Discover exciting career opportunities within our community!

Our new Jobs page connects you with talented individuals seeking new challenges. Explore a variety of roles and connect directly with potential candidates.

Multiple positions
Achira
New York
Posted on October 24, 2025 | Posted by Rachel Clune
We are currently searching for a mix of machine learners and software engineers, see a list of open positions.
Don’t see the perfect role listed? Submit your resume here.
Flatiron Research Fellow, Structural & Molecular Biophysics and Biomolecular Design, Center for Computational Biology
Flatiron Institute
162 5th Avenue, NY, NY 10010
Posted on October 24, 2025 | Posted by Doug Renfrew
Description
The Center for Computational Biology (CCB) of the Simons Foundation’s Flatiron Institute is actively seeking enthusiastic, full-time post-doctoral Flatiron Research Fellows to join its Structural & Molecular Biophysics  and Biomolecular Design groups for a joint appointment in 2026, as part of the Collaboration on Molecular Physics and Sampling Strategies (COMPASS).
The goal at CCB is to advance the understanding of fundamental and historically challenging biological processes by developing theory, innovative modeling tools for large-scale biophysical simulations, and computational frameworks for analyzing increasingly large and complex experimental datasets. Living systems are built hierarchically; as such, CCB’s research activities span several scales of biological organization, bridging the gap between microscopic detail and large-scale behaviors, and providing natural continuity between our groups’ efforts. CCB currently comprises more than 45 research and data scientists at career stages from recent Ph.D. graduates through senior scientists, as well as visiting scientists, guest researchers, graduate students, interns, and administrative support staff. For a full description of CCB research areas and scientific staff, please see our website.
The Structural & Molecular Biophysics group uses long timescale molecular dynamics (MD) simulations, integrated with experimental observables (especially cryo-electron microscopy data), and machine learning tools to better capture the dynamics of biological macromolecules and to understand their function. Complementing this  work, the Biomolecular Design group applies the current understanding of the theory of protein folding and function to design new, synthetic heteropolymers, built from exotic chemical building blocks, which fold into new structures inaccessible to natural proteins, and which perform new functions.  In addition to giving rise to useful new molecules that can serve as drugs, nanomaterials, or catalysts, this also serves as the ultimate test of our understanding of protein folding.
Together through the Molecular Ensemble Sampling and Simulation (MESS) collaboration, the groups are working together to advance computational methods for the design and understanding of molecular motion, and addressing current obstacles to accuracy and tractability.  The successful candidate will carry out a research project to advance these goals.  Particular foci include 1) engineering open-source software infrastructure to facilitate analysis of macromolecular motion and design of motile macromolecules, 2) integration of physics-based simulation and machine learning methods, 3) development of enhanced approximation methods (implicit solvation, coarse-graining, etc.) to improve the tractability of currently expensive calculations, 4) the incorporation of molecular design tools to interpret cryo-EM data, or 5) the design of molecules of potential medical interest.
Strong applicants with backgrounds in computational biology/biochemistry/biophysics, applied and computational mathematics, computer science/engineering,  machine learning, and related fields are particularly encouraged to apply.
POSITION DESCRIPTION
Flatiron Research Fellows in CCB are individuals at the postdoctoral level with backgrounds in one or more of the following areas: applied mathematics, statistics, computational biology, biophysics, computer science, engineering, mathematical physics, or related disciplines.
Fellows are expected to carry out an active research program that can be independently directed and/or involve substantial collaboration with other members of CCB or the Flatiron Institute. In addition to their research, Fellows help build the rich scientific community at CCB and the Flatiron Institute by participating in seminars, colloquia, and group meetings; developing their software, mathematical and computational expertise through internal education opportunities; and sharing their knowledge through scientific publications, presentations, and/or software releases, with the financial support of the Institute. Fellows have access to the Flatiron Institute’s powerful scientific computing resources.
Responsibilities include but are not limited to:
  • Performing theoretical and computational research
  • Developing, implementing and maintaining scientific software
  • Participating in the organization of CCB and Flatiron-wide collaborative activities including seminars, workshops and meetings
  • Participating in the preparation of manuscripts for publication and of presentations at scientific conferences
  • Assisting in student mentorship
  • Sharing expertise and providing training and guidance to CCB staff and visitors as needed.
FRF positions are generally two-year appointments that can be renewed for a third year, contingent on performance. Fellows will be based, and have a principal office or workspace, at the Simons Foundation’s offices in New York City.  Fellows may also be eligible for subsidized housing within walking distance of the Flatiron Institute.
For more information about careers at the Flatiron Institute, please click here.
Qualifications
Education
  • Ph.D. in a relevant field (applied mathematics, statistics, computational biology, biophysics, computer science, engineering, mathematical physics, or related disciplines)
 Related Skills & Other Requirements
  • Demonstrated abilities in mathematical modeling, analysis and/or scientific computation, scientific software and algorithm development, data analysis and inference, and image analysis
  • Ability to do original and outstanding research in computational biology, and expertise in computational methods, data analysis, software and algorithm development, modeling machine learning, and scientific simulation
  • Ability to work well in an interdisciplinary environment, and to collaborate with experimentalists
  • Strong oral and written communication, data documentation, and presentation skills
COMPENSATION AND BENEFITS
  • The full-time annual compensation for this position is $91,000.
  • In addition to competitive salaries, the Simons Foundation provides employees with an outstanding benefits package.
Application Instructions
To apply, please submit the following via the application portal:
  1. Cover Letter, which should include a summary of applicants’ most significant contributions in graduate school
  2. Curriculum vitae with publications list and, if relevant, links to software
  3. Research statement of no more than three (3) pages describing the applicant’s past important results, current and future research interests which may include both scientific topics and algorithm and software development, and potential synergies with activities at CCB
  4. Two (2) letters of recommendation
Applications for available positions that begin in 2025 will generally be reviewed beginning November 2025, and will be considered on a rolling basis until the positions are filled. For full consideration, candidates are strongly encouraged to submit their complete application by November 30, 2025.
SELECTION CRITERIA
Applications will be evaluated based on:
  • Past research accomplishments
  • The proposed research program
  • The synergy of applicant’s expertise and research proposal topic with existing CCB staff and research programs, and potential to cross boundaries between CCB groups and/or the Flatiron Institute’s other research centers that are part of the MESS collaboration.
Any queries about the application process or about CCB should be directed to ccbjobs@flatironinstitute.org. Queries about CCB may also be directed to scientific staff at CCB.
Ladder Rank Faculty Position – Assistant, Associate, or Full Professor
UC San Francisco
San Francisco, CA
Posted on October 24, 2025 | Posted by Julia Koehler Leman
Application Window
Open date: October 21, 2025
Next review date: Sunday, Nov 30, 2025 at 11:59pm (Pacific Time)
Apply by this date to ensure full consideration by the committee.
Final date: Wednesday, Apr 21, 2027 at 11:59pm (Pacific Time)
Applications will continue to be accepted until this date, but those received after the review date will only be considered if the position has not yet been filled.
Position description
Ladder Rank Faculty Position – Assistant, Associate, or Full Professor
Job #JPF05842
• Pharmaceutical Chemistry / SCHOOL OF PHARMACY / UC San Francisco
Position description
Ladder Rank Faculty Position – Assistant, Associate, or Full Professor
Department of Pharmaceutical Chemistry
University of California, San Francisco
The UCSF Department of Pharmaceutical Chemistry is seeking faculty active in all areas of computational chemistry and machine learning related to that area to join our vibrant, collaborative, and supportive discovery research community at the Mission Bay Campus in San Francisco. The Department of Pharmaceutical Chemistry includes diverse research in the areas of computational and synthetic chemistry, biophysics, chemical biology, systems and synthetic biology, enabling technologies, and drug discovery. Our department is characterized by a culture of collaboration and innovation in biomedical science.
We seek creative, innovative scientists who define and address fundamental questions in computational chemistry and machine learning for chemistry and chemical biology-related problems. We provide faculty with resources to launch their program, including a strong mentoring culture, a competitive start-up package, administrative support, and facilities for advanced computation, light and cryo-electron microscopy, mass spectrometry, high-throughput small molecule screening, cytometry, and state-of-the-art animal care.
Tenure-track faculty candidates are expected to hold a Ph.D., to have demonstrated substantial research accomplishment and potential, and to be committed to the mentorship of students in research. The successful candidate will establish a dynamic and interactive research program and join one or more of our top-ranked interdisciplinary graduate programs (see https://graduate.ucsf.edu/list-programs).
Faculty appointment will be made at a professorial rank commensurate with current academic standing. UCSF offers competitive salaries, research set-up funds, and recruitment allowances, and has numerous opportunities for faculty development and further training in mentorship.
The posted UC salary scales set the minimum pay determined by rank and step at appointment. See Table 5. The minimum base salary range for this position is $121,900 -$319,800. This position includes membership in the health sciences compensation plan which provides for eligibility for additional compensation.
Review will begin on Nov 30, 2025 and continue until the position is filled. Interviews will occur in two phases: video conference in December and January followed by in-person visits in January and February. Please direct inquiries about the position and suggestions of potential candidates to https://aprecruit.ucsf.edu/JPF05842.
Application Requirements
Document requirements
  • Cover Letter
  • Curriculum Vitae - CV must clearly list current and/or pending qualifications (e.g. board eligibility/certification, medical licensure, etc.).
  • Summary of Research Accomplishments (ca 1 page)
  • Description of Future Research Plans (ca 2-5 pages)
  • A Teaching Statement, including Formal and Informal Mentoring Activities (Optional)
  • Copies of Major Publications (Optional)
Reference requirements
3 references (contact information only)
Job location
San Francisco, CA
Application Requirements
Document requirements
  • Cover Letter
  • Curriculum Vitae - CV must clearly list current and/or pending qualifications (e.g. board eligibility/certification, medical licensure, etc.).
  • Statement of Research -

    Summary of Research Accomplishments (ca 1 page)

    Description of Future Research Plans (ca 2-5 pages)

  • Statement of Teaching - A Teaching Statement, including Formal and Informal Mentoring Activities

    (Optional)

  • Copies of Major Publications (Optional) (Optional)
Reference requirements
  • 3 required (contact information only)
About UC San Francisco
As a University employee, you will be required to comply with all applicable University policies and/or collective bargaining agreements, as may be amended from time to time. Federal, state, or local government directives may impose additional requirements.
The University of California is an Equal Opportunity Employer. All qualified applicants will receive consideration for employment without regard to race, color, religion, sex, sexual orientation, gender identity, national origin, disability, age, protected veteran status, or other protected status under state or federal law.
UCSF is committed to welcoming and serving all people, honoring the dignity of every individual without preference or prejudice, in support of its public mission and in alignment with our PRIDE values and Principles of Community.
As a condition of employment, the finalist will be required to disclose if they are subject to any final administrative or judicial decisions within the last seven years determining that they committed any misconduct.
• “Misconduct” means any violation of the policies or laws governing conduct at the applicant’s previous place of employment, including, but not limited to, violations of policies or laws prohibiting sexual harassment, sexual assault, or other forms of harassment, or discrimination, as defined by the employer.
UC Sexual Violence and Sexual Harassment Policy
UC Anti-Discrimination Policy
APM - 035: Affirmative Action and Nondiscrimination in Employment
Job location
San Francisco, CA
Tenure-Track Faculty Position(s) in Artificial Intelligence and Machine Learning for Drug Discovery
University of Michigan-Ann Arbor
Ann Arbor, Michigan
Posted on October 20, 2025 | Posted by Terra Sztain
Open Date
Sep 19, 2025
Deadline
Nov 30, 2025 at 11:59 PM Eastern Time
Description
The University of Michigan (U-M) invites applications for three tenure-track faculty positions in the area of Artificial Intelligence (AI) and Machine Learning (ML) in Drug Discovery. This is a unique cluster hire initiative spanning the College of Pharmacy, Life Sciences Institute (LSI), and Medical School. We welcome applications from both early and mid-career candidates with strong records of research excellence in AI/ML-driven approaches to drug discovery.
Successful candidates will be appointed within the unit most appropriate to their expertise while fostering interdisciplinary collaborations across the university.
Strategic Impact and Vision
 
This cluster hire aligns with U-M’s Vision 2034, emphasizing:
●       Research Innovation: Advancing AI/ML methodologies for drug discovery and improving therapeutic success rates.
●       Interdisciplinary Collaboration: Strengthening connections between computational and experimental drug development experts.
●       Economic and Societal Impact: Translating discoveries into startup ventures and industry partnerships to drive drug commercialization.
●       Education and Workforce Development: Training the next generation of scientists in AI/ML-enabled drug development.
About the Positions
 
Drug development faces significant challenges, including high costs, long timelines, and a 90% failure rate in clinical trials. AI and ML have the potential to enhance drug discovery by improving the identification of disease and drug targets, accelerating the identification of drug candidates, optimizing the design of therapeutics, and guiding predictions of clinical outcomes. The goal of this cluster hire is to advance U-M’s leadership in drug discovery by integrating cutting-edge AI and ML methodologies into the drug discovery process, enhancing efficiency, reducing failure rates, and supporting therapeutic innovation.
Resources and Collaborative Environment
U-M provides an exceptionally collaborative and resource-rich environment for AI/ML and drug discovery research, including:
●       Michigan Drug Discovery (MDD): A hub for academic-industry partnerships, drug screening, medicinal chemistry, and translational research.
●       Broad Campus Collaboration: A Highly collaborative network with faculty from departments like the Department of Pharmacology, Computational medicine and bioinformatics, Michigan Institute for Data Sciences, LSA, and College of engineering.
●       Core Facilities: High-throughput screening, medicinal chemistry, structural biology, cryo-electron microscopy, pharmacokinetics, bioinformatics, and AI-driven data analytics.
●       Innovation and Commercialization Support: Access to incubator space, business mentoring, venture funding, and technology licensing through Innovation Partnerships.
●       AI & Digital Health Innovation: A Presidential initiative providing deidentified multimodal health data, genetic data, data storage and processing, and research implementation services.
●       e-HAIL Initiative: A collaboration between Michigan Medicine and the College of Engineering, advancing AI in healthcare and biomedical research.
●       Newly Established U-M and Los Alamos National Laboratory Partnership: A strategic collaboration providing additional computational and experimental resources.
Responsibilities
●       Develop and sustain an externally funded research program in AI/ML-driven drug discovery.
●       Publish high-impact research in leading scientific journals.
●       Teach and mentor students and trainees across all learning and development stages.
●       Collaborate with faculty across U-M to drive AI/ML applications in drug development.
●       Engage with industry and government agencies to secure funding and foster translational research efforts.
●       Contribute to the development of a new AI/ML-driven drug discovery center, integrating efforts across the College of Pharmacy, LSI, and Medical School, and other units in the University of Michigan.
●       Contribute to the service missions of the department, university, and profession.
Qualifications
  • Ph.D., M.D., or equivalent degree in pharmaceutical sciences, medicinal chemistry, pharmacology, computational biology, biomedical informatics, chemical engineering, bioinformatics, computer science, or a related field.
  • Demonstrated excellence in research with a strong record of peer-reviewed publications and competitive funding.or the potential for building an independent externally-funded program
  • Expertise in applying AI/ML methodologies to drug discovery, pharmacology, chemistry, bioinformatics, or computational biology.
  • A commitment to teaching, mentoring, and training students and postdoctoral fellows in AI/ML-driven drug discovery.
  • Interest in interdisciplinary collaboration and contributing to drug discovery and therapeutic innovation.
Application Instructions
Review of applications will begin immediately. Application deadline November 30, 2025. 
To apply, please submit the following materials:
Cover letter specifying the preferred tenure home unit (College of Pharmacy or Medical School) and how their expertise aligns with the AI/ML drug discovery focus areas.
  • Curriculum vitae.
  • Statement of research interests and vision (2–3 pages).
  • Statement of teaching philosophy and mentoring approach (1–2 pages).
  • Names and contact information for three references.
All application materials should be submitted through the Interfolio Portal: https://apply.interfolio.com/174339
For informal inquiries, please contact the search committee chair, Dr. Duxin Sun (duxins@umich.edu)
Background Screening
The University of Michigan conducts background checks on all job candidates upon acceptance of a contingent offer and may use a third-party administrator to do so. Background checks include both a criminal background check and an institutional reference check regarding any misconduct. As part of this process, candidates will be required to complete a self-disclosure form and an authorization to release information form.
Equal Opportunity Statement
The College of Pharmacy and the University of Michigan seek to recruit and retain a diverse workforce as a reflection of our commitment to serve our diverse constituents, and to maintain the excellence of the Department, College, and University. The University of Michigan is supportive of the needs of dual career couples, and is an equal opportunity employer that complies with all applicable federal and state laws regarding nondiscrimination. It is committed to a policy of equal opportunity for all persons and does not discriminate on the basis of race, color, national origin, age, marital status, sex, sexual orientation, gender identity, gender expression, disability, religion, height, weight, or veteran status in employment, educational programs and activities, and admissions.
Senior Scientist, Computational Biology
Quantum-Si
San Diego, CA
Posted on October 8, 2025 | Posted by Kristin Blacklock

