List of works by Ole Lund

A Bacterial Analysis Platform: An Integrated System for Analysing Bacterial Whole Genome Sequencing Data for Clinical Diagnostics and Surveillance

scientific article

A community resource benchmarking predictions of peptide binding to MHC-I molecules

scientific article

A novel approach for characterisation of conformational allergen epitopes combining phage display and high-throughput sequencing.

scientific article published on 17 March 2014

Abundance and diversity of the faecal resistome in slaughter pigs and broilers in nine European countries

scientific article published on 23 July 2018

Accurate approximation method for prediction of class I MHC affinities for peptides of length 8, 10 and 11 using prediction tools trained on 9mers.

scientific article published on 14 April 2008

Amino Acid Similarity Accounts for T Cell Cross-Reactivity and for “Holes” in the T Cell Repertoire

scientific article

An Aboriginal Australian genome reveals separate human dispersals into Asia

scientific article (publication date: 7 October 2011)

An integrative approach to CTL epitope prediction: a combined algorithm integrating MHC class I binding, TAP transport efficiency, and proteasomal cleavage predictions.

scientific article published in August 2005

An interactive database for the investigation of high-density peptide microarray guided interaction patterns and antivenom cross-reactivity

scientific article published on 24 June 2020

AnOxPePred: using deep learning for the prediction of antioxidative properties of peptides

scientific article published on 08 December 2020

Antibody Cross-Reactivity in Antivenom Research

scholarly article by Line Ledsgaard et al published 27 September 2018 in Toxins

Application of Whole-Genome Sequencing Data for O-Specific Antigen Analysis and In Silico Serotyping of Pseudomonas aeruginosa Isolates

scientific article

ArrayPitope: Automated Analysis of Amino Acid Substitutions for Peptide Microarray-Based Antibody Epitope Mapping

scientific article

Automated benchmarking of peptide-MHC class I binding predictions

scientific article published on 25 February 2015

Automated download and clean-up of family specific databases for kmer-based virus identification

scientific article published on 08 October 2020

Bacterial whole genome-based phylogeny: construction of a new benchmarking dataset and assessment of some existing methods

scientific article

Benchmarking of methods for genomic taxonomy

scientific article published on 26 February 2014

Benchmarking of methods for identification of antimicrobial resistance genes in bacterial whole genome data.

scientific article

Benchtop Whole-Genome Sequencing for Identification of Nosocomial Outbreaks in Tanzania

scientific article published on 22 February 2016

Bistability in autoimmune diseases.

scientific article published on 19 January 2011

CD4+ T cells with an activated and exhausted phenotype distinguish immunodeficiency during aviremic HIV-2 infection

scientific article published on 11 August 2016

CHTyper, a Web Tool for Subtyping of Extraintestinal Pathogenic Escherichia coli based on the fumC and fimH Alleles

scientific article published on 7 February 2018

CPHmodels-3.0--remote homology modeling using structure-guided sequence profiles

scientific article published on 11 June 2010

CTL epitopes for influenza A including the H5N1 bird flu; genome-, pathogen-, and HLA-wide screening.

scientific article published on 29 December 2006

Ceftriaxone use in a tertiary care hospital in Kilimanjaro, Tanzania: A need for a hospital antibiotic stewardship programme

scientific article published on 05 August 2019

Characterization of HIV-specific CD4+ T cell responses against peptides selected with broad population and pathogen coverage

scientific article

ChemProt-2.0: visual navigation in a disease chemical biology database

scientific article

ChemProt-3.0: a global chemical biology diseases mapping

scientific article published on 13 February 2016

Computational immunology meets bioinformatics: the use of prediction tools for molecular binding in the simulation of the immune system

scientific article

Concepts in Mechanism Based Modeling

Contaminating viral sequences in high-throughput sequencing viromics: a linkage study of 700 sequencing libraries

scientific article published on 04 May 2019

Coronavirus 3CLpro proteinase cleavage sites: possible relevance to SARS virus pathology

scientific article

Correction: MGmapper: Reference based mapping and taxonomy annotation of metagenomics sequence reads

