"Staff Scientist (Computational – Connectome) - Genetics"

Position Summary

The Cremins lab works at the spatial biology-technology interface to understand chromatin-to-synapse communication during neural circuit activation in the mammalian brain. We aim to understand how chromatin works through long-range physical folding mechanisms to encode neuronal specification and long-term synaptic plasticity in healthy and diseased neural circuits. We pursue a multi-disciplinary approach integrating data across biological scales in the brain, including molecular Chromosome-Conformation-Capture sequencing technologies, single-cell imaging, optogenetics, genome engineering, induced pluripotent stem cell differentiation to neurons/organoids, and in vitro and in vivo electrophysiological measurements.

Our long-term scientific goal is to dissect the fundamental mechanisms by which chromatin architecture causally governs genome function and, ultimately, long-term synaptic plasticity and neural circuit features in healthy mammalian brains as well as during the onset and progression of neurodegenerative and neurodevelopmental disease states.

Our long-term mentorship goal is to develop a diverse cohort of next-generation scientists cross-trained in molecular and computational approaches. We seek to create a positive, high-energy environment with open and honest communication to empower individuals to discover and refine their purpose and grow into the best versions of themselves.

The candidate will work with a dynamic team of graduate students to develop new code and statistical methods to analyze newly created data in the Cremins lab to map the neural connectome at synapse resolution. Imaging data includes in situ sequencing signals procured across hundreds of fields of view. Pipelines to be developed will focus on base calling of nucleotides, cell segmentation, registration of spots across cycles, drift correction, and assembly of barcode counts files, and the interpretation of barcodes as a given neuron in specific x, y, z coordinates. Candidates will be expected to organize, manage, and curate the imaging data to make it available to the scientific community on public portals. All code should be written by PEP8 standards and of quality to provide it freely available to the community via bitbucket.

This role is ideal for you if you have a strong interest and motivation toward working with new data never produced or analyzed before, and thrive in a fast paced environment discovering new answers. Candidates will independently search the published literature and available code to develop a portfolio of novel computational tools for processing multi-modal imaging data. The candidate will contribute to the preparation of multiple manuscripts, including making figures and writing methods and results. This role is ideal for you if you enjoy the excitement of a bleeding-edge scientific laboratory and welcome the challenge of a fast-paced environment and working collaboratively in a positive, warm, and community-focused scientific culture.

Job Description

Primary Duties & Responsibilities:

• Assists with grant preparation and reporting (writing methods, results, and making figures for papers).
• Following instructions and discussions with the principal investigator, and lab members write methods sections and figures for research papers where the analysis is used in the manuscript.
• Search literature and identify code and statistical tools for developing image analysis pipelines.
• Develops new code in python at PEP8 standards for solving problems toward creating neural connectome maps (all codes should be written by PEP8 standards and of quality to provide it freely available to the community via bitbucket).
• Backup code on bitbucket and oversee the revision of the code to integrate with other algorithms.
• Algorithm development initially will involve solving problems such as:
  1. base calling of in situ nucleotide imaging data;
  2. cell segmentation;
  3. registration of spots representing nucleotides;
  4. drift correction using a fiducial;
  5. assembly of counts files of combinatorial barcodes;
  6. the interpretation of barcodes as a given neuron in specific x, y, z coordinates.
• Organizes the data on the lab cluster according to lab protocols and standards every week.
• Keeping of careful records for sequencing runs and sample names for each project.
• Training on and overseeing the formatting and cleaning of the data to make it publicly available according to the requirements of the NIH and NSF and paper journals.
• Performs other duties as assigned.

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.

The above statements are intended to describe the general nature and level of work performed by people assigned to this classification. They are not intended to be construed as an exhaustive list of all job duties performed by the personnel so classified. Management reserves the right to revise or amend duties at any time.

Required Qualifications

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)

Preferred Qualifications

• Exceptional commitment to upholding the collaborative ethos of the Cremins laboratory.
• Strong skills in verbal and written communication with a dedication to open transparent communication with mentors and peers.
• Demonstrated ability to handle daily laboratory challenges with a dedication to the values of reconciliation, unity, mutual honor, and respect.
• Excellent interpersonal skills, independent thinking, and a desire to work in a complex and high-energy environment with honor and respect shown to all lab members across rank and the PI.

Education:

Ph.D. - Doctor of Philosophy

Skills:

Algorithms, Analytical Problem Solving, Communication, Computer Literacy, Data Analysis, Data Interpretations, Detail-Oriented, Independent Thinking, Organizing, Python (Programming Language)

Salary Range

$48,000.00 - $86,900.00 / Annually