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ORCIDMorten Nielsen 0001
Person information
- affiliation: Technical University of Denmark, Center for Biological Sequence Analysis, Lyngby, Denmark
- affiliation: Universidad Nacional de San Martín, Buenos Aires, Argentina
- affiliation (PhD 1999): McGill University, Department of Physics, Montreal, QC, Canada
Other persons with the same name
- Morten Nielsen — disambiguation page
- Morten Nielsen 0002
![[0000-0002-9078-0594]](https://dblp.uni-trier.de/img/orcid-mark.12x12.png "0000-0002-9078-0594")
— Aalborg University, Department of Mathematical Sciences, Denmark (and 2 more) - Morten Nielsen 0003 — Technical University of Denmark, Wind Energy Department, Roskilde, Denmark
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2020 – today
- 2024
[j46]Eve Richardson, Raphael Trevizani, Jason A. Greenbaum, Hannah Carter, Morten Nielsen, Bjoern Peters:
The receiver operating characteristic curve accurately assesses imbalanced datasets. Patterns 5(6): 100994 (2024)- 2023
- [j45]Daniel Marrama, William D. Chronister, Luise Westernberg, Randi Vita, Zeynep Kosaloglu-Yalçin, Alessandro Sette, Morten Nielsen, Jason A. Greenbaum, Bjoern Peters:
PEPMatch: a tool to identify short peptide sequence matches in large sets of proteins. BMC Bioinform. 24(1): 485 (2023) - [j44]Zeynep Kosaloglu-Yalçin, Nina Blazeska, Randi Vita, Hannah Carter, Morten Nielsen, Stephen Schoenberger, Alessandro Sette, Bjoern Peters:
The Cancer Epitope Database and Analysis Resource (CEDAR). Nucleic Acids Res. 51(D1): 845-852 (2023) - 2022
- [j43]Raphael Trevizani, Zhen Yan, Jason A. Greenbaum, Alessandro Sette, Morten Nielsen, Bjoern Peters:
A comprehensive analysis of the IEDB MHC class-I automated benchmark. Briefings Bioinform. 23(4) (2022) - [j42]Magnus Haraldson Høie, Erik Nicolas Kiehl, Bent Petersen, Morten Nielsen, Ole Winther, Henrik Nielsen, Jeppe Hallgren, Paolo Marcatili:
NetSurfP-3.0: accurate and fast prediction of protein structural features by protein language models and deep learning. Nucleic Acids Res. 50(W1): 510-515 (2022) - 2021
- [j41]Jonathan Hare, David Morrison, Morten Nielsen:
Sampling SARS-CoV-2 Proteomes for Predicted CD8 T-Cell Epitopes as a Tool for Understanding Immunogenic Breadth and Rational Vaccine Design. Frontiers Bioinform. 1 (2021) - 2020
- [j40]Birkir Reynisson, Bruno Alvarez, Sinu Paul, Bjoern Peters, Morten Nielsen:
NetMHCpan-4.1 and NetMHCIIpan-4.0: improved predictions of MHC antigen presentation by concurrent motif deconvolution and integration of MS MHC eluted ligand data. Nucleic Acids Res. 48(Webserver-Issue): W449-W454 (2020) - [j39]Sinu Paul, Nathan P. Croft, Anthony W. Purcell, David C. Tscharke, Alessandro Sette, Morten Nielsen, Bjoern Peters:
Benchmarking predictions of MHC class I restricted T cell epitopes in a comprehensively studied model system. PLoS Comput. Biol. 16(5) (2020)
2010 – 2019
- 2019
- [j38]Emilio Fenoy, José M. G. Izarzugaza, Vanessa Isabell Jurtz, Søren Brunak, Morten Nielsen:
A generic deep convolutional neural network framework for prediction of receptor-ligand interactions - NetPhosPan: application to kinase phosphorylation prediction. Bioinform. 35(7): 1098-1107 (2019) - [j37]Swapnil Mahajan, Zhen Yan, Martin Closter Jespersen, Kamilla Kjærgaard Jensen, Paolo Marcatili, Morten Nielsen, Alessandro Sette, Bjoern Peters:
