Job:Bioinformatics Engineer, Molecular Diagnostics Labs, UCLA Health
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7 weeks ago

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.
scientist clinical variant bioinformatician engineer • 295 views
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