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.
Principal Applied Researcher
Microsoft Research AI for Science
Multiple Locations
Full-Time
Posted on October 3, 2025 | Posted by Frank Noe
Overview
At Microsoft Research AI for Science, we believe machine learning and artificial intelligence has the potential to transform scientific modelling and discovery crucial for solving the most pressing problems facing society including sustainable materials and discovery of new drugs.
We seek a highly motivated Senior RSDE to join our Biomolecular Emulator (BioEmu) team. The BioEmu project aims to model the dynamics and function of proteins - how they change shape, bind to each other, and bind small molecules. This approach will help us to understand biological function and dysfunction on a structural level and lead to more effective and targeted drug discovery. Our BioEmu-1 model was published in Science (see our blog post for links to our open-source software and other resources and this explainer video).
Qualifications
Required:
  • PhD or equivalent experience in Computer Science, Machine Learning, Applied Mathematics, Computational Biology, or related field.
  • Strong software engineering in Python (packaging, testing, CI), with systems thinking for data‑intensive ML.
  • Deep learning experience (PyTorch/JAX/TensorFlow) and solid foundations in linear algebra, probability, and statistics.
  • Proven experience designing robust data pipelines for large‑scale ML (HPC or cloud).
  • Ability to reason about learning signal and to assess information content of real‑world scientific datasets.
  • Excellent collaboration and communication in interdisciplinary teams.
Preferred:
  • Hands‑on cryo‑EM experience (e.g., map reconstruction, refinement, or pipeline tooling).
  • CUDA or C++ for performance‑critical components; experience with mixed precision and memory‑efficient training.
  • Experience integrating experimental data into ML models (e.g., constraints/priors from cryo‑EM, binding assays, spectroscopy).
  • Familiarity with MD data, structure prediction systems, or protein design work-flows.
  • Experience with cost‑optimization for data collection and cloud utilization; clear track record of building reliable, maintainable research software at scale.
  • Experience with structural biology or molecular biology data/techniques (e.g., cryo‑EM, binding assays, spectroscopy, expression, sequencing)
#Research #AI for Science
Responsibilities
  • Data integration for structure & dynamics: Build ingestion/curation pipelines for structural/biophysical data (mmCIF/PDB, EM maps/particles, binding/biophysics, spectroscopy); implement map/volume preprocessing (e.g., resolution filtering, normalization) and alignment to model inputs/outputs.
  • Cryo‑EM expertise: Operationalize end‑to‑end flows from raw image stacks/particles to 3D maps and model‑ready tensors; interoperate with community formats (e.g., EMDB/EMPIAR, mmCIF) and link to sequences/annotations.
  • Signal & information content: Design dataset diagnostics (e.g., mutual‑information‑like measures, effective sample size, SNR proxies) to quantify what data teach the model; build active‑learning loops that maximize learning per euro of data collection time.
  • Model‑aware data services: Implement scalable, versioned data services and feature stores that feed training/evaluation; design loaders/augmentations optimized for throughput and correctness (GPU‑aware).
  • Training‑at‑scale engineering: Own distributed data pipelines and orchestration for large runs on Azure; profile and tune I/O, storage tiers, data locality, and caching; monitor cost, utilization, and failure modes.
  • Quality, governance, and reproducibility: Codify schemas/ontologies, metadata contracts, unit/integration tests, and lineage; automate validation and data drift detection; maintain documentation and examples.
  • Partner across disciplines: Work closely with ML researchers, structural biologists, and drug designers; translate experimental constraints into robust computational workflows; communicate clearly and proactively.
Senior Applied Researcher
Microsoft Research AI for Science
Multiple Locations
Full-Time
Posted on October 3, 2025 | Posted by Frank Noe
Overview
At Microsoft Research AI for Science, we believe machine learning and artificial intelligence has the potential to transform scientific modelling and discovery crucial for solving the most pressing problems facing society including sustainable materials and discovery of new drugs.
We seek a highly motivated Senior Applied Researcher to join our Biomolecular Emulator (BioEmu) team. The BioEmu project aims to model the dynamics and function of proteins - how they change shape, bind to each other, and bind small molecules. This approach will help us to understand biological function and dysfunction on a structural level and lead to more effective and targeted drug discovery. Our BioEmu-1 model was published in Science (see our blog post for links to our open-source software and other resources and this explainer video).
Qualifications
Required:
  • PhD or equivalent research experience in Chemistry, Biophysics, Physics, Computer Science, Bioinformatics or a related field.
  • Demonstrated passion and proven excellence in computational molecular biology, biophysics, or bioinformatics via impactful projects, publications, or open‑source code.
  • Experience with biomolecular modeling/bioinformatics (e.g., folding systems, structural analysis, MD simulation, structure/genome databases).
  • Excellent technical communication for interdisciplinary work.
  • Comfortable with real‑world data that lack structure/cleanliness/completeness.
  • Proficiency in Python and data analysis packages (NumPy, SciPy, Pandas).
Preferred:
  • Experience with deep learning methods and software packages (PyTorch, JAX, Tensorflow).
  • Experience with structural biology or molecular biology data/techniques (e.g., cryo‑EM, binding assays, spectroscopy, expression, sequencing).
  • Background or advanced training in structural biology; familiarity with structure prediction and/or MD work-flows.
#Research #AI for Science
Responsibilities
  • Model biomolecular structure and dynamics at scale: Use BioEmu, structure/sequence databases, and complementary tools to analyze proteins and complexes.
  • Innovate and improve analysis technologies: Develop and implement scalable technologies to analyze and quantify conformational transitions, structural flexibility, and changes in complex formation for many biomolecular complexes.
  • Generate biological hypotheses and insights: Integrate biomolecular structure and dynamics data to generate experimentally-testable predictions and biological insights.
  • Collaborate with experimentalists: collaborate with wetlab scientists to test computational predictions. Learn to read and interpret their data and work together to challenge and improve hypothesis of biomolecular function.
  • Support drug‑targeting strategies: Partner with leading drug discovery experts to identify targets and propose mechanisms of action.
  • Operationalize at scale: Build robust Python pipelines; automate large‑scale inference and analysis jobs on Azure with reproducible work-flows.
  • Partner across disciplines: communicate clearly with ML researchers and experimental/computational biologists; present results and influence project direction.
  • Work autonomously and as a team player, regularly reporting insights, risks, and next steps.
  • Aim for impact: translate findings into artifacts others can use (code, datasets, internal reports, and when appropriate - papers).
Senior Research Data Engineer
Microsoft Research AI for Science
Multiple Locations
Full-Time
Posted on October 3, 2025 | Posted by Frank Noe
Overview
At Microsoft Research AI for Science, we believe machine learning and artificial intelligence has the potential to transform scientific modelling and discovery crucial for solving the most pressing problems facing society including sustainable materials and discovery of new drugs.
We seek a highly motivated Senior RSDE to join our Biomolecular Emulator (BioEmu) team. The BioEmu project aims to model the dynamics and function of proteins - how they change shape, bind to each other, and bind small molecules. This approach will help us to understand biological function and dysfunction on a structural level and lead to more effective and targeted drug discovery. Our BioEmu-1 model was published in Science (see our blog post for links to our open-source software and other resources and this explainer video).
Qualifications
Required:
  • PhD or equivalent experience in Computer Science, Machine Learning, Applied Mathematics, Computational Biology, or related field.
  • Strong software engineering in Python (packaging, testing, CI), with systems thinking for data‑intensive ML.
  • Deep learning experience (PyTorch/JAX/TensorFlow) and solid foundations in linear algebra, probability, and statistics.
  • Proven experience designing robust data pipelines for large‑scale ML (HPC or cloud).
  • Ability to reason about learning signal and to assess information content of real‑world scientific datasets.
  • Excellent collaboration and communication in interdisciplinary teams.
Preferred:
  • Hands‑on cryo‑EM experience (e.g., map reconstruction, refinement, or pipeline tooling).
  • CUDA or C++ for performance‑critical components; experience with mixed precision and memory‑efficient training.
  • Experience integrating experimental data into ML models (e.g., constraints/priors from cryo‑EM, binding assays, spectroscopy).
  • Familiarity with MD data, structure prediction systems, or protein design work-flows.
  • Experience with cost‑optimization for data collection and cloud utilization; clear track record of building reliable, maintainable research software at scale.
  • Experience with structural biology or molecular biology data/techniques (e.g., cryo‑EM, binding assays, spectroscopy, expression, sequencing)
#Research #AI for Science
Senior Machine Learning Researcher
Microsoft Research AI for Science
Multiple Locations
Full-Time
Posted on October 3, 2025 | Posted by Frank Noe
Overview
At Microsoft Research AI for Science, we believe machine learning and artificial intelligence has the potential to transform scientific modelling and discovery crucial for solving the most pressing problems facing society including sustainable materials and discovery of new drugs.
We seek a highly motivated Senior Researcher to join our Biomolecular Emulator (BioEmu) team. The BioEmu project aims to model the dynamics and function of proteins - how they change shape, bind to each other, and bind small molecules. This approach will help us to understand biological function and dysfunction on a structural level and lead to more effective and targeted drug discovery. Our BioEmu-1 model was published in Science (see our blog post for links to our open-source software and other resources and this explainer video).
Qualifications
Required:
  • PhD or equivalent research experience in Computer Science, Machine Learning, Physics, or a related field.
  • Demonstrated leadership in ML architecture and algorithm design.
  • Strong expertise in deep learning (model design, large-scale training, evaluation and reproducibility), statistics and linear algebra.
  • Proficiency in Python and modern ML/scientific frameworks (e.g., PyTorch, JAX, TensorFlow, NumPy, SciPy, Pandas).
  • Peer-reviewed publications in leading venues (e.g., NeurIPS, ICML, ICLR or leading journals).
  • Excellent technical communication for collaborating in an interdisciplinary team.
  • Curiosity and drive to apply deep learning to biological problems.
  • Comfort with real‑world, noisy/heterogeneous data.
Preferred:
  • ML Engineering skills (e.g., model optimization and deployment, code design, CUDA).
  • Experience with biomolecular modeling or bioinformatics (e.g., folding systems, structural analysis/visualization, MD simulation, structure/genome databases).
  • Ability to work with and interpret real‑world biological data (e.g., cryo‑EM, protein binding affinities, structural/biophysical measurements).
#Research #AI for Science
Responsibilities
  • Invent novel deep learning techniques for models of biomolecular structure, dynamics, and function.
  • Design, implement, and iterate on model architectures and training algorithms (e.g., diffusion/sequence–structure models, representation learning); run rigorous ablations and baselines.
  • Define success where standards don’t exist: proposing sound benchmarks and uncertainty‑aware metrics that reflect real‑world utility.
  • Build high‑quality research code (Python/PyTorch) with reproducible work-flows and robust data pipelines.
  • Partner across disciplines—communicate clearly with ML researchers and experimental/computational biologists; present results and influence direction.
  • Work autonomously and as a team player, reporting insights, risks, and next steps with crisp written/visual summaries.
  • Thrive with imperfect, heterogeneous data, using principled curation, augmentation, and probabilistic evaluation.
  • Aim for impact: try ideas quickly and fail-fast when they don't work. Rapidly convert working ideas to artifacts others can use (code, models, datasets, papers, patents).
Assistant Professor in Adaptive, Lifelike Biosynthetic Materials
TU Eindhoven (TU/e)
Posted on September 20, 2025 | Posted by Alena Khmelinskaia
We are seeking a passionate and collaborative researcher who is eager to take on cross-disciplinary challenges at the interface of soft matter and bioengineering. Inspired by nature’s ingenuity in material design, you integrate experimental and computational approaches to create tailored materials with novel functionalities. As our next Assistant Professor in Experimental Soft Matter & Bioengineering, you will have the opportunity to establish your own independent research line and build a team within a dynamic, ambitious, and collaborative academic environment. 
The position
TU Eindhoven (TU/e) is a university of technology located in the heart of the high-tech industry in the Netherlands. The Department of Chemical Engineering and Chemistry and the Institute for Complex Molecular Systems at TU/e are ambitious academic centers renowned for their top research and education in areas such as Soft Matter, Polymer Science, Supramolecular Chemistry, Adaptive Materials, Functional Materials, (Bio)nanotechnology, Protein Engineering and Biomaterials. Our researchers develop fundamental insights to engineer next-generation adaptive materials to address societal challenges in areas such as sustainability, health, and energy. The department invites applications for a new faculty position in the following area:
Experimental Soft Matter and Bioengineering. The solutions to the major societal challenges that we face require adaptive materials, custom-tailored in composition and in structure, which can be reconfigured for optimal performance and recycling. Developing such materials requires designable interactions between both molecular and macromolecular building blocks in complex mixtures. Bio-engineering and soft matter science are ideally positioned to address the fascinating fundamental research questions related to this radical transformation. We can draw inspiration from and build on existing biological building blocks, such as structural proteins and enzymes, and can design their material properties with a soft matter approach to tunable physical interactions between the constituent building blocks.
Recent advances in computationally-assisted design of materials and proteins have accelerated this development and opened up a large design space that can be explored to create materials that address our societal needs regarding sustainability and function. As assistant professor, you will contribute to current research activities within the molecules and materials clusters of the department in general, and the self-organizing soft matter and bio-organic chemistry laboratories specifically. You will develop a curiosity-driven, original, challenging research direction aligned with and complementary to existing expertise in the department. Examples of interesting directions are AI-accelerated materials design, computational protein design, functional reaction-assembly networks with (bio)chemical feedback or adaptive soft, lifelike (bio)synthetic materials. This could lead to learning and information processing in soft matter or molecular systems, enabled by the quantitative, spatiotemporal characterization of their hierarchical organization, formation, interactions, dynamics and function.
The position will be embedded in an interdisciplinary team of highly qualified researchers studying self-assembly processes in biological and bio-inspired soft matter aiming to advance our mechanistic understanding and establish guiding principles towards the rational design of novel (bioinspired) soft materials.
Do you want to work together in a research unit, in an open-atmosphere department, and set up and expand your own, independent research line and team? Then please apply now!
You will be offered the opportunity to establish an independent, largely externally funded research program in collaboration with colleagues at our department and at national and international institutions.
Job Requirements  
We encourage you to apply if you have a PhD degree and at least two years of postdoctoral experience.
  • PhD in soft matter research, polymer science, or a comparable domain.
  • Affinity/experience with machine learning approaches
  • Ability to conduct high quality academic research, demonstrated for instance by a relevant PhD thesis and publication(s).
  • Ability to teach, shown by experience or assistance in teaching and positive evaluations of these teaching efforts.
  • Creative and dedicated to (multidisciplinary) collaboration.
  • Excellent communication skills.
  • Ability to be, or willingness to become, a good leader.
  • Empathy and good listening skills.
  • Flexibility and resilience.
  • Excellent proficiency (written and oral) in English.
Conditions of employment
A meaningful job in a dynamic and ambitious university, in an interdisciplinary setting and within an international network. You will work on a beautiful, green campus within walking distance of the central train station. In addition, we offer you:
  • Salary in accordance with the Collective Labour Agreement for Dutch Universities, scale 11 (min. € 4.728 max. € 6.433).
  • A year-end bonus of 8.3% and annual vacation pay of 8%.
  • A dedicated mentoring program to help you get to know the university and the Dutch (research) environment.
  • A Development Track with the prospect of becoming an Associate Professor. If you have a more senior profile, a tailor-made career proposal will be considered.
  • High-quality training programs for academic leadership and teaching.
  • An excellent technical infrastructure, on-campus children's day care and sports facilities.
  • Partially paid parental leave and an allowance for commuting, working from home and internet costs.
  • A Staff Immigration Team is available for international candidates, as are a tax compensation scheme (the 30% facility) and partner career support.
Information and application
About us  
Eindhoven University of Technology is an internationally top-ranking university in the Netherlands that combines scientific curiosity with a hands-on attitude. Our spirit of collaboration translates into an open culture and a top-five position in collaborating with advanced industries. Fundamental knowledge enables us to design solutions for the highly complex problems of today and tomorrow.
The Department of Chemical Engineering and Chemistry focusses on solving societal challenges in health, sustainable energy and circularity using expertise in molecules, materials and chemical processes. We collaborate with academia and industry to enlarge our chain of knowledge. Our top-notch research is internationally renowned and facilitated by a state-of-the-art research infrastructure. High-quality education and research, strong collaboration, independence of researchers and talent development are our core values.
We believe that diversity broadens our research scope and enhances the quality of our education. Our Irène Curie Fellowship aims to advance talented female researchers, in order to thrive and be successful in top positions in science, contributing to the societal goal of promoting equal opportunities. The program addresses the aspirations and needs of women in industry, academia, and research institutes in order to support their ambition to become a professor at our university.
Curious to hear more about what it's like as a professor at TU/e? Please watch the video.
More information
Do you recognize yourself in this profile and would you like to know more? Please contact one of the hiring managers:  Prof. Dr. Ir. Ilja Voets, i.voets@tue.nl or +31 40 247 5303 or Prof. Dr. Ir. Jan van Hest, j.c.m.v.hest@tue.nl or +31 40 247 3737.
Are you inspired to know more about working at TU/e? Please visit www.tue.nl/jobs
Visit our website for more information about the application process or the conditions of employment. You can also contact Thomas Slegers, Senior Recruiter, t.slegers@tue.nl or +31 6 1483 5214.
Are you inspired and would like to know more about working at TU/e? Please visit our career page.
Application 
This vacancy is part of the Irène Curie Fellowship and is currently only open to female candidates. Male applicants will not be considered for the position.
We invite you to submit a complete application. The application should include a:
  • Cover letter in which you describe your motivation and qualifications for the position.
  • Curriculum vitae, including a list of your publications and the contact information of three references.
  • Description of your scientific interests and plans (1-2 pages).
  • Statement of your teaching goals and experience (1-2 pages).
We look forward to receiving your application and will screen it as soon as possible.
Referentienummer: 2025/411
PhD student – Development and application of site-specific phospho-encoding systems 80 %
University of Zürich
Posted on September 16, 2025 | Posted by Chun-Chen Yao
Start of employment as soon as possible
We are a newly established research group at the University of Zürich, focusing on the structural effects of posttranslational modifications within intrinsically disordered proteins. Our work combines biomolecular NMR with interdisciplinary approaches to answer fundamental questions in structural biology.

We believe that open communication, integrity, and mutual respect are the foundation of excellent research. Our goal is to foster a positive and inclusive work culture where every member feels valued and encouraged to contribute their ideas. Candidates should enjoy working collaboratively and be motivated to engage in interdisciplinary science.

Further information about our research can be found on our website.

Your responsibilities
You will develop and apply innovative genetic code expansion tools to achieve site-selective incorporation of la-beled phospho-tyrosine. Your tasks will encompass utilization of state-of-the-art bionformatic tools for protein design, perform high-throughput cell uptake tests, perform selection assays and express, purify and analyze tar-get model proteins.
Your profile
Requirements:
  • A first-class Master's degree in chemistry, biochemistry, bioinformatics or a related field, awarded prior to the start of the contract or soon to be finished
  • Background in protein design, computational biology or related field
  • Working knowledge in at least one relevant coding language (Python, R, or C++)
  • Excellent communication skills and excellent command of English, both spoken and written
Desirable:
  • Experience in sterile cell culturing technique
  • Familiarity with protein expression and purification
  • Interest in protein biophysics and structural biology
Information on your application
Please submit your application by 15th of October 2025, including a cover letter, a CV and the contact details of two references. Short-listed applicants will be interviewed either in person or via a video call.
Computational Biophysicist
Apoha
Posted on September 10, 2025 | Posted by Michael Chungyoun
About Apoha
At Apoha, we are building the Liquid Brain® — a programmable physical sensing platform creating rich, multidimensional fingerprints of materials to unlock faster and smarter material design. Our mission is to redefine how materials are sensed, understood, and designed across industries.

Why Join Us?

We’re Apoha, the team behind the Liquid Brain®.
We're pioneering Sensory Intelligence by decoding molecular behaviour. The first step in our journey to giving machines the senses they never had? Building a Liquid Brain® platform capable of improving life-saving drugs, by assessing the developability of antibodies earlier (those proteins our immune system makes to fight off bacteria and viruses).
We’re a group of scientists, engineers, and operators who’ve built and launched successful products at Goldman Sachs, Apple, Amazon, and published 50+ high impact research papers across biophysics, materials science, and thermodynamics—and been featured by Scientific American as one of “13 Discoveries That Could Change Everything”.
At Apoha, science isn’t just the foundation of our product—it’s woven into our every day. Whether it’s a journal club over coffee, a spirited scientific discussion unravelling a complex problem, or a full-company Quarter Demo Day that sparks wild new ideas, we’ve built a place where academic rigor meets startup energy.
Our team is small, flat, and talent-dense across disciplines. We gravitate towards people who are collaborative, curious, and take pride in owning their work end-to-end. We enjoy spirited debate, thinking way beyond the state of the art, and building products that could change how we understand biological materials—forever. We believe in the power of on-site collaboration, and our UK-based team works together in our London office to foster creativity, speed, and connection.
Our investors include Redalpine, Acequia Capital, Seedcamp, Nucleus Capital, Plug and Play, Wilbe and others—and we’re just getting started.
What We Offer
  • Competitive compensation + stock options
  • Private health insurance
  • Bi-weekly team lunches + regular socials
  • The rare chance to shape the DNA of a company
  • Access to cutting-edge science, a stellar team, and the chance to change the game
At Apoha, we are committed to fostering a diverse and inclusive workplace. We strongly encourage applications from candidates of all backgrounds, including those from underrepresented groups in tech and science.
The Role
We are hiring an early career scientist with a strong foundation in computational biology, structural bioinformatics, computational chemistry, biophysics, or systems biology, and the ambition to grow rapidly into scientific leadership. You may be a recent PhD graduate with exceptional aptitude and broad curiosity, or an industry scientist with 3+ years of computational drug discovery / R&D experience seeking a dynamic environment to amplify your growth and impact.
What you'll do
  • Develop and expand in-silico molecular representations that capture structural, dynamic, and functional aspects of proteins, antibodies, biologics, and small molecules, with a focus on informing drug discovery and design decisions.
  • Apply both state-of-the-art AI/ML models (deep learning, generative models, property predictors) and biophysical/computational chemistry simulations (molecular dynamics, docking, quantum chemistry, free-energy methods) to build predictive models that guide multi-objective design (e.g., potency, stability, selectivity, developability).
  • Evaluate the sensitivity, robustness, and predictive power of computational representations against experimental assay data, high-throughput screening results, and simulation outputs; calibrate models to close the loop between prediction and measurement.
  • Build frameworks that link molecular representations to structure–function and structure–activity relationships (SAR/QSAR), supporting candidate generation, ranking, and trade-off analysis.
  • Shape strategies for computationally guided protein and small-molecule library design, ensuring broad, efficient coverage of relevant biophysical and chemical property space.
  • Collaborate with ML, data science, and product teams to deliver reproducible workflows, pipelines, and design tools that make insights accessible to internal users and customers.
  • Publish, present, and communicate findings that demonstrate measurable improvements in computational drug discovery, protein engineering, and molecular design outcomes.
Who You Are
  • PhD or Master’s in computational biology, structural bioinformatics, biophysics, bioinformatics, computational chemistry, cheminformatics, or a related discipline.
  • Essential: Strong proficiency in Python for scientific computing, data analysis, and modelling (experience with scientific libraries such as NumPy, SciPy, scikit-learn, PyTorch or TensorFlow).
  • Hands-on experience with machine learning for biomolecular property prediction and/or physics-based modelling (e.g., molecular dynamics, coarse-grained models, statistical mechanics, protein folding/stability, docking, or quantum chemistry).
  • Solid grounding in statistics, applied mathematics, and data-driven modelling, with ability to analyse large-scale multi-omics, structural, or chemical datasets.
Important to Have
  • Industry drug discovery / biotechnology R&D experience (3+ years) desirable, but exceptional PhD graduates will be considered.
  • Evidence of research excellence (peer-reviewed publications, software packages, impactful computational analyses).
  • Advantageous: experience with design algorithms (search/optimisation, active learning, generative AI for molecules) and with cloud/HPC workflows or distributed computing.
DescriptionAssociate or Full Professor of Data Science
University of Oregon
Eugene, Oregon 97403, United States of America
Posted on September 9, 2025 | Posted by Parisa Hosseinzadeh
We enthusiastically invite established interdisciplinary scholars to apply to join and collaboratively develop our Department of Data Science. We invite applications from researchers working in Data Science, broadly defined, including those who contribute to data analysis methodology for applied domain(s), as well as those whose research focuses directly on the methodology itself (e.g., computer science, statistics, or applied math). We are building a Data Science department that promotes social good and enhances belonging in the field. Strong faculty candidates will therefore have demonstrated impactful contributions to both inclusive education and broader societal impact. We encourage applications from candidates with a history of collaboration with domain experts.

