PubRank

Morten Nielsen

Author PubWeight™ 111.07‹?›

Top papers

Rank Title Journal Year PubWeight™‹?›
1 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 2008 4.53
2 Improved method for predicting linear B-cell epitopes. Immunome Res 2006 4.32
3 NetMHCpan, a method for MHC class I binding prediction beyond humans. Immunogenetics 2008 3.59
4 A generic method for assignment of reliability scores applied to solvent accessibility predictions. BMC Struct Biol 2009 3.56
5 Prediction of residues in discontinuous B-cell epitopes using protein 3D structures. Protein Sci 2006 3.06
6 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 2008 2.69
7 Peptide binding predictions for HLA DR, DP and DQ molecules. BMC Bioinformatics 2010 2.53
8 Definition of supertypes for HLA molecules using clustering of specificity matrices. Immunogenetics 2004 2.39
9 An integrative approach to CTL epitope prediction: a combined algorithm integrating MHC class I binding, TAP transport efficiency, and proteasomal cleavage predictions. Eur J Immunol 2005 2.19
10 Immune epitope database analysis resource (IEDB-AR). Nucleic Acids Res 2008 2.14
11 Immune epitope database analysis resource. Nucleic Acids Res 2012 2.09
12 Large-scale validation of methods for cytotoxic T-lymphocyte epitope prediction. BMC Bioinformatics 2007 2.05
13 Prognostic factors for survival and resection in patients with initial nonresectable locally advanced pancreatic cancer treated with chemoradiotherapy. Int J Radiat Oncol Biol Phys 2011 2.05
14 Modeling the adaptive immune system: predictions and simulations. Bioinformatics 2007 1.95
15 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 2012 1.81
16 From lanosterol to cholesterol: structural evolution and differential effects on lipid bilayers. Biophys J 2002 1.67
17 CTL epitopes for influenza A including the H5N1 bird flu; genome-, pathogen-, and HLA-wide screening. Vaccine 2006 1.66
18 NetMHCcons: a consensus method for the major histocompatibility complex class I predictions. Immunogenetics 2011 1.57
19 Pan-specific MHC class I predictors: a benchmark of HLA class I pan-specific prediction methods. Bioinformatics 2008 1.53
20 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. Immunogenetics 2013 1.49
21 Reliable B cell epitope predictions: impacts of method development and improved benchmarking. PLoS Comput Biol 2012 1.44
22 NetCTLpan: pan-specific MHC class I pathway epitope predictions. Immunogenetics 2010 1.37
23 [Treatment of unresectable locally advanced pancreatic cancer with combined radiotherapy and chemotherapy]. Ugeskr Laeger 2008 1.37
24 Prediction of epitopes using neural network based methods. J Immunol Methods 2010 1.35
25 Correction for phylogeny, small number of observations and data redundancy improves the identification of coevolving amino acid pairs using mutual information. Bioinformatics 2009 1.30
26 Structural analysis of B-cell epitopes in antibody:protein complexes. Mol Immunol 2012 1.28
27 No evidence for the use of DIR, D-D fusions, chromosome 15 open reading frames or VH replacement in the peripheral repertoire was found on application of an improved algorithm, JointML, to 6329 human immunoglobulin H rearrangements. Immunology 2006 1.28
28 Peptide binding to HLA class I molecules: homogenous, high-throughput screening, and affinity assays. J Biomol Screen 2009 1.27
29 Broadly immunogenic HLA class I supertype-restricted elite CTL epitopes recognized in a diverse population infected with different HIV-1 subtypes. J Immunol 2008 1.25
30 Peptide-MHC class I stability is a better predictor than peptide affinity of CTL immunogenicity. Eur J Immunol 2012 1.24
31 Major histocompatibility complex class I binding predictions as a tool in epitope discovery. Immunology 2010 1.21
32 NNAlign: a web-based prediction method allowing non-expert end-user discovery of sequence motifs in quantitative peptide data. PLoS One 2011 1.20
33 Machine learning competition in immunology - Prediction of HLA class I binding peptides. J Immunol Methods 2011 1.18
34 MISTIC: Mutual information server to infer coevolution. Nucleic Acids Res 2013 1.14
