"Senior Scientist (Computational) - 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.

Will be responsible for both specific research projects as well as the oversight of the computational infrastructure and computational code and data analysis standards for the laboratory. Will play a leadership role in working with those who have built an in-house computational cluster with backup servers in a second location to facilitate movement of all of the lab’s data off the cluster and onto local storage for substantial cost savings for the lab. After this initial project, with mentoring from the Principal Investigator, the computational scientist will oversee and develop algorithms for analyzing ensemble genomics data, single cell genomics data, single cell merFISH and sequential oligopaints imaging data, as well as novel molecular connectomics data. They will develop code and data sharing standards for the lab, and create SOPs for interfacing with GEO and bitbucket. They will train the laboratory on code backup in bitbucket and computational lab notebooks. Along with the PI, they will co-lead specific complex interdisciplinary neuroscience projects and spearhead algorithm development for crucial papers in the lab. After the building of infrastructure, ample opportunities for creative advances, grant writing, and drafting/editing manuscripts will be available. The individual will be responsible for mentoring at minimum 1-3 junior analysts to ensure all sequencing and imaging data is housed, formatted, and stored on the computational cluster (and their own in-house servers) according to Cremins lab protocols.

Job Description

Primary Duties & Responsibilities:

• Collaborates on designing, conducting and reporting of research projects.
• Leads the process of monthly cleaning of servers and network attached storage across a 25 person laboratory to facilitate major long-term cost savings for the lab. 
• Oversees the code development and data storage and accessibility needs of the laboratory toward discovery-based science across all genomics, imaging, and connectome data. Develops key algorithm in collaboration with other graduate students, postdocs, and scientists in the laboratory to advance the laboratories papers and discoveries.
• Trains to achieve mastery and excellence in code to call compartments, TADs, subTADs, loops in Hi-C/Micro-C data, as well as in peak calling of Cut&Run and Cut&Tag data. Oversees trainees to ensure code and parameter selection implemented at highest standards.
• Creates algorithms to analyze data generated by their projects to create paper figures and make discoveries, guides lab members to write and edit methods sections and figures for research papers where the analysis is used in the manuscript.
• Assists with grant preparation and reporting (Editing, formatting, and facilitating stylistic and grammatical edits for lab’s annual grant progress reports, coordinating team members to arrange scientific content to meet grant progress deadline).
• Prepares and submits papers on research (Assists PI in filling out of paperwork, including, but not limited to: dbGAP and ENCODE data portal approvals, Grant and University-related paperwork, yearly RRPR reports for every one of the lab’s grants - including coordinating with the subTeam members to get the content assembled).
• Develops hypotheses to be tested and ways of testing it (Given concepts/ideas, and/or data from individual lab members, creates algorithms to analyze data generated by their projects to create paper figures and makes discoveries, develops new code to find patterns in single cell genomics and single cell imaging data, guides lab members to write and edit methods sections and figures for research papers where the analysis is used in the manuscript).
• Complies with established safety procedures and maintains required documentation (Oversees junior computational scientist to ensure data is organized, managed, and curated on the cluster and servers to find biological patterns in a wide range of genetic and epigenetic sequencing and imaging data to facilitate the paper figures of lab members, oversees and writes established SOPs for data storage and movement onto GEO and NIH portals for public data accessibility, trains new lab members on algorithms, bitbucket, data naming conventions, and GEO).
• Manages research project with other institutions and investigators.
• Performs other duties as assigned.

Working Conditions:

• Works in a laboratory environment with potential exposure to biological, chemical and radioactive hazards.
• Must be physically able to wear protective equipment and to provide standard care to research animals.

Required Qualifications

Education:

Phd Or Terminal Degree Or Combination Of Education And Experience May Substitute For Minimum Education.

Work Experience:

Postdoctoral (3 Years)

Preferred Qualifications:

• Familiar with genomics assays and their computational pipelines, image processing (segmentation, spot calling, drift correction).
• Exceptional commitment to upholding the collaborative ethos of the Cremins laboratory.
• Demonstrated ability to handle daily laboratory challenges with a dedication to the values of reconciliation, unity, mutual honor, and respect.

Skills:

Analytical Problem Solving, Detail-Oriented, Image Processing, Laboratory Instrumentation, Laboratory Processes, Laboratory Techniques, Linux Environments, Oral Communications, Organizational Processes, Python for Data Analysis, R Programming, Teamwork, Working Independently, Written Communication

Salary Range

$63,400.00 - $115,000.00 / Annually