Job Code: 4752 Job Grade: I The Department of Medicine, Division of Cardiovascular Medicine is looking for a Computational Biologist to join Dr. Euan Ashley's team at Stanford University. Dr. Ashley's research focuses on leveraging emerging technologies such as genomics and wearable sensors to provide insights into precision medicine (https://ashleylab.stanford.edu/).
Our team runs the Bioinformatics core for a large NIH study (>$180M) tasked with building a molecular map of physical activity (MoTrPAC - https://commonfund.nih.gov/moleculartransducers/overview). The program's goal is to study the molecular changes that occur during and after exercise to advance the understanding of how physical activity improves and preserves health. This incredible project will integrate very large volumes of clinical (imaging, EKG, wearable) and densely time sampled molecular data (DNA, RNA, ATAC, EPI sequencing, metabolomics, proteomics and the microbiome). The bioinformatics core will build cutting edge infrastructure to manage, analyze and disseminate this resource to the research community through the Google Cloud Platform. Our portal will push the boundaries of biomedical data analytics to provide insight on basic research and translational science such as the developments of new therapeutics.
The role of Computational Biologist will focus on modeling of the large amounts of molecular and clinical data being generated by the consortium. You will work with stakeholders across the network to best understand data structures to model metadata schemas and be the point person for data transactions to the Bioinformatics core. Your understanding of molecular data and experimental design will be a key resource in enabling high quality data to flow into our systems to enable analytical insights.
Prioritize and extract data from a variety of sources such as notes, survey results, medical reports, and laboratory data, and maintain its accuracy and completeness.
Determine additional data collection and reporting requirements.
Design and customize reports based upon data in the database. Oversee and monitor regulatory compliance for utilization of the data.
Use system reports and analyses to identify potentially problematic data, make corrections, and eliminate root cause for data problems or justify solutions to be implemented by others.
Create complex charts and databases, perform statistical analyses, and develop graphs and tables for publication and presentation.
Serve as a resource for non-routine inquiries such as requests for statistics or surveys.
Test prototype software and participate in approval and release process for new software.
Provide documentation based on audit and reporting criteria to investigators and research staff.
Complies with and supports University and government health & safety regulations & policies.
* - Other duties may also be assigned DESIRED QUALIFICATIONS:
Graduate degrees that emphasize engineering, computer science and statistics are preferred
Domain expertise in at least two omics such as WGS, RNA-Seq, RRBS, proteomics, metabolomics, microbiome
An understanding of data modeling including ontologies and database design
Experience with Python and Linux bash scripting
Experience with experimental design protocols
Basic knowledge of code management such as git and Jenkins
Exposure to data analytics toolsets such as R, SciPy/NumPy, Matlab
Exposure to cloud computing through Amazon, Google
Exposure to container systems such as setting up virtual machines and Docker instances
EDUCATION & EXPERIENCE (REQUIRED):
Bachelor's degree and three years of relevant experience or combination of education and relevant experience. Experience in a quantitative discipline such as economics, finance, statistics or engineering.
KNOWLEDGE, SKILLS AND ABILITIES (REQUIRED):
Substantial experience with MS Office and analytical programs.
Excellent writing and analytical skills.
Ability to prioritize workload.
Sitting in place at computer for long periods of time with extensive keyboarding/dexterity.
Occasionally use a telephone.
Rarely writing by hand.
* - Consistent with its obligations under the law, the University will provide reasonable accommodation to any employee with a disability who requires accommodation to perform the essential functions of his or her job.
Some work may be performed in a laboratory or field setting.
WORK STANDARDS (from JDL)
Interpersonal Skills: Demonstrates the ability to work well with Stanford colleagues and clients and with external organizations.
Promote Culture of Safety: Demonstrates commitment to personal responsibility and value for safety; communicates safety concerns; uses and promotes safe behaviors based on training and lessons learned.
Subject to and expected to comply with all applicable University policies and procedures, including but not limited to the personnel policies and other policies found in the University's Administrative Guide, http://adminguide.stanford.edu.
Location: School of Medicine, California, United States Schedule: Classification Level:
Stanford is an equal opportunity employer and all qualified applicants will receive consideration without regard to race, color, religion, sex, sexual orientation, gender identity, national origin, disability, veteran status, or any other characteristic protected by law.
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