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Engineer I, Machine Learning - Alltrna

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Job Title
Engineer I, Machine Learning
Job Location
Cambridge, Massachusetts, United States
Job Description

About Alltrna

Flagship Pioneering has conceived of and created companies such as Moderna Therapeutics (NASDAQ: MRNA), Editas Medicine (NASDAQ: EDIT), Omega Therapeutics (NASDAQ: OMGA), Seres Therapeutics (NASDAQ: MCRB), and Indigo Agriculture. Since its launch in 2000, Flagship has applied its unique hypothesis-driven innovation process to originate and foster more than 100 scientific ventures. In 2021, Flagship Pioneering was ranked 12th globally on Fortune’s “Change the World” list, an annual ranking of companies that have made a positive social and environmental impact through activities that are part of their core business strategies.

Alltrna is the world’s first tRNA platform company to decipher tRNA biology and pioneer tRNA therapeutics to treat thousands of diseases. Alltrna unlocks tRNA biology to correct disease. The company's platform incorporates AI/ML tools to learn the tRNA language and deliver diverse programmable molecules with broad therapeutic potential. Alltrna has an unprecedented opportunity to advance a single tRNA medicine to unify treatment across a wide range of diseases with the same underlying genetic mutation. Alltrna was founded in 2018 by Flagship Pioneering. For more info, visit

About The Role 

At Alltrna, we pair high throughput experimental approaches with predictive models to drive and accelerate the development of novel RNA-based therapeutics. We are seeking an innovative, collaborative, and highly motivated ML engineer to join our experienced team in expanding our drug design platform. As a engineer in our Computational & Molecular Biology team, you will work closely with fellow data scientists and molecular biologists to develop and hone sequence-to-function models that leverage in-house assay data. This is a great opportunity for an early career computer scientist, data scientist, or computational biologist to gain end-to-end industry experience in the blooming field of RNA drug discovery ­­­­­­­­­­­­­­­­­­­− from developing and benchmarking algorithms, to training models on in vitro data, and ending in production models that can be used to explore novel compounds.

Core Responsibilities

  • Developing machine learning models on in vitro sequence-activity measurements
  • Perform hyperparameter optimization and benchmarking on in-house datasets to evaluate model performance
  • Support explanatory analyses that promote understanding of model features and design strategies.
  • Communicate results within and outside Alltrna’s Computational Biology team and participate in scientific discussions

Qualifications and skills

  • Has a graduate degree in Computer Science, Computational Biology, Bioinformatics, Statistics, Mathematics, Physics, or another quantitative field (MS or PhD)
  • Fluent in Python (+ Pandas, Numpy) and at least one common ML library (TensorFlow/Keras, PyTorch, scikit-learn, etc.)
  • Familiar with code management (version control/Git, unit tests, Jupyter notebooks, docstrings)
  • Good verbal, communication, and collaboration skills

       Preferred Qualifications:

  • Experience with one or more of the following deep learning architectures: Transformers, GNNs, VAEs, or GANs
  • Comfortable working in a cloud-computing environment (AWS, GCP).
  • Prior experience with hyperparameter optimization and evaluation of machine learning algorithms
  • Prior model development experience in a research setting, such as a conference publication, thesis work, or previous engineer.

What We’ll Offer You

  • Comprehensive, competitive healthcare and dental coverage through Blue Cross Blue Shield, vision coverage through VSP, family leave, paid time off, 401k retirement plan, disability and life insurance, and fully covered parking/commuter benefits.
  • A dynamic early-stage work environment and highly interdisciplinary, talented, and collaborative team.
  • Participation in an unprecedented opportunity to advance a single tRNA medicine to restore disrupted protein production, regardless of target, for thousands of diseases with the same underlying genetic mutation.
  • Professional growth opportunities through mentoring, training, immersion in cross-functional projects, and opportunities to learn and try new things.

Our Core Values 

  1. PATIENTS DESERVE BETTER. We are transforming medicine, boldly building a new future for patients.
  2. CURIOSITY SPARKS DISCOVERY. We ardently explore the unknown, catalyzing new scientific breakthroughs.
  3. COURAGE PROPELS US FORWARD. We take thoughtful risks without fear of failure, growing with each experience.
  4. OUR PURPOSE FUELS US. We each lead and work with focus and passion to design groundbreaking tRNA medicines.
  5. WE ARE ONE TEAM. We are united on trust and collaboration, embracing all voices and experiences.


Flagship Pioneering and our ecosystem companies are committed to equal employment opportunity regardless of race, color, ancestry, religion, sex, national origin, sexual orientation, age, citizenship, marital status, disability, gender identity or Veteran status.
Recruitment & Staffing Agencies: Flagship Pioneering and its affiliated Flagship Lab companies (collectively, “FSP”) do not accept unsolicited resumes from any source other than candidates. The submission of unsolicited resumes by recruitment or staffing agencies to FSP or its employees is strictly prohibited unless contacted directly by Flagship Pioneering’s internal Talent Acquisition team. Any resume submitted by an agency in the absence of a signed agreement will automatically become the property of FSP, and FSP will not owe any referral or other fees with respect thereto.

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Alltrna Headquarters Location

Cambridge, MA

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Alltrna Company Size

Between 20 - 100 employees

Alltrna Founded Year


Alltrna Total Amount Raised


Alltrna Funding Rounds

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  • Series B

    $109,000,000 USD

  • Series Unknown

    $50,000,000 USD

Alltrna's Industries