Project Title: Secondary molecular analysis for viral pathogens identified by High Throughput
Sequencing on non-routine diagnostic plant samples
Background: This study will evaluate the established HTS protocols against traditional diagnostic methods on non-routine diagnostic samples received at the USDA-APHIS-CPHST-Beltsville Laboratory. Multiple computational pipelines developed for the specific detection of viruses using the data generated by HTS technologies such as VirFind (Ho and Tzanetakis 2014), VirusDetect (Zheng et al. 2017), and VirusSeeker (Zhao et al. 2017) will be considered in this study. The plant viruses identified by bioinformatic analysis need to be further confirmed by an additional molecular tool in order to validate the analysis and confirm the presence of the identified organisms.
Position Description: This position serves as a molecular biology analyst in the APHIS Plant Protection and Quarantine, Science, and Technology Beltsville Laboratory. The incumbent will conduct research and confirmatory molecular work to help the Agency evaluate high throughput sequencing protocols against traditional diagnostic methods on non-routine diagnostic samples. The ideal candidate must have knowledge and experience in basic molecular biology technologies and principles (e.g. DNA/RNA, PCR, Sequencing) and Good Laboratory Practices (GLPs).
Education Requirement: Bachelor’s or Master’s degree in biological sciences.
Methods: This project is in its second year and has already generated a large amount of data that needs further molecular confirmation. The confirmatory molecular work proposed for the student, while not time-sensitive, will help refine our bioinformatic analysis and interpretation of HTS data for virus identification of diagnostic samples.
Apply here by May 11th
