Staff Scientist - Pathology & Immunology

Washington University; Northern (KY); Hybrid; USD 90,000 - 130,000; Full time

Benefits offered by this job

Vacation time

Holidays

Transit U-Pass

Tuition reimbursement

Health insurance

Job summary

Washington University in St. Louis seeks a skilled computational biologist to develop and maintain pipelines for single-cell and multi-omic data analysis, including scRNA-seq and spatial transcriptomics.

You will work with 10x Genomics platforms, perform end-to-end analyses, and deliver reproducible workflows and publication-ready visualizations. You will collaborate with experimental biologists to test hypotheses, guide experimental design, and train team members in best practices for

Qualifications

• Develop and maintain robust computational pipelines for single-cell and multi-omic data analysis.
• Experience with scRNA-seq and spatial transcriptomics workflows.
• Familiarity with 10x Genomics platforms and related datasets.
• Strong collaboration with experimental biologists and ability to interpret results in biology context.
• Ability to train lab members in computational analyses and reproducible research practices.

Responsibilities

• Develop, implement, optimize, and maintain computational pipelines for single-cell and multi-omic data analysis.
• Perform end-to-end analysis of scRNA-seq datasets including QC, normalization, integration, clustering, and differential expression.
• Provide reproducible workflows using scripting and workflow-management tools; maintain documentation.
• Generate publication-quality visualizations and contribute to manuscripts, grants, and talks.
• Advise on experimental design for sequencing and spatial-omics studies; manage data and metadata resources.

Job description

* 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.Washington University in St. Louis' collective success is significantly attributed to the passion and outstanding efforts of our community. Our staff, faculty and trainees are committed to excellence and dedicated to carrying out our missions of research, teaching and patient care.WashU prides itself on being a place where people matter, and serious work is done. Our people work together in an inclusive community that celebrates diverse perspectives, collaboration and innovation. We are a community of individuals inspired to work together to develop big ideas and tackle challenging problems.We value the well-being of our people. WashU strives to create a positive employee experience where staff, faculty and trainees thrive, both personally and professionally. Our employees find meaning, connection and vitality in their work and life with a healthy work-life balance and support to learn, grow and make an impact at WashU, the community and the world.**Useful Links****Accommodation**If you are unable to use our online application system and would like an accommodation, please email [e-mail] or call the dedicated accommodation inquiry number at 314-935-1149 and leave a voicemail with the nature of your request.**Regulatory Postings**Know Your Rights: Workplace Discrimination is Illegal Poster(;)