Morten Nielsen

Massimo Andreatta, Ole Lund, Morten Nielsen: Simultaneous alignment and clustering of peptide data using a Gibbs sampling approach. Bioinformatics 29(1): 8-14 (2013)

Rémi Gribonval, Morten Nielsen: The restricted isometry property meets nonlinear approximation with redundant frames. Journal of Approximation Theory 165(1): 1-19 (2013)

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 Bioinformatics 13: 235 (2012)

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 Research 40(Web-Server-Issue): 281-287 (2012)

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 Research 40(Web-Server-Issue): 525-530 (2012)

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 Bioinformatics 11: 568 (2010)

Tommy Clausen, Allan Nordlunde Hjorth, Morten Nielsen, David Pisinger: The off-line group seat reservation problem. European Journal of Operational Research 207(3): 1244-1253 (2010)

Morten Nielsen, Claus Lundegaard, Ole Lund, Thomas Nordahl Petersen: CPHmodels-3.0 - remote homology modeling using structure-guided sequence profiles. Nucleic Acids Research 38(Web-Server-Issue): 576-581 (2010)

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 Computational Biology 6(11) (2010)

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

Hao Zhang, Claus Lundegaard, Morten Nielsen: Pan-specific MHC class I predictors: a benchmark of HLA class I pan-specific prediction methods. Bioinformatics 25(1): 83-89 (2009)

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. Bioinformatics 25(9): 1125-1131 (2009)

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. Bioinformatics 25(10): 1293-1299 (2009)

Morten Nielsen, Ole Lund: NN-align. An artificial neural network-based alignment algorithm for MHC class II peptide binding prediction. BMC Bioinformatics 10: 296 (2009)

Rémi Gribonval, Morten Nielsen: Beyond sparsity: Recovering structured representations by l¹{\ell}^1 minimization and greedy algorithms. Adv. Comput. Math. 28(1): 23-41 (2008)

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. Bioinformatics 24(11): 1397-1398 (2008)

Morten Nielsen, Hrvoje Sikic: Quasi-greedy systems of integer translates. Journal of Approximation Theory 155(1): 43-51 (2008)

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 Research 36(Web-Server-Issue): 509-512 (2008)

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 Research 36(Web-Server-Issue): 513-518 (2008)

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 Computational Biology 4(7) (2008)

Morten Nielsen: On polynomial symbols for subdivision schemes. Adv. Comput. Math. 27(2): 195-209 (2007)

Claus Lundegaard, Ole Lund, Can Kesmir, Søren Brunak, Morten Nielsen: Modeling the adaptive immune system: predictions and simulations. Bioinformatics 23(24): 3265-3275 (2007)

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 Bioinformatics 8 (2007)

Morten Nielsen, Claus Lundegaard, Ole Lund: Prediction of MHC class II binding affinity using SMM-align, a novel stabilization matrix alignment method. BMC Bioinformatics 8 (2007)

Morten Nielsen: An example of an almost greedy uniformly bounded orthonormal basis for L_p(0, 1). Journal of Approximation Theory 149(2): 188-192 (2007)

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 Computational Biology 2(6) (2006)

Rémi Gribonval, Morten Nielsen: Sparse approximations in signal and image processing. Signal Processing 86(3): 415-416 (2006)

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. Bioinformatics 20(9): 1388-1397 (2004)

Rémi Gribonval, Morten Nielsen: On the Strong Uniqueness of Highly Sparse Representations from Redundant Dictionaries. ICA 2004: 201-208

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

Lasse Borup, Morten Nielsen: Approximation with brushlet systems. Journal of Approximation Theory 123(1): 25-51 (2003)

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 Computation 15(12): 2931-2942 (2003)

Lasse Borup, Morten Nielsen: Fast adaptive expansions in local trigonometric bases. Signal Processing 83(2): 445-451 (2003)

Rémi Gribonval, Morten Nielsen: Sparse representations in unions of bases. IEEE Transactions on Information Theory 49(12): 3320-3325 (2003)

Rémi Gribonval, Morten Nielsen: Sparse decompositions in "incoherent" dictionaries. ICIP (1) 2003: 33-36

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

Rémi Gribonval, Morten Nielsen: Approximate Weak Greedy Algorithms. Adv. Comput. Math. 14(4): 361-378 (2001)

Morten Nielsen: On the Construction and Frequency Localization of Finite Orthogonal Quadrature Filters. Journal of Approximation Theory 108(1): 36-52 (2001)

Peter H. Carstensen, Morten Nielsen: Characterizing modes of coordination: a comparison between oral and artifact based coordination. GROUP 2001: 81-90

Peter H. Carstensen, Morten Nielsen: Towards Computer Support for Cooperation in Time-Critical Work Settings. HCI (1) 1997: 101-104