The colleague we hire will join an engaged and collaborative faculty to co-create a supportive department that makes positive and impactful contributions to the University, to the public of Oregon, and to the globe. To do so, the colleague will contribute to identification of strategic opportunities for our growing department that guide future faculty hiring, foster and support the department's faculty in research excellence, co-create a constructive department culture and continue to expand our educational mission at the undergraduate and graduate level. Some current efforts of the department are to improve outreach to underserved student populations to bolster admissions, and to develop internship and other programs to aid graduates in career placement.

Strong candidates will have demonstrated their ability and vision for building positively engaged spaces, programs, or organizations. Strong candidates will also have a history of excellent research scholarship; as befits an interdisciplinary department, we are open to various metrics of research success beyond grants, citations, and publications (including policy impact, community engagement in research, collaborative projects, etc.). Strong candidates will also have demonstrated excellence in and commitment to teaching, translation of knowledge, or advising/mentoring of students (including out-of-classroom education). We are excited to grow a mutually supportive culture of impactful teaching and research in our new department. We welcome candidates who understand the barriers facing members of groups who have been historically excluded from data science and higher education (as evidenced by life experiences and educational background), and who have experience in improving belonging with respect to teaching, mentoring, outreach, life experiences, or service. We seek to hire an established scholar (appointable to associate or full professor), which includes faculty currently going through the tenure process and researchers with careers in federal agencies.
More information about the Data Science department can be found at https://scds.uoregon.edu/ds. Particular strengths of collaborative research at UO include astronomy, biomedical data science, climate science and modeling, cell and developmental biology, data ethics, earth science, ecology, education, environmental science, evolution, linguistics, neuroscience, physics, spatial information sciences and sport and wellness, although we welcome applicants from other disciplines.

Department of Data Science

Data Science is a new department that has grown out of a long-standing initiative to increase scholarship and education in quantitative methodology at the University of Oregon. We envision the Data Science Department to be a hub of ethical methodological data science research, with strong connections to domain areas of application, overall facilitating interdisciplinary collaboration across the university. Current faculty and affiliates reflect strengths in machine learning, biological modeling, data ethics, data sovereignty, computer science, environmental data science, climate change policy and modeling, evolutionary genetics, and forensic genetics. The University of Oregon is a public university committed to exceptional teaching, discovery, and service, with a mission to foster the next generation of transformational leaders and informed participants in the global community. The department offers a rapidly growing Data Science undergraduate program, offered for the first time in Fall 2020 and projected to have > 700 undergraduate majors in 2027. This program aims to help students learn the technical data science skills to do socially/environmentally-connected interdisciplinary work with real world impact. Faculty in the department of Data Science can work with PhD students and integrate in specialized research communities through affiliations with world-class research Institutes on campus (e.g., the Institute of Neuroscience; the Institute of Ecology and Evolution; Center for the Study of Women in Society).
Minimum Requirements
  • PhD in discipline related to data science (ex: statistics, computer science, applied mathematics, or a domain field with strong involvement in data science methodology applied in that field)
  • Appointable to the rank of Associate or Full Professor upon initiation of the position
Preferred Qualifications
  • Demonstrated success in collaboratively co-organizing spaces that prioritize belonging
  • Exemplary evidence of impact beyond academia through research, teaching, and/or service
  • Demonstrated experience leading a productive and impactful research program aligned with the goals of the department
Application Submission Instructions
Candidates are asked to apply online at https://academicjobsonline.org/ajo/jobs/30328 by submitting the following required application materials:
  • Cover letter*
  • Curriculum Vitae
 *A cover letter (3 page max) summarizing your interest in and suitability for the position, including an overview and/or highlights of your a) research program, b) teaching experiences and interests, c) service contributions to science, academia, and the broader public, and d) professional contributions to creating welcoming and supportive scientific and learning spaces for individuals from a wide range of backgrounds and perspectives, with the goal of fostering a strong sense of belonging and mutual respect.
Applicants advancing to a later stage will be asked to submit:
  • Research statement
  • Teaching statement
  • Service statement
  • Three references (no actual letters, just names and email addresses)
Applications will be accepted until October 31st or until the post has been filled. If you are unable to use this online resource, please contact datascience@uoregon.edu to arrange alternate means of submitting application materials. Applicants who advance to subsequent rounds will be asked to provide a research statement, teaching statement, service statement, and references.
About the University of Oregon
 
The University of Oregon is building a faculty committed to meeting the needs of our changing student body and creating essential knowledge for society. We encourage applications from individuals who want to join an institution committed to addressing complex problems at all scales, and critical thinking and cross-disciplinary dialogue. We believe the way to create the faculty we need is to develop the most inclusive applicant pool. Goal 03 of our new (2024) strategic plan, titled Oregon Rising, is to create a flourishing community. As outlined in Oregon Rising, “Flourishing is the holistic development and thriving of every individual in our diverse community achieved through growth, well-being, resilience, trust, belonging, robust connection, and sense of purpose. A flourishing community is built on collective experience and is made stronger by our shared commitment to one another.
Application Materials Required:
Submit the following items online at this website to complete your application:
  • Cover letter
  • Curriculum Vitae
And anything else requested in the position description.
Further Info:
541-346-3273
Department of Data Science
120 Deschutes Hall
1202 University of Oregon
1477 E. 13th Ave.
Eugene, OR 97403-1202
Senior Computational Scientist
AstraZeneca
Cambridge
Posted on September 8, 2025 | Posted by Alex Zlobin

Title: Computational Structural Biologist

Location: Cambridge
Salary: Competitive
Introduction to the role:
The Computational Structural Biology (CSB) team is growing our broad-ranging expertise encompasses structural bioinformatics, protein structure prediction, molecular dynamics simulations, free-energy calculations, protein docking, and in silico prediction of physico-chemical properties of biomolecules using advanced computational methods. The team sits as part of the wider Protein Sciences dept. which poses leading capabilities in Protein Structure Prediction, Crystallography, Cryo-Electron Microscopy, Protein Expression and Biophysics.
This role will see you collaborating with structural biologists, protein scientists, biophysicists, chemists, biologists and computational scientists across all of AZs therapy areas. You will work proactively across multiple projects within an interdisciplinary, collaborative, dynamic environment to help develop high-quality lead proteins, ultimately leading to new clinical candidate drugs.
This is an outstanding opportunity to develop and work with ground-breaking, technology and apply it to bio-therapeutic discovery and development projects in a dynamic and interdisciplinary environment.
Accountabilities:
  • Predict, analyse and interpret protein structure using computational modelling tools like Boltz-2, Bindcraft, AlphaFold, RFdiffusion, RFpeptides, molecular dynamics simulations and ML/AI.
  • Apply and develop Protein/peptide design methods.
  • Apply and develop Free-energy calculations for molecular interactions.
  • Apply molecular dynamics simulations methods to understand protein dynamics and motions.
  • Generate scripts and workflows to enable automated analyses.
  • Apply and develop deep learning and molecular dynamics-based approaches to biologics drug discovery.
  • Be part of and contribute to multidisciplinary drug discovery project teams
Essential criteria:
  • PhD in Computer Sciences applied to Biochemical systems and /or Postdoc/ biotech/industry experience.
  • Demonstrated expertise in protein or peptide design.
  • Demonstrated proficiency in utilizing free energy calculations for biochemical analysis and protein design using AI technologies.
  • Expertise preparing and running complex molecular dynamics simulations of biochemical systems.
  • Strong experience in programming with Python for molecular structures.
  • Good track record of publications, strong research skills, and a history of innovation and achievements.
  • Strong experience using molecular modeling packages like Biovia, MOE, Schrodinger, etc.
  • Outstanding teamwork and excellent communication skills.
Desirable criteria:
  • Advanced methods protein and peptide design will be an advantage.
    Advanced methods for free-energy calculations will be an advantage.
    Experience applying methods for protein design with ML/AI will be an advantage.
    Relevant areas of experience might include development and implementation of new deep learning methodologies and generative models.
    Experience in molecular dynamics simulations or protein structure prediction with fully open-source programs is highly desired (e.g. Boltz-2, OpenFold, ProteniX, Rosetta, OpenFF, etc).
    Relevant post-doctoral experience will be advantageous, as would be experience of working in a biotech or pharma company.
    Experience using high performance computing clusters and cloud computing (e.g. AWS, Azure, etc).
    Experience using multiple molecular dynamics simulation packages (Charmm. Gromacs. Etc).
What is next?
Are you ready to make a difference?
Apply today and join us in our mission to improve global public health!
We welcome your applications not later than 18th September 2025.
Where can I find out more?
Follow AstraZeneca on LinkedIn https://www.linkedin.com/company/1603/
Follow AstraZeneca on Facebook https://www.facebook.com/astrazenecacareers/
Center Coordinator
University of Copenhagen
Posted on September 6, 2025 | Posted by Amelie Stein
The Novo Nordisk Foundation Center for Protein Design (CPD) seeks to appoint a Center Coordinator from as soon as possible to 31 July 2032.
We are looking for an energetic and ambitious Center Coordinator to lead and provide the driving force for the administrative team of a large new research center in protein design. The successful applicant should be motivated by working closely with researchers and administrative staff in an inclusive and highly collaborative environment with ambitions to establish the Center for Protein Design as an internationally recognized nucleus for cutting-edge research in protein design.
About us
The Center for Protein Design (CPD) will be embedded across the Faculty of Science (the Department of Biology) and the Faculty of Health and Medical Sciences (the Department of Drug Design and Pharmacology). It will be physically located in newly refurbished offices and laboratories in the Department of Drug Design and Pharmacology on Nørre Campus at the University of Copenhagen. The Center will collaborate with local, national, and international partners from academia and industry to deliver world-leading research and training in fundamental and applied protein design.
The overall mission of the CPD is to tackle key challenges and grasp new opportunities in protein design by interfacing with the basic sciences – biology, chemistry, computer science, and physics – to advance fundamental understanding of protein structure and function, and to enable frontier protein design. In addition, through an open and collaborative network of experts across these disciplines and other fields – such as biotechnology, medicine, and pharmacology – the CPD will use designed proteins to address challenges in healthcare and sustainability.
The CPD is funded by a large grant from the Novo Nordisk Foundation and started on 1 August 2025. The intention is that the Center Coordinator will play a proactive role in establishing and developing the Center from its very beginning.  This will begin with helping to coordinate taking over and establishing the new CPD offices and laboratories with the official launch of the Center, which are anticipated to be in spring 2026.
Additional information about the Novo Nordisk Foundation Center for Protein Design is available upon request from Louise Thers Nielsen ltni@science.ku.dk and Center Director, Professor Dek Woolfson d.n.woolfson@bio.ku.dk.
The position
The Center Coordinator will work in partnership with the Center Director, Professor Dek Woolfson, and will be responsible for the administrative operation of the Center and assisting in forming the foundations to fulfil the ambitions of the CPD. The Center Coordinator will be the administrative point of contact for the management, researchers, and administrative teams within the Center, in the two host departments, and the centralised administrative units across the University of Copenhagen (UCPH). This will include for example: UCPH Finance, Campus Services, HR, Communication, and IT; equivalent groups at the external CPD Spokes and Strategic Partners in Denmark and abroad; and the Novo Nordisk Foundation.  In addition, the Center Coordinator will be expected to help develop new internal (UCPH) and external partnerships; thus, together with the Center Director, they will be internally and outwardly facing points of contacts for the CPD. As such the Center Coordinator will be a key part of the CPD Management and Leadership team.
Your tasks will include – but are not limited to:
  • Development of the best administrative framework and processes for CPD together with the Center Director and the two host departments
  • Administrative management of the Center grant (and other grants) and reporting to the Novo Nordisk Foundation (and other foundations and agencies). This will be done alongside the Center Director, and in collaboration with UCPH's financial officer for the grant and administrative teams within the center and in the two host departments as appropriate.
  • As a sparring partner for the Center Director and the CPD Management Teams in relation to, e.g. center finances, recruitment, management and planning more generally.
  • Coordination of the tasks in the CPD administrative team.
  • Support to the Center Director/Management in strategy development and processes.
  • Develop fund-raising/income-generation strategies and business plans for the growth and development of the Center with the Center Director, Senior Management Team, and UCPH Innovation/Lighthouse and central administration as appropriate.
  • Coordination of employment and onboarding of researchers, many of whom may come from abroad.
  • Support the planning of teaching and research for academic staff in conjunction with the Center Director to ensure equitable workloads across the Center.
  • Ensure the Center implements and monitors relevant policies and strategies to meet statutory and regulatory compliance such as risk management, business continuity, Safety and Health, and data protection.
  • Coordination of activities with the Novo Nordisk Foundation.
  • Planning and overseeing the Center activities such as internal and external meetings, e.g. within the Management Teams, with academic and industrial collaborators and visitors, with the Novo Nordisk Foundation, with the Strategic Advisory Board, and the Annual CPD Research Conference.
  • Assistance in connection with purchase, installation, maintenance and management of research equipment, which will likely be a significant investment for the CPD. This will be done with the CPD Experimental Officer(s) and Technical Team.
  • Coordination with UCPH’s communication department in relation to communication to ensure that CPD becomes a local, national, and international, one-stop shop for information on research activities in protein design.
  • Ongoing dialogue with stakeholders, incl. researchers, funders, publics, journalists, companies, and other relevant organisations.
  • Facilitation of communication and dissemination of research results through, e.g. the CPD's annual reports, website, newsletters, and articles about CPD's research to a wider audience – in collaboration with UCPH’s communication department as appropriate.
  • Participate in Department, Faculty or University committees, working groups and new initiatives, leading these where appropriate.
  • Work with the Department/Faculty technical teams on operational requirements in the CPD’s highly technical environment to support training and research.
  • Advising and helping the CPD Director and Senior Leadership Group to foster and develop new internal (UCPH) and external partnerships.
In other words, the Center Coordinator will play a pivotal role in the CPD, working in partnership with the Director and the Management Teams on all aspects of the Center management, establishment, vision, and growth.
Our expectations
We expect that you will:
  • have an academic degree at Master's level or higher, ideally in a scientific discipline.
  • have substantial transferable/relevant experience in a management support position gained within a large, complex organisation.
  • have a proven ability to interact effectively with staff at all levels and with a wide range of internal and external contacts, commanding respect and dealing with highly complex issues.
  • speak and write English fluently.
  • have excellent intercultural communication skills and an understanding of the world of research.
  • have numerical skills and in-depth knowledge of Excel and can manage budgets.
  • take responsibility for providing consistent and high-quality professional administrative and management support and follow through on tasks.
  • have experience of producing detailed reports and, ideally, contributing to the development and presentation of business cases.
  • have experience of working in, or managing a specialist, technical environment.
  • work independently and in a structured manner and can keep an extraordinary overview of ongoing issues, challenges, and opportunities for the CPD.
  • at the same time, be able to work closely and well with others, especially in the senior academic and management team of the CPD.
  • are proactive, flexible, have a solution-oriented mindset and excel in collaborating and creating networks and relationships across professional groups, internally as well as externally.
  • are able to understand the larger context and perspective at the same time as having an eye for detail.
  • possess a pioneering spirit.
We offer
You will have an interesting and developing job at the CPD and you can expect a high level of activity and a challenging working day in a rapidly growing center. The tasks will initially cover a very broad range as everyone will have to help in solving the tasks related to the establishment of CPD.
We aim to establish a coherent Center administration that professionally and proactively supports CPD's research activities, and thereby underpins the best working environment to deliver world-leading research and training in protein design.
Salary and employment conditions
The position is as senior consultant in accordance with the Collective Agreement for Academics in the Danish State. Remuneration in accordance with the AC collective agreement is determined by seniority. It will be possible to negotiate additional supplements based on qualifications. The position is full-time and the average weekly working hours are 37 hours.
Your employment will be at CPD, the Department of Biology, the Faculty of Science, the University of Copenhagen.
The application process
If you are interested in the position, please send an electronic application in English with attachments (incl. CV, and relevant documentation for your academic degree) via the Job Portal (click on the link "APPLY FOR THE POSITION" at the bottom of the advertisement) no later than 1 October 2025 23:59 CEST.
We want to reflect the surrounding society and encourage everyone, regardless of personal background, to apply for the position.
Further information
For further information about the position, see: New Danish research centre to make designed proteins with vast potential – University of Copenhagen, or contact Louise Thers Nielsen ltni@science.ku.dk .
Part of the International Alliance of Research Universities (IARU), and among Europe’s top-ranking universities, the University of Copenhagen promotes research and teaching of the highest international standard. Rich in tradition and modern in outlook, the University gives students and staff the opportunity to cultivate their talent in an ambitious and informal environment. An effective organisation – with good working conditions and a collaborative work culture – creates the ideal framework for a successful academic career.
Contact
Louise Thers Nielsen
Info
Application deadline: 01-10-2025
Employment start: Start as soon as possible
Working hours: Full time
Department/Location: Department of Biology
ChemBE Systems/Data Science/Artificial Intelligence Professor
Johns Hopkins University
Baltimore, MD, 21218
Posted on September 2, 2025 | Posted by Jeffrey Gray
Description
Faculty position in Chemical and Biomolecular Engineering
Johns Hopkins
The Johns Hopkins University’s Department of Chemical and Biomolecular Engineering seeks applicants a tenure-track/tenured faculty positions.  Candidates with research and teaching interests in Systems Theory (Design -from plant level to molecular- and/or Control) with a strong component in Data Science/Artificial Intelligence relevant to chemical and biomolecular engineering will be considered.
Candidates in these areas will contribute to the Department of Chemical and Biomolecular Engineering and Johns Hopkins University community and mission to educate tomorrow’s leaders in ChemBE and pioneer technological advancements to address critical global challenges in energy, materials design, and precision medicine, to build a stronger, cleaner, and healthier future.
Candidates in the Systems/Data Science/Artificial Intelligence area will perform original research at the interface between chemical engineering modeling/scientific computation and modern Data Science and Machine Learning. Possible efforts include but are not limited to modern design and optimization (e.g. in the role of AI in the transition from automated to autonomous process operations). Creative uses of DSAI in materials/chemicals/process discovery/design, or towards novel computational approaches to atomistic simulations or biological systems modeling are of direct interest.
The Department of Chemical and Biomolecular Engineering is highly collaborative with an established track record of national leadership and developing new disciplines within chemical and biomolecular engineering.  The Department has large, vibrant educational programs at the undergraduate, master’s, and Ph.D. levels as well as post-doctoral level.
This past year, Johns Hopkins announced a major new investment in data science and the exploration of artificial intelligence that will be included in a new data science and translation institute, a new state-of-the-art facility and recruitment of 110 new faculty over the next five years. The institute will bring together world-class experts in artificial intelligence, machine learning, applied mathematics, computer engineering, and computer science to fuel data-driven discovery in support of research activities across the institution including within the Chemical and Biomolecular Engineering department.
In addition to its role in this initiative, the department is a leader in other major research centers and institutes at Johns Hopkins, including the Ralph O’Connor Sustainable Energy Institute (ROSEI), the Institute for Nanobiotechnology (INBT), the Advanced Mammalian Biomanufacturing Innovation Center (AMBIC), International Biomanufacturing Network (IBIoNe) MINDS (Mathematical Institute for Data Science), the Maryland Area Research Computing Center (MARCC), the Hopkins Extreme Materials Institute (HEMI).  Faculty also collaborate frequently with scholars in the Johns Hopkins School of Medicine, Applied Physics Laboratory, Bloomberg School of Public Health, and the Krieger School of Arts and Sciences.
Applicants should have a Ph.D. in chemical and biomolecular engineering or a related field, a track record of outstanding research, and a commitment to excellence in education and student mentoring. The Johns Hopkins Department of Chemical and Biomolecular Engineering recognizes the value and experience of individuals of different backgrounds. The Department and Johns Hopkins University are strongly dedicated to fostering an inclusive, diverse, and welcoming environment for all faculty, staff, and students, and to improving and sustaining equitable structures throughout our community.
The expected base pay range for this position at a rank of Assistant Professor is $150,000-$200,000.
The referenced salary range reflects base pay, which is based on faculty rank and years in rank. This salary range does not include all components of the WSE/ChemBE faculty compensation program or pay from participation in WSE/ChemBE incentive compensation programs. Therefore, the actual compensation paid to the selected candidate may vary from the salary range stated herein. For more information, please contact the hiring department.
 
