Scientist I, Single-Cell Genomics

About the role

The Allen Institute for Cell Science seeks a collaborative Scientist I to support computational analysis of single-cell RNA-seq datasets in projects focused on cell-state transitions during tissue morphogenesis in human iPSC-derived 3D culture systems. This role is well suited to a scientist with strong biological grounding, quantitative skills, and an interest in using data analysis to generate clear biological insight.

Responsibilities

• Perform analysis of single-cell RNA-seq datasets to characterize cell states, state transitions, and biological heterogeneity in human iPSC-derived 3D culture systems
• Develop reproducible analysis workflows, code, and visualizations using sound data-analysis practices
• Build and maintain R Shiny applications and related outputs to support data exploration and internal scientific decision-making
• Collaborate with experimental and computational colleagues to interpret biological findings from data and align analysis plans with project goals, sample design, and metadata needs
• Support data organization, documentation, and version control to enable effective collaboration and reuse
• Stay current with methods and literature in single-cell genomics
• Communicate findings clearly through presentations, figures, documentation, and manuscript contributions

Requirements

• PhD in cell biology, developmental biology, stem cell biology, computational biology, bioengineering, biophysics, or a related field, or equivalent combination of education and experience
• Experience analyzing single-cell RNA-seq datasets
• Proficiency in R and/or Python for biological data analysis
• Experience developing reproducible analysis workflows and clear data visualizations

Preferred

• Proficiency in Linux-based computing environments and version control tools such as Git
• Ability to build interactive data-exploration applications, such as R Shiny apps
• Background in developmental biology, stem cell biology, morphogenesis, or cell-state transitions
• Experience working with iPSC-derived model systems or 3D cell culture systems
• Understanding of wet-lab assay design considerations and practical limitations of single-cell or spatial experiments
• Knowledge of spatial biology approaches, including spatial transcriptomics and/or multiplexed protein imaging
• Ability to work effectively on interdisciplinary projects with experimental and computational collaborators
• Strong organizational, written, and verbal communication skills
• Publishation record demonstrating contribution to single-cell or related biological data analysis

Physical Demands

Fine motor movements in fingers/hands to operate computers and other office equipment; repetitive motion with equipment.

Position Type/Expected Hours of Work

This role is currently working onsite and is expected to work onsite for the majority of working hours. The primary work location for this role is 700 Dexter Ave N., with the flexibility to work remotely on a limited basis.

Annualized Salary Range

$86,150 - $106,650*

*Final salary depends on the required education for the role, experience, level of skills relevant to the role, and work location, where applicable.

Benefits

Employees (and their families) are eligible to enroll in benefits per eligibility rules outlined in the Allen Institutes Benefits Guide. These benefits include medical, dental, vision, and basic life insurance. Employees are also eligible to enroll in the Allen Institutes 401k plan. Paid time off is also available as outlined in the Allen Institutes Benefits Guide. Details on the Allen Institutes benefits offering are located at the following link to the Benefits Guide: https://alleninstitute.org/careers/benefits.