Bioinformatics Engineer II; Hybrid

Join to apply for the Bioinformatics Engineer II (Hybrid Opportunity) role at Stanford University School of Medicine

Join to apply for the Bioinformatics Engineer II (Hybrid Opportunity) role at Stanford University School of Medicine

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The Department of Medicine, Division of Cardiovascular Medicine at Stanford University is seeking a talented Bioinformatics Engineer to join the Bioinformatics Core (BIC) of the Molecular Transducers of Physical Activity Consortium (MoTrPAC). As part of this groundbreaking national research consortium, you will help unravel the molecular mechanisms underlying the benefits of physical activity. Under the supervision of co-PIs Dr. Euan Ashley and Dr.

Matthew Wheeler, you will play a crucial role in shaping the future of personalized exercise science and public health. Dr. Euan Ashley's research interests focus on the application of genomics and other omics data to improve clinical care, with an emphasis on cardiovascular disease and personalized medicine. Dr. Matthew Wheeler's research centers on the integration of large-scale molecular and clinical data to understand the genetic basis of cardiovascular diseases and to develop novel therapeutic strategies.

As a key member of the MoTrPAC team, your expertise in data engineering and bioinformatics software development will form the bedrock of our research infrastructure. You will be responsible for architecting and implementing the scalable data pipelines, standardized data models (like OMOP), and robust bioinformatic applications that transform raw, complex omics data into clean, analysis-ready datasets for the entire consortium, under the supervision of our lead informatician.

Your work is critical for our team to apply advanced statistical and machine learning methods, directly contributing to our understanding of complex biological systems and the development of personalized medicine.

This innovative project integrates large volumes of clinical and densely time-sampled molecular data, pushing the boundaries of biomedical data analytics. Our portal ((Use the "Apply for this Job" box below).) will push the boundaries of biomedical data analytics to provide insight into the basic and translational science of exercise. Working alongside our multidisciplinary team, you will be at the forefront of understanding how physical activity preserves and improves health, ultimately making a lasting impact on human well-being.

Responsibilities

As a Bioinformatics Engineer II, you will take ownership of critical data engineering and software development tasks that form the backbone of the MoTrPAC project. Your primary responsibilities will include:

• Data Engineering & ETL Pipelines:
  Engineer, maintain, and enhance robust ETL (Extract, Transform, Load) pipelines to process, clean, and map diverse data types. This includes managing pipelines for human and animal phenotype data to generate clean, summary datasets for public and consortium release.
• Data Standardization:
  Lead the transformation of MoTrPAC clinical data into standardized formats like the OMOP Common Data Model (CDM), enabling large-scale, federated data analysis and integration.
• Scientific Visualization Workflows:
  Develop and automate workflows to generate scientific visualizations (e.g., ATAC-seq tracks for IGV) that compare accessibility differences between study cohorts and support biological interpretation by our research team.
• Bioinformatics Tooling & Software Development:
  Refactor, extend, and package bioinformatic tools (e.g., Python packages) to streamline complex processes, such as the generation of mwTab files for metabolomics data submission.
• Data Management and Tracking:
  Design and implement data tracking systems to provide clear visibility into the status of raw and processed assays across cloud storage environments, improving data accessibility and usability for all consortium members.
• Collaboration and Communication:
  Collaborate with a multidisciplinary team of scientists and engineers to interpret large-scale multi-omics data and prepare reports and presentations to communicate findings effectively.

• 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…