 Priority given to applications received before 10/17/2025.
Application Instructions
Interested candidates should submit a cover letter that addresses outreach and belonging or diversity efforts, CV, references, and research and teaching statements.
Application Process
This institution is using Interfolio's Faculty Search to conduct this search. Applicants to this position receive a free Dossier account and can send all application materials, including confidential letters of recommendation, free of charge.
Equal Employment Opportunity Statement
Salary Range
The referenced salary range represents the minimum and maximum salaries for this position and is based on Johns Hopkins University's good faith belief at the time of posting.  Not all candidates will be eligible for the upper end of the salary range.  The actual compensation offered to the selected candidate may vary and will ultimately depend on multiple factors, which may include the successful candidate's geographic location, skills, work experience, internal equity, market conditions, education/training and other factors, as reasonably determined by the University.
Total Rewards
Johns Hopkins offers a total rewards package that supports our employees' health, life, career and retirement. More information can be found here: https://hr.jhu.edu/benefits-worklife/.
Equal Opportunity Employer
The Johns Hopkins University is committed to equal opportunity for its faculty, staff, and students. To that end, the university does not discriminate on the basis of sex, gender, marital status, pregnancy, race, color, ethnicity, national origin, age, disability, religion, sexual orientation, gender identity or expression, veteran status or other legally protected characteristic. The university is committed to providing qualified individuals access to all academic and employment programs, benefits and activities on the basis of demonstrated ability, performance and merit without regard to personal factors that are irrelevant to the program involved.
Pre-Employment Information
If you are interested in applying for employment with The Johns Hopkins University and require special assistance or accommodation during any part of the pre-employment process, please contact the HR Business Services Office at jhurecruitment@jhu.edu. For TTY users, call via Maryland Relay or dial 711. For more information about workplace accommodations or accessibility at Johns Hopkins University, please visit accessibility.jhu.edu.
Background Checks
The successful candidate(s) for this position will be subject to a pre-employment background check including education verification.
Diversity and Inclusion
The Johns Hopkins University values diversity, equity and inclusion and advances these through our key strategic framework, the JHU Roadmap on Diversity and Inclusion.
Vaccine Requirements
Johns Hopkins University strongly encourages, but no longer requires, at least one dose of the COVID-19 vaccine. The COVID-19 vaccine does not apply to positions located in the State of Florida. We still require all faculty, staff, and students to receive the seasonal flu vaccine. Exceptions to the COVID and flu vaccine requirements may be provided to individuals for religious beliefs or medical reasons. Requests for an exception must be submitted to the JHU vaccination registry. This change does not apply to the School of Medicine (SOM). SOM hires must be fully vaccinated with an FDA COVID-19 vaccination and provide proof of vaccination status. For additional information, applicants for SOM positions should visit https://www.hopkinsmedicine.org/coronavirus/covid-19-vaccine/ and all other JHU applicants should visit https://covidinfo.jhu.edu/health-safety/covid-vaccination-information/.
The following additional vaccine requirements may apply, depending upon your campus. Please contact the hiring department for more information.
The pre-employment physical for positions in clinical areas, laboratories, working with research subjects, or involving community contact requires documentation of immune status against Rubella (German measles), Rubeola (Measles), Mumps, Varicella (chickenpox), Hepatitis B and documentation of having received the Tdap (Tetanus, diphtheria, pertussis) vaccination. This may include documentation of having two (2) MMR vaccines; two (2) Varicella vaccines; or antibody status to these diseases from laboratory testing. Blood tests for immunities to these diseases are ordinarily included in the pre-employment physical exam except for those employees who provide results of blood tests or immunization documentation from their own health care providers. Any vaccinations required for these diseases will be given at no cost in our Occupational Health office.
Computational Enzyme Engineer
Lawrence Livermore National Laboratory (LLNL)
Livermore, CA
Posted on August 12, 2025 | Posted by Sudeep Sarma

Company Description

Join us and make YOUR mark on the World!
Are you interested in joining some of the brightest talent in the world to strengthen the United States’ security? Come join Lawrence Livermore National Laboratory (LLNL) where our employees apply their expertise to create solutions for BIG ideas that make our world a better place.
We are dedicated to fostering a culture that values individuals, talents, partnerships, ideas, experiences, and different perspectives, recognizing their importance to the continued success of the Laboratory’s mission.
Pay Range
$140,700 - $214,032
$140,700 - $178,392 Annually for the SES.2 level
$168,780 - $214,032 Annually for the SES.3 level
This is the lowest to highest salary we in good faith believe we would pay for this role at the time of this posting; pay will not be below any applicable local minimum wage.  An employee’s position within the salary range will be based on several factors including, but not limited to, specific competencies, relevant education, qualifications, certifications, experience, skills, seniority, geographic location, performance, and business or organizational needs.
This position will be filled at either level based on knowledge and related experience as assessed by the responsibilities (outlined below) will be assigned if hired at the higher level.
Job Description
We have an opening for a Computational Enzyme Engineer to join ongoing projects developing innovative biologics, therapeutics and vaccines against infectious diseases as part of the Center for Predictive Bioresilience (CPB). CPB is an exciting and fast-paced engineering center combining predictive computational modeling, machine learning, and experimental biology to develop medical countermeasures.
You will be responsible for leveraging cutting-edge computational tools and algorithms like RFDiffusion, RosettaFold, ProteinMPNN and AlphaFold to design and engineer proteins and enzymes with enhanced activity, specificity, and stability. This role involves building and training predictive models for enzyme engineering using machine learning and deep learning tools, as well as performing extensive data analysis on experimental protein engineering datasets (including activity and sequence/structure information) to continuously refine and improve these models. You will also develop and implement computational methods, utilizing 3D structures and/or sequences, to optimize enzyme characteristics, and will design protein libraries and datasets for high-throughput screening. Collaboration with interdisciplinary teams of biologists, chemists, and other engineers is crucial to integrate computational insights seamlessly with experimental design and execution. This position will be in the Computational Engineering Division (CED), within the Engineering Directorate, matrixed to the CPB.
In this role, you will
  • Utilize advanced computational tools and algorithms (such as RFDiffusion, RosettaFold, ProteinMPNN and AlphaFold) to contribute to and actively participate in the design and engineering of novel proteins and enzymes with desired properties (e.g., enhanced activity, specificity, or stability).
  • Collaborate with team members and participate in building and training predictive models for enzyme engineering using techniques like machine learning and deep learning, including providing input, recommending enhancements, and solving problems of moderate complexity.
  • Analyze large datasets from experimental protein engineering efforts (including enzyme activity data and sequence/structure information) to refine and improve computational models.
  • Develop and implement moderately complex computational methods, potentially utilizing 3D structures and/or sequences as input to enhance enzyme stability, solubility, and activity.
  • Document methods and implementation methodologies, activities, sequences, and requirements in both informal and formal reports and presentations.
  • Design protein libraries and datasets for high-throughput screening and hit identification.
  • Analyze data, deliver results, engage with, and participate in a talented team to identify, create, implement, benchmark, and scale cutting-edge techniques that integrate biophysics and AI for computational protein design, with a focus on therapeutic modalities including antibodies.
  • Design, test, deploy, and maintain high-quality pipelines on HPC and cloud infrastructures, ensuring scalable and robust solutions.
  • Balance multiple projects/tasks and priorities of customers and partners to ensure deadlines are met, while working independently with limited direction within the scope of the assignment.n.
  • Perform other duties as assigned.
Additional job responsibilities at the SES.3 level
  • Lead projects that develop advanced computational protein design strategies to meet diverse scientific and technical challenges.
  • Independently determine the appropriate technical objectives, criteria, and approaches to satisfy and execute project deliverables.
  • Provide solutions to abstract and complex problems using in-depth analysis, drawing from advanced level technical knowledge and best practices, and collaborate in the development of innovative methods/technology to guide and ensure successful completion of project and organizational goals.
  • Represent the organization as the primary technical contact by sharing relevant knowledge, providing opinions and recommendations, and exerting influence to fulfill deliverables as a team.
  • Lead and mentor junior staff and students.
Qualifications
  • Master's degree in biochemistry, biophysics, bioinformatics, computational chemistry, computer science, AI/ML, or a related technical discipline focused on solving biological problems using computational approaches, or the equivalent combination of education and related experience.
  • Comprehensive knowledge of or experience in developing and implementing novel methods and algorithms for computational protein design.
  • Proficiency in programming with languages such as Python, C/C++, or Java.
  • Proficient written, and verbal communication skills necessary to work and collaborate effectively in a multi-disciplinary environment, and to present and explain technical information.
  • Demonstrated strong record of documentation of executed work.
  • Ability to prioritize, balance, and keep several parallel threads of work in simultaneous, smooth motion.
Additional qualifications at the SES.3 level
  • Advanced level knowledge and significant experience in computational protein design or a related technical field.
  • Ability to independently develop and execute complex analyses and to prepare and finalize tailored reports.
  • Significant experience leading interdisciplinary teams, including setting clear expectations, delegating to subordinates and peers, and ensuring successful, timely completion of objectives.
  • Advanced verbal and written communication, facilitation, and interpersonal skills necessary to effectively collaborate and lead in a team environment and to present and explain technical information, influence and guide team members, and provide advice to management.
Qualifications We Desire
  • PhD in biochemistry, biophysics, bioinformatics, computational chemistry, computer science, AI/ML, or a related technical discipline focused on solving biological problems using computational approaches.
  • Demonstrated understanding of fundamental biochemistry and enzyme engineering concepts including kinetics, reaction mechanisms, transition states, and rational design.
  • Experience with classic computational approaches to estimating enzymatic properties such as thermodynamic stability and net charge and mathematical modeling of enzyme reaction dynamics.
  • Familiarity with non-canonical amino acids and their use in protein design.
  • Experience with design and modeling tools such as Rosetta, RFDiffusion, ProteinMPNN, AlphaFold, etc.
  • Background in developing generative AI, structure-, or sequence-based methods for therapeutic protein design.
  • Familiarity with training generative AI models, applying bioinformatics approaches to sequence analysis, and managing large databases of protein structures and sequences.
  • Experience with modern deep learning frameworks (e.g., PyTorch, JAX, SageMaker) and cloud services (e.g., Git, Docker, AWS Batch, Step Functions, EKS).
Additional Information
#LI-Hybrid
Position Information
This is a Flexible Term appointment, which is for a definite period not to exceed six years.  If final candidate is a Career Indefinite employee, Career Indefinite status may be maintained (should funding allow).
Why Lawrence Livermore National Laboratory?
Security Clearance
None required.  However, if your assignment is longer than 179 days cumulatively within a calendar year, you must go through the Personal Identity Verification process.  This process includes completing an online background investigation form and receiving approval of the background check.  (This process does not apply to foreign nationals.)
National Defense Authorization Act (NDAA)
The 2025 National Defense Authorization Act (NDAA), Section 3112, generally prohibits citizens of China, Russia, Iran and North Korea without dual US citizenship or legal permanent residence from accessing specific non-public areas of national security or nuclear weapons facilities.  The restrictions of NDAA Section 3112 apply to this position.  To be qualified for this position, Candidates must be eligible to access the Laboratory in compliance with Section 3112.
Pre-Employment Drug Test
External applicant(s) selected for this position must pass a post-offer, pre-employment drug test. This includes testing for use of marijuana as Federal Law applies to us as a Federal Contractor.
Wireless and Medical Devices
Per the Department of Energy (DOE), Lawrence Livermore National Laboratory must meet certain restrictions with the use and/or possession of mobile devices in Limited Areas. Depending on your job duties, you may be required to work in a Limited Area where you are not permitted to have a personal and/or laboratory mobile device in your possession.  This includes, but not limited to cell phones, tablets, fitness devices, wireless headphones, and other Bluetooth/wireless enabled devices.
If you use a medical device, which pairs with a mobile device, you must still follow the rules concerning the mobile device in individual sections within Limited Areas.  Sensitive Compartmented Information Facilities require separate approval. Hearing aids without wireless capabilities or wireless that has been disabled are allowed in Limited Areas, Secure Space and Transit/Buffer Space within buildings.
How to identify fake job advertisements
Please be aware of recruitment scams where people or entities are misusing the name of Lawrence Livermore National Laboratory (LLNL) to post fake job advertisements. LLNL never extends an offer without a personal interview and will never charge a fee for joining our company. All current job openings are displayed on the Career Page under “Find Your Job” of our website. If you have encountered a job posting or have been approached with a job offer that you suspect may be fraudulent, we strongly recommend you do not respond.
Equal Employment Opportunity
We are an equal opportunity employer that is committed to providing all with a work environment free of discrimination and harassment. All qualified applicants will receive consideration for employment without regard to race, color, religion, marital status, national origin, ancestry, sex, sexual orientation, gender identity, disability, medical condition, pregnancy, protected veteran status, age, citizenship, or any other characteristic protected by applicable laws.
Reasonable Accommodation
Our goal is to create an accessible and inclusive experience for all candidates applying and interviewing at the Laboratory.  If you need a reasonable accommodation during the application or the recruiting process, please use our online form to submit a request.
California Privacy Notice
The California Consumer Privacy Act (CCPA) grants privacy rights to all California residents. The law also entitles job applicants, employees, and non-employee workers to be notified of what personal information LLNL collects and for what purpose. The Employee Privacy Notice can be accessed here.
PostDoctoral Position in Structural Bioinformatics
National Institutes of Health
USA-MD-Bethesda
Posted on July 28, 2025 | Posted by Brian Pierce

The Structural Bioinformatics Core Section (SBIS) at the National Institute of Allergy and Infectious Diseases (NIAID), Vaccine Research Center (VRC), located on the main NIH campus in Bethesda, MD, is opening a postdoctoral position in the areas of computational biology and structural bioinformatics.