35 HLArestrictor--a tool for patient-specific predictions of HLA restriction elements and optimal epitopes within peptides. Immunogenetics 2010 1.11
36 Amino acid similarity accounts for T cell cross-reactivity and for "holes" in the T cell repertoire. PLoS One 2008 1.11
37 Simultaneous alignment and clustering of peptide data using a Gibbs sampling approach. Bioinformatics 2012 1.08
38 The PickPocket method for predicting binding specificities for receptors based on receptor pocket similarities: application to MHC-peptide binding. Bioinformatics 2009 1.08
39 The MHC motif viewer: a visualization tool for MHC binding motifs. Curr Protoc Immunol 2010 1.07
40 Networks of high mutual information define the structural proximity of catalytic sites: implications for catalytic residue identification. PLoS Comput Biol 2010 1.07
41 MHCcluster, a method for functional clustering of MHC molecules. Immunogenetics 2013 1.01
42 Interdisciplinary analysis of HIV-specific CD8+ T cell responses against variant epitopes reveals restricted TCR promiscuity. J Immunol 2010 1.00
43 The validity of predicted T-cell epitopes. Trends Biotechnol 2006 0.99
44 MHC motif viewer. Immunogenetics 2008 0.99
45 The peptide-binding specificity of HLA-A*3001 demonstrates membership of the HLA-A3 supertype. Immunogenetics 2008 0.97
46 Induction of foot-and-mouth disease virus-specific cytotoxic T cell killing by vaccination. Clin Vaccine Immunol 2010 0.96
47 State of the art and challenges in sequence based T-cell epitope prediction. Immunome Res 2010 0.95
48 Human leukocyte antigen (HLA) class I restricted epitope discovery in yellow fewer and dengue viruses: importance of HLA binding strength. PLoS One 2011 0.94
49 NetMHCstab - predicting stability of peptide-MHC-I complexes; impacts for cytotoxic T lymphocyte epitope discovery. Immunology 2014 0.93
50 Limitations of Ab initio predictions of peptide binding to MHC class II molecules. PLoS One 2010 0.92
51 Selecting informative data for developing peptide-MHC binding predictors using a query by committee approach. Neural Comput 2003 0.92
52 Porcine major histocompatibility complex (MHC) class I molecules and analysis of their peptide-binding specificities. Immunogenetics 2011 0.91
53 Modular DNA-programmed assembly of linear and branched conjugated nanostructures. J Am Chem Soc 2004 0.91
54 Different binding motifs of the celiac disease-associated HLA molecules DQ2.5, DQ2.2, and DQ7.5 revealed by relative quantitative proteomics of endogenous peptide repertoires. Immunogenetics 2014 0.91
55 Influence of dose calculation algorithms on the predicted dose distribution and NTCP values for NSCLC patients. Med Phys 2011 0.90
56 Identification of CD8+ T cell epitopes in the West Nile virus polyprotein by reverse-immunology using NetCTL. PLoS One 2010 0.89
57 Predictions versus high-throughput experiments in T-cell epitope discovery: competition or synergy? Expert Rev Vaccines 2012 0.88
58 Humans with chimpanzee-like major histocompatibility complex-specificities control HIV-1 infection. AIDS 2008 0.87
59 Characterizing the binding motifs of 11 common human HLA-DP and HLA-DQ molecules using NNAlign. Immunology 2012 0.87
60 Disentangling evolutionary signals: conservation, specificity determining positions and coevolution. Implication for catalytic residue prediction. BMC Bioinformatics 2012 0.86
61 Dataset size and composition impact the reliability of performance benchmarks for peptide-MHC binding predictions. BMC Bioinformatics 2014 0.85
62 A DNA tile actuator with eleven discrete states. Angew Chem Int Ed Engl 2011 0.85
63 Systematic characterisation of cellular localisation and expression profiles of proteins containing MHC ligands. PLoS One 2009 0.85
64 HLA class I binding 9mer peptides from influenza A virus induce CD4 T cell responses. PLoS One 2010 0.85
65 Sortilin facilitates signaling of ciliary neurotrophic factor and related helical type 1 cytokines targeting the gp130/leukemia inhibitory factor receptor beta heterodimer. Mol Cell Biol 2010 0.84
66 Modeling lipid-sterol bilayers: applications to structural evolution, lateral diffusion, and rafts. Methods Enzymol 2004 0.84
