Staff Scientist; Computational - Genomics - Genetics

Position Summary

Scheduled

Hours:

40

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 organize, manage, and curate big data on the cluster and find biological patterns in a wide range of genetic and epigenetic sequencing and imaging data to facilitate the paper figures of lab members. Candidate will train on the lab’s fundamental algorithms and run them in a collaborative manner with other team members to generate paper figures and make discoveries.

Collaborative code building for team member papers will involve mastery and application of existing algorithms and tools for understanding and detecting TADs, subTADs, loops, and compartments in Hi-C and Micro

C data and integrating the 3D genome features with underlying chromatin marks. As the candidate advances in training, they will develop new algorithms to find TADs and loops in single cell genomics data, as well as to analyze in situ DNA FISH and merFISH data.

This role is ideal for you if you have a strong interest and motivation toward publishing results and 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 according to a positive, warm, and community-focused scientific culture.

• Following instructions and discussions with the principal investigator, designs research protocols, including writing methods, results, and making figures for papers.
• Performs computational tasks under direction and collaboration with other graduate students, postdocs, and scientists in the laboratory (given concepts/ ideas, and/ or data from individual lab members, creates algorithms to analyze data generated by their projects to create paper figures and make discoveries).
• Trains to achieve mastery and excellence in code to call compartments, TADs, subTADs, loops in Hi-C/Micro-C/snm3c data, as well as in peak calling of Chip-seq, Cut&Run and Cut&Tag data and genome structures variants calling from whole genome sequencing data.
• In collaboration with lab members, writes methods sections and figures for research papers where the analysis is used in the manuscripts.
• As the position advances, begins to develop new code to find patterns in single-cell genomics and single-cell imaging data.
• Organizes the lab cluster according to lab protocols and standards every week.
• Leads the movement of data from base space to the cluster and the keeping of careful records for sequencing runs and sample names for each project.
• Runs established codes for read mapping and peak calling for lab’s foundational data across projects.
• Training on and overseeing…