We are seeking a highly motivated recent postgraduate for a full-time postdoctoral position in computational protein design. This position offers hands-on experience at the interface of machine learning, structural biology, and protein engineering. You’ll work closely with a multidisciplinary team developing next-generation tools to design proteins with novel functions.
What you’ll do:
 Drive the development of novel algorithms for de novo protein design aimed at advancing next-generation vaccines and therapeutics
 Apply state-of-the-art tools, including protein language models, diffusion models, and molecular simulations, to tackle design challenges
 Partner with experimental teams to validate in silico predictions and guide iterative protein optimization
Qualifications:
 Ph.D. in computational biology, bioinformatics, computer science, or related discipline
 Strong coding skills in Python; experience with PyTorch, Rosetta, AlphaFold, or related frameworks is a plus
 Background in protein modeling, structure prediction, or generative AI preferred
 Strong publication record and ability to work independently and collaboratively
 Oral and written communication skills
 Clear sense of organization, purpose, and accountability
 Eagerness to learn and contribute in a fast-paced, collaborative environment
To apply: Interested applicants should send a curriculum vitae via email to: Reda Rawi, PhD
reda.rawi@nih.gov using the following email subject: “PostDoc applicant – FirstName, LastName”
PostBaccalaureate Position in Structural Bioinformatics
National Institutes of Health
USA-MD-Bethesda
Posted on July 28, 2025 | Posted by Brian Pierce
The Structural Bioinformatics Core Section (SBIS) at the National Institute of Allergy and Infectious Diseases (NIAID), Vaccine Research Center (VRC), located on the main NIH campus in Bethesda, MD, is opening a postbaccalaureate position in the areas of computational biology and structural bioinformatics.
We are seeking a highly motivated recent graduate for a full-time postbaccalaureate position in computational protein design. This position offers hands-on experience at the interface of machine learning, structural biology, and protein engineering. You’ll work closely with a multidisciplinary team developing next-generation tools to design proteins with novel functions.
This is a great opportunity for candidates considering graduate school or a future in computational biology.
What you’ll do:
 Assist in and lead the development and application of protein language models and structure-guided design pipelines
 Analyze protein sequences and structures using bioinformatics and AI tools
 Contribute to ongoing research projects and author/co-author publications
Qualifications:
 Bachelor’s degree in bioinformatics, computer science, or a closely related field
 Proficiency in either Python or R
 Prior experience in machine learning
 High interest in applying computational tools to biological problems including vaccine and therapeutics development
 Oral and written communication skills
 Eagerness to learn and contribute in a fast-paced, collaborative environment
To be eligible, candidates must also be U.S. citizens or permanent residents.
To apply: Interested applicants should send a curriculum vitae via email to: Reda Rawi, PhD reda.rawi@nih.gov using the following email subject: “PostBac applicant – FirstName, LastName”
Scientist, Computational Biology
Visterra Inc.
Waltham, MA
Posted on July 14, 2025 | Posted by Brahm Yachnin
About the job
Summary
Visterra is seeking a highly talented and motivated Scientist to join our Protein Design and Modeling group, reporting to the Sr. Director of Research. This role focuses on leveraging and advancing cutting-edge methods for the design of novel therapeutics. The successful candidate will contribute to challenging design initiatives and collaborate closely with both computational and experimental scientists to develop, refine, and deploy tools for structure prediction, protein engineering, and data analysis. Candidates should have a strong foundation in protein engineering and a demonstrated ability to utilize modern protein design and modeling technologies. We’re looking for someone who is driven, intellectually curious, a critical thinker, and thrives in a collaborative, interdisciplinary environment. This is a full-time, on-site position located at Visterra’s offices in Waltham, MA.
Key duties and responsibilities
  • Develop, implement, and apply innovative deep learning and AI-based methods for protein structure prediction, design, and optimization.
  • Evaluate and implement emerging computational tools, algorithms, and best practices in the field of machine learning-driven protein engineering.
  • Integrate computational modeling and advanced analytics with experimental workflows to design and optimize antibodies and other therapeutic proteins.
  • Collaborate closely with other computational and experimental scientists to support iterative design of therapeutic proteins and antibodies.
  • Independently analyze scientific results, troubleshoot computational and data-driven challenges, and develop creative solutions and workflows to address challenges.
  • Prepare technical documents and deliver clear, effective presentations on project progress, findings, and strategy to internal teams.
  • Develop research plans and manage multiple concurrent projects or workflows.
  • May include supervision and mentorship of direct reports.
Minimum Qualifications
  • A Ph. D. or equivalent in computational biology, bioinformatics, structural biology, or a related discipline with significant and extensive experience in protein design.
  • Strong foundation in deep learning, particularly as applied to protein structure modeling (e.g. AlphaFold, ProteinMPNN, RFdiffusion).
  • Demonstrated experience applying machine learning to solve real-world problems in protein engineering or design.
  • Familiarity with experimental approaches for protein characterization (e.g. expression, purification, biophysics, and binding assays).
  • Proficient in Python and deep learning frameworks (e.g. PyTorch).
  • Proficient with Linux, including experience using high performance computing environments.
  • Ability to work in multi-disciplinary teams, displaying excellent interpersonal skills.
  • Exceptional communication skills (written and verbal), with a proven ability to convey complex ideas in a clear, precise, and actionable manner to diverse teams at all levels of the organization.
Preferred Qualifications:
  • Experience developing custom ML/AI models for biological sequence or structure generation.
  • Experience using Rosetta-based methods for protein design and modeling.
  • Prior experience engineering therapeutic antibodies or other biologics.
  • Familiarity with cloud computing or GPU-accelerated infrastructure.
  • Track record of publications in the field of computational protein design.
Management responsibilities: This position may include supervisory responsibilities
Travel: Possible travel to local and national conferences
Company
Visterra is a clinical stage biotechnology company committed to developing innovative biologic therapies (antibodies and therapeutic proteins) for the treatment of kidney diseases and other hard-to-treat diseases. Our proprietary technology platform enables the design and engineering of precision antibody or protein-based drug candidates to modulate key disease targets. We are developing a robust pipeline of novel therapies for patients with unmet needs.
Visterra is a wholly-owned subsidiary of Otsuka America, Inc., which is a U.S. holding company and a wholly owned subsidiary of Otsuka Pharmaceutical Co., Ltd. of Japan. Visterra has approximately 125 employees and is located in Waltham, Massachusetts.
Assistant or Associate Professor
Dana-Farber Cancer Institute and Biological Chemistry and Molecular Pharmacology at Harvard Medical School
Boston, MA
Posted on July 11, 2025 | Posted by Sergey Ovchinnikov
Job Ref:
45259
Location:
450 Brookline Ave, Boston, MA 02215
Category:
Faculty/Health Educator
Employment Type:
Full time
Work Location:
Onsite: 100% onsite
Overview
ASSISTANT/ASSOCIATE PROFESSOR, DEPARTMENT OF CANCER BIOLOGY DANA FARBER CANCER INSTITUTE and DEPARTMENT OF BIOLOGICAL CHEMISTRY AND MOLECULAR PHARMACOLOGY HARVARD MEDICAL SCHOOL
The Departments of Cancer Biology at the Dana-Farber Cancer Institute and Biological Chemistry and Molecular Pharmacology at Harvard Medical School invite applicants for a tenure-track faculty position at the rank of Assistant/Associate Professor.
We offer an inspiring, supportive and collaborative work environment that includes diverse faculty with research interests spanning chemical biology, structural biology, cancer biology, systems pharmacology, cell biology, immunology, biochemistry, biophysics, computer science, protein engineering and medicine.
We strongly encourage team science, entrepreneurship and mentorship of scientists and physicians from a variety of backgrounds. The two Departments are known for exceptional scientific and scholarly resources, interdisciplinary research and a family-friendly and supportive environment.
Located in Boston and the surrounding communities, Dana-Farber Cancer Institute is a leader in life changing breakthroughs in cancer research and patient care. We are united in our mission of conquering cancer, HIV/AIDS and related diseases. We strive to create an inclusive, diverse, and equitable environment where we provide compassionate and comprehensive care to patients of all backgrounds, and design programs to promote public health particularly among high-risk and underserved populations. We conduct groundbreaking research that advances treatment, we educate tomorrow's physician/researchers, and we work with amazing partners, including other Harvard Medical School-affiliated hospitals.
Responsibilities
We seek imaginative and creative scientists interested in building an innovative research program in cancer chemical biology.
The candidate should possess the ability to work collaboratively with other scientists within the Chemical Biology Program and their host departments and should espouse the scholarly qualities required to teach and mentor doctoral students and postdoctoral fellows. Candidates should be committed to a safe and supportive culture based on principles of creativity, collegiality, responsibility, rigor, and integrity.
The successful candidate will participate in the teaching and training of graduate students  in Ph.D. programs at Harvard University, such as those in Biological and Biomedical Sciences and Chemical Biology, which attract extraordinary graduate students.  Applicants will be housed at the Dana Farber Cancer Institute and will be members of the Dana-Farber Chemical Biology Program.
Qualifications
A Ph.D. or M.D./Ph.D. in areas of chemistry, chemical biology, molecular biology, cancer biology or related fields is required.
A core expertise in chemical biology, medicinal chemistry, drug discovery, development and design, especially as it pertains to advancing understanding and treatment of cancer, is preferred. Candidates who combine these interest with expertise and interest in developing and applying AI/ML methodology to design new therapeutic modalities and/or understand their mechanism of action are also encouraged to apply.
Required documents (to be submitted as a single PDF):
  • curriculum vitae (including bibliography)
  • description of research accomplishments (one page maximum)
  • summary of future research interests (three pages maximum)
After you apply through the portal, please ask your three to four references to email their Letters of Recommendation to: chemical_biology@dfci.harvard.edu
Applications will be considered starting now until October 31, 2025. 
At Dana-Farber Cancer Institute, we work every day to create an innovative, caring, and inclusive environment where every patient, family, and staff member feels they belong.  As relentless as we are in our mission to reduce the burden of cancer for all, we are equally committed to diversifying our faculty and staff.  Cancer knows no boundaries and when it comes to hiring the most dedicated and diverse professionals, neither do we. If working in this kind of organization inspires you, we encourage you to apply.
Dana-Farber Cancer Institute is an equal opportunity employer and affirms the right of every qualified applicant to receive consideration for employment without regard to race, color, religion, sex, gender identity or expression, national origin, sexual orientation, genetic information, disability, age, ancestry, military service, protected veteran status, or other characteristics protected by law.
Wetlab Internship
Lausanne, Switzerland
Posted on July 8, 20225 | Posted by Martin Pacesa
We are looking for a motivated student for a 6 month paid wetlab internship in Lausanne, Switzerland, working on protein design, protein purification and biophysical protein interaction screening in the group of Prof. Bruno Correia.
Applicant needs to have European or Swiss citizenship and to have completed their Masters degree in the last 6 months or will graduate this summer at a European or Swiss university. Possibility for long term employment if further funding is acquired.
Please send your motivation letter (0.5-1 page) and CV to applications@mpacesa.com. Looking forward working with some talented people!
Sr Scientist I/II Informatics - Peptide Design
AbbVie
Chicago, IL
Posted on June 30, 2025 | Posted by John Karanicolas
Company Description
AbbVie's mission is to discover and deliver innovative medicines and solutions that solve serious health issues today and address the medical challenges of tomorrow. We strive to have a remarkable impact on people's lives across several key therapeutic areas – immunology, oncology, neuroscience, and eye care – and products and services in our Allergan Aesthetics portfolio. For more information about AbbVie, please visit us at www.abbvie.com. Follow @abbvie on XFacebookInstagramYouTubeLinkedIn and Tik Tok.
Job Description
AbbVie seeks a knowledgeable, self-motivated, and creative scientist for cyclic peptide design in for computational chemistry / drug discovery. The selected candidate will join our Computational Drug Discovery group within the Discovery Research organization. AbbVie has recently gained the capability to synthesize millions of custom cyclic peptide sequences in a “programmable” manner, and to individually characterize their interaction with a desired protein partner. The candidate will be expected to leverage this opportunity to computationally design novel cyclic peptides as an entry-point to this platform.
The candidate will have the opportunity to develop and advance physics-based modeling as well as AI/ML technologies at the heart of computer-aided peptide design. The candidate should have broad experience with computational techniques with a focus on the state-of-the-art methods in machine learning applied to chemical and biological data. The key responsibilities of this position are to identify, develop, optimize, validate, and deploy innovative methods for modeling cyclic peptides and their interactions with proteins. The candidate should have a working knowledge of chemistry and the ability to work collaboratively with a broad variety of disciplines including other members of our internal computational chemistry and cheminformatics groups to accelerate drug discovery from hit identification through candidate selection.
You will have access to state-of-the-art modeling, simulation, and machine learning technologies as well as computing infrastructure, and be able to leverage rich collections of data to accelerate drug discovery in a fast-paced and creative environment.
Key Responsibilities:
  •  Developing, implementing and deploying programs and computational solutions employing Machine Learning/Deep learning and Cheminformatics
  • Ability to implement, debug, and maintain computational tools in common programming languages (Python, etc…) and proficiency with cloud computing capabilities
  • Familiarity with modern deep learning architectures including GNN, CNN, RNN, Transformer, GCNN and MPNN, and machine learning paradigms such as generative models, GAN, and active learning
Qualifications
Qualifications:
  • Bachelor’s Degree or equivalent education and typically, 10 years of experience, Master’s Degree or equivalent education and typically 8 years of experience, PhD and no experience necessary.
  • MS, or PhD in Chemistry/Computer Science/Machine Learning/Cheminformatics/Chemical Engineering or related education with experience developing machine learning models related to chemical and biological data, preferred.
  • Expertise in AI/ML-enabled molecular generation, pose generation, sequence design, and/or affinity prediction are preferred
  • Strong analytical and problem-solving skills with demonstrated ability to think critically and creatively, and provide solutions both individually and collaboratively with internal experts to develop and optimize the computational discovery infrastructure including cloud resources
  • Excellent ability to communicate clearly and concisely with colleagues and collaborators including an ability to explain complex ideas to non-specialists
  • Strong programming skills in Python and experience with data science stack including numpy, pandas, scikit-learn, and other related scientific libraries
  • The level of the position will be determined by the skill set of the candidates
Additional Information
Applicable only to applicants applying to a position in any location with pay disclosure requirements under state or local law: ​​
​​
  • The compensation range described below is the range of possible base pay compensation that the Company believes in good faith it will pay for this role at the time of this posting based on the job grade for this position. Individual compensation paid within this range will depend on many factors including geographic location, and we may ultimately pay more or less than the posted range. This range may be modified in the future.​​
  • We offer a comprehensive package of benefits including paid time off (vacation, holidays, sick), medical/dental/vision insurance and 401(k) to eligible employees.​​
  • This job is eligible to participate in our short-term incentive programs. ​​
​​
Note: No amount of pay is considered to be wages or compensation until such amount is earned, vested, and determinable. The amount and availability of any bonus, commission, incentive, benefits, or any other form of compensation and benefits that are allocable to a particular employee remains in the Company's sole and absolute discretion unless and until paid and may be modified at the Company’s sole and absolute discretion, consistent with applicable law. ​
AbbVie is an equal opportunity employer and is committed to operating with integrity, driving innovation, transforming lives and serving our community.  Equal Opportunity Employer/Veterans/Disabled.
US & Puerto Rico applicants seeking a reasonable accommodation, click here to learn more:
Tenure Track Professor in Chemical Biology
Aix-Marseille University (AMU)
Marseille, France
Posted on June 16, 2025 | Posted by Matthew O'Meara
OPEN POSITION AT THE CANCER RESEARCH CENTER OF MARSEILLE
Tenure Track Professor in Chemical Biology
(Chaire Professeur Junior)
Aix-Marseille University (AMU), Marseille, France
Key words: cancer research chemical biology chemo-informatics chemistry l
Aix-Marseille University opens a tenure track professor (CPJ) in chemical biology to strengthen research and teaching at
the interface of chemistry and biology. The scientific objective is to accelerate the discovery and development of innovative
therapeutic molecules and advanced drug delivery systems, addressing major health challenges such as cancer,
cardiovascular, infectious, genetic, and neurodegenerative diseases. The recruited professor will leverage interdisciplinary
expertise in organic synthesis, chemo-informatics, and drug design, utilizing cutting-edge platforms and collaborations to
design novel compounds and optimize existing therapies, including the use of artificial intelligence for target identification
and functional screening. On the educational side, the chair will enhance the university’s training programs in Health
Engineering and Biology-Health Masters, by providing high-level theoretical and practical teaching in both French and
English. The professor will also supervise students at the master’s and doctoral levels, fostering research-based learning
and contributing to continuing and professional education. This initiative will reinforce the university’s national and
international competitiveness in innovative chemistry-biology research and education, while addressing societal and
environmental concerns related to therapeutic innovation.
In this context, the Cancer Research Centre of Marseille (CRCM), an international center affiliated to national (Inserm,
CNRS) and local (Aix-Marseille University, Paoli-Calmettes Cancer Institute) institutions, is seeking to expand its activities
in the field of chemical biology (e.g., medicinal chemistry, chemical probe development, activity-based probes, chemical
genetics, targeted protein degradation, chemo-informatics, chemical proteomics, etc.) and is actively looking to support
strong candidates with complementary expertise who could apply for the upcoming CPJ tenure-track position in Chemical
Biology to be opened by Aix-Marseille Université (AMU) in 2025.
With 450 members in 4 Departments dedicated to Cell Communication and Microenvironment, Genome Integrity, Onco-
Hematology and Immuno-Oncology, and Translational/Clinical research, the CRCM combines excellent research and
access to high education in oncology and immunology, state-of-the-art technological support and a collegial set of teams
offering a fertile and outstanding environment to develop fundamental, translational or clinical projects for patient benefits.
Applicants should propose a competitive, innovative research program aligned with the AMU CPJ objectives and with
cancer biology and translational research for candidates wishing to join the CRCM. Candidates must hold a PhD, have
significant postdoctoral experience, a strong publication record, and demonstrate the potential to obtain external funding.
Funding: 4-year salary + funding package (470 k€ including salary)
Candidates should express their interest in applying by sending before June 27th, 2025 to
bernardst@ipc.unicancer.fr: 1) A curriculum vitae; 2) A concise presentation of the current research; 3) The name and
email address of three referees.
The CRCM provides equal employment opportunities to all employees and applicants for employment and prohibits all
forms of discrimination and harassment of any type.
Senior Principal Scientist, AI/ML Antibody Design & Engineering
Regeneron
Tarrytown, New York, United States of America
Posted on June 6, 2025 | Sent by Anum Glasgow
Job Description
Save
We are seeking a highly talented and motivated Senior Principal Scientist specializing in AI Machine Learning to lead the design and engineering of our next-generation antibody-based protein therapies. The ideal candidate shall have a strong background and passion in both computational biology, with expertise in programming, large language models, in silico protein design tools, and knowledge in structural biology and antibody engineering. You will help drive both internal development and external partnership to create/validate AI/ML tools to enable our quest for next-gen antibody therapies. By closely working with antibody engineers, structural biologists and AI/ML scientists from a cross functional team, you have a unique opportunity to shape the future of our AI/ML strategy and deliver on future biotherapies from our state-of-art research facilities.
A typical day in the life of a Senior Principal Scientist AI/ML Antibody Design and Engineering may include the following responsibilties:
  • Utilize AI and machine learning techniques to design novel antibodies and bi/multi-specific antibodies that would be challenging to achieve from screening
  • Develop novel AI and machine learning tools to enable de novo antibody discovery with unique properties and in silico co-optimization of affinity, expression, stability and PK/half-life.
  • Apply deep learning and generative AI techniques to train/enhance LLM or other relevant language models using internal datasets
  • Use in silico protein/antibody engineering design tools such as Rosetta to drive for structure-based design and engineering
  • Leverage deep target biology from broad therapeutic areas to enable desired novel MoAs through molecular design
  • Collaborate and support scientists from antibody engineering, therapeutic areas and other tech centers with biotherapeutic design
  • Guide and lead AI/ML scientists across multiple functions to have a synergized AI/ML strategy and drive sustained delivery of novel molecular entities to pipeline
  • Serve as an expert in computational biologic design to keep up with the latest advancements in AI, machine learning, and protein engineering fields
  • Maintain data analysis and records in well-organized fashion
  • Present data clearly to teams and managements
This role may be for you if:
  • You are a result-driven innovator and a problem solver
  • You have a strong background in computational biology, programming, deep learning algorithms, structural biology and protein engineering
  • You have expertise with advanced machine learning models related to antibody engineering, such as language model, geometric deep learning, generative model and multi-modal model
  • You have proficiency in programming languages such as Python, R and C++
  • You have competence to work with large dataset and cloud computing infrastructure
  • You can efficiently coordinate multiple projects in a collaborative environment
  • You have strong organizational, time-management, and presentation skills
  • You enjoy working in a fast-paced, innovative and cross-functional team
To be considered for this opportunity, you must have a PhD in Computational Biology, Bioinformatics, Computer Science, Structural Biology or a related field, with 7-10 years of relevant experience. You must have a strong track record of innovation and research accomplishments in developing AI/ML methods and using deep learning tools to successfully solve antibody/protein engineering challenges. Experience in using structural modeling and design tools (e.g. Rosetta) is strongly preferred. Experience in constructing DNA and protein production for screening in silico design is preferred.
Does this sound like you? Apply now to take your first step towards living the Regeneron Way! We have an inclusive and diverse culture that provides comprehensive benefits, which often include (depending on location) health and wellness programs, fitness centers, equity awards, annual bonuses, and paid time off for eligible employees at all levels!
Regeneron is an equal opportunity employer and all qualified applicants will receive consideration for employment without regard to race, color, religion or belief (or lack thereof), sex, nationality, national or ethnic origin, civil status, age, citizenship status, membership of the Traveler community, sexual orientation, disability, genetic information, familial status, marital or registered civil partnership status, pregnancy or parental status, gender identity, gender reassignment, military or veteran status, or any other protected characteristic in accordance with applicable laws and regulations. The Company will also provide reasonable accommodation to the known disabilities or chronic illnesses of an otherwise qualified applicant for employment, unless the accommodation would impose undue hardship on the operation of the Company's business.
For roles in which the hired candidate will be working in the U.S., the salary ranges provided are shown in accordance with U.S. law and apply to U.S.-based positions. For roles which will be based in Japan and/or Canada, the salary ranges are shown in accordance with the applicable local law and currency. If you are outside the U.S, Japan or Canada, please speak with your recruiter about salaries and benefits in your location.
Please note that certain background checks will form part of the recruitment process. Background checks will be conducted in accordance with the law of the country where the position is based, including the type of background checks conducted. The purpose of carrying out such checks is for Regeneron to verify certain information regarding a candidate prior to the commencement of employment such as identity, right to work, educational qualifications etc.
(Senior) Machine Learning Engineer, Bayesian Optimization
Flagship Labs 109
Cambridge, MA USA
Posted on June 5, 2025 | Posted by Ben Stranges
Company overview:
Flagship Labs 109, Inc. (FL109) is a privately held, early-stage technology company pioneering the use of artificial intelligence, physics and hardware to transform the way we see biology. FL109 was conceived by Flagship Pioneering, which brings the courage, long-term vision, and resources needed to realize unreasonable results. Become part of our mission-driven team and help envision the future of science.
Overview:
We are seeking a (Senior) Machine Learning Engineer with deep expertise in Bayesian optimization, protein design, and generative modeling to help lead the development of next-generation AI systems in the protein space. This role will focus on solving state-of-the-art problems structural biology and protein design. You will collaborate closely with a multidisciplinary team of scientists to push the boundaries of biological understanding and generative protein modeling, with opportunities to mentor others while translating research into production-ready tools, experimental designs, and powerful new datasets.
Key Responsibilities:
  • Apply Bayesian optimization and other active learning techniques to diverse problems.
  • Develop, train, and fine-tune generative models (ex: diffusion models, transformers) for encoding and designing protein structures and sequences.
  • Collaborate with diverse functions (ex: structural biologists, protein engineers) to incorporate physical, structural, or biological priors into the model.
  • Deliver models and insights to guide experimental design and data generation.
  • Mentor junior engineers and contribute to the direction of the ML engineering function.
  • Track and present model performance, research progress, and infrastructure improvements to internal stakeholders.
Required Qualifications:
  • PhD or MSc in Computer Science, Machine Learning, Computational Biology, Biophysics, or a related field.
  • 2+ years of experience in developing and deploying machine learning models in industry or applied research settings.
  • Strong background in Bayesian optimization, active learning, or experimental design for high-dimensional biological problems.
  • Experience with large-scale generative models (ex: diffusion models, transformers) and distributed training (multi-GPU, multi-node).
  • Proficiency in Python and modern ML frameworks such as PyTorch or TensorFlow.
  • Hands-on experience with ML infrastructure, including cloud services (AWS, or Azure) and container orchestration (Kubernetes, Docker).
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 generation of over 500 patents, initiation of over 50 clinical trials for novel therapeutic agents and an aggregate value of more than $90 billion. 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 is 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.
Research Professorship in microbial systems biology, synthetic biology and/or protein engineering
KULeuven
Leuven, Belgium
Posted on June 4, 2025 | Posted by Anastassia Vorobieva
About the role
We are recruiting a full-time Research Professor (BOFZAP) to join the Centre of Microbial
and Plant Genetics, Faculty of Bioscience Engineering, KU Leuven. We welcome
applications from internationally oriented candidates with a strong research profile in the
field of microbial systems biology, synthetic biology and/or protein engineering.
The new colleague will be expected to develop a research program around the study of
fundamental properties of microbes, microbial biomolecules and on translating insights
from these systems into practical applications. The research should preferably adopt a
systems-level approach and make use of high-throughput methodologies. Effective
application of advanced machine learning analysis and data integration approaches,
potentially through collaboration, is considered a strong asset. Application areas may
include, but are not limited to, synthetic biology for enzyme, strain, or ecosystem
engineering aimed at addressing important societal and sustainability challenges. The
research will be embedded within the ongoing research programs of the Centre of
Microbial and Plant Genetics and should ideally complement existing initiatives.
A good command of English is required. Teaching duties as a Research Professor are
initially limited, allowing you time to establish your research program. You will contribute to
the Faculty of Bioscience Engineering's bachelor's and master's programs and supervise
master's theses. Teaching responsibilities will be defined in consultation and aligned with
your expertise. Knowledge of Dutch is not required at the time. However, since most
bachelor-level teaching is Dutch, you are expected to acquire a working knowledge of the
language over time. KU Leuven offers language training to support this.

