Bent Petersen
A5001809968- Genomics and Phylogenetic Studies
- Genetic diversity and population structure
- Bacteriophages and microbial interactions
- Genetic and phenotypic traits in livestock
- Chromosomal and Genetic Variations
- Forest Insect Ecology and Management
- Forensic and Genetic Research
- RNA and protein synthesis mechanisms
- Wildlife Ecology and Conservation
- Mosquito-borne diseases and control
- Protein Structure and Dynamics
- Machine Learning in Bioinformatics
- Plant and animal studies
- Plant biochemistry and biosynthesis
- Insect and Pesticide Research
- Microbial Community Ecology and Physiology
- Cancer-related molecular mechanisms research
- Antibiotic Resistance in Bacteria
- Environmental DNA in Biodiversity Studies
- Plant and Fungal Species Descriptions
- Gut microbiota and health
- Archaeology and ancient environmental studies
- Bioinformatics and Genomic Networks
- Evolution and Paleontology Studies
- Genetic Mapping and Diversity in Plants and Animals
AIMST University
2018-2025
University of Copenhagen
2018-2024
Aims Community College
2019-2022
Technical University of Denmark
2009-2019
Natural History Museum Aarhus
2018-2019
Natural History Museum of Denmark
2019
Globe University
2019
Institute of Avian Research
1999
To better determine the history of modern birds, we performed a genome-scale phylogenetic analysis 48 species representing all orders Neoaves using phylogenomic methods created to handle data. We recovered highly resolved tree that confirms previously controversial sister or close relationships. identified first divergence in Neoaves, two groups named Passerea and Columbea, independent lineages diverse convergently evolved land water bird species. Among Passerea, infer common ancestor core...
Antimicrobial resistance (AMR) is a serious threat to global public health, but obtaining representative data on AMR for healthy human populations difficult. Here, we use metagenomic analysis of untreated sewage characterize the bacterial resistome from 79 sites in 60 countries. We find systematic differences abundance and diversity genes between Europe/North-America/Oceania Africa/Asia/South-America. taxonomy only explains minor part variation that observe. no evidence cross-selection...
Estimation of the reliability specific real value predictions is nontrivial and efficacy this often questionable. It important to know if you can trust a given prediction therefore best methods associate with score or index. For discrete qualitative predictions, conventionally estimated as difference between output scores selected classes. Such an approach not feasible for that predict biological feature single rather than classification. As solution challenge, we have implemented method...
The ability to predict local structural features of a protein from the primary sequence is paramount importance for unraveling its function in absence experimental information. Two main factors affect utility potential prediction tools: their accuracy must enable extraction reliable information on proteins interest, and runtime be low keep pace with sequencing data being generated at constantly increasing speed. Here, we present NetSurfP-2.0, novel tool that can most important unprecedented...
Abstract Ancient DNA research has been revolutionized following development of next-generation sequencing platforms. Although a number such platforms have applied to ancient samples, the Illumina series are dominant choice today, mainly because high production capacities and short read production. Recently potentially attractive alternative platform for palaeogenomic data generation developed, BGISEQ-500, whose sequence output comparable with series. In this study, we modified standard...
Significance The domestication of the horse revolutionized warfare, trade, and exchange people ideas. This at least 5,500-y-long process, which ultimately transformed wild horses into hundreds breeds living today, is difficult to reconstruct from archeological data modern genetics alone. We therefore sequenced two complete genomes, predating by thousands years, characterize genetic footprint domestication. These ancient genomes reveal predomestic population structure a significant fraction...
Significance Thirty years after the first DNA fragment from extinct quagga zebra was sequenced, we set another milestone in equine genomics by sequencing its entire genome, along with genomes of surviving species. This extensive dataset allows us to decipher genetic makeup underlying lineage-specific adaptations and reveal complex history speciation. We find that Equus diverged New World, spread across Old World 2.1–3.4 Mya, finally experienced major demographic expansions collapses...
Abstract Recent advances in machine learning and natural language processing have made it possible to profoundly advance our ability accurately predict protein structures their functions. While such improvements are significantly impacting the fields of biology biotechnology at large, methods downside high demands terms computing power runtime, hampering applicability large datasets. Here, we present NetSurfP-3.0, a tool for predicting solvent accessibility, secondary structure, structural...
Abstract The tuatara ( Sphenodon punctatus )—the only living member of the reptilian order Rhynchocephalia (Sphenodontia), once widespread across Gondwana 1,2 —is an iconic species that is endemic to New Zealand 2,3 . A key link now-extinct stem reptiles (from which dinosaurs, modern reptiles, birds and mammals evolved), provides insights into ancestral amniotes 2,4 Here we analyse genome tuatara, which—at approximately 5 Gb—is among largest vertebrate genomes yet assembled. Our analyses...