scientific article published on 12 June 2017

Critical role of glycosylation in determining the length and structure of T cell epitopes

scientific article published on 24 September 2009

Cross-recognition of a pit viper (Crotalinae) polyspecific antivenom explored through high-density peptide microarray epitope mapping

scientific article published on 14 July 2017

Definition of supertypes for HLA molecules using clustering of specificity matrices

scientific article published on 13 February 2004

Degree of predicted minor histocompatibility antigen mismatch correlates with poorer clinical outcomes in nonmyeloablative allogeneic hematopoietic cell transplantation

scientific article published on 28 March 2010

Development of a web tool for Escherichia coli sub-typing based on fimH alleles

scientific article

Direct whole-genome sequencing of Plasmodium falciparum specimens from dried erythrocyte spots

scientific article published on 23 February 2018

Distance distributions in proteins: a six-parameter representation

scientific article published on 01 September 1996

Ebolavirus comparative genomics

scientific article (publication date: September 2015)

Epitope mapping and topographic analysis of VAR2CSA DBL3X involved in P. falciparum placental sequestration

scientific article

Erratum to: Evaluating next-generation sequencing for direct clinical diagnostics in diarrhoeal disease.

scientific article

Evaluating next-generation sequencing for direct clinical diagnostics in diarrhoeal disease.

scientific article

Evaluation of peptide selection approaches for epitope-based vaccine design

scientific article published on October 2013

Evaluation of whole genome sequencing for outbreak detection of Salmonella enterica

scientific article published on 04 February 2014

Genome-based in silico identification of new Mycobacterium tuberculosis antigens activating polyfunctional CD8+ T cells in human tuberculosis

scientific article published on 17 December 2010

Genotyping using whole-genome sequencing is a realistic alternative to surveillance based on phenotypic antimicrobial susceptibility testing

scientific article

Global Genomic Epidemiology of Salmonella enterica Serovar Typhimurium DT104.

scientific article

Global monitoring of antimicrobial resistance based on metagenomics analyses of urban sewage

scientific article published on 08 March 2019

HLA class I binding 9mer peptides from influenza A virus induce CD4 T cell responses

scientific article

High throughput resistance profiling of Plasmodium falciparum infections based on custom dual indexing and Illumina next generation sequencing-technology

scientific article

High-affinity human leucocyte antigen class I binding variola-derived peptides induce CD4+ T cell responses more than 30 years post-vaccinia virus vaccination.

scientific article published in March 2009

High-density peptide microarray exploration of the antibody response in a rabbit immunized with a neurotoxic venom fraction

scientific article

High-throughput immuno-profiling of mamba (Dendroaspis) venom toxin epitopes using high-density peptide microarrays

scientific article

High-throughput sequencing enhanced phage display enables the identification of patient-specific epitope motifs in serum

scientific article published on 6 August 2015

Hospital Epidemiology of Methicillin-Resistant Staphylococcus aureus in a Tertiary Care Hospital in Moshi, Tanzania, as Determined by Whole Genome Sequencing

scientific article published on 2 January 2018

HostPhinder: A Phage Host Prediction Tool

scientific article published on 4 May 2016

Human leukocyte antigen (HLA) class I restricted epitope discovery in yellow fewer and dengue viruses: importance of HLA binding strength

scientific article

Humans with chimpanzee-like major histocompatibility complex-specificities control HIV-1 infection

scientific article

Identification and assembly of genomes and genetic elements in complex metagenomic samples without using reference genomes

scientific article published on 6 July 2014

Identification of CD8+ T cell epitopes in the West Nile virus polyprotein by reverse-immunology using NetCTL.

scientific article

Identification of Known and Novel Recurrent Viral Sequences in Data from Multiple Patients and Multiple Cancers

scientific article

Identification of MHC class II restricted T-cell-mediated reactivity against MHC class I binding Mycobacterium tuberculosis peptides

scientific article published on 7 February 2011

Identification of Y-Chromosomally Encoded Minor Histocompatibility Antigens Using a Reverse Immunology Approach

scholarly article by Bo Kok Mortensen et al published February 2013 in Biology of Blood and Marrow Transplantation