Research Unit and Academic Setting
KU Leuven is a research-intensive university, consistently listed among the top institutions
worldwide. It has strong fundamental and applied research, and is considered amongst
Europe’s most innovative universities. Research at KU Leuven is strongly inter- and
multidisciplinary in nature, and the university strives for international excellence. In this
context, it actively collaborates with research partners in Belgium and abroad and offers
students an academic education that is rooted in high-quality scientific research.

The CMPG consists of 10 professors active in biological and biotechnological research.
This includes fundamental research on bacterial and yeast physiology, using microbes as
model systems to study core biological processes, and applied research in fermentation
and the control of bacterial infections and contaminations. Further, several groups work on
the development and application of advanced computational biology analyses. Three
groups are part of the VIB research institute. The unit organizes the masters of Cellular and
Genetic Engineering and Bioinformatics within the Faculty of Bioscience Engineering. The
Faculty is recognized for the academic strength of its students.

What we offer
We offer full-time employment as a BOF-ZAP research professor in a supportive and
research-driven academic context. A start-up package is included, with funding for a PhD
student and experimental expenses, and equipment. You will be based in our shared
laboratory space and have access to CMPG equipment, the VIB/KU Leuven Core Facilities
(see VIB Core Facilities, KU Leuven Core Facilities, and KU Leuven Institutes), as well as
the university’s high-performance computing facility.
KU Leuven actively supports international professors and their families with immigration
and administrative procedures, housing, childcare, Dutch language courses, and partner
career guidance.
You will work in Leuven, a historic, dynamic and lively city located in the heart of Belgium,
within 20 minutes from Brussels, the capital of the European Union, and less than two
hours from Paris, London and Amsterdam. The CMPG is located in the castle Arenberg
campus, just outside the city centre.
Depending on your record and qualifications, you will be appointed to or tenured in one of
the grades of the senior academic staff: assistant professor, associate professor,
professor or full professor. In principle, junior researchers are appointed as assistant
professor on the tenure track for a period of 5 years; after this period and a positive
evaluation, they are permanently appointed (or tenured) as an associate professor.

Procedure and additional information
The recruitment procedure will proceed through the annual university BOF-ZAP Research
Professor call. Candidates interested in this position are invited to submit their application
by emailing CMPG at to zap_recruitment_cmpg@kuleuven.be by June 30th 2025. Add to
your application the following documents:

1. A short Biosketch (max 2 pages) outlining your experience and future vision and
ambition as an academic in research, education and service to society. This can be
included as a separate document or directly in your email.
2. A Curriculum Vitae including an overview of your education and publications.
3. A research plan outlining the development of 2-3 research lines over the next five
years.
A selection of candidates will be invited for an interview and campus visit - either virtual or
in person -in August. Following this, the CMPG will select a candidate to proceed with the
university’s appointment process.
This starts with a formal pre-application by September 2, followed by submission of the
full application in October 2025. The university interview will take place between
November 11 and December 11. During this period, the candidate will be invited to visit
our facilities, present their research, and meet with CMPG professors and staff.
The final appointment decision will be made in February 2026. Information on the
BOFZAP procedure can be found here and the general call is published here.
Contact
For more information about the procedure or content of the position you can contact the
head of the CMPG, Prof. dr. Rob Jelier via zap_recruitment_cmpg@kuleuven.be .
Senior Scientist, Computational Biology
Quantum-Si
Branford, CT / San Diego, CA
Posted on June 4, 2025 | Posted by Kristin Blacklock
We are seeking a highly motivated and experienced Senior Scientist with expertise in computational biology, protein structural modeling and engineering, 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 protein engineering, machine learning, and structural biology, leveraging state-of-the-art algorithms experimental feedback to develop novel protein scaffolds with tailored binding characteristics.
The ideal candidate will have a deep background in Computational Biology, Bioengineering, Structural Biology, 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 protein modeling software (e.g. AlphaFold, ProteinMPNN). Knowledge of fine-tuning or generating new machine-learning models 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
  • PhD. in Computational Biology, Bioengineering, Structural Biology, or a related computational/scientific field
  • Proven expertise in protein structure prediction and design using cutting-edge modeling software (AlphaFold, ProteinMPNN, RFDiffusion, ESM, Rosetta, etc.)
  • Strong understanding of protein-protein and protein-peptide interactions, as well as hands-on experience conducting in silico analyses to evaluate these interactions
  • Experience developing custom computational methods or ML approaches to guide 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!):
  • Publications showcasing the use of advanced protein design tools (e.g., AlphaFold, RFDiffusion, ProteinMPNN) to develop proteins with targeted functions or novel structural features
  • Experience designing binders against unstructured peptide regions, including terminal epitopes or motifs
  • Experience with ML model development or fine-tuning, particularly for structure-function prediction or generative protein design.
  • Experience integrating experimental feedback loops into computational pipelines to improve design success.
  • 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.
Research Scientist, Amazon Special Projects
Amazon
Posted on May 29, 2025 | Posted by Karla-Luise Herpoldt
DESCRIPTION
We are a team of doers working passionately to apply advanced technology to solve real-world problems. As a Research Scientist at the intersection of machine learning and the life sciences, you will participate in developing exciting products for customers. Our team rewards curiosity while maintaining a laser-focus in bringing products to market. Competitive candidates are responsive, flexible, and able to succeed within an open, collaborative, entrepreneurial, startup-like environment. At both academic and applied research in this product area, you have the opportunity to work together with a diverse and talented team of scientists, engineers, and product managers and collaborate with others teams.

Here at Amazon, we embrace our differences. We are committed to furthering our culture of inclusion. We have ten employee-led affinity groups, reaching 40,000 employees in over 190 chapters globally. We have innovative benefit offerings, and host annual and ongoing learning experiences. Amazon’s culture of inclusion is reinforced within our Leadership Principles, which remind team members to seek diverse perspectives, learn and be curious, and earn trust

Work/life Balance
Our team puts a high value on work-life balance. It isn’t about how many hours you spend at home or at work; it’s about the flow you establish that brings energy to both parts of your life. We believe striking the right balance between your personal and professional life is critical to life-long happiness and fulfillment. We offer flexibility in working hours and encourage you to find your own balance between your work and personal lives

Mentorship & Career Growth
Our team is dedicated to supporting new members. We have a broad mix of experience levels and tenures, and we’re building an environment that celebrates knowledge sharing and mentorship. Our senior members enjoy one-on-one mentoring and thorough, but kind, code reviews. We care about your career growth and strive to assign projects based on what will help each team member develop into a better-rounded engineer and enable them to take on more complex tasks in the future

Key job responsibilities
We are looking for an experienced computational focused candidate with experience predicting, folding, and designing proteins. The candidate can expect to work on a team working collaboratively with software developers, engineers, and like-minded scientists on a fast paced project.

A day in the life
New data has just landed and promoted to our datalake. You load the data and verify it's overall integrity by visualizing variation across target subsets. You realize we may have made progress toward our goals and begin to test the validity of your nominal results. At midday you grab lunch with new coworkers and learn about their fields or weird interests (there are many). You meet with peers in the afternoon to discuss your findings and breakdown the remaining tasks to finalize your group report.

BASIC QUALIFICATIONS
- PhD
- Experience investigating the feasibility of applying scientific principles and concepts to business problems and products
- Experience analyzing both experimental and observational data sets
PREFERRED QUALIFICATIONS
- Knowledge of R, MATLAB, Python or similar scripting language
- Experience with agile development
- 4+ years of quantitative field research experience

Amazon is an equal opportunity employer and does not discriminate on the basis of protected veteran status, disability, or other legally protected status.

Our inclusive culture empowers Amazonians to deliver the best results for our customers. If you have a disability and need a workplace accommodation or adjustment during the application and hiring process, including support for the interview or onboarding process, please visit https://amazon.jobs/content/en/how-we-hire/accommodations for more information. If the country/region you’re applying in isn’t listed, please contact your Recruiting Partner.

Our compensation reflects the cost of labor across several US geographic markets. The base pay for this position ranges from $136,000/year in our lowest geographic market up to $212,800/year in our highest geographic market. Pay is based on a number of factors including market location and may vary depending on job-related knowledge, skills, and experience. Amazon is a total compensation company. Dependent on the position offered, equity, sign-on payments, and other forms of compensation may be provided as part of a total compensation package, in addition to a full range of medical, financial, and/or other benefits. For more information, please visit https://www.aboutamazon.com/workplace/employee-benefits. This position will remain posted until filled. Applicants should apply via our internal or external career site.

Scientist and Lab Operations Coordinator
Madison, Wisconsin
Staff-Full Time
Posted on May 23, 2025 | Posted by Hannah Wayment-Steele
Job Summary:
The Wayment-Steele Lab seeks a Research Scientist to lead experimental operations within our highly interdisciplinary team, integrating both computational "dry" and experimental "wet" lab approaches. Our research aims to achieve a predictive understanding of biomolecular dynamics and the mechanisms underlying biological function. In this role, you will spearhead the lab's wet-lab initiatives, focusing on experimentally testing computational models and developing high-throughput assays.
Responsibilities:
Identifies research problems, designs research methodologies, performs research, and prepares and/or presents results for presentation to professional organizations or for scholarly publications to help advance research.
  • 5% Identifies research problems and develops complex research methodologies and procedures
  • 45% Collects and analyzes complex research data, conducts experiments and interviews, and documents results according to established policies and procedures under general supervision
  • 5% Conducts literature reviews, prepares reports and materials, and disseminates information to appropriate entities
  • 5% Attends and assists with the facilitation of scholarly events and presentations in support of continued professional development and the dissemination of research information
  • 5% Writes or assists in developing grant applications and proposals to secure research funding
  • 25% May supervise the day-to-day activities of a research unit as needed
  • 5% Serves as a unit subject matter expert and liaison to internal and external stakeholders providing advanced level information and representing the interests of a specialized research area
  • 5% Monitors program budget and approves unit expenditures
Institutional Statement on Diversity:
Diversity is a source of strength, creativity, and innovation for UW-Madison. We value the contributions of each person and respect the profound ways their identity, culture, background, experience, status, abilities, and opinion enrich the university community. We commit ourselves to the pursuit of excellence in teaching, research, outreach, and diversity as inextricably linked goals.

The University of Wisconsin-Madison fulfills its public mission by creating a welcoming and inclusive community for people from every background - people who as students, faculty, and staff serve Wisconsin and the world.

For more information on diversity and inclusion on campus, please visit: Diversity and Inclusion

Education:
Preferred
Terminal Degree in Biochemistry, Biophysics, Bioengineering or other related field
Qualifications:
Required:
1) Experience with protein expression and purification for structural biology research
2) Knowledge of molecular biology protocol development
3) Knowledge of lab operations, including maintenance of equipment, inventory management, and day-to-day operations including mentoring students in bench techniques
4) Experience with communicating technical information to a varied audience

Preferred:
1) Experience in preparing large-scale protein libraries
2) Familiarity with data analysis in python or related programming languages

Work Type:
Full Time: 100%

It is anticipated this position requires work be performed in-person, onsite, at a designated campus work location.

Appointment Type, Duration:
Ongoing/Renewable
Salary:
Minimum $70,000 ANNUAL (12 months)
Depending on Qualifications
The minimum salary for this position is $70,000. However, final salary will depend on experience and qualifications. Employees in this position can expect to receive benefits such as generous vacation, holidays, and paid time off; competitive insurances and savings accounts; retirement benefits. Additional benefits information can be found at: or https://www.wisconsin.edu/ohrwd/benefits/download/fasl.pdf
Additional Information:
The successful applicant will be responsible for ensuring eligibility for employment in the United States by the start of the appointment.
How to Apply:
Click on the "Apply Online" button to start the application process. You will be prompted to upload the following documents/Application Materials:

CV (required) - Detail your educational and professional background (3-5 pages)
Cover letter (required) - Refer to your related work experience
References - Finalists will be asked to provide contact information for three (3) references, including your current/most recent supervisor. References will not be contacted without prior notice.

It's important that your cover letter and resume reflect your experience for this position related to the Qualifications section. Your application materials will be used during our evaluation to determine your qualifications as they relate to the job. The most qualified applicants will be invited to participate in the next step of the selection process.

Contact:
Stefanie Lannoye
stefanie.lannoye@wisc.edu
608-261-1029
Relay Access (WTRS): 7-1-1. See RELAY_SERVICE for further information.
Official Title:
Scientist II(RE044)
Department(s):
A07-COL OF AG & LIFE SCIENCES/BIOCHEMISTRY
Employment Class:
Academic Staff-Renewable
Job Number:
315518-AS
The University of Wisconsin-Madison is an Equal Opportunity Employer.
Qualified applicants will receive consideration for employment without regard to, including but not limited to, race, color, religion, sex, sexual orientation, national origin, age, pregnancy, disability, or status as a protected veteran and other bases as defined by federal regulations and UW System policies. We promote excellence by acknowledging skills and expertise from all backgrounds and encourage all qualified individuals to apply. For more information regarding applicant and employee rights and to view federal and state required postings, click here

To request a disability or pregnancy-related accommodation for any step in the hiring process (e.g., application, interview, pre-employment testing, etc.), please contact the Division Disability Representative (DDR) in the division you are applying to. Please make your request as soon as possible to help the university respond most effectively to you.

Employment may require a criminal background check. It may also require you and your references to answer questions regarding sexual violence and sexual harassment.

The University of Wisconsin System will not reveal the identities of applicants who request confidentiality in writing, except that the identity of the successful candidate will be released. See Wis. Stat. sec. 19.36(7).

The Annual Security and Fire Safety Report contains current campus safety and disciplinary policies, crime statistics for the previous 3 calendar years, and on-campus student housing fire safety policies and fire statistics for the previous 3 calendar years. UW-Madison will provide a paper copy upon request; please contact the University of Wisconsin Police Department.

Director of Computational Biology & Bioinformatics
Institute for Protein Innovation
Posted on May 19th, 2025 | Posted by Sergey Ovchinnikov
Purpose
The Director of Computational Biology and Bioinformatics will lead and manage our computational
protein science and bioinformatics team. The successful candidate will be responsible for developing
and implementing computational strategies to support cutting-edge research and development in the
fields of protein science, antibody discovery, proteomics, systems biology, scientific databases, machine
learning, and others. This role will involve collaboration with cross-functional teams to drive the
discovery and development of novel molecules, technologies, and scientific publications. This individual
will be a key member of IPI's scientific leadership team.

Primary Areas of Responsibility
1. Drive the development of new computational tools, pipelines, and platforms to enhance data
analysis capabilities. These include but are not limited to in vitro antibody discovery data, protein
biophysical characterization, proteomic analysis, and others.
2. Collaborate with experimental protein scientists, data scientists, and other stakeholders to design
and interpret experiments, providing data-driven recommendations.
3. Work closely with other departments to ensure computational support for various research and
development projects. This group will initially support IPI's research platforms, internal databases, and
external product catalogs of antigens and antibodies.
4. Ensure the integration and analysis of large datasets to generate actionable biological insights.
5. Lead and mentor a team of computational protein scientists and bioinformaticians, fostering a
collaborative and innovative work environment.
6. Develop and execute strategic plans for the computational protein scientists and bioinformatics
group aligned with the organization’s goals.
7. Manage project timelines, budgets, and resources to ensure successful project delivery.
8. Communicate complex computational analyses and results to both technical and non-technical
audiences.
9. Stay current on the latest advancements in computational protein science and bioinformatics and
incorporate relevant technologies and methodologies.
10. Promote adopting best practices in data management, reproducibility, and collaborative research.

Qualifications
· PhD in related field. Expertise in protein science or biochemistry strongly preferred
· 7+ years of management experience, including leading teams of 5 or more computational staff
· A strong track record in the field demonstrated through publications, patents, and/or products is
required
· Experience applying AI/machine learning tools in a biological setting
· Experience with cloud computing and high-performance computing environments
· Experience mentoring junior staff

