Research Scientist​/Engineer

Position: Research Scientist/Engineer 3
** Job Description
**** The Division of Metabolism, Endocrinology and Nutrition (MET) has an outstanding opportunity for a Research Scientist/Engineer 3 position to support studies within the Pyle and Bjornstad Laboratories.
** Housed within the University of Washington Medicine Diabetes Institute at the South Lake Union campus, the Pyle laboratory applies translational data science to bridge complex biostatistics and bioinformatics findings into medical insights. The Bjornstad and Pyle laboratories focus on metabolic and hemodynamic mechanisms underlying the development of diabetic kidney disease (DKD) and cardiovascular disease (CVD) in Type 1 (T1D) and Type 2 (T2D) diabetes and obesity.

This position is engaged in the field of Spatial transcriptomics and bioinformatics. This position supports the analysis of spatial transcriptomic data generated from kidney biopsy tissue using 10x Genomics platforms including Visium, Visium HD, and Xenium Prime 5K. The role involves processing, quality control, and interpretation of spatially resolved gene expression data to understand disease mechanisms in diabetic kidney disease and obesity-related kidney disease.

A key focus includes cell type deconvolution, integration with single-cell RNA-seq reference data, identification of spatially variable genes, and pathway enrichment analysis. This position requires effective communication of results through manuscript writing and presentations s position will work under general guidance, receiving instruction on specific assignment objectives, and will collaborate with investigators on spatial transcriptomic analyses, data visualization, and preparation of abstracts, talks, and manuscripts.

Research Sponsors/Stakeholders:
Novo Nordisk and NIH##
** DUTIES AND RESPONSIBILITIES
***** Spatial Transcriptomics and Data Analysis 60%**
* • Process and quality-control 10x Genomics Visium, Visium HD, and Xenium Prime 5K spatial transcriptomics data from human and mouse kidney tissue
• Perform spatial preprocessing with Space Ranger and downstream integration across samples using Seurat and BPCells
• Perform cell type deconvolution and mapping by integrating spatial data with single-cell RNA-seq reference objects using RCTD (spacexr) workflow
• Identify spatially variable genes and cluster-specific markers to prioritize biological pathways and candidate genes for downstream investigation
• Perform differential expression and pathway enrichment analysis using decouple

R, cluster

Profiler, and GSEA
• Perform image stitching and alignment using Image

J and Loupe Browser for spatial preprocessing
• Integrate multi-sample spatial datasets to enable scalable normalization, clustering, and cross-sample comparison
• Develop protocol-specific systems and documents including process flows, training manuals, and Standard Operating Procedures (SOPs).
• Maintain subject level documentation and prepares documents, equipment and/or supplies
• Provide the biostatistical/data science expertise and leadership in study design, study oversight, data management, data analysis and manuscript preparation to assist all levels of biomedical investigators and clinicians on new research activities across a wide range of disciplines
• Provide mentorship to collaborators, trainees, and team members
• Acts as a subject matter expert and authority in the areas of data management and data analysis
• Serve as an expert resource to PIs and other stakeholders
*** Bioinformatics Programming 20%**
* • Assist with the design and development of major bioinformatics-related programming projects
• Write custom scripts to access databases, analyze data, and create reproducible visual representations of results
• Write custom web tools for PIs and other stakeholders
*** Laboratory support 20%**
* • Collaborate on the preparation and presentation of data for publications in peer-reviewed journals, ensuring clarity and adherence to publication standards.
• Assist Team Leads, Supervisors, and management in developing and implementing effective processes, procedures, and quality improvement initiatives that enhance team performance.
• Develop and disseminate a variety of tools designed to…