Identification of a novel UTY-encoded minor histocompatibility antigen

scientific article published in August 2012

Identification of acquired antimicrobial resistance genes

scientific article published on 10 July 2012

Immune epitope database analysis resource

scientific article

Immune epitope database analysis resource (IEDB-AR).

scientific article published on 31 May 2008

Immune system simulation online

scientific article published on 17 June 2011

ImmunoGrid: towards agent-based simulations of the human immune system at a natural scale

scientific article published on June 2010

Improved Resistance Prediction in Mycobacterium tuberculosis by Better Handling of Insertions and Deletions, Premature Stop Codons, and Filtering of Non-informative Sites

scientific article published on 31 October 2019

Improved method for predicting linear B-cell epitopes

scientific article

Improved prediction of MHC class I and class II epitopes using a novel Gibbs sampling approach

scientific article published on 12 February 2004

In silico Genotyping of Escherichia coli Isolates for Extraintestinal Virulence Genes by Use of Whole-Genome Sequencing Data

scientific article published on 15 July 2020

In silico detection and typing of plasmids using PlasmidFinder and plasmid multilocus sequence typing

scientific article

In silico prediction of human pathogenicity in the γ-proteobacteria ⬇️

scientific article

Insight into antigenic diversity of VAR2CSA-DBL5ε domain from multiple Plasmodium falciparum placental isolates

scientific article

Insights from 20 years of bacterial genome sequencing

scientific article

Interdisciplinary analysis of HIV-specific CD8+ T cell responses against variant epitopes reveals restricted TCR promiscuity.

scientific article published on 2 April 2010

LRE-Finder, a Web tool for detection of the 23S rRNA mutations and the optrA, cfr, cfr(B) and poxtA genes encoding linezolid resistance in enterococci from whole-genome sequences

scientific article published on 01 June 2019

Large scale automated phylogenomic analysis of bacterial isolates and the Evergreen Online platform

scientific article published on 20 March 2020

Large scale automated phylogenomical analysis of bacterial whole-genome isolates and the Evergreen platform

Large-scale validation of methods for cytotoxic T-lymphocyte epitope prediction

scientific article

Limitations of Ab initio predictions of peptide binding to MHC class II molecules

scientific article

Low-bandwidth and non-compute intensive remote identification of microbes from raw sequencing reads

scientific article

MGmapper: Reference based mapping and taxonomy annotation of metagenomics sequence reads

scientific article

MHC class II epitope predictive algorithms.

scientific article

MHC motif viewer

scientific article published on 3 September 2008

MHC-I-restricted epitopes conserved among variola and other related orthopoxviruses are recognized by T cells 30 years after vaccination

scientific article published on 12 September 2008

MHCcluster, a method for functional clustering of MHC molecules

scientific article published on 18 June 2013

MR1-restricted MAIT cells display ligand discrimination and pathogen selectivity through distinct T cell receptor usage

scientific article

MULTIPRED2: a computational system for large-scale identification of peptides predicted to bind to HLA supertypes and alleles

scientific article published on 2 December 2010

Machine learning competition in immunology - Prediction of HLA class I binding peptides.

scientific article published on 29 September 2011

Major histocompatibility complex class I binding predictions as a tool in epitope discovery.

scientific article published on 26 May 2010

Meta-analysis of proportion estimates of Extended-Spectrum-Beta-Lactamase-producing Enterobacteriaceae in East Africa hospitals

scientific article

Meta-genomic analysis of toilet waste from long distance flights; a step towards global surveillance of infectious diseases and antimicrobial resistance

scientific article published on 10 July 2015

MetaPhinder-Identifying Bacteriophage Sequences in Metagenomic Data Sets

scientific article

Metaphylogenetic analysis of global sewage reveals that bacterial strains associated with human disease show less degree of geographic clustering

scientific article published on 20 February 2020

Modeling the adaptive immune system: predictions and simulations

scientific article published on 28 November 2007

Modelling the human immune system by combining bioinformatics and systems biology approaches

scientific article published on 27 October 2006

Molecular epidemiology of virulence and antimicrobial resistance determinants in Klebsiella pneumoniae from hospitalised patients in Kilimanjaro, Tanzania

scholarly article by Tolbert Sonda et al published 20 July 2018 in European Journal of Clinical Microbiology & Infectious Diseases