Postdoctoral Scholar, In Silico Discovery
Johnson & Johnson Services, Inc.
Cambridge / United States of America
Posted on May 13, 2025 | Posted by Rebecca Alford
This job posting is anticipated to close on May 20 2025. We may however extend this time period, in which case the posting will remain available on www.careers.jnj.com to accept additional applications.
Description
At Johnson & Johnson, we believe health is everything. Our strength in healthcare innovation empowers us to build a world where complex diseases are prevented, treated, and cured, where treatments are smarter and less invasive, and solutions are personal. Through our expertise in Innovative Medicine and MedTech, we are uniquely positioned to innovate across the full spectrum of healthcare solutions today to deliver the breakthroughs of tomorrow, and profoundly impact health for humanity. Learn more at https://www.jnj.com
Job Function:
Career Programs
Job Sub Function:
Post Doc – Drug Discovery & Pre-Clinical/Clinical Development
Job Category:
Career Program
All Job Posting Locations:
Cambridge, Massachusetts, United States of America
Job Description:
Our expertise in Innovative Medicine is informed and inspired by patients, whose insights fuel our science-based advancements. Visionaries like you work on teams that save lives by developing the medicines of tomorrow.
Join us in developing treatments, finding cures, and pioneering the path from lab to life while championing patients every step of the way. Learn more at https://www.jnj.com/innovative-medicine
We are seeking a dedicated Postdoctoral Scholar to join the In Silico Discovery team within the Therapeutics Discovery organization in Cambridge, MA.
The focus of this position is to develop and apply pioneering computational methods to accelerate the discovery of orally bioavailable peptide therapeutics. The successful candidate will be a highly motivated and technically skilled individual with a strong background in computational chemistry or computational biophysics. This postdoctoral position will last 24 months and offers an exciting opportunity to drive innovation in this emerging therapeutic modality.
Key Responsibilities include:
  • Developing novel physics- and ML-based approaches to peptide structure prediction and design
  • Developing novel physics- and ML-based approaches to predicting molecular properties that drive membrane permeability and oral bioavailability
  • Evaluating existing methods to computationally screen peptide candidates for desired properties
  • Working directly with wet-lab scientists across Therapeutics Discovery to design and optimize peptides with specific properties
  • Presenting work in oral or written form at conferences, internal meetings and journals
Required Knowledge, Skills, and Abilities:
  • A Ph.D. in chemistry, biophysics, computational chemistry, chemical engineering, or a related field. Degree must be completed within the past 3 years or to be completed within the upcoming 6 months.
  • Advanced working knowledge of computational molecular modeling including both application of existing tools and development of new tools
  • Advanced fluency in Python and related data-science packages (e.g. Pandas, NumPy, sci-kit learn)
  • Experience using Schrodinger, Rosetta, MOE, GROMACS, NAMD, OpenMM or other molecular simulation software.
  • Proven scientific excellence as evidenced by publications, patents, and presentations.
  • Excellent interpersonal, communication, and presentation skills.
Preferred Knowledge, Skills and Abilities:
  • Experience with high performance computing including either on-premises and cloud computing architectures.
  • Experience with ML packages for protein modeling and design such as AlphaFold, RFDiffusion, ProteinMPNN, etc.
  • Familiarity with cheminformatics toolkits (e.g., rdkit, OpenEye)
Johnson & Johnson is an Equal Opportunity Employer. All qualified applicants will receive consideration for employment without regard to race, color, religion, sex, sexual orientation, gender identity, age, national origin, disability, protected veteran status or other characteristics protected by federal, state or local law. We actively seek qualified candidates who are protected veterans and individuals with disabilities as defined under VEVRAA and Section 503 of the Rehabilitation Act.
Johnson and Johnson is committed to providing an interview process that is inclusive of our applicants’ needs. If you are an individual with a disability and would like to request an accommodation, please email the Employee Health Support Center (ra-employeehealthsup@its.jnj.com) or contact AskGS to be directed to your accommodation resource.
The anticipated base pay range for this position is :
$77,000-$124,200
Additional Description for Pay Transparency:
The Company maintains highly competitive, performance-based compensation programs. Under current guidelines, this position is eligible for an annual performance bonus in accordance with the terms of the applicable plan. The annual performance bonus is a cash bonus intended to provide an incentive to achieve annual targeted results by rewarding for individual and the corporation’s performance over a calendar/performance year. Bonuses are awarded at the Company’s discretion on an individual basis. Employees and/or eligible dependents may be eligible to participate in the following Company sponsored employee benefit programs: medical, dental, vision, life insurance, short- and long-term disability, business accident insurance, and group legal insurance. Employees may be eligible to participate in the Company’s consolidated retirement plan (pension) and savings plan (401(k)). This position is eligible to participate in the Company’s long-term incentive program. Employees are eligible for the following time off benefits: Vacation – up to 120 hours per calendar year Sick time - up to 40 hours per calendar year; for employees who reside in the State of Washington – up to 56 hours per calendar year Holiday pay, including Floating Holidays – up to 13 days per calendar year of Work, Personal and Family Time - up to 40 hours per calendar year Additional information can be found through the link below. http://www.careers.jnj.com/employee-benefits The compensation and benefits information set forth in this posting applies to candidates hired in the United States. Candidates hired outside the United States will be eligible for compensation and benefits in accordance with their local market.
Senior Scientist
Kellogg Lab
Posted on May 11, 2025 | Posted by
Elizabeth H. Kellogg & Alexandre Zanghellini
Be at the forefront of the gene editing revolution and contribute to developing next generation therapies for children. Top-tier compensation and benefits, supportive and collaborative team environment with unique opportunities and exciting potential for career advancement.
Job Description
Overview
As part of the Structural Biology Department at St. Jude Children’s Research Hospital, the Kellogg lab seeks a talented computational biologist who is looking to make high-impact contributions on exciting challenges at the scientific frontier of genome-editing. The Kellogg lab uses cutting edge genetics, cryo-electron microscopy, machine-learning, and protein design to develop novel genome-editing tools. Located on the 6th floor of the new Inspiration4 Advanced Research Center (opened in 2021), the Kellogg lab leads the forefront of research in understanding the biology of CRISPR-associated transposons (Science, 2023, Molecular Cell, 2023, Science, 2023, Nature, 2023, PNAS, 2022, Science, 2021, and more) and is well supported by the NIH, Pew Biomedical Foundation, and the Cystic Fibrosis Foundation to develop novel approaches to engineer programmable transposons for clinical gene replacement therapy. The Kellogg lab is a highly interdisciplinary scientific environment, routinely working with generously supported St. Jude research core facilities: Cryo-EM Center, the Protein Technology Center, the Single-
Molecule Imaging Center, the Center for Advanced Genome Editing, and the Cell & Tissue
Imaging Center. The Kellogg lab is a scientifically enriching environment with regular CRISPR supergroup discussions with Dr. Shengdar Tsai. In addition, the Kellogg lab is an active member of RosettaCommons and the Rosetta community. In this position, the candidate will be exposed to multiple, cutting edge techniques spanning cryo-electron microscopy, computational protein design, machine learning, and advanced genomics in a world class research environment aimed at advancing cures for genetic disorders.
About you
The successful candidate will be an independent learner with strong critical thinking skills and excellent communication skills. We are looking for someone with an outstanding independent track-record and stellar academic background. The ideal candidate is passionate about research and committed to developing tomorrow’s cures for children with devastating genetic disorders.
Our ideal candidate has extensive experience in one of the following (or more): bioinformatic analyses (metagenomic mining is a major plus), reconstructing evolutionary trajectories, protein structure prediction, or computational protein design. Scientists are expected to operate independently by leading new research directions in the Kellogg lab. The candidate will be mentored in manuscript preparation and be given opportunities for career advancement via conference attendance and oral presentation sponsorship.
Responsibilities:
• Develop new research directions under close mentorship of Dr. Kellogg.
• Stay up to date with latest CRISPR and protein engineering literature, conduct regular literature reviews in collaboration with Dr. Kellogg and other Kellogg lab members.
• Collaborate with other Kellogg lab members to design & clone large DNA libraries using state of the art machine learning methods
• Map phylogenetic relationships of CRISPR-associated systems to map functional interactions.
• Develop innovative sequence profile machine-learning based protein design pipelines in collaboration with Dr. Kellogg
• Collaborate with Kellogg lab members to develop novel tools/assays to collectively advance lab research goals.
• Mentor Kellogg lab members in executing internally developed computational analyses
and pipelines.
• Prepare manuscripts and present research at relevant conferences, including but not limited to: CRISPR, genome-engineering, or protein design conferences.
Opportunities for Professional Growth
• The candidate will be given opportunities to participate in interdisciplinary scientific research and be mentored in developing leadership skills.
• The candidate will be given opportunities to develop new skills, including experimental biochemistry and/or structure determination in collaboration with Kellogg lab members.
• The candidate will be given opportunities to attend diverse scientific conferences in the areas of computational protein design (including the Rosetta community), machine learning, genome-editing, and transposon biology.
• The candidate will be given opportunities for oral presentations at local and national
venues as well as opportunities to develop independent research directions.
St Jude Children’s Research Hospital is consistently named as one of Fortune magazine’s “Best
Companies to Work for” and top 10 “Best Places to Work in Academia” by the Scientist Magazine.
St Jude is located in Memphis, Tennessee, the 28th most populous city in America. Memphis is a historic city with an affordable cost of living along with world class dining and strong cultural tradition in music and theater. Memphis enjoys a mild, sunny climate year-round and has some of the largest outdoor green spaces of any big city.
St. Jude Employees receive:
• Competitive compensation packages commensurate with experience.
• Excellent healthcare plans with zero to low health premium costs.
• Generous retirement benefits with contributions from St. Jude
• Onsite health clinic, pharmacy, and exercise facilities.
• Paid parental leave and adoption assistance.
• Immigration Services
• Tuition Reimbursement
The Kellogg lab is committed to building a lab culture that is based on respect, diversity, and inclusion which contributes to a dynamic, innovative, and creative scientific environment that is fundamentally based on empathy and intellectual curiosity. The Kellogg lab is known for their rigor and fast pace, consistently aiming for ambitious goals that greatly expand the boundaries of
human knowledge. The Kellogg lab is proud to be home to ambitious, curious, and fun-loving
scientists of all nationalities and backgrounds.
Minimum Education
Ph.D. in a relevant scientific field is required.
Minimum Experience
• At least one first author publication from a reputable journal.
• Strong candidates from a related field (ancestral sequence reconstruction, genomics, computational protein engineering, computational structure prediction, or CRISPR) are encouraged to apply.
This Position May be Ideal For:
• Ph.D.s with post-degree experience looking to establish an experimental line of inquiry prior to pursuing an independent research position.
• Experienced Computational Biologists looking for a stimulating, collaborative,
and interdisciplinary lab environment committed to creating tomorrow’s genome-editing tools.
To virtually meet Dr. Kellogg, check out The Plunge, a Cryo-EM Podcast she and two
colleagues hosted. Dr. Kellogg was also recently featured on Cryo-Talk to talk about her life & work.
Computational Protein Design Scientist
Center for Protein Design
Posted on May 11, 2025 | Posted by
Elizabeth H. Kellogg & Alexandre Zanghellini
Be at the forefront of AI and protein design revolution (recognized by the 2024 Nobel Prize in
Chemistry) and contribute to developing next generation therapies for children. Top-tier
compensation and benefits, supportive and collaborative team environment with strong
mentoring opportunities and exciting potential for career advancement.
Ideal Candidates
 Are you passionate about innovative research that has the potential to dramatically
improve patients’ lives and change the world?
 Are you excited to push the envelope in what AI-guided protein design can do in
medicine?
 Do you love using and developing innovative AI methodologies to engineer new
proteins?
 Do you want to pursue new frontiers in systems level biological design (e.g. redesigning
metabolic and signaling networks in cells)?
 Are you motivated by a fast-paced collegial environment with a diversity of technical
expertise and a strong emphasis on creative and rigorous science?
 Is open communication one of your strengths? Do you proactively address issues head
on?
If you’ve answered “yes” to all of these, then we’d love to meet with you! But first, here are
more details about the role…
Job Description
Overview
The newly opened Center for Protein Design at St Jude is looking to expand our world-class
protein design team with an accomplished protein designer. As a scientist in the Center for
Protein Design, you will be leading one or several research programs, spearheading
computational design efforts to create proteins with new functions, developing AI methods for
the advancement of your projects, and being directly involved with the experimental
characterization of your designs.
Attributes of successful candidates:
 A desire to lead protein design programs from start to finish with a focus on successful
outcomes.
 Strong attention to details coupled with a deep understanding of (1) protein design
algorithms and (2) protein structure and function.
 A proactive, fast learner who can operate independently and possesses strong
communication skills.
 A leader with a contagious ‘can-do’ attitude.
 Excellent organization and presentation skills coupled to a collaborative attitude.
Opportunities for Professional Growth
 You will have the opportunity to take an active role in leadership within the Center for
Protein Design as it expands and grows.
 As an integral and critical member of the Center for Protein Design at St Jude, you will
also be able to participate in internal meetings and interact with other groups and faculty
at St Jude to advance applications of protein design. You will be working alongside
internationally recognized scientists who are leaders in such disciplines as AI/machine
learning (Dr. Madan Babu), NMR (Dr. Charalampos Kalodimos), cryo-EM/ET (Dr.
Elizabeth Kellogg and Dr. Georgios Skiniotis), single-molecule experiments (Dr. Scott
Blanchard) and more.
 You will also collaborate with the wider community at St Jude (such as the Departments
of Immunology, Host-Microbe Interactions, Pharmacy and Pharmaceutical Sciences, and
Chemical Biology and Therapeutics), which is full of very smart, helpful, and fun
individuals with unique and diverse scientific strengths.
 The candidate will be given opportunities to participate in interdisciplinary scientific
research and be mentored in developing leadership skills.
 You will have opportunities to attend scientific conferences surrounding the fields of
protein and systems design such as the Gordon Research Conferences, RosettaCON and
SynBioBeta. Through extensive links that Dr. Zanghellini has nurtured with industry, you
will also get exposure to the biopharma and venture capital ecosystems.
About the Center for Protein Design
The Center for Protein Design is a new institutional center established in November 2024 and
housed in the Center of Excellence for Data-Driven Discovery within the Structural Biology
department at St Jude. The Center is led by Dr. Alexandre Zanghellini, Executive Fellow at St
Jude. Dr. Zanghellini has 20 years of experience in protein design, including academia with
Nobel Laureate Dr. David Baker, where his seminal contributions to the field of enzyme design
were cited more than 3000 times, and in industry as CEO of Arzeda, a venture-backed protein
design company he co-founded that translates protein design innovations into successful
commercial products.
The Center for Protein Design’s mission is to advance our understanding of protein structure-
function relationships to design proteins and cell therapies that restore hope against catastrophic
pediatric diseases. We use cutting edge deep-learning, biophysics and experimental approaches
to develop new functional proteins for protein and cell therapies, including enzyme therapeutics,
gene editing systems and CAR-T cell engineering. The Center is also pushing the boundary in
new methodology development in computational protein design, leveraging the large amount of
data that is generated by various groups and departments at St Jude.
As an institutional center, the Center for Protein Design collaborates across many departments at
St Jude such as Structural Biology, Immunology, Host-Microbe Interactions, and Pharmacology.
The Center for Protein Design is a highly interdisciplinary environment which marries basic
science with a strong translational component, leveraging St Jude Research Hospital cGMP
manufacturing and clinical expertise.
About St Jude
St Jude Children’s Research Hospital is consistently named as one of Fortune magazine’s “Best
Companies to Work for” and top 10 “Best Places to Work in Academia” by the Scientist
Magazine. St Jude is located in Memphis, Tennessee, the 28 th most populous city in America.
Memphis is a historic city with an affordable cost of living along with world class dining and
strong cultural tradition in music and theater. Memphis enjoys a mild, sunny climate year-round
and has some of the largest outdoor green spaces of any big city.
St. Jude Employees receive:
 St Jude offers a well-defined career ladder with potential for growth and advancement.
Industry-competitive salaries are based on your degree and years of experience.
 Excellent healthcare plans with zero to low health premium costs.
 Generous retirement benefits with contributions from St. Jude.
 Onsite health clinic, pharmacy, and exercise facilities.
 Paid parental leave and adoption assistance.
 Immigration services.
 Tuition reimbursement.
 For a complete description of our benefits for this position, click here.
The Center for Protein Design is committed to building a lab culture that is rooted in respect,
diversity, and inclusion. This foundation promotes a dynamic, innovative, and impactful
scientific environment driven by empathy and intellectual curiosity.
Minimum Requirements:
 PhD in biochemistry, biophysics, bioengineering, structural biology or computer science
with a strong emphasis in computational protein design (Rosetta structure-based design)
and recent generative AI methods (AlphaFold, RoseTTAFold, ESM-3, LLMs etc).
 A proven track record of success in protein design projects, from concept to experimental
characterization.
Desired qualifications:
 An outstanding academic and professional track record of achievement.
 Demonstrated experience in not only using but also developing computational or AI
protein design algorithms is a strong plus.
 Practical experience in experimental biochemistry, molecular biology, structural biology
or biophysics is a plus.
 Experience or interest in biotechnology industry.
 Independence, critical thinking, and experience with mentoring and collaborative
interdisciplinary work is strongly valued.
This Position May be Suitable For:
 Recent graduates or postdocs from leading protein design academic labs.
 Computational scientists with a desire to focus on computational protein design.
 Scientists from the biotechnology or pharmaceutical industry that wish to marry
academic research with translational opportunities in translational biologics drug
development.
To be considered, please contact alexandre.zanghellini@stjude.org. Applications will be
considered until the position is filled.
Experimental Protein Scientist / Biochemist
Center for Protein Design
Posted on May 11, 2025 | Posted by
Elizabeth H. Kellogg & Alexandre Zanghellini
Be at the forefront of AI and protein design revolution (recognized by the 2024 Nobel Prize in
Chemistry) and contribute to developing next generation therapies for children. Top-tier
compensation and benefits, supportive and collaborative team environment with strong
mentoring opportunities and exciting potential for career advancement.
Ideal Candidates
 Are you passionate about innovative research that has the potential to dramatically
improve patients’ lives and change the world?
 Are you excited to push the envelope in what AI-guided protein design can do in
medicine?
 Do you love developing and conducting challenging protein functional assays, striving
for efficiency and automation?
 Do you want to pursue new frontiers in systems level biological design (e.g. redesigning
metabolic and signaling networks in cells)?
 Are you motivated by a fast-paced collegial environment with a diversity of technical
expertise and a strong emphasis on creative and rigorous science?
 Is open communication one of your strengths? Do you proactively address issues head
on?
If you’ve answered “yes” to all of these, then we’d love to meet with you! But first, here are
more details about the role…
Job Description
Overview
The newly opened Center for Protein Design at St Jude is looking to expand our world-class
team with an accomplished scientist. As a biochemist in the Center for Protein Design, you will
be leading the experimental side of several protein design research programs, including devising
and executing accurate and high-throughput assays to validate proteins with new functions in-
vitro and in-vivo. Working hand-in-hand with our computational protein design team, you will
play a critical scientific leadership role in protein design projects, from the conceptual to the
validation and translational phases. As the Center for Protein Design continues to grow, you will
also have the opportunity to participate in the development of a state-of-the-art roboticized
platform for the expression and characterization of our designer proteins at high-throughput.
Attributes of successful candidates:
 A desire to actively participate in computational protein design research programs from
start to finish with a focus on successful outcomes.
 Exceptional biochemical skills with a strong attention to details and perseverance to
obtain solid experimental results.
 A proactive, fast learner who can operate independently and possesses strong
communication skills.
 A leader (vs. follower) with a contagious ‘can-do’ attitude.
 Excellent organization and presentation skills coupled to a collaborative attitude.
Opportunities for Professional Growth
 You will have the opportunity to take an active role in leadership within the Center for
Protein Design as it expands and grows.
 As an integral and critical member of the Center for Protein Design at St Jude, you will
also be able to participate in internal meetings and interact with other groups and faculty
at St Jude to advance applications of protein design. You will be working alongside
internationally recognized scientists who are leaders in such disciplines as AI/machine
learning (Dr. Madan Babu), NMR (Dr. Charalampos Kalodimos), cryo-EM/ET (Dr.
Elizabeth Kellogg and Dr. Georgios Skiniotis), single-molecule experiments (Dr. Scott
Blanchard) and more.
 You will also collaborate with the wider community at St Jude (such as the Departments
of Immunology, Host-Microbe Interactions, Pharmacy and Pharmaceutical Sciences, and
Chemical Biology and Therapeutics), which is full of very smart, helpful, and fun
individuals with unique and diverse scientific strengths.
 The candidate will be given opportunities to participate in interdisciplinary scientific
research and be mentored in developing leadership skills.
 You will have opportunities to attend scientific conferences surrounding the fields of
protein and systems design such as the Gordon Research Conferences, RosettaCON and
SynBioBeta. Through extensive links that Dr. Zanghellini has nurtured with industry, you
will also get exposure to the biopharma and venture capital ecosystems.
About the Center for Protein Design
The Center for Protein Design is a new institutional center established in November 2024 and
housed in the Center of Excellence for Data-Driven Discovery within the Structural Biology
department at St Jude. The Center is led by Dr. Alexandre Zanghellini, Executive Fellow at St
Jude. Dr. Zanghellini has 20 years of experience in protein design, including academia with
Nobel Laureate Dr. David Baker, where his seminal contributions to the field of enzyme design
were cited more than 3000 times, and in industry as CEO of Arzeda, a venture-backed protein
design company he co-founded that translates protein design innovations into successful
commercial products.
The Center for Protein Design’s mission is to advance our understanding of protein structure-
function relationships to design proteins and cell therapies that restore hope against catastrophic
pediatric diseases. We use cutting edge deep-learning, biophysics and experimental approaches
to develop new functional proteins for protein and cell therapies, including enzyme therapeutics,
gene editing systems and CAR-T cell engineering. The Center is also pushing the boundary in
new methodology development in computational protein design, leveraging the large amount of
data that is generated by various groups and departments at St Jude.
As an institutional center, the Center for Protein Design collaborates across many departments at
St Jude such as Structural Biology, Immunology, Host-Microbe Interactions, and Pharmacology.
The Center for Protein Design is a highly interdisciplinary environment which marries basic
science with a strong translational component, leveraging St Jude Research Hospital cGMP
manufacturing and clinical expertise.
About St Jude
St Jude Children’s Research Hospital is consistently named as one of Fortune magazine’s “Best
Companies to Work for” and top 10 “Best Places to Work in Academia” by the Scientist
Magazine. St Jude is located in Memphis, Tennessee, the 28 th most populous city in America.
Memphis is a historic city with an affordable cost of living along with world class dining and
strong cultural tradition in music and theater. Memphis enjoys a mild, sunny climate year-round
and has some of the largest outdoor green spaces of any big city.
St. Jude Employees receive:
 St Jude offers a well-defined career ladder with potential for growth and advancement.
Industry-competitive salaries are based on your degree and years of experience.
 Excellent healthcare plans with zero to low health premium costs.
 Generous retirement benefits with contributions from St. Jude.
 Onsite health clinic, pharmacy, and exercise facilities.
 Paid parental leave and adoption assistance.
 Immigration services.
 Tuition reimbursement.
 For a complete description of our benefits for this position, click here.
The Center for Protein Design is committed to building a lab culture that is rooted in respect,
diversity, and inclusion. This foundation promotes a dynamic, innovative, and impactful
scientific environment driven by empathy and intellectual curiosity.
Minimum Requirements:
 PhD level in biochemistry or protein science.
 A proven track record in DNA cloning, protein expression and purification, assay
development (LC/GC-MS, HPLC, Spectrophotometry).
Desired qualifications:
 Previous experience in protein design & engineering is strongly favored.
 Experience with yeast, phage or ribosome display or development of high-throughput
screens and selection systems in bacterial or mammalian cells is a strong plus.
 An outstanding academic and professional track record of achievements.
 Biotechnology industry experience, especially with the development of automation and
data management systems is a strong plus.
 Independence, critical thinking, and experience with mentoring and collaborative
interdisciplinary work is also strongly valued.
This Position May be Suitable For:
 Recent graduates or postdocs from leading biochemistry, enzymology and protein science
academic labs.
 Scientists from the biotechnology or pharmaceutical industry that wish to marry
academic research with translational opportunities in biologics drug development.
To be considered, please contact alexandre.zanghellini@stjude.org. Applications will be
considered until the position is filled.
Lab Manager
Center for Protein Design
Posted on May 11, 2025 | Posted by
Elizabeth H. Kellogg & Alexandre Zanghellini
Be at the forefront of AI and protein design revolution (recognized by the 2024 Nobel Prize in Chemistry) and
contribute to developing next generation therapies for children. Top-tier compensation and benefits, supportive
and collaborative team environment with strong mentoring opportunities and exciting potential for career
advancement.
Ideal Candidates
 Are you passionate about innovative research that has the potential to dramatically improve patients’
lives and change the world?
 Are you excited to push the envelope in what AI-guided protein design can do in medicine?
 Are you naturally organized and structured? Do you enjoy creating processes that improve efficiency
and productivity?
 Are you motivated by “Team”? Is your success your colleagues success?
 Is open communication one of your strengths? Do you proactively address issues head on?
If you’ve answered “yes” to all of these, then we’d love to meet with you! But first, here a are more details
about the role…
Job Description
Overview
The Center for Protein Design at St Jude seeks a proactive and organized Lab Manager with strong
communication skills to build and maintain lab operations, ensuring it runs smoothly while fostering an
inclusive, supportive, and welcoming environment for all Center members.
Attributes of successful candidates:
 A proactive, fast learner who can operate independently and possesses strong communication skills.
 A leader with a contagious ‘can-do’ attitude.
 Excellent organization skills and a collaborative attitude.
 Strong biochemistry technique with experience performing recombinant protein production, low and
high-throughput enzyme assays, protein-protein binding measurements, and standard molecular cloning
procedures (or equivalent).
o Experience with cell-free expression, deep sequencing (NGS), FACS, liquid handling (Biomek
or equivalent) and lab automation are a plus.
Responsibilities:
Scientific Operations (70%):
 Work to build up lab operations for the Center for Protein Design through assisting with equipment
purchase, installation and maintenance, and hiring processes related to lab operations.
 Develop and establish strategies and processes to streamline lab organization, inventory, and ordering
while also developing and maintaining standard lab operation protocols and procedures.
 Maintain and operate the Center for Protein Design lab equipment
 The lab manager may be asked to participate in mentoring technicians and junior scientists.
Scientific Research (30%):
 Lead new research directions in in vitro and in vivo assays for protein design.
 Record experimental observations, present results, and collaborate with multiple computational and
experimental scientists in the Center for Protein Design.
Opportunities for Professional Growth
 You will have the opportunity to help build the lab for the Center of Protein Design, as well as develop
and optimize lab workflows and define exacting lab standards.
 As an integral and critical member of the Center for Protein Design at St Jude, you will also be able to
participate in internal meetings and interact with other groups and faculty at St Jude to advance
applications of protein design. You will be working alongside internationally recognized scientists who
are leaders in such disciplines as AI/machine learning (Dr. Madan Babu), NMR (Dr. Charalampos
Kalodimos), cryo-EM/ET (Dr. Elizabeth Kellogg and Dr. Georgios Skiniotis), single-molecule experiments
(Dr. Scott Blanchard) and more.
 You will also collaborate with the wider community at St Jude (such as the Departments of
Immunology, Host-Microbe Interactions, Pharmacy and Pharmaceutical Sciences, and Chemical
Biology and Therapeutics), which is full of very smart, helpful, and fun individuals with unique and
diverse scientific strengths.
 The candidate will be given opportunities to develop new skills, including but not limited to machine
learning, AI and translational aspects of protein design.
 The candidate will be given opportunities to participate in interdisciplinary scientific research and be
mentored in developing leadership skills.
 You will have opportunities to attend scientific conferences surrounding the fields of protein design and
biochemistry technique.
About the Center for Protein Design
The Center for Protein Design is a new institutional center established in November 2024 and housed in the
Center of Excellence for Data-Driven Discovery within the Structural Biology department at St Jude. The
Center is led by Dr. Alexandre Zanghellini, Executive Fellow at St Jude. Dr. Zanghellini has 20 years of
experience in protein design, including academia with Nobel Laureate Dr. David Baker, where his seminal
contributions to the field of enzyme design were cited more than 3000 times, and in industry as CEO of Arzeda,
a venture-backed protein design company he co-founded that translates protein design innovations into
successful commercial products.
The Center for Protein Design’s mission is to advance our understanding of protein structure-function
relationships to design proteins and cell therapies that restore hope against catastrophic pediatric diseases. We
use cutting edge deep-learning, biophysics and experimental approaches to develop new functional proteins for
protein and cell therapies, including enzyme therapeutics, gene editing systems and CAR-T cell engineering.
The Center is also pushing the boundary in new methodology development in computational protein design,
leveraging the large amount of data that is generated by various groups and departments at St Jude.
As an institutional center, the Center for Protein Design collaborates across many departments at St Jude such
as Structural Biology, Immunology, Host-Microbe Interactions, and Pharmacology. The Center for Protein
Design is a highly interdisciplinary environment which marries basic science with a strong translational
component, leveraging St Jude Research Hospital cGMP manufacturing and clinical expertise.
About St Jude
St Jude Children’s Research Hospital is consistently named as one of Fortune magazine’s “Best Companies to
Work for” and top 10 “Best Places to Work in Academia” by the Scientist Magazine. St Jude is located in
Memphis, Tennessee, the 28 th most populous city in America. Memphis is a historic city with an affordable cost
of living along with world class dining and strong cultural tradition in music and theater. Memphis enjoys a
mild, sunny climate year-round and has some of the largest outdoor green spaces of any big city.
St. Jude Employees receive:
 St Jude offers a well-defined career ladder with potential for growth and advancement. Industry-
competitive salaries are based on your degree and years of experience.
 Excellent healthcare plans with zero to low health premium costs.
 Generous retirement benefits with contributions from St. Jude.
 Onsite health clinic, pharmacy, and exercise facilities.
 Paid parental leave and adoption assistance.
 Immigration services.
 Tuition reimbursement.
 For a complete description of our benefits for this position, click here.
The Center for Protein Design is committed to building a lab culture that is rooted in respect, diversity, and
inclusion. This foundation promotes a dynamic, innovative, and impactful scientific environment driven by
empathy and intellectual curiosity.
Minimum Requirements:
 Bachelor’s degree in biochemistry, protein engineering, synthetic biology, molecular biology,
bioengineering, or related discipline.
 3 years of relevant professional experience in biochemistry, protein engineering, high-throughput
methods, or related disciplines.
Desired qualifications:
 Ph.D. degree in biochemistry, molecular biology or related discipline with experience working in a
protein engineering environment.
 Experience in biotechnology industry and with lab automation a strong plus.
 An outstanding academic and professional track record of achievement.
 Experience with managing and mentoring wet lab-oriented researchers.
This Position May be Suitable For:
 Graduates with strong biochemistry research experience and leadership qualities looking for growth
opportunities.
 Experienced protein engineers or synthetic biologists passionate about lab operations.
 Protein engineering or synthetic biology professionals interested in switching from industry to an
academic environment focused on curiosity driven science and interdisciplinary research.
To be considered, please contact alexandre.zanghellini@stjude.org. Applications will be considered until
position is filled.
Postdoctoral Fellow – Protein design applied to genome-editing
Kellogg lab
Posted on May 11, 2025 | Posted by
Elizabeth H. Kellogg & Alexandre Zanghellini
Be at the forefront of AI and protein design revolution (recognized by the 2024 Nobel Prize in Chemistry) and
contribute to developing next generation genome-editing therapies for children. Top-tier compensation and
benefits, supportive and collaborative team environment with strong mentoring opportunities and exciting
potential for career advancement.
Ideal Candidates
• Are you passionate about innovative research that has the potential to dramatically improve patients’
lives and change the world?
• Are you excited to push the envelope in what AI-guided protein design can do in medicine?
• Do you love learning and developing innovative AI methodologies to engineer new proteins
• Are you motivated by a fast-paced collegial environment with a diversity of technical expertise and a
strong emphasis on creative and rigorous science?
• Is open communication one of your strengths? Do you proactively address issues head on?
If you’ve answered “yes” to all of these, then we’d love to meet with you! But first, here a are more details
about the role...
Job Description
Overview
The Kellogg lab is looking to hire multiple postdoctoral fellows in the area of computational protein design to
expand their genome-editing research portfolio. We are looking for expertise in machine-learning method
development or application to relevant protein design problems. Examples include diffusion models, large
language models, or graph neural networks. Candidates should have a strong background in
software/computation, lab bench experience is viewed as a plus.
Attributes of successful candidates:
• A desire to lead protein design programs from start to finish with a focus on successful outcomes
• Strong attention to details coupled with a deep understanding of (1) protein design algorithms and (2)
protein structure and function
• A proactive, fast learner who can operate independently and possesses strong communication skills.
• A leader with a contagious ‘can-do’ attitude.
• Excellent organization and presentation skills coupled to a collaborative attitude.
Opportunities for Professional Growth
• You will have the opportunity to take an active role in leadership within the Kellogg lab as we grow
further.
• As an integral and critical member of the Kellogg lab at St Jude, you will also be able to participate in
internal meetings and interact with other groups and faculty at St Jude to advance applications of protein
design. You will be working alongside with internationally recognized scientists who are leaders in such
disciplines as AI/machine learning, protein engineering, cryo-EM/ET, NMR, single-molecule
experiments and more.
• You will also collaborate with the wider community at St Jude, which is full of very smart, helpful, and
fun individuals with unique and diverse scientific strengths.
• The candidate will be given opportunities to participate in interdisciplinary scientific research and be
mentored in developing leadership skills.
• You will have opportunities to attend scientific conferences surrounding the fields of protein and
systems design and get exposure to the biopharma industry.
About the Kellogg lab
The Kellogg lab uses cutting edge structural techniques, biochemistry, genetics, and protein design to develop
novel genome-editing tools. By addressing key bottlenecks in current research, the Kellogg lab is a leader in the
field (Science, 2023, Molecular Cell, 2023, Science, 2023, Nature, 2023, PNAS, 2022, Science, 2021, and more),
and has generous support via: the NIH, Pew Biomedical Foundation, and the Cystic Fibrosis Foundation to
develop novel approaches to engineer programmable transposons for clinical gene replacement therapy.
The Kellogg lab is a highly interdisciplinary scientific environment, routinely working with the Cryo-EM Center,
the Protein Technology Center, the Single-Molecule Imaging Center, the Center for Advanced Genome Editing,
and the Cell & Tissue Imaging Center. It is a scientifically enriching environment with regular CRISPR
supergroup discussions (with Dr. Shengdar Tsai) and Cryo-EM supergroup meetings (with Dr. Mario Halic, Dr.
Ji Sun, and Dr. Chia-Hsueh Lee along with other Structural Biology faculty).
To virtually meet Dr. Kellogg, check out The Plunge, a Cryo-EM Podcast she and two colleagues hosted.
Dr. Kellogg was also recently featured on Cryo-Talk to talk about her life & work.
About St Jude
St Jude Children’s Research Hospital is consistently named as one of Fortune magazine’s “Best Companies to
Work for” and top 10 “Best Places to Work in Academia” by the Scientist Magazine. St Jude is located in
Memphis, Tennessee, the 28th most populous city in America. Memphis is a historic city with an affordable cost
of living along with world class dining and strong cultural tradition in music and theater. Memphis enjoys a mild,
sunny climate year-round and has some of the largest outdoor green spaces of any big city.
St. Jude Employees receive:
• St Jude offers a well-defined career ladder with potential for growth and advancement. Industry-
competitive salaries are based on your degree and years of experience.
• Excellent healthcare plans with zero to low health premium costs.
• Generous retirement benefits with contributions from St. Jude.
• Onsite health clinic, pharmacy, and exercise facilities.
• Paid parental leave and adoption assistance.
• Immigration services.
• Tuition reimbursement.
• For a complete description of our benefits for this position, click here.
The Kellogg lab is committed to building a lab culture that is rooted in respect, diversity, and inclusion. This
foundation promotes a dynamic, innovative, and impactful scientific environment driven by empathy and
intellectual curiosity.
Minimum Requirements:
• PhD level in protein design & engineering with a strong emphasis in computational (Rosetta structure
based design) and recent generative AI methods (AlphaFold, ROSETTAFold, ESM-3, LLMs etc) OR
bioinformatics.
• A proven track record of success in protein design projects, from concept to experimental characterization.
Desired qualifications:
• Ph.D. degree in biochemistry, biophysics, bioengineering, structural biology or computer science with a
strong emphasis on computational and AI methods and/or bioinformatics.
• An outstanding academic and professional track record of achievement.
• Demonstrated experience in not only using but developing computational or AI protein design algorithms
a strong plus
• Practical experience in experimental biochemistry, molecular biology, structural biology or biophysics a
plus.
• Experience or interest in biotechnology industry desired.
• Independence, critical thinking, and experience with mentoring and collaborative interdisciplinary work
is strongly valued.
This Position May be Suitable For:
• Recent graduates or postdocs from leading protein design academic labs
• Computational scientists with a desire to focus on computational protein design
• Scientists from the biotechnology industry that wish to marry academic research with translational
opportunities in clinical genome-editing
To be considered, please email: Elizabeth.Kellogg@stjude.org with your C.V. and a brief statement describing
research areas that you’d like to pursue as a postdoctoral fellow.
Computational Biochemist
Menten AI
Remote
Posted on March 20, 2025 | Posted by Pat Finneran

