ML Enzyme Engineer Consultant en Flagship Pioneering, Inc.

Who We Are

Flagship Pioneering is a bioplatform innovation company that invents and builds platform companies, each with the potential for multiple products that transform human health or sustainability. Since its launch in 2000, Flagship has originated and fostered more than 100 scientific ventures, resulting in more than $90 billion in aggregate value. Many of the companies Flagship has founded have addressed humanity’s most urgent challenges: vaccinating billions of people against COVID-19, curing intractable diseases, improving human health, preempting illness, and feeding the world by improving the resiliency and sustainability of agriculture.  Flagship has been recognized twice 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, and has been twice named to Fast Company’s annual list of the World’s Most Innovative Companies. Learn more about Flagship at www.flagshippioneering.com.

Role Summary
We are seeking a consulting ML Enzyme Designer to build and optimize computational pipelines that prioritize protein sequences for experimental screening in enzyme discovery and engineering. The successful candidate will integrate evolutionary analysis, structural/functional prediction, and machine learning approaches to identify the most promising candidates for downstream testing in expression, stability and functional assays.

Minimum 10 hours per week.

Key Responsibilities

• Pipeline Development: Design and implement computational pipelines for ranking and prioritizing enzyme sequences for screening.
• Data Integration: Incorporate sequence, structural, and functional features (e.g., conservation, diversity, active site motifs, predicted stability) into multi-criteria scoring systems.
• Machine Learning Models: Apply and adapt ML/AI methods (Bayesian optimization, reinforcement learning, active learning) to iteratively refine prioritization based on experimental feedback.
• Phylogenetic & Evolutionary Analysis: Utilize tools like PAML, HyPhy, and FastML for detecting positive selection, ancestral sequence reconstruction, and evolutionary modeling.
• Biological Insight Extraction: Leverage knowledge of enzyme mechanism, structural biology, and biocatalysis to ensure that computational outputs map to experimentally relevant hypotheses.
• Collaboration: Work closely with experimental biochemists, structural biologists, and protein engineers to validate computational predictions and feed results back into model refinement.

Core Competencies

• Computational Biology & Bioinformatics
• Multiple sequence alignment, phylogenetics, and ancestral sequence reconstruction (ASR).
• Structural modeling and function prediction of enzymes.
• Machine Learning for Biology
• Experience with supervised, unsupervised, and generative models.
• Familiarity with active learning approaches for iterative design-test-learn cycles.
• Data Engineering & Pipeline Design
• Ability to build scalable, reproducible workflows (e.g., with Snakemake, Nextflow, or cloud-based tools).
• Scientific Rigor
• Strong grounding in molecular evolution, enzyme catalysis, and protein engineering.
• Capable of translating algorithmic outputs into biologically meaningful predictions.

Required Skills

• Proficiency in Python/R with ML libraries (PyTorch, TensorFlow, scikit-learn).
• Experience with phylogenetics and molecular evolution tools (HyPhy, PAML, FastML).
• Familiarity with enzyme engineering concepts, including thermostability, substrate promiscuity, and directed evolution.
• Experience handling genomic/proteomic datasets (NCBI, UniProt, PDB).
• Strong understanding of protein structure-function relationships, including catalytic residues and structural motifs.
• Excellent communication skills for interdisciplinary collaboration.

Preferred Qualifications

• PhD or working toward PhD in Computational Biology, Bioinformatics, Biophysics, or related field.
• Prior experience in enzyme discovery or biocatalyst engineering.
• Track record of integrating computational predictions into experimental pipelines.

About Flagship

Flagship Pioneering is a bioplatform innovation company that invents and builds platform companies, each with the potential for multiple products that transform human health or sustainability. Since its launch in 2000, Flagship has originated and fostered more than 100 scientific ventures, resulting in more than $90 billion in aggregate value. Many of the companies Flagship has founded have addressed humanity’s most urgent challenges: vaccinating billions of people against COVID-19, curing intractable diseases, improving human health, preempting illness, and feeding the world by improving the resiliency and sustainability of agriculture.  Flagship has been recognized twice 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, and has been twice named to Fast Company’s annual list of the World’s Most Innovative Companies. Learn more about Flagship at www.flagshippioneering.com.

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. 

At Flagship, we recognize there is no perfect candidate. If you have some of the experience listed above but not all, please apply anyway. Experience comes in many forms, skills are transferable, and passion goes a long way. We are dedicated to building diverse and inclusive teams and look forward to learning more about your unique background.

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.