A5064396074- Genomics and Phylogenetic Studies
- Forensic and Genetic Research
- Environmental DNA in Biodiversity Studies
- Identification and Quantification in Food
- Bioinformatics and Genomic Networks
- Genomics and Rare Diseases
- Genetic Associations and Epidemiology
- Protein Structure and Dynamics
- Isotope Analysis in Ecology
- Asthma and respiratory diseases
- Food Allergy and Anaphylaxis Research
- Enzyme Structure and Function
- Genetic Mapping and Diversity in Plants and Animals
- Metabolism, Diabetes, and Cancer
- Liver Disease Diagnosis and Treatment
- Gut microbiota and health
- Cancer Genomics and Diagnostics
- Allergic Rhinitis and Sensitization
- Metabolomics and Mass Spectrometry Studies
- Diabetes, Cardiovascular Risks, and Lipoproteins
- vaccines and immunoinformatics approaches
- Literature Analysis and Criticism
- Scientific Computing and Data Management
- Molecular Biology Techniques and Applications
- Folate and B Vitamins Research
Technical University of Denmark
2006-2024
PURPOSE: Historically, cancer predisposition syndromes (CPSs) were rarely established for children with cancer. This nationwide, population-based study investigated how frequently had or likely to have a CPS. METHODS: Children (0–17 years) in Denmark newly diagnosed invited participate whole-genome sequencing of germline DNA. Suspicion CPS was assessed according Jongmans’/McGill Interactive Pediatric OncoGenetic Guidelines (MIPOGG) criteria and familial diagnoses verified using registries....
Reliable prediction of free energy changes upon amino acid substitutions (ΔΔGs) is crucial to investigate their impact on protein stability and protein-protein interaction. Advances in experimental mutational scans allow high-throughput studies thanks multiplex techniques. On the other hand, genomics initiatives provide a large amount data disease-related variants that can benefit from analyses with structure-based methods. Therefore, computational field should keep same pace new tools for...
The presence of gaps in an alignment nucleotide or protein sequences is often inconvenience for bioinformatical studies. In phylogenetic and other analyses, instance, gapped columns are discarded entirely from the alignment. MaxAlign a program that optimizes prior to such analyses. Specifically, it maximizes number (or amino acid) symbols present gap-free – area by selecting optimal subset exclude can be used analyses as well situations where this form improvement useful. work we test...
Motivation DNA damage patterns, such as increased frequencies of C>T and G>A substitutions at fragment ends, are widely used in ancient studies to assess authenticity detect contamination. In metagenomic studies, fragments can be mapped against multiple references or de novo assembled contigs identify those likely ancient. Generating comparing profiles samples that stem from modern contaminants, however, both tedious time-consuming. Although tools exist for estimating single reference...
Current mitochondrial DNA (mtDNA) haplogroup classification tools map reads to a single reference genome and perform inference based on the detected mutations this reference. This approach biases assignments towards prohibits accurate calculations of uncertainty in assignment. We present HaploCart , probabilistic mtDNA classifier which uses pangenomic graph framework together with principles Bayesian inference. demonstrate that our significantly outperforms available by being more robust...
Excess liver iron content is common and linked to the risk of hepatic extrahepatic diseases. We aimed identify genetic variants influencing use genetics understand its link other traits
Abstract Motivation Allergy is a pathological immune reaction towards innocuous protein antigens. Although only narrow fraction of plant or animal proteins induce allergy, atopic disorders affect millions children and adults cost billions in healthcare systems worldwide. In silico predictors can aid the development more food sources. Previous allergenicity used sequence similarity, common structural domains, amino acid physicochemical features. However, these strongly rely on similarity to...
The role of genomic variants in disease, including cancer, continues to expand thanks the advent advanced sequencing techniques integrated into clinical practice. rapid growth identification has led classification many as Variants Uncertain Significance (VUS) or with conflicting evidence, posing challenges their interpretation and application. Here we introduce MAVISp ( M ulti-layered A ssessment V arIants by S tructure for p roteins), a modular structural framework variant interpretation....
Abstract Ancient environmental DNA (aeDNA) is a crucial source of information for past reconstruction. However, the computational analysis aeDNA involves inherited challenges ancient (aDNA) and typical difficulties eDNA samples, such as taxonomic identification abundance estimation identified groups. Current methods fall into those that only perform mapping followed by purport to do estimation. The former leaves estimates users, while latter are not designed large metagenomic datasets often...
Abstract Summary: InterMap3D predicts co-evolving protein residues and plots them on the 3D structure. Starting with a single sequence, automatically finds set of homologous sequences, generates an alignment fetches most similar structure from Protein Data Bank (PDB). It can also accept user-generated alignment. Based alignment, are then predicted using three different methods: Row Column Weighing Mutual Information, Information/Entropy Dependency. Finally, high-quality images highlighted....
