Computational Scientist - Spatial Profiling/Multiplexed Imaging...

Full and partial remote work options are available with hiring manager approval. Periodic travel to Farmington and/or Bar Harbor campuses expected in the future.

Summary

The Jackson Laboratory (JAX) is seeking a computational biologist to join a single-cell imaging and informatics team embedded within the Computational Sciences group. The successful candidate will apply statistical, machine learning, and deep learning approaches to predict phenotypes in cancer and non-malignant disease from imaging and spatial expression data generated by cutting-edge technologies within JAX's Single Cell Biology Laboratory (SCBL). These platforms include spatial transcriptomics, which provides unbiased, spatially-resolved expression profiles of mixtures of cells, and imaging mass cytometry (IMC), which affords a highly multiplexed (~40 proteins) perspective of individual cells. SCBL's platforms continue to evolve and will soon include CODEX and multiplex FISH. The primary responsibilities of the... Computational Scientist involve providing analysis of tissue imaging data and interpreting their results across a range of biological and translational domains. The Computational Scientist will apply and optimize published methods and pipelines when they exist and develop novel methods when they do not. In doing so, they will accelerate adoption of advanced imaging and spatially-aware technologies at JAX.

The Computational Scientist will stay current in the latest image analysis methods and their biological application by attending and presenting at conferences. They will expand their professional network through collaborations with faculty across JAX campuses and with external investigators and consortia (e.g., PDXNet). Finally, they will have significant growth opportunities to develop novel and evaluate existing methods in the rapidly evolving field of highly multiplexed image analysis and to deploy them in advancing biological discoveries.

A Successful Computational Scientist will have:

• Prior exposure to or interest in analysis of highly multiplexed imaging (e.g., CyCIF, CODEX, IMC, MIBI) or spatial transcriptomics (e.g., 10x Visium, GeoMx) data.
• Expertise applying and developing statistical and machine learning approaches to address questions in biology, such as: regression, random forests, ensemble methods, clustering, survival analysis, and dimensionality reduction.

Characteristic distinction from Assistant to Full Computational Scientist includes increased ability to work independently, liaise directly with biologists, develop in-depth knowledge in selected biological disciplines, provide biological interpretation of results, contribute to or lead grant submissions, and mentor more junior Computational Scientists.

Responsibilities:

• Analyze imaging and spatial transcriptomics data (e.g., H&E, IMC, CODEX, 10x Visium), from quality control through generation of results, in collaboration with faculty on the Farmington, CT and Bar Harbor, ME campuses and under minimal supervision.
• Develop and publish novel methods for imaging/spatial transcriptomics data, making them accessible to the community as well-documented packages/libraries shared in online repositories (e.g., github, Bioconductor).
• Attend and present at scientific meetings to maintain and advance technological and scientific expertise at JAX.
• Provide leading contributions to internal and external grant applications.
• Participate in departmental and project activities, participate in conducting courses and workshops at JAX, help students and scientists, participate in CS meetings and present results to JAX community and at conferences and workshops as assigned.

Qualifications:

• PhD in Computational Biology, Bioinformatics, Computer Science, Biostatistics, Physics, or relevant area.
• Associate/Full level: Possess Assistant level qualifications plus additional 2-4 years (associate) / 5-10 years (full) of experience excluding time spent to obtain PhD.
• Excellent verbal and written communication skills.
• Demonstrated ability to develop and execute a scientific narrative, as indicated by lead author, peer-reviewed publications in impactful journals.
• Proficiency in Python and/or R in a Linux environment.
• Strong initiative, and motivation to learn new technologies and biological domains.
• An ability to explore and research new challenges creatively and with limited supervision.

The ideal candidate will have one or more of the following:

• A solid understanding of biology (molecular, cancer, or immunology) and prior experience collaborating with biologists and clinicians.
• Experience with image analysis / computer vision libraries (e.g., Scikit-image, OpenCV).
• Experience analyzing spatial transcriptomics and/or related single-cell RNA-seq data (e.g., using Seurat or Scanpy).
• Proficiency with image visualization tools and libraries (e.g., QuPath, Fiji, napari).
• Familiarity with deep learning libraries (e.g., tensorflow), particularly as applied to image analysis.
• Experience with software development environments (e.g., git/github, conda, Docker).

About JAX:

The Jackson Laboratory (JAX) is an independent, nonprofit biomedical research institution with more than 2,400 employees. Headquartered in Bar Harbor, Maine, it has a National Cancer Institute-designated Cancer Center in Augusta, Maine, a genomic medicine institute in Farmington, Connecticut, and facilities in Ellsworth, Maine, Sacramento, California, and Shanghai, China. Its mission is to discover precise genomic solutions for disease and empower the global biomedical community in the shared quest to improve human health.

JAX employees work in a collaborative, value-driven, and team-based environment where the focus is on advancing science and improving patients' lives. Researchers apply genetics to increase the understanding of human disease and advance treatments and cures for cancer, neurological and immune disorders, diabetes, aging, and heart disease. JAX was voted among the top 15 “Best Places to Work in Academia” in the United States in a poll conducted by The Scientist magazine!

EEO Statement:

The Jackson Laboratory provides equal employment opportunities to all employees and applicants for employment in all job classifications without regard to race, color, religion, age, mental disability, physical disability, medical condition, gender, sexual orientation, genetic information, ancestry, marital status, national origin, veteran status, and other classifications protected by applicable state and local non-discrimination laws