Published in Genome Biology
The integration of a viral genome into the host genome has a major impact on the trajectory of the infected cell. Integration location and variation within the associated viral genome can influence both clonal expansion and persistence of infected cells. Methods based on short-read sequencing can identify viral insertion sites, but the sequence of ...
A novel, genetically-stabilized type 2 oral polio vaccine (nOPV2), developed to assist in the global polio eradication program, was recently the first-ever vaccine granted Emergency Use Listing by the WHO. Lot release tests for this vaccine included-for the first time to our knowledge-the assessment of genetic heterogeneity using next-generation se...
Published in Molecular ecology resources
Metabarcoding of Metazoa using mitochondrial genes may be confounded by both the accumulation of PCR and sequencing artefacts and the co-amplification of nuclear mitochondrial pseudogenes (NUMTs). The application of read abundance thresholds and denoising methods is efficient in reducing noise accompanying authentic mitochondrial amplicon sequence ...
Published in Annals of hematology
SF3B1 is a highly mutated gene in myelodysplastic syndrome (MDS) patients, related to a specific subtype and parameters of good prognosis in MDS without excess blasts. More than 40% of MDS patients carry at least two myeloid-related gene mutations but little is known about the impact of concurrent mutations on the outcome of MDS patients. In applyi...
Published in BioData Mining
GenoVault is a cloud-based repository for handling Next Generation Sequencing (NGS) data. It is developed using OpenStack-based private cloud with various services like keystone for authentication, cinder for block storage, neutron for networking and nova for managing compute instances for the Cloud. GenoVault uses object-based storage, which enabl...
Published in BMC Medical Genomics
BackgroundBasal cell carcinoma (BCC) represents by far the most common non-melanoma skin cancer (NMSC) in the world with an increasing incidence of 3% to 10% per year, especially in patients under the age of 40. While variants in the sonic Hedgehog and cell cycle regulation pathways account for the majority of BCC cases in adults, the molecular eti...
Published in Frontiers in Microbiology
Fecal pollution in coastal areas is of a high concern since it affects bathing and shellfish harvesting activities. Wild waterbirds are non-negligible in the overall signal of the detectable pollution. Yet, studies on wild waterbirds’ gut microbiota focus on migratory trajectories and feeding impact on their shape, rare studies address their compar...
Published in Frontiers in Oncology
Purpose Thymic epithelial tumors (TETs) are relatively rare neoplasms, including thymomas (types A, AB, B1, B2, and B3) and thymic carcinomas (TCs). The current knowledge about the biological properties of TETs is limited due to their low incidence. This study aimed to detect genetic alterations in TETs using next-generation sequencing(NGS) and exp...
Recent studies have highlighted the importance of ice-algal blooms in driving darkening and therefore surface melt of the Greenland Ice Sheet (GrIS). However, the contribution of fungal and bacterial communities to this microbially driven albedo reduction remains unconstrained. To address this significant knowledge gap, fungi were isolated from key...
The CRISPR/Cas9 genome editing system has already proved its efficiency, versatility and simplicity in numerous applications in human, animal, microbe and plant cells. Together with the vast amount of genome and transcriptome databases available, it represents an enormous potential for plant breeding and research. Although most changes produced wit...
