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.

40 hours per week.

• 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.
• Develop 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:
  • base calling of in situ nucleotide imaging data;
  • cell segmentation;
  • registration of spots representing nucleotides;
  • drift correction using a fiducial;
  • assembly of counts files of combinatorial barcodes;
  • 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.

• 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.

Master’s degree or combination of education and/or experience may substitute for minimum education.

No specific certification/professional license is required for this position.

Laboratory Operations (3 Years).

Not Applicable.

A driver’s license is not required for this position.

• Ph.D. – Doctor of Philosophy.
• 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.

R10

$48,000.00 – $86,900.00 / Annually