Staff Scientist - Pathology & Immunology

Washington University in St. Louis; St. Louis (MO); On-site; USD 48,000 - 87,000; Full time

Job summary

Washington University in St. Louis seeks a Staff Scientist in Computational Biology and Multi-Omics to develop and maintain pipelines for high-dimensional genomic and spatial-omics analyses.

The role centers on single-cell sequencing, multi-omics integration, and collaboration with experimental teams to translate data into biological insights. The ElTanbouly Lab emphasizes in vivo mouse models, primary cell culture, flow cytometry, and 10x Genomics technologies, with opportunities to expand to

Qualifications

• Master's degree or equivalent; several years in bioinformatics or computational biology.
• Experience designing, implementing, and maintaining robust computational pipelines for single-cell and multi-omics data.
• Strong collaboration with experimental biologists and ability to translate complex datasets into biological insights.

Responsibilities

• Design research protocols and data management procedures under the PI.
• Develop and optimize pipelines for scRNA-seq and multi-omic data analysis.
• Establish workflows for 10x Genomics datasets (scRNA-seq, Xenium, scATAC, multi-ome).
• Perform end-to-end scRNA-seq analyses including QC, normalization, integration, clustering, and annotation.
• Create reproducible workflows and well-documented analysis pipelines.

Skills

Analytical Problem Solving

Collegiality

Communication

Computer Literacy

Data Analysis

Data Interpretations

Detail-Oriented

Teamwork and Cooperation

Willingness to Learn

Education

Master’s degree

Ph.D. - Doctor of Philosophy

Tools

10x Genomics Xenium

Job description

Position Summary

Location

SAINT LOUIS, MO 63110

Scheduled Hours

40

Position Summary

We are seeking a highly motivated Staff Scientist in Computational Biology and Multi-Omics to develop, implement, and maintain computational pipelines for the analysis of high-dimensional genomic and spatial-omics datasets. The successful candidate will work closely with experimental scientists to analyze complex biological datasets, develop reproducible computational workflows, and integrate information across multiple molecular and cellular modalities.

The ElTanbouly Lab will primarily use in vivo mouse models, in vitro primary cell culture, flow cytometry and multi-omic approaches to uncover new pathways regulating plasma cell biology, fate and longevity.

The position will have a particular emphasis on single-cell RNA sequencing (scRNA-seq), scATAC-seq, bulk transcriptomics/epigenomics and spatial transcriptomics, including 10x Genomics Xenium, with opportunities to work with additional genomic, transcriptomic, proteomic, and imaging-based datasets.

The Ideal Candidate Will:

• combine strong computational and quantitative skills with an interest in biological discovery and will play a central role in translating large-scale multi-omic datasets into biologically meaningful insights.
• have several years of experience in the bioinformatics or computational biology fields.

Job Description

Primary Duties & Responsibilities:

• Following instructions and discussions with the principal investigator, designs research protocols, including developing procedures for the collection, verification and management of data.
• 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.

Working Conditions:

• Works in a laboratory environment with potential exposure to biological and chemical hazards.
• Must be physically able to wear protective equipment and to provide standard care to research animals.

Education

Master’s degree or combination of education and/or experience may substitute for minimum education.

Certifications/Professional Licenses

No specific certification/professional license is required for this position.

Work Experience

Laboratory Operations (3 Years)

Skills

Not Applicable

Driver's License

A driver's license is not required for this position.

More About This Job

WashU seeks highly motivated individuals who are able to perform duties in a manner consistent with our core mission and guiding principles.

Preferred Qualifications

Ph.D. - Doctor of Philosophy

Work Experience

No additional work experience unless stated elsewhere in the job posting.

Skills

Analytical Problem Solving, Collegiality, Communication, Computer Literacy, Data Analysis, Data Interpretations, Detail-Oriented, Teamwork and Cooperation, Willingness to Learn

Grade

R10

Salary Range

$48,000.00 - $86,900.00 / Annually

The salary range reflects base salaries paid for positions in a given job grade across the University. Individual rates within the range will be determined by factors including one's qualifications and performance, equity with others in the department, market rates for positions within the same grade and department budget.

Questions

For frequently asked questions about the application process, please refer to our External Applicant FAQ.

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.

All qualified individuals must be able to perform the essential functions of the position satisfactorily and, if requested, reasonable accommodations will be made to enable employees with disabilities to perform the essential functions of their job, absent undue hardship.

Pre-Employment Screening

All external candidates receiving an offer for employment will be required to submit to pre-employment screening for this position. The screenings will include criminal background check and, as applicable for the position, other background checks, drug screen, an employment and education or licensure/certification verification, physical examination, certain vaccinations and/or governmental registry checks. All offers are contingent upon successful completion of required screening.

Benefits Statement

Personal

• 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%.

Wellness

• Wellness challenges, annual health screenings, mental health resources, mindfulness programs and courses, employee assistance program (EAP), financial resources, access to dietitians, and more!

Family

• We offer 4 weeks of caregiver leave to bond with your new child. Family care resources are also available for your continued childcare needs. Need adult care? We've got you covered.
• 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.

For policies, detailed benefits, and eligibility, please visit: https://hr.wustl.edu/benefits/

EEO Statement

Washington University in St. Louis is committed to the principles and practices of equal employment opportunity. It is the University’s policy to provide equal opportunity and access to persons in all job titles without regard to race, ethnicity, color, national origin, citizenship (where prohibited by federal law), age, religion, sex, sexual orientation, gender identity or expression, disability, protected veteran status, or genetic information.