Benchmark datasets of immune receptor-epitope structural complexes. BMC Bioinform. 20(1): 490:1-490:7 (2019) - [j36]Sandeep Kumar Dhanda, Swapnil Mahajan, Sinu Paul, Zhen Yan, Haeuk Kim, Martin Closter Jespersen, Vanessa Isabell Jurtz, Massimo Andreatta, Jason A. Greenbaum, Paolo Marcatili, Alessandro Sette, Morten Nielsen, Bjoern Peters:
IEDB-AR: immune epitope database - analysis resource in 2019. Nucleic Acids Res. 47(Webserver-Issue): W502-W506 (2019) - 2018
- [j35]Massimo Andreatta, Thomas Trolle, Zhen Yan, Jason A. Greenbaum, Bjoern Peters, Morten Nielsen:
An automated benchmarking platform for MHC class II binding prediction methods. Bioinform. 34(9): 1522-1528 (2018) - [j34]Wenguang Shao, Patrick G. A. Pedrioli, Witold Wolski, Christian Scurtescu, Emanuel Schmid, Juan Antonio Vizcaíno, Mathieu Courcelles, Heiko Schuster, Daniel Kowalewski, Fabio Marino, Cecilia S. Lindestam Arlehamn, Kerrie Vaughan, Bjoern Peters, Alessandro Sette, Tom H. M. Ottenhoff, Krista E. Meijgaarden, Natalie Nieuwenhuizen, Stefan H. E. Kaufmann, Ralph Schlapbach, John C. Castle, Alexey I. Nesvizhskii, Morten Nielsen, Eric W. Deutsch, David S. Campbell, Robert L. Moritz, Roman A. Zubarev, Anders Jimmy Ytterberg, Anthony W. Purcell, Miguel Marcilla, Alberto Paradela, Qi Wang, Catherine E. Costello, Nicola Ternette, Peter A. van Veelen, Cécile A. C. M. van Els, Albert J. R. Heck, Gustavo A. de Souza, Ludvig Magne Sollid, Arie Admon, Stefan Stevanovic, Hans-Georg Rammensee, Pierre Thibault, Claude Perreault, Michal Bassani-Sternberg, Ruedi Aebersold, Etienne Caron:
The SysteMHC Atlas project. Nucleic Acids Res. 46(Database-Issue): D1237-D1247 (2018) - 2017
- [j33]Diego J. Zea, Diego Anfossi, Morten Nielsen, Cristina Marino Buslje:
MIToS.jl: mutual information tools for protein sequence analysis in the Julia language. Bioinform. 33(4): 564-565 (2017) - [j32]Vanessa Isabell Jurtz, Alexander Rosenberg Johansen, Morten Nielsen, José Juan Almagro Armenteros, Henrik Nielsen, Casper Kaae Sønderby, Ole Winther, Søren Kaae Sønderby:
An introduction to deep learning on biological sequence data: examples and solutions. Bioinform. 33(22): 3685-3690 (2017) - [j31]Martin Closter Jespersen, Bjoern Peters, Morten Nielsen, Paolo Marcatili:
BepiPred-2.0: improving sequence-based B-cell epitope prediction using conformational epitopes. Nucleic Acids Res. 45(Webserver-Issue): W24-W29 (2017) - [j30]Morten Nielsen, Massimo Andreatta:
NNAlign: a platform to construct and evaluate artificial neural network models of receptor-ligand interactions. Nucleic Acids Res. 45(Webserver-Issue): W344-W349 (2017) - [j29]Massimo Andreatta, Bruno Alvarez, Morten Nielsen:
GibbsCluster: unsupervised clustering and alignment of peptide sequences. Nucleic Acids Res. 45(Webserver-Issue): W458-W463 (2017) - 2016
- [j28]Massimo Andreatta, Morten Nielsen:
Gapped sequence alignment using artificial neural networks: application to the MHC class I system. Bioinform. 32(4): 511-517 (2016) - 2015
- [j27]Thomas Trolle, Imir G. Metushi, Jason A. Greenbaum, Yohan Kim, John Sidney, Ole Lund, Alessandro Sette, Bjoern Peters, Morten Nielsen:
Automated benchmarking of peptide-MHC class I binding predictions. Bioinform. 31(13): 2174-2181 (2015) - [j26]Michael Schantz Klausen, Mads Valdemar Anderson, Martin Closter Jespersen, Morten Nielsen, Paolo Marcatili:
