Principal Deep Learning/AI Engineer, Bioinformatics
$205,100–$307,700 year
On-site · San Diego, California, United States
Job Summary
The Principal Deep Learning/AI Engineer, Bioinformatics is a senior hands-on technical expert responsible for inventing, implementing, and validating AI- and ML-driven bioinformatics methods that directly power sequencing and analysis products. This technical role requires algorithm design, model development, and efficiency for real-world applications, and includes responsibilities such as leading a focused team, ensuring scientific validity of AI methods, creating gold-standard datasets, and driving data strategy. Candidates typically need a PhD or equivalent experience in relevant fields, 10+ years of algorithm and ML model development experience, and expertise in genomics data workflows.
Required Qualifications
- Typically requires a minimum of 15 years of related experience with a Bachelor’s degree; or 12 years and a Master’s degree; or a PhD with 8 years of experience; or equivalent experience
- PhD (strongly preferred) or MS with equivalent depth in Bioinformatics, Computational Biology, Computer Science, Statistics, or a related field
- 10+ years of hands-on experience developing algorithms and ML models for biological data, with sustained personal technical contribution
- Proven track record of shipping AI/ML-driven bioinformatics methods into production software used by external customers
- Deep expertise in genomics data types and workflows (FASTQ/BAM/CRAM/VCF, reference genomes, annotations, pipelines)
- Strong applied ML background, including deep learning, probabilistic modeling, and rigorous model evaluation
- Demonstrated ability to work close to the code and data, including reviewing implementations and results.
Desired Qualifications
- Experience with sequencing-instrument–adjacent AI (basecalling, signal processing, error modeling, run QC)
- Experience operating in regulated or clinical software environments
- Publications and/or patents in AI, ML, or bioinformatics with clear product relevance
- Experience optimizing models for scale, latency, and cost in production environments
- Hands on experience leveraging AI tools for development work
Additional Requirements
- Illumina conducts background checks on applicants for whom a conditional offer of employment has been made. Qualified applicants with arrest or conviction records will be considered for employment in accordance with applicable local, state, and federal laws.
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