Senior Scientist, Computational Biology

We are seeking a highly motivated and experienced Senior Scientist with expertise in computational biology and machine learning to join the Data Science & Algorithms Team. This role focuses on designing and optimizing protein binders with high affinity for N-terminal amino acid targets, a critical component of our Next-Generation Protein Sequencing kit.  

You will work at the intersection of machine learning, protein engineering, and structural biology, leveraging state-of-the-art algorithms and experimental feedback to develop novel protein scaffolds with tailored binding characteristics.  

The ideal candidate will have a deep background in Computational Biology, Bioinformatics, Data Science, or a related field with 5+ years of relevant academic or industry experience.  The candidate also must have a strong knowledge of programming languages (e.g. Python, Bash) and experience with developing or fine-tuning machine learning models. Candidates with a demonstrated ability to apply machine learning to protein design, structure-function prediction, or generative modeling are especially encouraged to apply. Familiarity with state-of-the-art protein modeling software (e.g. AlphaFold, ProteinMPNN) is a plus. 

As part of our team, your core responsibilities will be:   

• Design, model, and computationally screen protein binders for selective binding to N-terminal amino acid motifs. 

• Develop and optimize binder scaffolds using a combination of structure-based design, ML-driven design, and generative protein modeling tools. 

• Collaborate with wet-lab teams to iteratively test, validate, and refine designs using experimental feedback. 

• Innovate new computational pipelines for high-throughput protein binder discovery. 

• Evaluate binding energetics, specificity, and structural feasibility using in silico approaches. 

Qualifications  

• Ph.D. in Computational Biology, Bioinformatics, Computer Science, Data Science, or a related computational/scientific field 

• Skilled in ML model development and/or fine-tuning, especially for protein structure-function prediction and generative protein design 

• Experience integrating experimental feedback loops into computational pipelines to improve design success 

• Experience developing custom computational methods or ML approaches to guide protein design toward desired structural/functional properties 

• Proficient in programming with Python (preferred) and/or other scripting languages such as Bash; familiarity with JupyterLab, Jupyter Notebooks, or similar virtual notebook environments for data analysis, interactive modeling, and prototyping. 

• Strong analytical thinking and practical problem-solving skills, including the ability to break problems into logical subproblems and devise efficient and flexible solutions 

• Excellent scientific communication and documentation skills, including data summarization and visualization using Python 

Ideally, you also have these skills/experiences/attributes (but it’s ok if you don’t!): 

• Strong understanding of protein-protein and protein-peptide interactions, as well as hands-on experience conducting in silico analyses to evaluate these interactions 

• Familiarity with protein structure prediction and design using cutting-edge modeling software (AlphaFold, ProteinMPNN, RFDiffusion, ESM, Rosetta, etc.) 

• Experience designing binders against unstructured peptide regions, including terminal epitopes or motifs 

• Familiarity with GPU-accelerated computing and scaling workflows using HPC or cloud resources 
• Experience with Git 

The estimated base salary range for this role based in the United States of America is: $130,000 - $155,000. Compensation decisions are dependent on several factors including, but not limited to, level of the position, an individual’s skills, knowledge and abilities, location where the role is to be performed, internal equity, and alignment with market data. Additionally, all full-time employees are eligible for our discretionary bonus program and equity as part of the compensation package.   

Quantum-Si does not accept agency resumes.  

Quantum-Si is an E-Verify and equal opportunity employer regardless of race, color, ancestry, religion, gender, national origin, sexual orientation, age, citizenship, marital status, disability or Veteran status. All your information will be kept confidential according to EEO guidelines.