Abstract Despite tremendous efforts in the past decades, relationships among main avian lineages remain heavily debated without a clear resolution. Discrepancies have been attributed to diversity of species sampled, phylogenetic method and choice genomic regions 1–3 . Here we address these issues by analysing genomes 363 bird 4 (218 taxonomic families, 92% total). Using intergenic coalescent methods, present well-supported tree but also marked degree discordance. The confirms that Neoaves...
The characterization of therapeutic phage genomes plays a crucial role in the success rate therapies. There are three checkpoints that need to be examined for selection candidates, namely, presence temperate markers, antimicrobial resistance (AMR) genes, and virulence genes. However, currently, no single-step tools available this purpose. Hence, we have developed tool capable checking all conditions required suitable candidates. This consists an ensemble machine-learning-based predictors...
Abstract Adaptation is the central feature and leading explanation for evolutionary diversification of life. also notoriously difficult to study in nature, owing its complexity logistically prohibitive timescale. Here, we leverage extensive contemporary historical collections Ambrosia artemisiifolia —an aggressively invasive weed primary cause pollen-induced hayfever—to track phenotypic genetic causes recent local adaptation across native ranges North America Europe, respectively. Large...
The PfEMP1 family of surface proteins is central for Plasmodium falciparum virulence and must retain the ability to bind host receptors while also diversifying aid immune evasion. interaction between CIDRα1 domains endothelial protein C receptor (EPCR) associated with severe childhood malaria. We combine crystal structures CIDRα1:EPCR complexes analysis 885 sequences, showing that EPCR-binding surfaces are conserved in shape bonding potential, despite dramatic sequence diversity....
Significance Yakutia is among the coldest regions in Northern Hemisphere, showing ∼40% of its territory above Arctic Circle. Native horses are particularly adapted to this environment, with body sizes and thick winter coats minimizing heat loss. We sequenced complete genomes two ancient nine present-day Yakutian elucidate their evolutionary origins. find that contemporary population descends from domestic livestock, likely brought by early horse-riders who settled region a few centuries ago....
Hundreds of thousands human genomes are now being sequenced to characterize genetic variation and use this information augment association mapping studies complex disorders other phenotypic traits. Genetic is identified mainly by short reads the reference genome or performing local assembly. However, these approaches biased against discovery structural variants in more parts genome. Hence, large-scale de novo assembly needed. Here we show that it possible construct excellent assemblies from...
North America is currently home to a number of grey wolf (Canis lupus) and wolf-like canid populations, including the coyote latrans) taxonomically controversial red, Eastern timber Great Lakes wolves. We explored their population structure regional gene flow using dataset 40 full genome sequences that represent extant diversity American wolves populations. This included 15 new genomes (13 wolves, 1 red timber/Great wolf), ranging from 0.4 15x coverage. In addition providing support for...
Most severe Plasmodium falciparum infections are experienced by young children. Severe symptoms precipitated vascular sequestration of parasites expressing a particular subset the polymorphic P. erythrocyte membrane protein 1 (PfEMP1) adhesion molecules. Parasites binding human endothelial C receptor (EPCR) through CIDRα1 domain certain PfEMP1 were recently associated with malaria in However, it has remained unclear to which extend EPCR-binding domains epitomize expressed malaria. Here, we...
Sled dog arctic adaptations go far back Dogs have been used for sledding in the Arctic as ∼9500 years ago. However, relationships among earliest sled dogs, other populations, and wolves are unknown. Sinding et al. sequenced an ancient dog, 10 modern wolf analyzed their genetic with dogs. This analysis indicates that dogs represent lineage going at least 9500 bred ancestors of precontact American gene flow between likely stopped before Science , this issue p. 1495
β-turns are the most common type of non-repetitive structures, and constitute on average 25% amino acids in proteins. The formation plays an important role protein folding, stability molecular recognition processes. In this work we present neural network method NetTurnP, for prediction two-class individual β-turn types, by use evolutionary information predicted sequence features. It has been evaluated against a commonly used dataset BT426, achieves Matthews correlation coefficient 0.50,...
An increasing number of studies are addressing the evolutionary genomics dog domestication, principally through resequencing dog, wolf and related canid genomes. There is, however, only one de novo assembled genome currently available against which to map such data - that a boxer (Canis lupus familiaris). We generated first lupus) as an additional choice reference, explored what implications may arise when previously published remapped this reference. Reassuringly, we find regardless...