The Department of Medicine, Division of Cardiovascular Medicine is looking for a Bioinformatics Engineer / Data Scientist to join the Bioinformatics Core (BIC) of the Molecular Transducers of Physical Activity Consortium (MoTrPAC) tasked with building a molecular map of physical activity (MoTrPAC - https://commonfund.nih.gov/moleculartransducers/overview). The Bioinformatics Core is supervised by co-PIs Dr. Euan Ashley and Dr. Matthew Wheeler in the Division of Cardiovascular Medicine 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/). Dr. Wheeler's research focuses on genomics, rare myocardial and skeletal muscle disease, and undiagnosed diseases (https://undiagnosed.stanford.edu). Group members have opportunities for cross-disciplinary collaboration and engagement with clinical, translational, wet lab, and dry lab researchers.
The BIC'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 integrates very large volumes of clinical and densely time sampled molecular data (genomic, epigenomic, transcriptomic, proteomic and metabolomic data). The bioinformatics core is building cutting edge infrastructure to manage, analyze and disseminate this resource to the research community through the Google Cloud Platform. Our portal (https://motrpac-data.org/) will push the boundaries of biomedical data analytics to provide insight into basic and translational science of exercise.
The role of Bioinformatics Engineer will focus on the development of pipelines and tools for the comprehensive analysis of large amounts of molecular and clinical data being generated by the consortium, with special emphasis on Metabolomics and Proteomics datasets. Your ability to participate in software development projects, understand MS-based molecular data and experimental design will be a key resource in enabling high-quality data to flow through 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.
Design and develop software applications that may involve sophisticated data manipulation.
*- Other duties may also be assigned, not all unique aspects of this job are covered by this job posting. A full job description will be shared during the interview process.
Graduate degrees that emphasize engineering, computer science, and statistics are preferred
Experience with mass spectrometry-based data analysis
Proficiency in Python and Linux bash scripting
Demonstrated adherence to best practices in software engineering, including usability, testing, and source code version control (e.g. git)
Experience with cloud computing environment
Exposure to container systems such as setting up virtual machines and Docker instances
Experience on a bioinformatics and/or software development team-based project
Familiarity with build/release/deploy and continuous integration frameworks
Familiarity with the R programming language
Biological domain knowledge
Experience in exercise science and/or untargeted metabolomics-based / proteomics projects
An understanding of data modeling including ontologies and database design
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.
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/.
Why Stanford is for You: Imagine a world without search engines or social platforms. Consider lives saved through first-ever organ transplants and research to cure illnesses. Stanford University has revolutionized the way we live and enrich the world. Supporting this mission is our diverse and dedicated 17,000 staff. We seek talent driven to impact the future of our legacy. Our culture and unique perks empower you with:
Freedom to grow. We offer career development programs, tuition reimbursement, or audit a course. Join a TedTalk, film screening, or listen to a renowned author or global leader speak.
A caring culture. We provide superb retirement plans, generous time-off, and family care resources.
A healthier you. Climb our rock wall, or choose from hundreds of health or fitness classes at our world-class exercise facilities. We also provide excellent health care benefits.
Discovery and fun. Stroll through historic sculptures, trails, and museums.
Enviable resources. Enjoy free commuter programs, ridesharing incentives, discounts and more.
*- Stanford is an equal employment opportunity and affirmative action employer. All qualified applicants will receive consideration for employment without regard to race, color, religion, sex, sexual orientation, gender identity, national origin, disability, protected veteran status, or any other characteristic protected by law. Additional Information
Location: School of Medicine, Stanford, 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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Located between San Francisco and San Jose in the heart of Silicon Valley, Stanford University is recognized as one of the world's leading research and teaching institutions. Leland and Jane Stanford founded the University to "promote the public welfare by exercising an influence on behalf of humanity and civilization." Stanford opened its doors in 1891, and more than a century later, it remains dedicated to finding solutions to the great challenges of the day and to preparing students for leadership in a complex world. The University's thriving diverse community is comprised of nearly 7000 undergraduate students, 12000 graduate students, 2000 faculty members, 1900 postdoctoral scholars, and over 11,000 academic and administrative staff in seven schools including several interdisciplinary research centers and institutes. The campus spreads over 8000 contiguous acres and nearly all undergraduates live on campus. Stanford offers bachelor's and master's degrees in addition to doctoral degrees (PhD, MD, DMA and JD) plus a number of professional and continuing education programs and certifications. More at http://facts.stanford.edu and http://www.stanford.edu. Stanford is an equal empl...oyment opportunity and affirmative action employer. All qualified applicants will receive consideration for employment without regard to race, color, religion, sex, sexual orientation, gender identity, national origin, disability, protected veteran status, or any other characteristic protected by law. Stanford also welcomes applications from others who would bring additional dimensions to the University’s research, teaching and clinical missions.