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Lista de obras de Ole Lund

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

artículo científico publicado en 2016

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

artículo científico publicado en 2006

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

artículo científico publicado en 2014

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

artículo científico publicado en 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

artículo científico publicado en 2008

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

artículo científico publicado en 2008

An Aboriginal Australian genome reveals separate human dispersals into Asia

artículo científico publicado en 2011

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

artículo científico publicado en 2005

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

artículo científico publicado en 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

artículo científico publicado en 2016

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

artículo científico publicado en 2017

Automated benchmarking of peptide-MHC class I binding predictions

artículo científico publicado en 2015

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

artículo científico publicado en 2020

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

artículo científico publicado en 2017

Benchmarking of methods for genomic taxonomy

artículo científico publicado en 2014

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

artículo científico publicado en 2016

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

artículo científico publicado en 2016

Bistability in autoimmune diseases ⬇️

artículo científico publicado el 19 de enero de 2011

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

artículo científico publicado en 2016

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

artículo científico publicado en 2018

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

artículo científico publicado en 2010

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

artículo científico publicado en 2006

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

artículo científico publicado en 2019

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

artículo científico publicado en 2012

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

artículo científico publicado en 2012

ChemProt-3.0: a global chemical biology diseases mapping

artículo científico publicado en 2016

Complement-Mediated Enhancement of HIV-1 Infection in Peripheral Blood Mononuclear Cells ⬇️

artículo científico publicado el 1 de enero de 1997

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

artículo científico publicado en 2010

Concepts in Mechanism Based Modeling

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

artículo científico publicado en 2019

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

artículo científico publicado en 2004

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

artículo científico publicado en 2017

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

artículo científico publicado en 2009

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

artículo científico

Definition of supertypes for HLA molecules using clustering of specificity matrices

artículo científico publicado en 2004

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

artículo científico publicado en 2010

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

artículo científico publicado en 2017

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

artículo científico publicado en 2018

Distance distributions in proteins: a six-parameter representation

artículo científico publicado en 1996

Ebolavirus comparative genomics

artículo científico publicado en 2015

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

artículo científico publicado en 2006

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

artículo científico publicado en 2017

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

artículo científico publicado en 2017

Evaluation of peptide selection approaches for epitope-based vaccine design

artículo científico publicado en 2013

Evaluation of whole genome sequencing for outbreak detection of Salmonella enterica

artículo científico publicado en 2014

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

artículo científico publicado en 2010

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

artículo científico publicado en 2012

Global Genomic Epidemiology of Salmonella enterica Serovar Typhimurium DT104.

artículo científico publicado en 2016

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

artículo científico publicado en 2019

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

artículo científico publicado en 2010

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

artículo científico publicado en 2017

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

artículo científico publicado en 2009

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

artículo científico publicado en 2017

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

artículo científico publicado en 2016

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

artículo científico publicado en 2015

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

artículo científico publicado en 2018

HostPhinder: A Phage Host Prediction Tool

artículo científico publicado en 2016

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

artículo científico publicado en 2011

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

artículo científico publicado en 2008

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

artículo científico publicado en 2014

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

artículo científico publicado en 2010

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

artículo científico publicado en 2016

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

artículo científico publicado en 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

artículo científico publicado en 2012

Identification of acquired antimicrobial resistance genes

artículo científico publicado en 2012

Immune epitope database analysis resource

artículo científico publicado en 2012

Immune epitope database analysis resource (IEDB-AR).

artículo científico publicado en 2008

Immune system simulation online

artículo científico publicado en 2011

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

artículo científico

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

artículo científico publicado en 2019

Improved method for predicting linear B-cell epitopes

artículo científico publicado en 2006

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

artículo científico publicado en 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

artículo científico publicado en 2014

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

artículo científico publicado en 2010

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

artículo científico publicado en 2010

Insights from 20 years of bacterial genome sequencing

artículo científico publicado en 2015

Integrating Genome-based Informatics to Modernize Global Disease Monitoring, Information Sharing, and Response ⬇️

artículo científico publicado el 1 de noviembre de 2012

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

artículo científico publicado en 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

artículo científico publicado en 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

artículo científico publicado en 2007

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

artículo científico publicado en 2010

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

artículo científico publicado en 2013

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

artículo científico publicado en 2017

MHC class II epitope predictive algorithms.

artículo científico publicado en 2010

MHC motif viewer

artículo científico publicado en 2008

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

artículo científico publicado en 2008

MHCcluster, a method for functional clustering of MHC molecules

artículo científico publicado en 2013

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

artículo científico publicado en 2014

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

artículo científico publicado en 2010

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

artículo científico publicado en 2011

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

artículo científico publicado en 2010

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

artículo científico publicado en 2016

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

artículo científico publicado en 2015

MetaPhinder-Identifying Bacteriophage Sequences in Metagenomic Data Sets

artículo científico publicado en 2016

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

artículo científico publicado en 2007

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

artículo científico publicado en 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

artículo científico publicado en 2015

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

artículo científico publicado en 2017

Multilocus sequence typing of total-genome-sequenced bacteria

artículo científico publicado en 2012

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

artículo científico publicado en 2014

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

artículo científico publicado en 2009

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

artículo científico publicado en 2011

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

artículo científico publicado en 2014

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

artículo científico publicado en 2008

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

artículo científico publicado en 2010

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.

artículo científico publicado en 2013

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

artículo científico publicado en 2011

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

artículo científico publicado en 2008

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

artículo científico publicado en 2007

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

artículo científico publicado en 2016

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

artículo científico publicado en 2017

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

artículo científico publicado en 2015

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

artículo científico publicado en 2013

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

artículo científico publicado en 2017

Peptide binding predictions for HLA DR, DP and DQ molecules

artículo científico publicado en 2010

PlasmidHostFinder: Prediction of Plasmid Hosts Using Random Forest

artículo científico publicado en 2022

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

artículo científico publicado en 2010

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

artículo científico publicado en 2017

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

artículo científico publicado en 2011

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

artículo científico publicado en 2007

Prediction of epitopes using neural network based methods

artículo científico publicado en 2010

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

artículo científico publicado en 2012

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

artículo científico publicado en 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

artículo científico publicado en 2019

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

artículo científico publicado en 2016

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

artículo científico publicado en 2008

RUCS: rapid identification of PCR primers for unique core sequences

artículo científico publicado en 2017

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

artículo científico publicado en 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

artículo científico publicado en 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.

artículo científico publicado en 2018

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

artículo científico publicado en 2003

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

artículo científico publicado en 2017

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

artículo científico publicado el 12 de junio de 2013

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

artículo científico publicado el 24 de octubre de 2012

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

artículo científico publicado en 2014

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

artículo científico publicado en 2019

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

artículo científico publicado en 2010

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

artículo científico publicado en 2012

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

artículo científico publicado en 2008

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

artículo científico publicado en 2016

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

artículo científico publicado en 2009

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

artículo científico publicado en 2014

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

artículo científico publicado en 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

artículo científico publicado en 2009

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

artículo científico publicado en 2005

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

artículo científico publicado en 2005

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

artículo científico publicado en 2008

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

artículo científico publicado en 2006

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

artículo científico publicado en 2007

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?

artículo científico publicado en 2015

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

artículo científico publicado en 2018

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