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 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
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
• 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