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Staff Data Scientist / Protein Design - Aether Biomachines

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Job Title
Staff Data Scientist / Protein Design
Job Location
Menlo Park, CA
Job Description

This is a (minimum four days/week in office) full-time position based in our Menlo Park, CA office. This position reports to the Director of Data Science of the Company.

Aether Biomachines is on a mission to build the post-scarcity future using peptide-based nanotechnology as the driving force for the next industrial revolution. By creating the world's most advanced high-throughput robotic laboratory, we are generating data at unprecedented scales to fuel deep learning algorithms. We're assembling a diverse and dynamic team of self-starters, engineers, sci-fi enthusiasts, and visionaries, and we invite you to join us on this journey.

We're breaking barriers in laboratory automation to power world-class machine learning models with faster, broader, and more robust robotic sample processing systems. We aim to transform peptides from niche catalysts into general-purpose molecular assemblers using our platform, enabling a future of abundance for the human race.

Aether's Machine Learning (“ML”) team is spearheading innovation in enzyme engineering by capitalizing on advanced computational methodologies. Faced with the intricate and multidimensional challenges of enzyme engineering, the ML team employs refined data-cleaning algorithms to curate and preprocess extensive volumes of experimental data meticulously. By deploying state-of-the-art predictive models, the team can accurately predict enzyme-substrate interactions, uncover novel enzymatic activities, and optimize enzyme performance across diverse experimental conditions. Furthermore, by utilizing cutting-edge multi-objective search and optimization algorithms, the ML team can concurrently navigate multiple solution spaces, adeptly navigating trade-offs between conflicting objectives to engineer optimal enzyme designs. Aether's innovative fusion of data science and biotechnology facilitates the creation of pioneering solutions that address pressing challenges within the biotech industry and unleash the boundless potential of enzymes for a wide array of applications.


What we are looking for in you

We seek an experienced and highly motivated Staff Data Scientist to join our ML team and contribute to the cutting-edge protein and enzyme design field. In this role, you will be responsible for developing novel machine learning models, particularly Physics-Informed GNNs, diffusion models, and large language models (LLMs), to advance the design and engineering of proteins and enzymes. Your work will play a pivotal role in driving the innovation and success of our enzyme engineering projects.


What you will be doing

  • Development Maintenance and use of  Physics-Informed GNNs
  • Development Maintenance and use of LLM-based machine learning models for enzyme design.
  • Hybridization of LLM and Diffusion models. 
  • Collaboration with cross-functional teams, including chemists, biochemists, and data scientists.
  • Analysis and interpretation of experimental data to validate and refine machine learning models.
  • Presentation of research findings, model performance, and insights to internal teams and external collaborators.
  • Staying current with advances in machine learning, computational biology, and protein engineering to inform model development and improvement.
  • Contributing to the preparation of scientific publications, technical reports, and patent applications.
  • Building internal tools for research teams to interpret and categorize data generated by protein and enzyme engineering experiments.

What you must have

  • Strong understanding of protein structure, function, and biochemistry.
  • Strong understanding of MD simulations. Experience with (QM/MM) methods for modeling enzyme-catalyzed reaction mechanisms is a plus.
  • Proven experience developing and applying machine learning models, in a biological or biochemical context.
  • Proficiency in Python and experience with machine learning frameworks such as TensorFlow, jax, or PyTorch and MD frameworks such as openmm. 
  • Strong problem-solving and critical-thinking skills, with a high level of attention to detail.

What you should have

Ph.D. in Computational Biology, Mathematics, Computer Science, or a related field or demonstrated exceptional ability outside of the context of a Ph.D.


Not sure you meet 100% of our qualifications? 

We encourage anyone who thinks they would excel at Aether to apply, no matter their background or how they identify.


Benefits and Perks

  • Full suite of health benefits (medical, dental, vision)
    • Aether pays 100% of the premiums for employees and 90% of the premiums for dependents.
  • Basic Life, AD&D, and Long Term Disability
  • Health Savings Account
    • $125 Aether contribution per month for individuals
    • $250 Aether contribution per month for employees with dependents/partners
  • Flexible Spending Accounts 
    • Health Care FSA
    • Dependent Care FSA
    • Commuter FSA
      • Up to $100 Aether match contribution per month
      • Lab Personnel: 
        • $200 per month Aether taxable bonus if you live more than 25 miles from the office
        • $100 per month Aether taxable bonus if you live less than 25 miles from the office
  • 401(k) Retirement Plan
  • Flexible Time Off for Full-Time employees and 11 Paid Holidays
  • Health Perks (EAP, Travel Assistance, Chiropractic and Acupuncture care)
  • Company Perks (Equity, Socials, holiday parties, LifeMart Discounts, and more!)
  • On-Site Services (Free EV charging, shuttle services, free meals while you work, free on-site fitness center, and more!)



Our company values diversity and believes diverse teams make innovation possible. We work on complex, difficult problems with no linear or clear solutions. We believe that a diverse team can bring different perspectives and approaches, and whose experiences reflect the full set of clients we seek to serve. As such, Aether Biomachines, Inc. is committed to a diverse representation among our employees. Legal authorization to work in the U.S. is required.  Aether may agree to sponsor an individual for an employment visa now or in the future if there is a shortage of individuals with particular skills for this job.  In compliance with federal law, all persons hired will be required to verify identity and eligibility to work in the United States and to complete the required employment eligibility verification form upon hire. This position is based in our California location.

This is the pay range for this position that we reasonably expect to pay. Individual compensation is based on various factors, including experience, education, skillset, and geographic location. This range is for the SF Bay Area, California location, and may be adjusted to the labor market in other geographic areas.
SF Bay Area Pay Range
$166,500$203,500 USD

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Aether Biomachines Headquarters Location

Menlo Park, CA

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Aether Biomachines Company Size

Between 20 - 50 employees

Aether Biomachines Founded Year


Aether Biomachines Total Amount Raised


Aether Biomachines Funding Rounds

View funding details
  • Series A

    $49,000,000 USD

  • Series Unknown

    $93,616 USD

Aether Biomachines' Investors