Published in BMC Biology
BackgroundNew sequencing technologies have lowered financial barriers to whole genome sequencing, but resulting assemblies are often fragmented and far from ‘finished’. Updating multi-scaffold drafts to chromosome-level status can be achieved through experimental mapping or re-sequencing efforts. Avoiding the costs associated with such approaches, ...
Published in Arthritis Research & Therapy
BackgroundSystemic sclerosis (SSc) is a rare disease with studies limited by small sample sizes. Electronic health records (EHRs) represent a powerful tool to study patients with rare diseases such as SSc, but validated methods are needed. We developed and validated EHR-based algorithms that incorporate billing codes and clinical data to identify S...
Published in Cancer Cell International
BackgroundThe incidence of cholangiocarcinoma (CCA) has risen in recent years, and it has become a significant health burden worldwide. However, the mechanisms underlying tumorigenesis and progression of this disease remain largely unknown. An increasing number of studies have demonstrated crucial biological functions of epigenetic modifications, e...
Published in Molecular Cytogenetics
BackgroundPrioritization of genomic data has become a useful tool for uncovering the phenotypic effect of genetic variations (e.g. copy number variations or CNV) and disease mechanisms. Due to the complexity, brain disorders represent a major focus of genomic research aimed at revealing pathologic significance of genomic changes leading to brain dy...
Published in Cell Division
BackgroundCell cycle regulation is a complex system consisting of growth-promoting and growth-restricting mechanisms, whose coordinated activity is vital for proper division and propagation. Alterations in this regulation may lead to uncontrolled proliferation and genomic instability, triggering carcinogenesis. Here, we conducted a comprehensive bi...
Published in BMC Bioinformatics
BackgroundEmerging evidence suggests retroviruses play a role in the pathophysiology of amyotrophic lateral sclerosis (ALS). Specifically, activation of ancient viral genes embedded in the human genome is theorized to lead to motor neuron degeneration. We explore whether connections exist between ALS and retroviruses through protein interaction net...
Published in Evolution: Education and Outreach
I reviewed a book Population Genomics that fills in the noticeable lack of a general introductory textbook to population genomics, one of the most exciting and rapidly developing branches of life sciences nowadays. Highly recommended to everybody willing to broaden knowledge about basics of genomics and get recent exciting insights into many evolut...
Published in BMC Research Notes
ObjectivesWe report a transcriptome acquisition for the bath sponge Spongia officinalis, a non-model marine organism that hosts rich symbiotic microbial communities. To this end, a pipeline was developed to efficiently separate between bacterial expressed genes from those of eukaryotic origin. The transcriptome was produced to support the assessmen...
Published in Journal of Animal Science and Biotechnology
BackgroundKetosis in dairy cows is associated with body fat mobilization during the peripartal period. Sub-clinical and clinical ketosis arise more frequently in cows that are overfed energy during the entire dry (last 50 to 45 days prior to parturition) or close-up period (last ~ 28 days prepartum).MethodsA retrospective analysis was performed on ...
Published in BMC Ecology
BackgroundThe use of environmental DNA (eDNA) has become an increasing important tool in environmental surveys and taxonomic research. High throughput sequencing of samples from soil, water, sediment, trap alcohol or bulk samples generate large amount of barcode sequences that can be assigned to a known taxon with a reference sequence. This process...
