ML Scientist: Nucleic Acid Design & Sequence Modeling

Lilasciences; San Francisco (CA); On-site; USD 176,000 - 304,000; Full time

Benefits offered by this job

Medical/dental/vision

Life and disability insurance

Flexible time off

Parental leave

Commuter benefits

Company lunch program

Job summary

Lila Sciences is seeking an ML Scientist I/II, Nucleic Acid Design to advance RNA and DNA sequence design. This scientist will develop models and design strategies for understanding and engineering nucleic acid sequences, including problems such as 3’ UTR optimization, 5’ UTR optimization, CDS optimization, and promoter / enhancer design.

You’ll work at the intersection of machine learning, sequence modeling, experimental design, and platform development.

Qualifications

• PhD or equivalent experience in ML, computational biology, bioengineering, CS, statistics, or related field.
• Hands-on experience building, training, and evaluating ML models for DNA or RNA.
• Strong foundation in modern ML methods with PyTorch/JAX or equivalent.

Responsibilities

• Build ML models for RNA and DNA sequence design across regulatory and coding sequence contexts.
• Develop methods spanning de novo generation, sequence property prediction, diverse set selection for experimental validation, and active learning strategies.
• Deeply investigate the biological mechanisms of designed sequences and propose hypotheses about why they succeed or fail.
• Partner with experimental scientists to propose informative assays, validation strategies, and learning loops.
• Collaborate with ML scientists and engineers to integrate nucleic acid design models into robust platforms and agent-driven frameworks.
• Stay current with research in nucleic acid biology, sequence design, and scientific ML, and share findings externally.

Skills

ML model development

DNA/RNA sequence design

PyTorch

JAX

Active learning

Experimental collaboration

Education

PhD or equivalent (ML/computational biology)

Tools

PyTorch

JAX

Job description

Lila Sciences is seeking an ML Scientist I/II, Nucleic Acid Design to advance RNA and DNA sequence design. This scientist will develop models and design strategies for understanding and engineering nucleic acid sequences, including problems such as 3’ UTR optimization, 5’ UTR optimization, CDS optimization, and promoter / enhancer design.

You’ll work at the intersection of machine learning, sequence modeling, experimental design, and platform development.