Genotyping and Bioinformatics Analysis and Reporting

This research project will:(1) Perform analysis of deep-sequencing data from hundreds of samples. The workflow will include creating sequencing quality control (QC reports). merging overlapping pairs. trimming low quality reads. mapping reads to database. conducting OTU clustering. conducting abundance analysis and diversity analysis. and performing phylogenetic analysis and single nucleotide polymorphism (SNP) analysis. (2) Receive. process. and analyze samples / specimen from the BAMC Pl (Government) and provide the consolidated report.(3) Communicate with the BAMC Pl regularly on a weekly basis to discuss processing status updates and observations from deep-sequencing data analysis. bioinformatics analysis and other information related to the deliverables.(4) Analysis results uploaded to AWS Gov. Cloud server or will be provided to the BAMC Pl. within 10workdays after completion of service.
 
 Dr. Wang's laboratory at University of Texas San Antonio (UTSA) will provide their bioinformatics experience and interdisciplinary expertise in the specific areas of bioinformatics. comparative genomics.molecular evolution. population genetics. and systems biology. to Brooke Army Medical Center (BAMC) to analyze genomic data generated for biomarker discoveries. Her team will be involved in the large-scale analysis of genomics data for prediction of biomarkers for bacteria diagnostics. BAMC has conducted several years of studies to identify the presence of the HPV virus via extracted DNA from pap smears and using patient genomics data to make it faster and cheaper to identify cancers. BAMC's goal of applying these research discoveries of future projects into a high-volume smooth-workflow process in which bacteria is extracted. then sent to a lab for sequencing and diagnosis. whose results are then published via an online web dashboard in an audience-appropriate communication based on the discovery of biomarkers from large-scale genotyping. Scope: Process and analyze large-scale genomic data for biomarker discovery on thousands of samples. Support interdisciplinary research with in depth knowledge and experience in bioinformatics and computational biology.molecular genetics. population and evolutionary genetics. and statistical modeling.