleri, Stephen S. Wilson, John Sidney, Ole Lund, Søren Buus, Alessandro Sette
2006 — conf
The Immune Epitope Database and Analysis Resource.
PRIB
Alessandro Sette, Huynh-Hoa Bui, John Sidney, Philip E. Bourne, Søren Buus, Ward Fleri, R. Kubo, Ole Lund, D. Nemazee, Julia V. Ponomarenko, Muthu Sathiamurthy, Scott Stewart, Scott Way, Stephen S. Wilson, Björn Peters
2005 — book
Immunological bioinformatics.
Ole Lund, Morten Nielsen, Claus Lundegaard, Can Kesmir, Søren Brunak
2004 J jnl
Coronavirus 3CL
BMC Bioinform.
Lars Kiemer, Ole Lund, Søren Brunak, Nikolaj Blom
2004 J jnl
Improved prediction of MHC class I and class II epitopes using a novel Gibbs sampling approach.
Bioinform.
Morten Nielsen, Claus Lundegaard, Peder Worning, Christina Sylvester-Hvid, Kasper Lamberth, Søren Buus, Søren Brunak, Ole Lund
2004 — conf
MHC Class I Epitope Binding Prediction Trained on Small Data Sets.
ICARIS
Claus Lundegaard, Morten Nielsen, Kasper Lamberth, Peder Worning, Christina Sylvester-Hvid, Søren Buus, Søren Brunak, Ole Lund
2003 — conf
Prediction of Protein Secondary Structure at High Accuracy Using a Combination of Many Neural Networks.
Mathematical Methods for Protein Structure Analysis and Design
Claus Lundegaard, Thomas Nordahl Petersen, Morten Nielsen, Henrik Bohr, Jakob Bohr, Søren Brunak, Garry Gippert, Ole Lund
2003 J jnl
Selecting Informative Data for Developing Peptide-MHC Binding Predictors Using a Query by Committee Approach.
Neural Comput.
Jens Kaae Christensen, Kasper Lamberth, Morten Nielsen, Claus Lundegaard, Peder Worning, Sanne Lise Lauemøller, Søren Buus, Søren Brunak, Ole Lund
1999 J jnl
MatrixPlot: visualizing sequence constraints.
Bioinform.
Jan Gorodkin, Hans Henrik Stærfeldt, Ole Lund, Søren Brunak
1999 A conf
Using Sequence Motifs for Enhanced Neural Network Prediction of Protein Distance Constraints.
ISMB
Jan Gorodkin, Ole Lund, Claus A. F. Andersen, Søren Brunak
1998 J jnl
O-GLYCBASE Version 3.0: a revised database of O-glycosylated proteins.
Nucleic Acids Res.
Jan E. Hansen, Ole Lund, Jette Nilsson, Kristoffer Rapacki, Søren Brunak
1997 J jnl
O-GLYCBASE version 2.0: a revised database of O-glycosylated proteins.
Nucleic Acids Res.
Jan E. Hansen, Ole Lund, Kristoffer Rapacki, Søren Brunak
1996 J jnl
O-GLYCBASE: a revised database of O-glycosylated proteins.
Nucleic Acids Res.
Jan E. Hansen, Ole Lund, Jens O. Nielsen, John-E. S. Hansen, Søren Brunak
1993 J jnl
Period doubling route to chaos in a model of HIV infection of the immune system: A comment on the Anderson-May model.
Simul. Pract. Theory
Ole Lund, Erik Mosekilde, Jan E. Hansen
1992 — conf
Period Doubling Route to Chaos in a Model of HIV infection of the Immune System.
EUROSIM
Ole Lund, Erik Mosekilde, Jan E. Hansen