The mission of the Allen Institute is to unlock the complexities of bioscience and advance our knowledge to improve human health. Using an open science, multi-scale, team-oriented approach, the Allen Institute focuses on accelerating foundational research, developing standards and models, and cultivating new ideas to make a broad, transformational impact on science.
As part of the NIH BRAIN Initiative Cell Atlas Network, the Allen Institute is helping to lead a major new international consortium effort to create a comprehensive cell atlas of the human and closely related non-human primate brain. This project aims to make the most detailed map of the human brain ever produced, linking cellular and molecular phenotypes to brain imaging and functional architecture. To tackle this ambitious goal, we are seeking talented and highly motivated individuals to help create these atlases and help to make them transformative for neuroscience and biomedical research through open data sharing.
We seek a Scientist with strong computational skills who will lead efforts to build whole-brain cellular atlases for humans, macaques, and marmosets by analyzing transcriptomic and epigenomic datasets with millions of cells. The successful candidate will develop scalable bioinformatics pipelines to build multiomic cell type taxonomies and assess cell type reproducibility across modalities. The candidate will also identify cell type-specific molecular features and establish cell type ontologies to capture the relationship between cell types based on multi-modal datasets. They will also play a key role in team efforts to characterize spatial distributions and morphological and electrophysiological properties of cells using probabilistic mapping tools.
The Allen Institute believes that team science significantly benefits from the participation of diverse voices, experiences, and backgrounds. High-quality science can only be produced when it includes different perspectives. We are committed to increasing diversity across every team and encourage people from all backgrounds to apply for this role.
Essential Functions
- Build scalable bioinformatic pipelines, including assessing sample quality, aligning taxonomies across brain regions, and generating marker gene panels to map cell types.
- Integrate transcriptomic, epigenomic, and spatial transcriptomic datasets to build robust taxonomies of cell types in the primate brain.
- Build robust and scalable computational tools to map published single-cell transcriptomic studies to the collected datasets and vice versa to assist cell type annotation.
- Participate in cross-team efforts to quantify the spatial distributions and other properties of cell types.
- Publish and present findings in peer-reviewed journals and scientific conferences.
- Prepare written and oral reports on a regular basis.
- Maintain clear and accurate communication with supervisor, team members, and external collaborators.
Required Education And Experience
- PhD degree in a quantitative field (Computational Neuroscience, Computer Science, Bioinformatics, Bioengineering, or related field); or an equivalent combination of degree and experience.
Preferred Education And Experience
- Strong background in scientific computing and analysis of large data sets.
- Proficiency in a high-level programming language such as Python and/or R.
- Prior experience analyzing single cell genomics datasets (transcriptomics, epigenomics).
- Proficiency in machine learning and statistical analysis approaches.
- Experience using cloud platforms (AWS, Google Cloud) for genomic data analysis.
- Experience working with very large data sets.
- Knowledgeable about human genetics and gene regulatory mechanisms.
- Experience working as part of a team to pursue collaborative research goals.
- Proven independent thinking and flexibility.
- Strong publication record.
- Strong written and verbal communication skills.
- Ability to meet aggressive timelines and deliverables in a collaborative environment.
Physical Demands
- Fine motor movements in fingers/hands to operate computers and other office equipment.
Position Type/Expected Hours of Work
- This role is currently able to work both remotely and onsite in a hybrid work environment. We are a Washington State employer, and the primary work location for all Allen Institute employees is 615 Westlake Ave N.; any remote work must be performed in Washington State.
Additional Comments
- Please note, this opportunity offers relocation assistance.
- Please note, this opportunity offers work visa sponsorship.
Annualized Salary Range
- $75,003 - $105,004 *
- Final salary depends on required education for the role, experience, and level of skills relevant to the role, along with work location, where applicable.
Benefits
- Employees (and their families) are eligible to enroll in benefits per eligibility rules outlined in the Allen Institute’s Benefits Guide. These benefits include medical, dental, vision, and basic life insurance. Employees are also eligible to enroll in the Allen Institute’s 401k plan. Paid time off is also available as outlined in the Allen Institute’s Benefits Guide. Details on the Allen Institute’s benefits offering are located at the following link to the Benefits Guide: .
It is the policy of the Allen Institute to provide equal employment opportunity (EEO) to all persons regardless of age, color, national origin, citizenship status, physical or mental disability, race, religion, creed, gender, sex, sexual orientation, gender identity and/or expression, genetic information, marital status, status with regard to public assistance, veteran status, or any other characteristic protected by federal, state or local law. In addition, the Allen Institute will provide reasonable accommodations for qualified individuals with disabilities.
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