Sezerman, U. | bioRxiv Science

bioRxiv2020

driveR: A Novel Method for Prioritizing Cancer Driver Genes Using Somatic Genomics Data

Cancer develops due to "driver" alterations. Numerous approaches exist for predicting cancer drivers from cohort-scale genomic data. However, methods for personalized analysis of driver genes are underdeveloped. In this study, we developed a novel personalized/batch analysis approach for driver gene prioritization utilizing somatic genomic data, called driveR. Combining genomic information and prior biological knowledge, driveR accurately prioritizes cancer driver genes via a multi-task learning model. Testing on 28 different datasets, this study demonstrates that driveR performs adequately, outperforms existing approaches, and is an accurate and easy-to-utilize approach for prioritizing driver genes in cancer genomes. driveR is available on CRAN: https://cran.r-project.org/package=driveR.

bioinformatics↗

bioRxiv2020

SARS-CoV-2 Isolation and Propagation from Turkish COVID-19 patients

The novel coronavirus pneumonia, which was named later as Coronavirus Disease 2019 (COVID-19), is caused by the Severe Acute Respiratory Syndrome Coronavirus 2, namely SARS-CoV-2. It is a positive-strand RNA virus that is the seventh coronavirus known to infect humans. The COVID-19 outbreak presents enormous challenges for global health behind the pandemic outbreak. The first diagnosed patient in Turkey has been reported by the Republic of Turkey Ministry of Health on March 11, 2020. Today, over ninety thousand cases in Turkey, and two million cases around the world have been declared. Due to the urgent need for vaccine and anti-viral drug, isolation of the virus is crucial. Here, we report one of the first isolation and characterization studies of SARS-CoV-2 from nasopharyngeal and oropharyngeal specimens of diagnosed patients in Turkey. This study provides an isolation and replication methodology, and cell culture tropism of the virus that will be available to the research communities. Article SummaryScientists have isolated virus from Turkish COVID-19 patients. The isolation, propagation, and plaque and immune response assays of the virus described here will serve in following drug discovery and vaccine testing.

microbiology↗