Bioinformatics Engineer, Molecular Diagnostics Labs, UCLA Health

You will be part of a team of molecular biologists, medical geneticists, and bioinformaticians working together to analyze new and archival clinical cases using high throughput sequencing. As one of a newer team of software engineers, you will have the unique opportunity to design new in-house infrastructure for the UCLA Molecular Diagnostics Laboratories at the Department of Pathology and Lab Medicine.

If interested, submit application here.

A successful applicant will operate in these major areas:

Bioinformatics Pipelines. Sequencing data alignment, variant calling, and clinical reporting.

• Current tools for workflow development include Docker, Nextflow, and Python.
• Current compute platforms include Azure CycleCloud, DNAnexus, and Illumina Dragen.
• Current storage platforms include SMB shares, Azure Blob Storage, and Amazon Glacier.
• Strong focus on code reusability and scientific reproducibility of all work, manual or automated.

Lab Automation. Help colleagues automate manual or tedious steps in their daily workflows.

• Write scripts to parse, update, or even obsolete spreadsheets used by the lab to track work.
• Build APIs and tools that talk to our EPIC Beaker Lab Information System to track samples.
• Build databases and UIs to track samples and their associated metadata.
• Build web-based or Win32 graphical user-interfaces to structure and simplify data entry.

Translational Research. Feature extraction, clinical correlation, and data visualization.

• Extract clinical covariates and molecular data from health records and pathology reports.
• Structure data using natural language processing, neural networks, and regular expressions.
• Speak with pathologists, clinicians, and molecular biologists to understand the data.
• Perform ad-hoc analyses in Jupyter Notebooks, R Markdown, or well documented scripts.

Qualifications

• BS or MS in Computer Science, Molecular Biology, or a related discipline.
• 3+ years’ experience or strong aptitude for software design and engineering.
• Expertise with command-line tools on Linux batch systems and cloud compute.
• Advanced skills in Python or R with attention to documentation and style.
• Familiarity with version control using git and continuous integration platforms.
• Familiarity with workflow specification (CWL/Nextflow) and executors (Toil/Snakemake).
• Excellent written and verbal communication skills with both biologists and coders.
• Enjoys working in a team but can solve problems independently.
• Self-motivated with a strong desire to learn and troubleshoot.
• Strong organizational skills and ability to manage ambiguity.