LYRA, a webserver for lymphocyte receptor structural modeling. Nucleic Acids Res. 43(Webserver-Issue): W349-W355 (2015) - 2014
- [j25]Yohan Kim, John Sidney, Søren Buus, Alessandro Sette, Morten Nielsen, Bjoern Peters:
Dataset size and composition impact the reliability of performance benchmarks for peptide-MHC binding predictions. BMC Bioinform. 15: 241 (2014) - [c4]Anne Bresciani, Jason Greenbaum, Cecilia S. Lindestam Arlehamn, Alessandro Sette, Morten Nielsen, Bjoern Peters:
The interplay of sequence conservation and T cell immune recognition. BCB 2014: 739-743 - 2013
- [j24]Massimo Andreatta, Ole Lund, Morten Nielsen:
Simultaneous alignment and clustering of peptide data using a Gibbs sampling approach. Bioinform. 29(1): 8-14 (2013) - [j23]Franco L. Simonetti, Elin Teppa, Ariel Chernomoretz, Morten Nielsen, Cristina Marino Buslje:
MISTIC: mutual information server to infer coevolution. Nucleic Acids Res. 41(Webserver-Issue): 8-14 (2013) - [j22]Leon Eyrich Jessen, Ilka Hoof, Ole Lund, Morten Nielsen:
SigniSite: Identification of residue-level genotype-phenotype correlations in protein multiple sequence alignments. Nucleic Acids Res. 41(Webserver-Issue): 286-291 (2013) - 2012
- [j21]Elin Teppa, Angela D. Wilkins, Morten Nielsen, Cristina Marino Buslje:
Disentangling evolutionary signals: conservation, specificity determining positions and coevolution. Implication for catalytic residue prediction. BMC Bioinform. 13: 235 (2012) - [j20]Martin Christen Frølund Thomsen, Morten Nielsen:
Seq2Logo: a method for construction and visualization of amino acid binding motifs and sequence profiles including sequence weighting, pseudo counts and two-sided representation of amino acid enrichment and depletion. Nucleic Acids Res. 40(Web-Server-Issue): 281-287 (2012) - [j19]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:
Immune epitope database analysis resource. Nucleic Acids Res. 40(Web-Server-Issue): 525-530 (2012) - [j18]Jens Vindahl Kringelum, Claus Lundegaard, Ole Lund, Morten Nielsen:
Reliable B Cell Epitope Predictions: Impacts of Method Development and Improved Benchmarking. PLoS Comput. Biol. 8(12) (2012) - 2010
- [j17]Peng Wang, John Sidney, Yohan Kim, Alessandro Sette, Ole Lund, Morten Nielsen, Björn Peters:
Peptide binding predictions for HLA DR, DP and DQ molecules. BMC Bioinform. 11: 568 (2010) - [j16]Morten Nielsen, Claus Lundegaard, Ole Lund, Thomas Nordahl Petersen:
CPHmodels-3.0 - remote homology modeling using structure-guided sequence profiles. Nucleic Acids Res. 38(Web-Server-Issue): 576-581 (2010) - [j15]Cristina Marino Buslje, Elin Teppa, Tomás Di Domenico, José María Delfino, Morten Nielsen:
Networks of High Mutual Information Define the Structural Proximity of Catalytic Sites: Implications for Catalytic Residue Identification. PLoS Comput. Biol. 6(11) (2010) - [c3]Claus Lundegaard, M. Buggert, A. C. Karlsson, Ole Lund, Carina Perez, Morten Nielsen:
PopCover: a method for selecting of peptides with optimal population and pathogen coverage. BCB 2010: 658-659
2000 – 2009
- 2009
- [j14]Hao Zhang, Claus Lundegaard, Morten Nielsen:
Pan-specific MHC class I predictors: a benchmark of HLA class I pan-specific prediction methods. Bioinform. 25(1): 83-89 (2009) - [j13]Cristina Marino Buslje, Javier Santos, José María Delfino, Morten Nielsen:
