A5041905317- Genomics and Phylogenetic Studies
- Microbial Community Ecology and Physiology
- Protist diversity and phylogeny
- Genetic Associations and Epidemiology
- Genomics and Rare Diseases
- Machine Learning in Bioinformatics
- Scientific Computing and Data Management
- Artificial Intelligence in Healthcare and Education
- RNA and protein synthesis mechanisms
- Geological Formations and Processes Exploration
- Distributed and Parallel Computing Systems
- COVID-19 diagnosis using AI
- Bioinformatics and Genomic Networks
- Research Data Management Practices
- Advanced Data Storage Technologies
- Vector-borne infectious diseases
- Insect symbiosis and bacterial influences
- Bacteriophages and microbial interactions
- Melanoma and MAPK Pathways
- Genetics, Bioinformatics, and Biomedical Research
- Interdisciplinary Research and Collaboration
- Forensic and Genetic Research
Uppsala University
2006-2024
Science for Life Laboratory
2011-2024
Here we describe the SweGen data set, a comprehensive map of genetic variation in Swedish population. These represent basic resource for clinical genetics laboratories as well sequencing-based association studies by providing information on variant frequencies cohort that is matched to national patient cohorts. To select samples this study, first examined structure population using high-density SNP-array from nation-wide over 10 000 Swedish-born individuals included Twin Registry. A total...
The SAR11 clade, here represented by Candidatus Pelagibacter ubique, is the most successful group of bacteria in upper surface waters oceans. In contrast to previous studies that have associated 1.3 Mb genome Ca. ubique with less than 1.5 genomes Rickettsiales, our phylogenetic analysis suggests closely related soil and aquatic Alphaproteobacteria large genomes. This implies clade Rickettsiales undergone reduction independently. A gene flux 46 representative alphaproteobacterial indicates...
Abstract Background The SAR11 group of Alphaproteobacteria is highly abundant in the oceans. It contains a recently diverged freshwater clade, which offers opportunity to compare adaptations salt- and freshwaters monophyletic bacterial group. However, there are no cultivated members genomes have been sequenced yet. Results We isolated ten single cells from three lakes assembled their genomes. A phylogeny based on 57 proteins indicates that organized into distinct microclusters. show evolved...
Background According to the endosymbiont hypothesis, mitochondrial system for aerobic respiration was derived from an ancestral Alphaproteobacterium. Phylogenetic studies indicate that ancestor is most closely related Rickettsiales. Recently, it suggested Candidatus Pelagibacter ubique, a member of SAR11 clade highly abundant in oceans, sister taxon mitochondrial-Rickettsiales clade. The availability ocean metagenome data substantially increases sampling Alphaproteobacteria inhabiting...
Many theories favor a fusion of 2 prokaryotic genomes for the origin Eukaryotes, but there are disagreements on origin, timing, and cellular structures cells involved. Equally controversial is source nuclear genes mitochondrial proteins, although α-proteobacterial contribution to genome well established. Phylogenetic inferences show that nuclearly encoded aminoacyl-tRNA synthetases (aaRSs) occupy position in tree not close any currently sequenced genomes, despite cohesive remarkably...
SAR11 is a globally abundant group of Alphaproteobacteria in the oceans that taxonomically not well defined. It has been suggested should be classified into novel order Pelagibacterales. Features such as conservation gene content and synteny have taken evidence also divergent member HIMB59 included order. However, this proposition controversial since phylogenetic analyses questioned monophyly grouping. Here, we performed reinvestigated genomic similarity HIMB59. Our analysis confirmed sister...
Abstract Here we describe the SweGen dataset, a high-quality map of genetic variation in Swedish population. This data represents basic resource for clinical genetics laboratories as well sequencing-based association studies, by providing information on frequencies variants cohort that is matched to national patient cohorts. To select samples this study, first examined structure population using high-density SNP-array from nation-wide based over 10,000 individuals. From sample collection,...
The European Genome-phenome Archive (EGA) is a service for archiving and sharing personally identifiable genetic phenotypic data, while the Genomic Data Infrastructure (GDI) project enabling access to genomic related clinical data across Europe. Both projects are focused on creating federated secure infrastructure researchers archive share with research community, support further research.This proposal focusing part of infrastructure. files encrypted in archives, using crypt4gh standard....
The European Genome-phenome Archive (EGA) (Freeberg et al., 2022) (also known as CentralEGA - cEGA) is a service for permanent archiving and sharing personally identifiable geneticand phenotypic data resulting from biomedical research projects. Federated EGA (EGAConsortium, n.d.), consisting of the Central nodes, will be distributednetwork repositories human -omics phenotypes. Each node thefederation responsible its own infrastructure connection to EGA.Currently, adoption deployment new...
Human genome and phenome data is classified as special categories under the EU GDPR legislation (Art. 9 GDPR). This requires care to be taken when processing reusing this for research. To enable in a compliant way, federated approach was applied existing European Genome-phenome Archive ([EGA(https://ega-archive.org/)]) (Freeberg et al., 2022), creating Federated EGA ([FEGA(https://ega-archive.github.io/ FEGA-onboarding/#what-is-federated-ega)]) (EGA Consortium, n.d.) 2022. The Nordic...