ZipRecruiter

Log In

1

Protein Engineering Jobs in Ontario (NOW HIRING)

Manifold Bio

CA$140K - CA$225K/yr

Your efforts will contribute to building production-ready ML infrastructure that enables breakthrough discoveries in protein therapeutics. You will be expected to take ownership of engineering ...

Maple Leaf Foods

Reliability Engineer

Hamilton, ON

CA$71K - CA$103K/yr

College or university education in Engineering or an Engineering Technologist Diploma (mechanical ... protein company on earth, and a deep commitment to sustainable protein across North America.An ...

BinSentry

Software Developer - HD

Kitchener, ON

With our technology, feed mills and protein producers are enhancing feed ordering efficiency ... Bachelor's degree in Computer Science, Software Engineering, or related field (or equivalent ...

BinSentry

Software Developer - HD

Kitchener, ON · On-site

CA$70K - CA$90K/yr

With our technology, feed mills and protein producers are enhancing feed ordering efficiency ... Bachelor's degree in Computer Science, Software Engineering, or related field (or equivalent ...

BinSentry

Senior Embedded Software Developer

Kitchener, ON · On-site

CA$125K - CA$165K/yr

With our technology, feed mills and protein producers are enhancing feed ordering efficiency ... Qualifications : * Bachelor's degree in Computer Engineering, Software Engineering, Computer ...

BinSentry

Senior Software Developer - HD

Kitchener, ON · On-site

CA$100K - CA$140K/yr

With our technology, feed mills and protein producers are enhancing feed ordering efficiency ... Bachelor's degree in Computer Science, Software Engineering, or related field (or equivalent ...

NITTA GELATIN NA INC

QA MANAGER

Toronto, ON · On-site

Experience in the gelatin, collagen, protein ingredients, meat, or food ingredients industry is ... Biology, Engineering, or related field. · Minimum 5 years of Quality Assurance leadership ...

BinSentry

Electronics Technician

Kitchener, ON · On-site

With our technology, feed mills, commercial grain handling facilities, and protein producers are ... Electronics Technologist Diploma or Electronics Engineering Degree * 3-5 years of experience in ...

BinSentry

Product Manager

Kitchener, ON · On-site

With our technology, feed mills, commercial grain handling facilities, and protein producers are ... Collaborate directly with the cross-functional engineering teams to identify and solve task-level ...

VitalBio

Scientist - II

Oakville, ON

CA$80K - CA$95K/yr

Collaborate closely with clinical, regulatory, engineering, quality, and manufacturing teams to ... Experience with nanoparticles, microfluidics, automated laboratory systems, protein conjugation ...

next page

Showing results 1-20

All JobsProtein Engineering JobsProtein Engineering Jobs in Ontario

Protein Engineering information

What is protein engineering?

A Protein Engineering job involves designing, modifying, and optimizing proteins for specific applications in medicine, biotechnology, and industry. Scientists in this field use computational modeling, directed evolution, and genetic engineering to enhance protein functions. Roles may include developing enzymes for drug production, improving therapeutic proteins, or creating biomaterials. This work often requires expertise in molecular biology, biochemistry, and structural biology.

What are the typical daily responsibilities of someone working in protein engineering?

A typical day in Protein Engineering involves designing and conducting experiments to modify protein sequences, expressing and purifying proteins, and analyzing their structure or function using techniques like chromatography and spectroscopy. You will often document your results, troubleshoot unexpected findings, and present data to colleagues or project teams. Collaboration with scientists in molecular biology, bioinformatics, and structural biology is common to ensure robust experimental design and data interpretation. The role may also include literature reviews to stay updated with the latest research and participating in team meetings to plan next steps or project timelines.

What are the key skills and qualifications needed to thrive in protein engineering, and why are they important?

To thrive in Protein Engineering, you need a solid background in biochemistry, molecular biology, and genetic engineering, typically supported by a relevant advanced degree. Experience with laboratory techniques such as PCR, site-directed mutagenesis, protein expression/purification, and analytical tools like mass spectrometry or chromatography is essential. Strong problem-solving abilities, attention to detail, and effective teamwork and communication skills help you stand out in this role. These competencies are crucial for designing novel proteins, collaborating in multidisciplinary teams, and ensuring successful project outcomes in biotech or pharmaceutical environments.

How much do protein engineers make?

Protein engineers typically earn a median salary ranging from $70,000 to $120,000 annually, depending on experience, education, and location. Advanced skills in molecular biology, bioinformatics, and laboratory techniques can lead to higher compensation, especially in biotech or pharmaceutical industries.

What do protein engineers do?

Protein engineers design and modify proteins to improve their functions or create new ones, often using techniques like directed evolution and computational modeling. They work in research labs, utilizing tools such as gene editing and structural analysis to develop applications in medicine, agriculture, and industry.

