Spatial Biology - Data Scientist

Axle Informatics is a bioinformatics and information technology company that offers innovative computer services, informatics, and enterprise solutions to research centers and healthcare organizations around the globe. With experts in software engineering, bioinformatics and program management, we focus on developing and applying technology tools and techniques to empower decision-making and accelerate the discovery in translational research. We work with some of the top research organizations and facilities in the country including multiple institutes at the National Institutes of health (NIH).

Axle Informatics is currently seeking a Spatial Biology - Data Scientist to support our federal client.

Responsibilities:

• Directly support client research core facilities by listening and understanding how their spatial biology data is generated experimentally, and by developing data analysis strategies that take into account experimental designs and constraints.
• Design and execute novel secondary statistical analysis workflows to extract high-level biological information from large single-cell datasets generated by spatial transcriptomics and spatial biology instruments and preprocessed at multiple client research core facilities.
• Work in a close collaborative fashion with other team members at client research core facilities to understand, optimize, and troubleshoot the data analysis workflows.
• Present their work on a regular basis at team meetings, intra-departmental meetings, and at international scientific conferences.
• Communicate and explain the rationale, technical details, and possible limitations behind their data analysis strategies workflows to audiences of other data scientists, biologists, and clinicians in client research organizations.
• Contribute to writing and dissemination of research through scientific publications.
• Communicate and explain the results of the data analysis workflows to audiences of other data scientists, biologists, and clinicians across the client research organization.
• Maintain and develop expertise about technological trends in spatial proteomics and spatial transcriptomics.

Minimum Qualifications:

• Track record of successful collaborative scientific projects as demonstrated by publicly available project portfolios on software repositories, webpages, and/or scientific publications in high-impact scientific journals.
• Ability and interest to communicate and explain the rationale, technical details, results, and possible limitations behind their data analysis workflows to both technical and non-technical audiences of other data scientists, biologists, and clinicians in client research organizations.
• Demonstrated adherence to good scientific computational and data management practices and scientific reproducibility principles, such as version control, code testing, code documentation, version control, scientific literate programming, etc.
• Ability and interest to listen to client scientific investigators and client research core facilities personnel to understand the biological rationale and experimental design underlying their scientific projects.
• Demonstrated problem-solving skills to identify and troubleshoot technical issues, conduct research, and develop innovative solutions in an independent manner.
• Excellent writing and presentation skills as shown by technical/scientific blog posts or web pages, software documentation, scientific publications, and presentation at technical or scientific conferences.
• MSc. with 8+ years or Ph.D. with 5+ years of industry/post-doctoral experience in Data Science, Bioinformatics, Computational Biology, Molecular Biology or similar.
• Extensive proficiency in R, Python, or other open-source scientific computational languages.
• Proficiency with modern computational software stacks for biological data visualization, spatial statistical modeling, and machine learning (e.g. Tidyverse, SciPy, Numpy, ScikitLearn, etc.).
• Extensive experience in setting up data biological data analysis workflows on either High-Performance Computing (HPC) platforms, or in the cloud.
• Highly motivated to work and thrive in a highly collaborative environment with other client team members.

Desired Qualifications:

• Working knowledge of spatial proteomics or transcriptomics instruments and their output file formats, including but not limited to: 10X Genomics Visium and Xenium, NanoString GeoMx and CosMx, Akoya CODEX/Phenocycler, or CITE-seq.
• Hands-on experience in using spatial statistic models for the secondary analysis of spatial biology or spatial transcriptomics data.
• Experience with deep learning frameworks (e.g. PyTorch, TensorFlow) for the analysis of imaging-based and/or NGS-based spatial data.
• Experience or familiarity with commercial or open-source analysis software for image and quantitative tissue analysis, such as HALO (Indica Labs), Visiopharm’s image analysis packages, QuPath, etc.
• Hands-on experience with the scientific software stack for the analysis of single-cell and spatial transcriptomics data (e.g., Seurat, Scanpy, Squidpy, etc.).
• Hands-on experience in developing or applying tissue imaging technologies to visualize and molecularly characterize human and mouse tissues (e.g., immunofluorescence, RNA-FISH, MERFISH, confocal microscopy, and high-throughput imaging).
• Hands-on experience with bioinformatics analysis of single-cell next-gen sequencing (NGS)

Benefits

• 100% Medical, Dental, and Vision Coverage for Employees
• Employee Referral Bonus
• Parking Reimbursement Account (PRK)
• Flexible Spending Accounts:
• Healthcare (FSA)
• Transportation Reimbursement Account (TRN)
• 401k matching
• Paid Time Off (including Holidays)
• Dependent Care Assistant Program (DCAP)

The diversity of Axle’s employees is a tremendous asset. We are firmly committed to providing equal opportunity in all aspects of employment and will not tolerate any illegal discrimination or harassment based on age, race, gender, religion, national origin, disability, marital status, covered veteran status, sexual orientation, status with respect to public assistance, and other characteristics protected under state, federal, or local law and to deter those who aid, abet, or induce discrimination or coerce others to discriminate.

Accessibility: If you need accommodation as part of the employment process please contact:

Email: [email protected]

Disclaimer: The above description is meant to illustrate the general nature of work and the level of effort being performed by individuals assigned to this position or job description. This is not restricted to a complete list of all skills, responsibilities, duties, and/or assignments required. Individuals may be required to perform duties outside of their position, job description, or responsibilities as needed.