WORK TERM: January 2023 - June 2023

Company Summary:

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

Position Summary:

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 co-op to join our experienced team in expanding our drug design platform. As a co-op 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.

Key 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

Basic Qualifications:

  • Currently pursuing a graduate degree in Computer Science, Computational Biology, Bioinformatics, Statistics, Mathematics, Physics, or another quantitative field (MS)
  • Available to start in January 2023
  • 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 co-op.

More About Flagship Pioneering

Flagship Pioneering conceives, creates, resources, and develops first-in-category life sciences companies to transform human health and sustainability. Since its launch in 2000, the firm has, through its Flagship Labs unit, applied its unique hypothesis-driven innovation process to originate and foster more than 100 scientific ventures, resulting in over $50B in aggregate value. To date, Flagship has deployed over $2.2B in capital toward the founding and growth of its pioneering companies alongside more than $18B of follow-on investments from other institutions. The current Flagship ecosystem comprises 41 transformative companies, including Axcella Health (NASDAQ: AXLA), Denali Therapeutics (NASDAQ: DNLI), Evelo Biosciences (NASDAQ: EVLO), Foghorn Therapeutics (NASDAQ: FHTX), Indigo Ag, Kaleido Biosciences (NASDAQ: KLDO), Moderna (NASDAQ: MRNA), Rubius Therapeutics (NASDAQ: RUBY), Sana Biotechnology (NASDAQ: SANA), Seres Therapeutics (NASDAQ: MCRB), and Sigilon Therapeutics (NASDAQ: SGTX).

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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