Senior Bioinformatics Scientist – AI/ML for Protein Engineering

Location: San Diego, California, United States; onsite role

Base salary: $129,400–$194,000 per year. Additional variable cash compensation and, for eligible roles, equity may be available.

Company

hirify.global develops genomic technologies for disease detection, diagnosis, treatment research, and sequencing applications.

What you will do

• Develop bioinformatics tools and pipelines for designing, engineering, and discovering novel enzymes.
• Apply protein language models, generative design, structure-based machine learning, and other AI methods to optimize enzyme function.
• Evaluate computational methods using protein sequence, structure, and experimental data.
• Create reusable scripts, templates, dashboards, and lightweight applications for routine analyses and computational recommendations.
• Analyze high-throughput screening and sequencing datasets to guide protein optimization.
• Collaborate with engineers, chemists, biophysicists, and protein scientists to deliver protein variants with desired properties.

Requirements

• At least 5 years of related experience with a bachelor’s degree, 3 years with a master’s degree, a PhD without experience, or equivalent experience.
• Practical experience applying AI/ML methods to protein or enzyme engineering.
• Programming skills in at least one major language, such as C/C++, Python, or R.
• Knowledge of protein sequence or structure modeling, protein-ligand interaction prediction, molecular simulation, statistical modeling, algorithm design, data analysis, or visualization.
• Strong communication, collaboration, innovation, and research and development skills.
• This role is not eligible for visa sponsorship.

Nice to have

• Experience with generative protein design, zero-shot variant scoring, supervised learning, model-guided library design, uncertainty-aware learning, and multi-parameter optimization.
• Experience with Rosetta, Protein MPNN, RFdiffusion, Boltz, AlphaFold, molecular dynamics, docking, or biophysical analysis.
• Experience with PyTorch, TensorFlow, JAX, AI agents, cloud or high-performance computing, GPU computing, and job schedulers.
• Experience with directed evolution, high-throughput screening, data standards, assay schemas, dashboards, Git, UNIX, and shell scripting.
• Knowledge of bioinformatics, genomics, proteomics, biochemistry, enzymology, molecular biology, and next-generation sequencing.

Culture & Benefits

• Collaborative, inclusive environment focused on genomics innovation and diverse perspectives.
• Health, dental, and vision coverage, retirement benefits, and paid time off.
• Family planning support and access to genomics sequencing.
• Variable cash programs and equity for eligible roles.
• Employee Resource Groups offering career development, cultural awareness, and social responsibility opportunities.