Computational Biology & Bioinformatics Lead

Institute for Protein Innovation; Boston (MA); On-site; USD 200,000 - 240,000; Full time

Benefits offered by this job

100% employer-paid medical, dental, and vision plans

401(k) with 6% employer match

Generous PTO package

Flexible spending accounts

Job summary

The Institute for Protein Innovation (IPI) in Boston is seeking a Computational Biology & Bioinformatics Lead to drive advances in protein science through machine learning and data systems. This role will lead a team responsible for modeling protein structures and biophysical properties, aiming to support transformative biomedical research across the Institute.

Ideal candidates will hold a PhD and have significant experience in computational biology, protein science, and team management. Benefits include a comprehensive medical and retirement plan, generous PTO, and further career development opportunities.

Qualifications

• 5+ years of relevant experience, including leading or mentoring computational staff.
• Experience building and training protein machine learning models.
• Experience with de novo protein and antibody design processes.

Responsibilities

• Train and benchmark models for protein folding and design.
• Develop pipelines for in vitro antibody discovery data.
• Manage cloud and high-performance computing environments.

Skills

Python

Machine learning

Deep learning frameworks

Protein science

Bioinformatics

Education

PhD in computational biology or related field

Tools

PyTorch

Cloud computing

Job description

The Institute for Protein Innovation (IPI) is a nonprofit research organization advancing protein science to accelerate research and improve human health. Founded in 2017 and located in Boston’s Longwood Medical Area, the Institute’s three-pronged strategy is to build protein tools, conduct related internal research and develop educational programs for the protein science and biological research communities.

With a significant endowment, IPI uniquely combines the freedom of academia with the high throughput and scale of industry to take on transformative projects. IPI has built a robust platform for discovering, developing, and distributing synthetic antibodies and other protein tools to share with the biomedical community. The Institute's deep protein expertise, collaborative spirit and research tools are powering new biomedical and therapeutic discoveries with a growing community of researchers at Harvard Medical School, Boston Children’s Hospital and other institutions across Greater Boston and beyond.

Purpose

Computational Biology & Bioinformatics Lead will help grow IPI's computational protein science team and be responsible for the machine learning and data systems that support work across the Institute. This includes the following functional teams: antibody and antigen discovery, protein characterization, neuroscience, lab automation and lab operations.

This role is responsible for training and applying foundation models for protein structure prediction and design, building models that predict biophysical properties from sequence and structure and turning large multimodal biological datasets into tools and portals that can be effectively utilized across the Institute.

This position provides a combination of hands‑on technical work with team leadership skills to fulfill responsibilities and achieve goals.

The position will collaborate closely with the Associate Director & Program Manager of the Antibody Platform and reports to the Senior Director of the Antibody Platform.

Primary Responsibilities

1. Train, fine‑tune, and benchmark foundation models for protein folding and design, including structure prediction models and generative models for de novo binder and antibody design, and integrate these models for routine use in antigen and antibody discovery projects.
2. Build and validate models that predict biophysical properties such as stability, aggregation, expression, binding affinity, and developability, using multimodal data across sequence, structure, next generation sequencing, proteomics, and assay results.
3. Run in silico binder and antibody design campaigns and pair them with experimental rounds so predictions are tested and the results feed back into the models.
4. Develop pipelines and platforms for in vitro antibody discovery data, protein biophysical characterization, proteomics, and next generation sequencing analysis.
5. Build and maintain web portals and databases for large biological datasets, including IPI's external antigen and antibody catalogs (for example OpenAntigens) and internal research databases.
6. Work with teams and groups across the Institute to design experiments, interpret and analyze results, and effectively integrate computational tools into established team workflows.
7. Manage cloud and high‑performance computing environments, including GPU infrastructure for model training and large‑scale analysis.
8. Lead and mentor a small team of computational biologists and bioinformaticians.
9. Effectively present computational analyses to technical and non‑technical audiences and contribute to publications, patents, and products.
10. Establish standards for data management, version control, reproducibility, and MLOps in the group.

Qualifications

Required

• PhD in computational biology, bioinformatics, biophysics, machine learning, or a related field, with a strong background in protein science or biochemistry.
• 5 or more years of relevant experience, including experience leading or mentoring computational staff or serving as a technical lead. Direct experience managing a team of two to four people is a plus.
• Strong Python and hands‑on experience with deep learning frameworks such as PyTorch.
• Experience developing, modifying, and applying protein machine learning models for structure prediction and design.
• Experience building or training models on multimodal biological data, with a track record shown through publications, patents, or products.
• Experience with de novo protein and antibody design and validation cycles.

Preferred. (strong candidates will bring several of these, but not all are required)

• Experience with next generation sequencing analysis.
• Experience building data portals, APIs, or databases for large biological datasets.
• Experience with cloud computing and high‑performance computing or GPU environments.
• Familiarity with antibody discovery, proteomics, or protein biophysical characterization assays.
• Experience integrating computational predictions with wet‑lab workflows, including LIMS or ELN systems.

$200,000 - $240,000 a year

Benefits

• 100% employer‑paid medical, dental, and vision plans
• Flexible spending accounts and a healthcare reimbursement account
• 401(k) plan with generous 6% employer match – immediately 100% vested
• Generous PTO package
• Commuter and parking reimbursement
• Career development opportunities

IPI provides competitive compensation and an excellent benefits package to support physical, mental and financial health. Highlights of benefits include: 100% employer‑paid medical, dental, and vision plans, flexible spending accounts, a healthcare reimbursement account, 401(k) plan with generous 6% employer match, generous PTO package, commuter and parking reimbursement, career development opportunities.

For more information, visit proteininnovation.org or follow us on social media, @ipiproteins. IPI is an independent 501(c)(3) nonprofit research organization and an equal‑opportunity employer. The Institute celebrates diversity and is committed to creating an inclusive environment for all employees. Please be advised that you will be required to provide evidence of your identity and eligibility for employment in the United States. IPI will not guarantee sponsorship of foreign nationals and retains complete discretion regarding providing sponsorship to any prospective or existing employee at time of hire or at any time in the future.