Staff Scientist - Pathology & Immunology

* Develop, implement, optimize, and maintain robust computational pipelines for single-cell and multi-omic data analysis, including scRNA-seq and spatial transcriptomic datasets.
* Establish and maintain workflows for 10x Genomics (preferably scRNAseq, Xenium, scATAC and multi-ome), smartseq datasets; related experience in image and transcript quality control, cell segmentation assessment, transcript assignment, cell-type annotation, spatial neighborhood analysis, and integration with complementary single-cell datasets.
* Perform end-to-end analysis of scRNA-seq datasets, including:+ raw data processing and quality control;+ normalization and dimensionality reduction;+ batch correction and data integration;+ clustering and cell-type annotation;+ differential gene-expression analysis;+ pathway and gene-set enrichment analysis;+ characterization of cellular heterogeneity and cell-state changes.
* Develop and run/conduct reproducible computational workflows using scripting and workflow-management tools and maintain well-documented analysis pipelines that can be reused across projects.
* Perform statistical analyses and develop publication-quality visualizations of complex multi-dimensional datasets.
* Work collaboratively with experimental biologists to formulate analytical strategies, interpret results in their biological context, and identify additional analyses or experiments needed to test emerging hypotheses.
* Provide guidance on experimental design for sequencing and spatial-omics studies, including considerations related to sample size, sequencing depth, batch effects, technical controls, and downstream analytical requirements.
* Establish procedures for computational quality control, data organization, metadata management, version control, and reproducibility.
* Manage analysis of large datasets using institutional high-performance computing environments and/or cloud-based computational resources.
* Troubleshoot computational workflows and identify technical or biological sources of unexpected results.
* Maintain awareness of new developments in single-cell genomics, spatial biology, computational biology, and multi-omic data integration and introduce useful new approaches into the laboratory's analytical framework.
* Contribute computational analyses, figures, and methodological descriptions to manuscripts, grant applications, presentations, and collaborative research projects.
* Maintain clear documentation of analytical methods, software versions, parameters, and computational workflows.
* Where appropriate, train and support laboratory members in computational analysis, data visualization, and best practices for reproducible research.
* Up to 22 days of vacation, 10 recognized holidays, and sick time.
* Competitive health insurance packages with priority appointments and lower copays/coinsurance.
* Take advantage of our free Metro transit U-Pass for eligible employees.
* WashU provides eligible employees with a defined contribution (403(b)) Retirement Savings Plan, which combines employee contributions and university contributions starting at 7%.
* WashU covers the cost of tuition for you and your family, including dependent undergraduate-level college tuition up to 100% at WashU and 40% elsewhere after seven years with us.

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