Correction for phylogeny, small number of observations and data redundancy improves the identification of coevolving amino acid pairs using mutual information. Bioinform. 25(9): 1125-1131 (2009) - [j12]Hao Zhang, Ole Lund, Morten Nielsen:
The PickPocket method for predicting binding specificities for receptors based on receptor pocket similarities: application to MHC-peptide binding. Bioinform. 25(10): 1293-1299 (2009) - [j11]Morten Nielsen, Ole Lund:
NN-align. An artificial neural network-based alignment algorithm for MHC class II peptide binding prediction. BMC Bioinform. 10: 296 (2009) - 2008
- [j10]Claus Lundegaard, Ole Lund, Morten Nielsen:
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. 24(11): 1397-1398 (2008) - [j9]Claus Lundegaard, Kasper Lamberth, Mikkel Harndahl, Søren Buus, Ole Lund, Morten Nielsen:
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. 36(Web-Server-Issue): 509-512 (2008) - [j8]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:
Immune epitope database analysis resource (IEDB-AR). Nucleic Acids Res. 36(Web-Server-Issue): 513-518 (2008) - [j7]Morten Nielsen, Claus Lundegaard, Thomas Blicher, Bjoern Peters, Alessandro Sette, Sune Justesen, Søren Buus, Ole Lund:
Quantitative Predictions of Peptide Binding to Any HLA-DR Molecule of Known Sequence: NetMHCIIpan. PLoS Comput. Biol. 4(7) (2008) - 2007
- [j6]Claus Lundegaard, Ole Lund, Can Kesmir, Søren Brunak, Morten Nielsen:
Modeling the adaptive immune system: predictions and simulations. Bioinform. 23(24): 3265-3275 (2007) - [j5]Mette V. Larsen, Claus Lundegaard, Kasper Lamberth, Søren Buus, Ole Lund, Morten Nielsen:
Large-scale validation of methods for cytotoxic T-lymphocyte epitope prediction. BMC Bioinform. 8 (2007) - [j4]Morten Nielsen, Claus Lundegaard, Ole Lund:
Prediction of MHC class II binding affinity using SMM-align, a novel stabilization matrix alignment method. BMC Bioinform. 8 (2007) - 2006
- [j3]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:
A Community Resource Benchmarking Predictions of Peptide Binding to MHC-I Molecules. PLoS Comput. Biol. 2(6) (2006) - 2005
- [b1]Ole Lund, Morten Nielsen, Claus Lundegaard, Can Kesmir, Søren Brunak:
Immunological bioinformatics. Computational molecular biology, AAAI Press 2005, ISBN 978-0-262-12280-1, pp. I-XII, 1-296 - 2004
- [j2]Morten Nielsen, Claus Lundegaard, Peder Worning, Christina Sylvester-Hvid, Kasper Lamberth, Søren Buus, Søren Brunak, Ole Lund:
Improved prediction of MHC class I and class II epitopes using a novel Gibbs sampling approach. Bioinform. 20(9): 1388-1397 (2004) - [c2]Claus Lundegaard, Morten Nielsen, Kasper Lamberth, Peder Worning, Christina Sylvester-Hvid, Søren Buus, Søren Brunak, Ole Lund:
MHC Class I Epitope Binding Prediction Trained on Small Data Sets. ICARIS 2004: 217-225 - 2003
- [j1]Jens Kaae Christensen, Kasper Lamberth, Morten Nielsen, Claus Lundegaard, Peder Worning, Sanne Lise Lauemøller, Søren Buus, Søren Brunak, Ole Lund:
Selecting Informative Data for Developing Peptide-MHC Binding Predictors Using a Query by Committee Approach. Neural Comput. 15(12): 2931-2942 (2003) - [c1]Claus Lundegaard, Thomas Nordahl Petersen, Morten Nielsen, Henrik Bohr, Jakob Bohr, Søren Brunak, Garry Gippert, Ole Lund:
Prediction of Protein Secondary Structure at High Accuracy Using a Combination of Many Neural Networks. Mathematical Methods for Protein Structure Analysis and Design 2003: 117-122
Coauthor Index
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