Computational Scientist, AI/ML & Protein Design

USA - South San Francisco, CA

Computational Scientist, AI/ML & Protein Design (Hybrid in South San Francisco, CA)

Job Description

Twist is seeking a Computational Scientist to join our Bioinformatics team to support Antibody Discovery, Development and NGS Analysis. You will work alongside research scientists, software engineers, and data scientists to develop cutting-edge computational solutions for protein design, contributing to accelerating and scaling Twist Biopharma Solutions' offerings. You will develop Large Language Model-based solutions for designing novel antibody sequences and therapeutic proteins, leveraging NGS data and experimental results to train and validate models. Our ideal candidate demonstrates expertise in AI/ML applications for biology and is comfortable with both machine learning frameworks and standard NGS bioinformatics tools. Strong communication skills and a balanced ability to work independently and as a team member are desired. 

What you’ll be doing:

  • Lead development of AI/ML-based solutions to design novel antibody sequences using Large Language Models (LLMs) and neural networks for sequence optimization. 
  • Build and deploy machine learning models for protein engineering, including sequence generation, affinity optimization, and developability prediction. 
  • Process and analyze NGS data, meta data from wet lab assays (expression, binding data, and developability assessment), and large biological datasets to create training datasets and validate AI-generated sequences.
  • Provide technical support and troubleshooting: Debug model performance issues, resolve data pipeline failures, troubleshoot experimental integration problems, and provide day-to-day operational support to ensure smooth team workflows and project continuity.
  • Develop software solutions for storing, querying, processing, and visualizing biological data and model outputs.
  • Utilize advanced data science techniques and frameworks, including deep learning (PyTorch, TensorFlow), analysis (pandas, numpy, scikit-learn), and visualization (matplotlib, plotly).
  • Collaborate with internal members throughout all phases of Biopharma R&D workflows, translating biological requirements into machine learning solutions and providing technical support.
  • Follow and establish software development best practices for Bioinformatics systems, including model versioning, experiment tracking, deployment pipelines, and code management.

What you’ll bring to the team:

  • PhD in Computational Biology, Machine Learning, or related scientific discipline with a minimum of 2-5 years related experience (industry experience preferred).
  • Deep understanding of LLMs and neural network models for biological sequence design, with hands-on experience in model development and deployment.
  • Demonstrated experience in antibody and/or other therapeutic proteins for AI-driven discovery and engineering applications.
  • Understanding of antibody discovery, affinity maturation, humanization, developability: Deep knowledge of antibody engineering workflows, CDR optimization, species humanization strategies, and therapeutic developability assessment including aggregation, immunogenicity, and stability considerations.
  • Proficiency in machine learning frameworks (PyTorch, TensorFlow) and experience with protein language models (ESM, Ablang, ProtTrans, or similar).
  • Strong experience in analyzing biological datasets (NGS, experimental assays), data preprocessing for ML, and utilizing common file formats (FASTA, FASTQ).
  • Understanding of cloud computing, MLOps workflows, model deployment, and CI/CD pipelines for AI systems.
  • Interest in learning and contributing to developing web applications (Django, React) and utilizing database management systems for biological discovery platforms.

About Twist Bioscience

Twist Bioscience synthesizes genes from scratch, known as “writing” DNA. Just as children learn to both read and write, the next phase of development for the genomics revolution is the ability to write DNA.

At Twist Bioscience, we work in service of people who are changing the world for the better. In fields such as health care, agriculture, industrial chemicals and data storage, our unique silicon-based DNA Synthesis Platform provides precision at a scale that is otherwise unavailable to our customers.

Twist Bioscience Corporation is an Equal Opportunity Employer. Twist Bioscience Corporation provides equal employment opportunities to all employees and applicants for employment without regard to race, color, religion, sex, sexual orientation, gender identity, national origin, age, disability, genetic characteristics, or any other category protected by law.

The base cash compensation for this California-based role is below. In addition to base salary, this role is eligible for bonus, equity, and a generous benefits package. Final compensation amounts are determined by multiple factors, including candidate skill, experience, expertise, and location and may vary from the amount listed above. Compensation may be different in other locations.

San Francisco Bay Area Pay Range

$140,085 - $177,866 USD

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