Ole Lund
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When Not to Kill Your Host in Competitive Bust-Boom Environments Open
Temperate phages, which can either kill their host cells or integrate into them, struggle to compete with purely virulent phages in environments with plenty of available hosts. This suggests that their survival strategy is fine-tuned for u…
View article: MAGinator enables strain-level quantification of<i>de novo</i>MAGs
MAGinator enables strain-level quantification of<i>de novo</i>MAGs Open
Motivation Metagenomic sequencing has provided great advantages in the characterization of microbiomes, but currently available analysis tools lack the ability to combine strain-level taxonomic resolution and abundance estimation with func…
View article: Deep integrative models for large-scale human genomics
Deep integrative models for large-scale human genomics Open
Polygenic risk scores (PRSs) are expected to play a critical role in precision medicine. Currently, PRS predictors are generally based on linear models using summary statistics, and more recently individual-level data. However, these predi…
The enhancing effect of intercropping sugar beet with chicory on the deep root growth and nutrient uptake Open
Crops with deeper rooting is an emerging tool for better exploitation of soil resources. However, there is a need for more in-depth understanding on how the increased rooting depth may be achieved. In this study a novel approach for obtain…
Additional file 1 of Whole genome sequencing reveals high clonal diversity of Escherichia coli isolated from patients in a tertiary care hospital in Moshi, Tanzania Open
Table S1. A pairwise genome comparison matrix of SNP differences for E. coli ST131. (XLS 34 kb)
Additional file 2 of Whole genome sequencing reveals high clonal diversity of Escherichia coli isolated from patients in a tertiary care hospital in Moshi, Tanzania Open
Table S2. A pairwise genome comparison matrix of SNP differences for E. coli ST10 clonal complex. (XLS 29 kb)
SourceFinder: a Machine-Learning-Based Tool for Identification of Chromosomal, Plasmid, and Bacteriophage Sequences from Assemblies Open
Extra-chromosomal genes encoding antimicrobial resistance, metal resistance, and virulence provide selective advantages for bacterial survival under stress conditions and pose serious threats to human and animal health. These accessory gen…
Improved prediction of blood biomarkers using deep learning Open
Blood and urine biomarkers are an essential part of modern medicine, not only for diagnosis, but also for their direct influence on disease. Many biomarkers have a genetic component, and they have been studied extensively with genome-wide …
Metagenomic DNA sequencing for semi-quantitative pathogen detection from urine: a prospective, laboratory-based, proof-of-concept study Open
EU Horizon 2020 Research and Innovation Programme.
PlasmidHostFinder: Prediction of Plasmid Hosts Using Random Forest Open
Antimicrobial resistance is a global health threat to humans and animals, causing high mortality and morbidity while effectively ending decades of success in fighting against bacterial infections. Plasmids confer extra genetic capabilities…
PlasmidHostFinder: Prediction of plasmid hosts using random forest Open
Plasmids play a major role facilitating the spread of antimicrobial resistance between bacteria. Understanding the host range and dissemination trajectories of plasmids is critical for surveillance and prevention of antimicrobial resistanc…
View article: Identification of Single-Nucleotide Polymorphisms in the Mitochondrial Genome and Kelch 13 Gene of Plasmodium falciparum in Different Geographical Populations
Identification of Single-Nucleotide Polymorphisms in the Mitochondrial Genome and Kelch 13 Gene of Plasmodium falciparum in Different Geographical Populations Open
The emergence of artemisinin-resistant Plasmodium falciparum parasites in Southeast Asia threatens malaria control and elimination. The interconnectedness of parasite populations may be essential to monitor the spread of resistance. Combin…
View article: Production Characteristics and Strategies for Adapting to the Impact of Climate Change on Cassava Whiteflies and Viruses in Tanzania
Production Characteristics and Strategies for Adapting to the Impact of Climate Change on Cassava Whiteflies and Viruses in Tanzania Open
Cassava is Africa’s most important food security crop and sustains about 700 million people globally. Survey interviews of 320 farmers in three regions of Tanzania to identify their production characteristics, and interviews with 20 intern…
Predicting Antimicrobial Resistance Using Partial Genome Alignments Open
Antimicrobial resistance causes thousands of deaths annually worldwide. Understanding the regions of the genome that are involved in antimicrobial resistance is important for developing mitigation strategies and preventing transmission.