Ancient DNA is highly degraded, resulting in very short sequences. Reads generated with modern high-throughput sequencing machines are generally longer than ancient molecules, therefore the reads often contain some portion of adaptors. It crucial to remove those adaptors, as they can interfere downstream analysis. Furthermore, overlapping portions when has been read forward and backward (paired-end) be merged correct errors improve quality. Several tools have developed for adapter trimming...
FeatureMap3D is a web-based tool that maps protein features onto 3D structures. The user provides sequences annotated with any feature of interest, such as post-translational modifications, protease cleavage sites or exonic structure and will then search the Protein Data Bank (PDB) for structures homologous proteins. results are displayed both an sequence alignment, where user-provided annotations well conservation between query target displayed, also publication-quality image selected...
Abstract 1. Ancient environmental DNA (eDNA) is a crucial source of in-formation for past reconstruction. However, the com-putational analysis ancient eDNA involves not only inherited challenges (aDNA) but also typical difficulties samples, such as taxonomic identification and abundance esti-mation identified groups. Current methods fall into those that perform mapping followed by taxo-nomic purport to do estima-tion. The former leaves estimates users, while latter are designed large...
Abstract Insights into peptide binding to HLA class II molecules is essential when studying the biological mechanisms behind cellular immunity, autoimmune diseases, and development of immunotherapies vaccines. Currently, most publicly available data used train state-of-the-art prediction methods for HLA-DR only includes DRB1 information. The role paralogue alleles, HLA-DRB3/4/5, their strong linkage disequilibrium often omitted typing HLA-II alleles. This leads ambiguities making disease...
Abstract Current mitochondrial DNA (mtDNA) haplogroup classification tools map reads to a single reference genome and perform inference based on the detected mutations this reference. This approach biases assignments towards prohibits accurate calculations of uncertainty in assignment. We present HaploCart , an mtDNA classifier which uses VG ’s pangenomic graph framework together with principles Bayesian inference. demonstrate that our significantly outperforms available by being more robust...
Abstract Ancient environmental DNA (aeDNA) is becoming a powerful tool to gain insights about past ecosystems. However, several methodological challenges remain, particularly for classifying the species level and conducting phylogenetic placement. Current methods, primarily tailored modern datasets, fail capture idiosyncrasies of aeDNA, including mixtures from closely related ancestral divergence. We introduce soibean , novel that utilises pangenomic graphs identifying ancient mitochondrial...
Abstract De novo assembly of ancient metagenomic datasets is a challenging task. Ultra-short fragment size and characteristic postmortem damage patterns sequenced DNA molecules leave current tools ill-equipped for ideal assembly. We present CarpeDeam , novel damage-aware de assembler designed specifically samples. Utilizing maximum-likelihood frameworks that integrate sample-specific patterns, recovers longer continuous sequences more protein from both simulated empirical compared to...
Abstract Aligning DNA sequences retrieved from fossils or other paleontological artifacts, referred to as ancient DNA, is particularly challenging due the short sequence length and chemical damage which creates a specific pattern of substitution (C→T G→A) in addition heightened divergence between sample reference genome thus exacerbating bias. This bias can be mitigated by aligning pangenome graphs incorporate documented organismic variation, but this approach still suffers patterns damage....
Ancient environmental DNA (aeDNA) is becoming a powerful tool to gain insights about past ecosystems, overcoming the limitations of conventional fossil records. However, several methodological challenges remain, particularly for classifying species level and conducting phylogenetic analysis. Current methods, primarily tailored modern datasets, fail capture idiosyncrasies aeDNA, including mixtures from closely related ancestral divergence. We introduce soibean, novel that utilises...
ABSTRACT Allergy is a pathological immune reaction towards innocuous protein antigens. Although only narrow fraction of plant or animal proteins induce allergy, atopic disorders affect millions children and adults cost billions in healthcare systems worldwide. In-silico predictors can aid the development more food sources. Previous allergenicity used sequence similarity, common structural domains, amino acid physicochemical features. However, these strongly rely on similarity to known...
Reliable prediction of free energy changes upon amino acidic substitutions (ΔΔGs) is crucial to investigate their impact on protein stability and protein-protein interaction. Moreover, advances in experimental mutational scans allow high-throughput studies thanks sophisticated multiplex techniques. On the other hand, genomics initiatives provide a large amount data disease-related variants that can benefit from analyses with structure-based methods. Therefore, computational field should keep...
Abstract The Li and Stephens (LS) haplotype-copying model is a seminal framework that represents target haplotype as an imperfect mosaic of set reference haplotypes. Using hidden Markov model, it can switch from different source haplotypes to recombinations. This has been used in several applications modern populations including phasing inference ancestry. However, recent publications have looked at the applicability using ancient individuals targets panels data. Previous research exploring...
Abstract Ancient DNA is highly degraded, resulting in very short sequences. Reads generated with modern high-throughput sequencing machines are generally longer than ancient molecules, therefore the reads often contain some portion of adaptors. It crucial to remove those adaptors, as they can interfere downstream analysis. Furthermore, overlapping portions when has been read forward and backward (paired-end) be merged correct errors improve quality. Several tools have developed for adapter...