Multidimensional Clusters of CD4+ T Cell Dysfunction Are Primarily Associated with the CD4/CD8 Ratio in Chronic HIV Infection

scientific article published on 24 September 2015

Multidrug-resistant Neisseria gonorrhoeae infection with ceftriaxone resistance and intermediate resistance to azithromycin, Denmark, 2017.

scientific article published in October 2017

Multilocus sequence typing of total-genome-sequenced bacteria

scientific article

Multiparametric bioinformatics distinguish the CD4/CD8 ratio as a suitable laboratory predictor of combined T cell pathogenesis in HIV infection

scientific article

NN-align. An artificial neural network-based alignment algorithm for MHC class II peptide binding prediction

scientific article

NNAlign: a web-based prediction method allowing non-expert end-user discovery of sequence motifs in quantitative peptide data

scientific article (publication date: 2011)

NetFCM: a semi-automated web-based method for flow cytometry data analysis

scientific article

NetMHC-3.0: accurate web accessible predictions of human, mouse and monkey MHC class I affinities for peptides of length 8-11

scientific article published on 7 May 2008

NetMHCIIpan-2.0 - Improved pan-specific HLA-DR predictions using a novel concurrent alignment and weight optimization training procedure.

scientific article

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.

scientific article published on 31 July 2013

NetMHCcons: a consensus method for the major histocompatibility complex class I predictions

scientific article published on 20 October 2011

NetMHCpan, a method for MHC class I binding prediction beyond humans

scientific article published on 12 November 2008

NetMHCpan, a method for quantitative predictions of peptide binding to any HLA-A and -B locus protein of known sequence

scientific article

New Genome-Wide Algorithm Identifies Novel In-Vivo Expressed Mycobacterium Tuberculosis Antigens Inducing Human T-Cell Responses with Classical and Unconventional Cytokine Profiles

scientific article

Norwegian patients and retail chicken meat share cephalosporin-resistant Escherichia coli and IncK/blaCMY-2 resistance plasmids

scientific article published on 7 January 2017

Novel variation and de novo mutation rates in population-wide de novo assembled Danish trios ⬇️

scientific article

PathogenFinder--distinguishing friend from foe using bacterial whole genome sequence data

scientific article

Patterns of infections, aetiological agents and antimicrobial resistance at a tertiary care hospital in northern Tanzania

scientific article published on 10 January 2017

Peptide binding predictions for HLA DR, DP and DQ molecules

scientific article

PlasmidHostFinder: Prediction of Plasmid Hosts Using Random Forest

scientific article published on 06 April 2022

Plasmodium falciparum population dynamics in a cohort of pregnant women in Senegal

scientific article

PointFinder: a novel web tool for WGS-based detection of antimicrobial resistance associated with chromosomal point mutations in bacterial pathogens

scientific article published in October 2017

Porcine major histocompatibility complex (MHC) class I molecules and analysis of their peptide-binding specificities

scientific article

Prediction of Acquired Antimicrobial Resistance for Multiple Bacterial Species Using Neural Networks

scientific article published on 21 January 2020

Prediction of MHC class II binding affinity using SMM-align, a novel stabilization matrix alignment method

scientific article

Prediction of epitopes using neural network based methods

scientific article published on 31 October 2010

Predictions versus high-throughput experiments in T-cell epitope discovery: competition or synergy?

