Principal Deep LearningAI Engineer, Bioinformatics

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Position 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 Illuminas sequencing and analysis products. This role is primarily technical in nature with deep personal ownership of algorithm design model development benchmarking and production readiness. The role partners with product and engineering to ensure AI methods are scientifically sound performant at scale and ready for real-world customer and/or clinical use while providing technical direction and mentorship.

Key Responsibilities

• Hands-on algorithm and model development: Design prototype and implement AI/ML methods for genomics and multiomics (e.g. basecalling variant calling error modeling QC anomaly detection methylation single-cell metagenomics assembly interpretation).
• Technical ownership of AI in products: Serve as the technical authority for AI features embedded in Illumina software and pipelines from concept through production release.
• People leadership: Lead a focused team to create enhance and sustain ML and AI products and tools.
• Benchmarking and validation: Define gold-standard datasets evaluation metrics and statistical validation approaches; personally review and approve model performance and scientific claims.
• Production ML rigor: Work directly with engineers to ensure models are reproducible versioned monitored and robust in production (training pipelines inference efficiency regression detection).
• Data-centric AI leadership: Drive data strategy for model performance including curation labeling augmentation and bias/edge-case analysis across instruments assays and populations.
• Technical design reviews: Lead architecture and design reviews for AI and bioinformatics components; set coding testing and documentation standards.
• AI adoption through technical excellence: Enable adoption by delivering models that measurably improve accuracy speed cost and usabilityrather than through programmatic or organizational mandates.
• Regulated and clinical readiness: Provide technical input and documentation for design controls traceability and validation where AI methods are used in regulated contexts.
• Mentorship and technical guidance: Mentor senior and junior scientists and engineers as a technical authority and reviewer.
• External technical engagement: Patent present and -on occasion- publish technical work; evaluate external methods tools and collaborations for technical fit and differentiation.

Required Qualifications

• Typically requires a minimum of 15 years of related experience with a Bachelors degree; or 12 years and a Masters 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.

Preferred Qualifications

• Experience with sequencing-instrumentadjacent 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.

Role Emphasis

This role is designed as a technical authority and hands-on expert. Success is measured by the quality robustness and real-world impact of AI/ML bioinformatics methods shipped into Illumina products.

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The estimated base salary range for the Principal Deep Learning/AI Engineer Bioinformatics role based in the United States of America is: $205100 - $307700. Should the level or location of the role change during the hiring process the applicable base pay range may be updated accordingly. The range reflects longterm growth in the role. Most candidates are hired between the minimum and middle of the range. Placement depends on experience skills location and internal equity. Additionally all employees are eligible for one of our variable cash programs (bonus or commission) and eligible roles may receive equity as part of the compensation package. We offer a wide range of benefits as innovative as our work including access to genomics sequencing family planning health/dental/vision retirement benefits and paid time off.

We are a company deeply rooted in belonging promoting an inclusive environment where employees feel valued and empowered to contribute to our mission. Built on a strong foundation Illumina has always prioritized openness collaboration and seeking alternative perspectives to propel innovation in genomics. We are proud to confirm a zero-net gap in pay regardless of gender ethnicity or race. We also have several Employee Resource Groups (ERG) that deliver career development experiences increase cultural awareness and offer opportunities to engage in social responsibility. We are proud to be an equal opportunity employer committed to providing employment opportunity regardless of sex race creed color gender religion marital status domestic partner status age national origin or ancestry physical or mental disability medical condition sexual orientation pregnancy military or veteran status citizenship status and genetic information. 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. Background check results may potentially result in the withdrawal of a conditional offer of employment. The background check process and any decisions made as a result shall be made in accordance with all applicable local state and federal laws. Illumina prohibits the use of generative artificial intelligence (AI) in the application and interview process. If you require accommodation to complete the application or interview process please contact To learn more visit: The position will be posted until a final candidate is selected or the requisition has a sufficient number of qualified applicants.