Deep integrative models for large-scale human genomics Open
Polygenic risk scores (PRSs) are expected to play a critical role in achieving precision medicine. Currently, PRS predictors are generally based on linear models using summary statistics, and more recently individual-level data. However, t…
Rapid Open-Source SNP-Based Clustering Offers an Alternative to Core Genome MLST for Outbreak Tracing in a Hospital Setting Open
Traditional genotyping methods for infection control of antimicrobial-resistant bacteria in healthcare settings have been supplemented by whole-genome sequencing (WGS), often relying on a gene-based approach, e.g., core genome multilocus s…
Machine learning predicts and provides insights into milk acidification rates of Lactococcus lactis Open
Lactococcus lactis strains are important components in industrial starter cultures for cheese manufacturing. They have many strain-dependent properties, which affect the final product. Here, we explored the use of machine learning to creat…
Genetic variation for tolerance to the downy mildew pathogen Peronospora variabilis in genetic resources of quinoa (Chenopodium quinoa) Open
Background Quinoa ( Chenopodium quinoa Willd.) is an ancient grain crop that is tolerant to abiotic stress and has favorable nutritional properties. Downy mildew is the main disease of quinoa and is caused by infections of the biotrophic o…
Additional file 2 of Genetic variation for tolerance to the downy mildew pathogen Peronospora variabilis in genetic resources of quinoa (Chenopodium quinoa) Open
Additional file 2: Supplementary File 1. List of genebank accessions and passport data; Mildew infection raw data; saponin and stomatal measurements.
Automated download and clean-up of family-specific databases for kmer-based virus identification Open
Summary Here, we present an automated pipeline for Download Of NCBI Entries (DONE) and continuous updating of a local sequence database based on user-specified queries. The database can be created with either protein or nucleotide sequence…
View article: ResFinder 4.0 for predictions of phenotypes from genotypes
ResFinder 4.0 for predictions of phenotypes from genotypes Open
Objectives WGS-based antimicrobial susceptibility testing (AST) is as reliable as phenotypic AST for several antimicrobial/bacterial species combinations. However, routine use of WGS-based AST is hindered by the need for bioinformatics ski…
<i>In Silico</i> Genotyping of Escherichia coli Isolates for Extraintestinal Virulence Genes by Use of Whole-Genome Sequencing Data Open
Extraintestinal pathogenic Escherichia coli (ExPEC) is the leading cause in humans of urinary tract infection and bacteremia. The previously published web tool VirulenceFinder ( http://cge.cbs.dtu.dk/services/VirulenceFinder/ ) uses whole-…
An interactive database for the investigation of high-density peptide microarray guided interaction patterns and antivenom cross-reactivity Open
Snakebite envenoming is a major neglected tropical disease that affects millions of people every year. The only effective treatment against snakebite envenoming consists of unspecified cocktails of polyclonal antibodies purified from the p…
MINTyper: An outbreak-detection method for accurate and rapid SNP typing of clonal clusters with noisy long reads Open
For detection of clonal outbreaks in clinical settings, we present a complete pipeline that generates a SNP-distance matrix from a set of sequencing reads. Importantly, the program is able to handle a separate mix of both short reads from …
View article: Accelerating surveillance and research of antimicrobial resistance – an online repository for sharing of antimicrobial susceptibility data associated with whole-genome sequences
Accelerating surveillance and research of antimicrobial resistance – an online repository for sharing of antimicrobial susceptibility data associated with whole-genome sequences Open
Antimicrobial resistance (AMR) is an emerging threat to modern medicine. Improved diagnostics and surveillance of resistant bacteria require the development of next-generation analysis tools and collaboration between international partners…