Research Scientist​/Engineer

Job Description

This position is engaged in the field of Spatial transcriptomics and bioinformatics. It 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. The position requires effective communication of results through manuscript writing and presentations at conferences.

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 decoupleR, cluster
  
  Profiler, 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 prepare 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 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
• Provide input and feedback to leadership on team members’ overall performance, opportunities for development, and process improvement initiatives

• 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
• Expe…