Washington University in St. Louis
Staff Scientist (Computational – Connectome) - Genetics
Washington University in St. Louis, Northfield, Vermont, us, 05663
Overview
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 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. Ideal for post-baccalaureate students eager to do PhD level research. Primary Duties & Responsibilities
Following instructions and discussions with the principal investigator, designs research protocols, including developing procedures for the collection, verification and management of data. Assists with grant preparation and reporting (writing methods, results, and making figures for papers). Performs complex statistical analysis of data collected and writes interpretative reports. In collaboration with lab members, writes methods sections and figures for research papers where the analysis is used in the manuscript. Organizes, manages, and curates the 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. Organizes the data on the lab cluster according to lab protocols and standards every week (keeping careful records for sequencing runs and sample names for each project). Backups code on bitbucket and oversees the revision of the code to integrate with other algorithms. Trains on and oversees the formatting and cleaning of the data to make it publicly available according to the requirements of the NIH and NSF and paper journals. Conducts literature searches related to the research project, identifies code and statistical tools for developing image analysis pipelines, and develops new code in Python at PEP8 standards for solving problems toward creating neural connectome maps. Algorithm development will involve 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) interpretation of barcodes as a given neuron in specific x, y, z coordinates. 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. Required Qualifications
Education:
Master’s degree or combination of education and/or experience may substitute for minimum education. Certifications:
No specific certification is required for this position. Work Experience:
Laboratory Operations (3 Years) Skills:
Not Applicable Driver\'s License:
A driver\'s license is not required for this position. More About This Job
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. Preferred Qualifications (Education and Experience)
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) Grade and Salary
Grade:
R10 Salary Range:
$48,000.00 - $86,900.00 / Annually Questions and Benefits
For frequently asked questions about the application process, please refer to our
External Applicant FAQ . Accommodation
If you are unable to use our online application system and would like an accommodation, please email CandidateQuestions@wustl.edu or call the dedicated accommodation inquiry number and leave a voicemail with the nature of your request. All qualified individuals must be able to perform the essential functions of the position satisfactorily and, if requested, reasonable accommodations will be made to enable employees with disabilities to perform the essential functions of their job, absent undue hardship. Pre-Employment Screening All external candidates receiving an offer for employment will be required to submit to pre-employment screening for this position. The screenings will include criminal background check and, as applicable for the position, other background checks, drug screen, an employment and education or licensure/certification verification, physical examination, certain vaccinations and/or governmental registry checks. All offers are contingent upon successful completion of required screening. Benefits
Benefits Statement Up to 22 days of vacation, 10 recognized holidays, and sick time. Competitive health insurance packages with priority appointments and lower copays/coinsurance. Metro U-Pass for eligible employees. Retirement Savings Plan starting at 7% contributions. EEO Statement Washington University in St. Louis is committed to equal employment opportunity and encourages applications from underrepresented groups. It is the University’s policy to provide equal opportunity and access to persons in all job titles without regard to race, ethnicity, color, national origin, age, religion, sex, sexual orientation, gender identity or expression, disability, protected veteran status, or genetic information.
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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 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. Ideal for post-baccalaureate students eager to do PhD level research. Primary Duties & Responsibilities
Following instructions and discussions with the principal investigator, designs research protocols, including developing procedures for the collection, verification and management of data. Assists with grant preparation and reporting (writing methods, results, and making figures for papers). Performs complex statistical analysis of data collected and writes interpretative reports. In collaboration with lab members, writes methods sections and figures for research papers where the analysis is used in the manuscript. Organizes, manages, and curates the 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. Organizes the data on the lab cluster according to lab protocols and standards every week (keeping careful records for sequencing runs and sample names for each project). Backups code on bitbucket and oversees the revision of the code to integrate with other algorithms. Trains on and oversees the formatting and cleaning of the data to make it publicly available according to the requirements of the NIH and NSF and paper journals. Conducts literature searches related to the research project, identifies code and statistical tools for developing image analysis pipelines, and develops new code in Python at PEP8 standards for solving problems toward creating neural connectome maps. Algorithm development will involve 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) interpretation of barcodes as a given neuron in specific x, y, z coordinates. 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. Required Qualifications
Education:
Master’s degree or combination of education and/or experience may substitute for minimum education. Certifications:
No specific certification is required for this position. Work Experience:
Laboratory Operations (3 Years) Skills:
Not Applicable Driver\'s License:
A driver\'s license is not required for this position. More About This Job
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. Preferred Qualifications (Education and Experience)
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) Grade and Salary
Grade:
R10 Salary Range:
$48,000.00 - $86,900.00 / Annually Questions and Benefits
For frequently asked questions about the application process, please refer to our
External Applicant FAQ . Accommodation
If you are unable to use our online application system and would like an accommodation, please email CandidateQuestions@wustl.edu or call the dedicated accommodation inquiry number and leave a voicemail with the nature of your request. All qualified individuals must be able to perform the essential functions of the position satisfactorily and, if requested, reasonable accommodations will be made to enable employees with disabilities to perform the essential functions of their job, absent undue hardship. Pre-Employment Screening All external candidates receiving an offer for employment will be required to submit to pre-employment screening for this position. The screenings will include criminal background check and, as applicable for the position, other background checks, drug screen, an employment and education or licensure/certification verification, physical examination, certain vaccinations and/or governmental registry checks. All offers are contingent upon successful completion of required screening. Benefits
Benefits Statement Up to 22 days of vacation, 10 recognized holidays, and sick time. Competitive health insurance packages with priority appointments and lower copays/coinsurance. Metro U-Pass for eligible employees. Retirement Savings Plan starting at 7% contributions. EEO Statement Washington University in St. Louis is committed to equal employment opportunity and encourages applications from underrepresented groups. It is the University’s policy to provide equal opportunity and access to persons in all job titles without regard to race, ethnicity, color, national origin, age, religion, sex, sexual orientation, gender identity or expression, disability, protected veteran status, or genetic information.
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