scientific article published on January 2012

Prevalence and risk factors for CTX-M gram-negative bacteria in hospitalized patients at a tertiary care hospital in Kilimanjaro, Tanzania

scientific article published on 20 February 2018

Proof of concept: used malaria rapid diagnostic tests applied for parallel sequencing for surveillance of molecular markers of anti-malarial resistance in Bissau, Guinea-Bissau during 2014-2017

scientific article published on 26 July 2019

Propionibacterium acnes: Disease-Causing Agent or Common Contaminant? Detection in Diverse Patient Samples by Next-Generation Sequencing

scientific article published on 27 January 2016

Quantitative predictions of peptide binding to any HLA-DR molecule of known sequence: NetMHCIIpan

scientific article

RUCS: rapid identification of PCR primers for unique core sequences

scientific article published on 30 August 2017

Rapid Whole-Genome Sequencing for Detection and Characterization of Microorganisms Directly from Clinical Samples.

scientific article published in August 2014

Rapid and precise alignment of raw reads against redundant databases with KMA

scientific article published on 29 August 2018

Rapid whole-genome sequencing for detection and characterization of microorganisms directly from clinical samples

scientific article published on 30 October 2013

Reads2Type: a web application for rapid microbial taxonomy identification

scientific article published on 25 November 2015

Real-time whole-genome sequencing for routine typing, surveillance, and outbreak detection of verotoxigenic Escherichia coli

scientific article published on 26 February 2014

SCCmecFinder, a Web-Based Tool for Typing of Staphylococcal Cassette Chromosome mec in Staphylococcus aureus Using Whole-Genome Sequence Data.

scientific article published in January 2018

Selecting informative data for developing peptide-MHC binding predictors using a query by committee approach.

scientific article

Sequencing and de novo assembly of 150 genomes from Denmark as a population reference

scientific article published in Nature

SigniSite: Identification of residue-level genotype-phenotype correlations in protein multiple sequence alignments

scientific article published on 12 June 2013

Simultaneous alignment and clustering of peptide data using a Gibbs sampling approach

scientific article published on 24 October 2012

Solving the problem of comparing whole bacterial genomes across different sequencing platforms

scientific article

Specific gut microbiome members are associated with distinct immune markers in allogeneic hematopoietic stem cell transplantation

Specific gut microbiome members are associated with distinct immune markers in pediatric allogeneic hematopoietic stem cell transplantation

scientific article published on 13 September 2019

State of the art and challenges in sequence based T-cell epitope prediction

scientific article

Structural analysis of B-cell epitopes in antibody:protein complexes

scientific article

Structural insight into epitopes in the pregnancy-associated malaria protein VAR2CSA

scientific article

Synthesis and Biological Evaluations of Cytotoxic and Antiangiogenic Triterpenoids-Jacaranone Conjugates

scientific article published on 2 May 2016

Systematic characterisation of cellular localisation and expression profiles of proteins containing MHC ligands

scientific article

T-bet and Eomes are differentially linked to the exhausted phenotype of CD8+ T cells in HIV infection

scientific article

Targeting of conserved gag-epitopes in early HIV infection is associated with lower plasma viral load and slower CD4(+) T cell depletion

scientific article published on 8 January 2013

The CGE Tool Box

The COMPARE Data Hubs

scientific article published on 01 January 2019

The PickPocket method for predicting binding specificities for receptors based on receptor pocket similarities: application to MHC-peptide binding

scientific article

The design and implementation of the immune epitope database and analysis resource

scientific article published on 14 May 2005

The immune epitope database and analysis resource: from vision to blueprint

scientific article

The peptide-binding specificity of HLA-A*3001 demonstrates membership of the HLA-A3 supertype

scientific article

The role of the proteasome in generating cytotoxic T-cell epitopes: insights obtained from improved predictions of proteasomal cleavage

The validity of predicted T-cell epitopes.

scientific article published on 12 October 2006

Towards a consensus on datasets and evaluation metrics for developing B-cell epitope prediction tools

scientific article

Using WGS to identify antibiotic resistance genes and predict antimicrobial resistance phenotypes in MDR Acinetobacter baumannii in Tanzania

article

What Can We Learn from a Metagenomic Analysis of a Georgian Bacteriophage Cocktail?

scientific article

Whole genome sequencing reveals high clonal diversity of Escherichia coli isolated from patients in a tertiary care hospital in Moshi, Tanzania.

scientific article

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