67 SigniSite: Identification of residue-level genotype-phenotype correlations in protein multiple sequence alignments. Nucleic Acids Res 2013 0.84
68 Designing bovine T cell vaccines via reverse immunology. Ticks Tick Borne Dis 2012 0.83
69 Degree of predicted minor histocompatibility antigen mismatch correlates with poorer clinical outcomes in nonmyeloablative allogeneic hematopoietic cell transplantation. Biol Blood Marrow Transplant 2010 0.83
70 Sensitivity of NTCP parameter values against a change of dose calculation algorithm. Med Phys 2007 0.81
71 Characterization of HIV-specific CD4+ T cell responses against peptides selected with broad population and pathogen coverage. PLoS One 2012 0.81
72 In silico prediction of human pathogenicity in the γ-proteobacteria. PLoS One 2010 0.81
73 Common variants of the ACE gene and aneurysmal subarachnoid hemorrhage in a Danish population: a case-control study. J Neurosurg Anesthesiol 2011 0.81
74 Use of "one-pot, mix-and-read" peptide-MHC class I tetramers and predictive algorithms to improve detection of cytotoxic T lymphocyte responses in cattle. Vet Res 2014 0.80
75 Modelling the human immune system by combining bioinformatics and systems biology approaches. J Biol Phys 2006 0.80
76 Structural properties of MHC class II ligands, implications for the prediction of MHC class II epitopes. PLoS One 2010 0.80
77 Characterization of binding specificities of bovine leucocyte class I molecules: impacts for rational epitope discovery. Immunogenetics 2014 0.79
78 Radiation dose response of normal lung assessed by Cone Beam CT - a potential tool for biologically adaptive radiation therapy. Radiother Oncol 2011 0.78
79 Chiral ordering and conformational dynamics for a class of oligo-phenylene-ethynylenes on Au(111). J Phys Chem B 2007 0.78
80 A modern approach for epitope prediction: identification of foot-and-mouth disease virus peptides binding bovine leukocyte antigen (BoLA) class I molecules. Immunogenetics 2015 0.78
81 Age dependent prognosis in concurrent chemo-radiation of locally advanced NSCLC. Acta Oncol 2014 0.77
82 The cancer exome generated by alternative mRNA splicing dilutes predicted HLA class I epitope density. PLoS One 2012 0.77
83 NetTepi: an integrated method for the prediction of T cell epitopes. Immunogenetics 2014 0.77
84 In silico peptide-binding predictions of passerine MHC class I reveal similarities across distantly related species, suggesting convergence on the level of protein function. Immunogenetics 2013 0.77
85 Isotoxic dose escalation in the treatment of lung cancer by means of heterogeneous dose distributions in the presence of respiratory motion. Int J Radiat Oncol Biol Phys 2011 0.76
86 Self-assembly of aluminium-salen coupled nanostructures from encoded modules with cleavable disulfide DNA-linkers. Chem Commun (Camb) 2004 0.76
87 Long-term results of concurrent radiotherapy and UFT in patients with locally advanced pancreatic cancer. Radiother Oncol 2009 0.76
88 CD4+ T cells with an activated and exhausted phenotype distinguish immunodeficiency during aviremic HIV-2 infection. AIDS 2016 0.75
89 In reply to Parlak and Topkan. Re: Prognostic factors for survival and resection in patients with initial nonresectable locally advanced pancreatic cancer treated with chemoradiotherapy. Int J Radiat Oncol Biol Phys 2013 0.75
90 The representitativeness of patient position during the first treatment fractions. Acta Oncol 2009 0.75
91 Influence of molecular geometry on the adsorption orientation for oligophenylene-ethynylenes on Au(111). J Phys Chem B 2007 0.75
92 Haplotype structure of the beta2-adrenergic receptor gene in 814 Danish Caucasian subjects and association with body mass index. Scand J Clin Lab Invest 2009 0.75
93 Improved prediction of Bovine Leucocyte Antigens (BoLA) presented ligands by use of mass spectrometry-determined ligand- and in-vitro binding data. J Proteome Res 2017 0.75
94 Bioinformatics identification of antigenic peptide: predicting the specificity of major MHC class I and II pathway players. Methods Mol Biol 2013 0.75