What are popular job titles related to Protein Engineering jobs in Ontario?

For Protein Engineering jobs in Ontario, the most frequently searched job titles are:

What job categories do people searching Protein Engineering jobs in Ontario look for?

The top searched job categories for Protein Engineering jobs in Ontario are:

Protein Engineering jobs near you
Infographic showing various Protein Engineering job openings in Ontario as of August 2026, with employment types broken down into 88% Full Time, 8% Part Time, 3% Contract, and 1% Nights. Highlights an 85% Physical, 4% Hybrid, and 11% Remote job distribution.

AI/ML Research Engineer

On-site

Manifold Bio
Biotechnology Research and Development • 1 - 10 employees
Learn more about Manifold Bioexternal

CA$140K - CA$225K/yr

Full-time

Medical, Dental, Vision, Retirement, PTO

Re-posted 9 days ago

Job description

Manifold Bio is a platform biotechnology company pioneering AI-guided protein design and massively multiplexed in vivo screening to unlock tissue-targeted medicines and organism-scale models of living systems. Using proprietary molecular barcoding technology, we screen hundreds of thousands of protein designs simultaneously in living systems, producing in vivo-validated datasets at a scale no one else can match. The datasets power our computational models, which leads to better drug designs, creating a flywheel that gets stronger with every campaign. Our team of protein engineers, biologists, and computational scientists works across this full stack to pursue programs both internally and with leading pharma companies.
 

Position

Manifold Bio is seeking a talented Machine Learning Research Engineer to join our growing AI team. You will work closely with our research scientists to implement, scale, and optimize machine learning systems that power our de novo antibody design platform and advance our protein design capabilities. Your efforts will contribute to building production-ready ML infrastructure that enables breakthrough discoveries in protein therapeutics. You will be expected to take ownership of engineering challenges in our ML pipeline, from data processing and model training to deployment and monitoring, while collaborating closely with our research team to translate cutting-edge ideas into robust, scalable systems.

This is an on-site role and can be based in either Boston, Massachusetts or San Francisco, California. Please only apply if you reside in these cities or are open to relocate. 

Responsibilities

  • Implement and optimize machine learning models for protein design
  • Build and maintain scalable data processing pipelines for large-scale protein and molecular datasets
  • Develop and deploy ML infrastructure for distributed training and inference across GPU clusters
  • Collaborate with research scientists to translate experimental ML approaches into production-ready code
  • Design and execute ML experiments with clear hypotheses and rigorous analysis
  • Optimize model performance and computational efficiency for large-scale protein design tasks
  • Build tools and utilities to support rapid prototyping and experimentation by the research team

Required Qualifications

  • Bachelor's or Master's degree in Computer Science, Machine Learning, Computational Biology, or related field
  • 2+ years of hands-on experience with PyTorch and/or JAX for deep learning applications
  • Strong proficiency in Python scientific computing stack (NumPy, Pandas, scikit-learn)
  • Experience with distributed computing and GPU optimization techniques
  • Familiarity with protein structure analysis, computational biology, or analogous problems in natural sciences
  • Understanding of modern deep learning architectures and optimization techniques
  • Experience implementing research papers or translating ML approaches to production systems
  • Proficiency with version control (Git), testing frameworks, and software engineering best practices
  • Strong problem-solving skills and ability to work independently on technical challenges
  • Excellent written and verbal communication skills for cross-functional collaboration

Preferred Qualifications

  • Experience training LLMs or diffusion generative models
  • Knowledge of cloud computing platforms (AWS, GCP) and containerization (Docker, Kubernetes)
  • Background in computational biology, bioinformatics, or structural biology
  • Experience with large-scale data engineering and ETL pipelines
  • Familiarity with MLOps practices and model deployment frameworks

This Role Might Be Perfect For You If

You are passionate about leveraging state of the art machine learning approaches to solve challenging disease areas

  • You enjoy translating research ideas into high impact, productionized, scalable code
  • You have rich AI/ML experience and are looking to pivot into biotech

If you're excited to build scalable ML systems that revolutionize protein therapeutic discovery, please reach out to careers@manifold.bio.

Base Salary Range: $140,000-225,000

This reflects the typical offer range for this role, based on experience, role scope, and internal equity. Final compensation decisions are made using a consistent leveling framework and consider the candidate's experience, interview performance, and expected impact.

This role is eligible for:

  • Annual performance-based target bonus
  • Stock options
  • Comprehensive medical, dental, and vision coverage
  • 401(k) plan
  • Flexible paid time off and holidays
  • Perks including on-site gym, onsite lunch, and commuter support

Our compensation ranges are reviewed annually to ensure alignment with market trends and internal equity.

Apply