Research Scientist/Engineer 3

University of Washington•Seattle, WA

23h•$80,244 - $132,612

About The Position

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 at conferences. This 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

Requirements

Bachelor’s degree in Bioinformatics, Computational Biology, Biostatistics, Data Science or a related field and four years of relevant experience. Equivalent education and/or experience may substitute for minimum qualifications except when there are legal requirements, such as a license, certification, and/or registration.
Advanced knowledge of basic statistical principles relevant in medical research
Experience with spatial transcriptomics platforms (10x Genomics Visium, Visium HD, and/or Xenium)
Ability to analyze and solve complex problems and apply quantitative analytical approaches
Demonstrated fluency in one or more programming languages (e.g., R, Python, Perl, Java, C++) and willingness to learn new programming languages as necessary
Familiarity with statistical analytical concepts and methods
Ability to communicate effectively, both in writing and orally
Ability to establish and maintain effective working relationships with employees at all levels throughout the institution
Outstanding customer service skills
Demonstrated commitment and leadership ability to advance diversity and inclusion
Knowledge of basic human anatomy, physiology medical terminology
Ability to interpret and master complex research protocol information
Ability to handle multiple projects simultaneously within rigorous timelines
Potential to work independently with minimal supervision and in a team atmosphere

Nice To Haves

Experience with 10x Genomics Xenium Prime 5K spatial transcriptomics platform
Experience with single-cell RNA-seq analysis and integration with spatial data (Seurat, spacexr/RCTD)

Responsibilities

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 decoupleR, clusterProfiler, and GSEA
Perform image stitching and alignment using ImageJ 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
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
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 access relevant clinical and sample data
Provide guidance and training to junior team members, fostering a culture of continuous learning and professional development.
Identify and analyze operational efficiency issues, communicating findings and recommendations to leadership for informed decision-making.
Proactively identify and recommend training and development opportunities for both new hires and existing team members to enhance skill sets and performance.
Provides input and feedback to leadership on team members’ overall performance, opportunities for development, and process improvement initiatives