About the job

Job Description
Menten AI is growing and seeks a full-time computational biochemist to develop new applications and tools. The ideal candidate will be responsible for identifying innovative solutions to complex problems within the cyclic peptide design and optimization space. We are expecting a researcher capable of working alongside the rest of the platform development team as we further advance our computational platform. We seek a researcher willing to acquire new skills and actively participate in our decision-making process as we scale and enhance our platform. We prioritize a team player who can embrace and contribute to our positive culture of mutual support and growth.
Location: Remote
Core Responsibilities
  • Develop new computational methods to accelerate the design and optimization of cyclic peptide therapeutics.
  • Work alongside machine learning developers or independently contribute to machine learning projects.
  • Analyze data and suggest directions for platform advancement based on scientific insights and platform performance.
  • Implement existing and novel methods into Menten AI’s computational platform for utilization at production scale.
  • Contribute to the maintenance of existing areas of the platform to ensure resilience, scalability, and scientific accuracy.
  • Report to the team on your progress and incorporate feedback from others, including application scientists at Menten AI.
  • Be a team player by identifying areas for improvement, aiming to enhance scientific results and computational efficiency to solve complex problems.
Requirements
  • Ph.D. in life sciences or computational disciplines.
  • Experience with developing in silico methodologies for optimization of peptides, biologics, or small molecules.
  • Proficiency in developing protocols with at least one of the following: Rosetta, PyRosetta, OpenMM, RDKit, GROMACS, AMBER, GAMESS
  • Ability to program in Python and familiarity with common packages such as BioPython, Pandas, NumPy, SciPy, and sci-kit-learn.
  • Skilled in collaborative research environments, contributing to shared repositories and adhering to best practices, including the use of git.
  • Willingness and interest to pick up new skills to solve complex problems.
Preferred
  • Having trained new AI models for predicting properties or generation of peptides, biologics, or small molecules.
  • Experience in the Biotechnology Industry
  • Previous experience in method development for cyclic peptide docking, scoring, or design.
  • Familiarity with Linux, SQL, and cloud computing (AWS, Google Cloud, or Azure).
  • Experience developing C++ code – Particularly C++ development in Rosetta is highly valued.
  • Experience in free energy calculations from molecular dynamics simulations or other QM/MM approaches.
Protein Modeling and Engineering Scientist
Draper
Posted on April 10, 2025 | Posted by Ting Pang

Draper is seeking a highly motivated and skilled Protein Modeling and Engineering Scientist to join a team developing cutting-edge biotechnology solutions for our Synthetic Biology R&D program area, which includes a new and expanded 13,000 square foot BSL-2 laboratory in our Kendall Square location.

The ideal candidate will be fluent in computational protein modeling/design strategies, with prior experience in protein modeling, structure prediction, and wet-lab characterization. This technical position requires computational work as well as collaboration with multidisciplinary teams to analyze data, presentation of findings, and brainstorming of new ideas.

The position also requires teamwork, tenacity, and attention to detail. We offer an atmosphere that fosters innovation, a supportive team environment, intellectual freedom and creativity, and an emphasis on career development.Job Description:

  • Demonstrated track record in computational protein modeling with wet-lab validation
  • 2+ years of experience using Rosetta, AlphaFold in protein modeling and validation
  • Strong understanding of protein biochemistry or biophysics related to protein structure/function
  • Fluency in one or more programming languages (Python preferred)
  • Strong leadership skills with experience in managing and mentoring scientific teams
  • Excellent communication, presentation, and organizational skills
  • Ability to thrive in a fast-paced, innovative, and collaborative environment
  • Interest in writing proposals/grants and participating in the formation of new programs to solve the nation’s most challenging problems
  • Strong Research experience in Bioinformatics, Computational Biology, Biochemistry, Biophysics, or a related Biological science field.
  • Preferred: 
    • Experience with development and application of AI/ML methods and models for protein structure analysis and modeling
    • Experience with cloud computing (i.e. AWS) and software
    • Expertise with experimental techniques in protein engineering and high-throughput analysis
    • Demonstrated ability to communicate ideas in proposal/grant formats
Applicants selected for this position will be required to obtain and maintain a U.S. Security Clearance.
Max Planck Research Group Leader (W2) in Molecular Design
Max Planck Institute for Polymer Research
Posted on April 4, 2025 | Posted by Alena Khmelinskaia

The Max Planck Institute for Polymer Research (MPIP) in Mainz invites applications for Max Planck Research Group Leaders (W2 Federal Civil Service Remuneration Act – Bundesbesoldungsgesetz) in Molecular Design.
Your profile
We are looking for exceptional early-career scientists conducting computational research with a proven record of accomplishment. The primary focus of this call is on candidates proposing research on biomolecular design by generative modeling. Prior achievements in developing new methods will be highly regarded.
We would particularly encourage proposals in the following research topics:
  • New Machine Learning-based approaches for de novo design of (bio)molecules
  • Applications of generative models to biological or materials science problems
Our offer
Max Planck Research Group Leaders at the MPIP receive a core support package with funds for personnel and consumables, which can be expanded by attracting external third-party funding. Access to the excellent high-performance computing infrastructure of the Max Planck Society, and, if desired, MPIP’s wet-lab infrastructure will be provided. Successful candidates will develop an independent research program in an interactive and cross-disciplinary environment. The MPIP also provides access to a rich collaborative network within the Max Planck Society and close links to our partner university, the Johannes Gutenberg University Mainz.
The successful candidate will be appointed for six years. Depending on the progress of the work and taking into account the financial possibilities and those under labour legislation, the Max Planck Research Group can be extended at maximum by three years on an individual basis according to scientific criteria and after a positive evaluation in each case. Remuneration will be paid on the basis of remuneration group W2 of the Federal Civil Service Remuneration Act (Bundesbesoldungsgesetz).
Your application
Applications should include:
  • a cover letter explaining your motivation to apply for this position
  • a Curriculum Vitae including publication list
  • a statement of scientific achievements (~500 words)
  • a two-page summary of your future research plans (~1000 words)
  • up to three of your most important papers
  • names and contact details of 3 academic references
Applications and inquiries should be sent to Prof. Dr. Frauke Gräter (fgraeter@mpip-mainz.mpg.de), scientific member and director at the Max Planck Institute for Polymer Research by May 11, 2025. The appointment can commence as early as October 1, 2025. Please refer to our websites for further information about MPIP.
  • The Max Planck Society strives for gender and diversity equality. We welcome applications from all backgrounds.
  • The Max Planck Society wishes to increase the number of women in those areas where they are underrepresented. Women are therefore explicitly encouraged to apply.
  • The Max Planck Society is committed to increasing the number of individuals with disabilities in its workforce and therefore encourages applications from such qualified individuals.
Senior Scientist GenAI/ML Protein Design
Merck
USA - Massachusetts - Cambridge (320 Bent Street)
Posted on March 31, 2025 | Posted by Tom Linsky
Job Description
Our Company's Discovery Biologics Disruptive Technologies group is seeking an exceptional generative AI protein engineer to drive the advancement and application of structure-based de novo design and optimization methods to support our biotherapeutic portfolio. In addition to planning and executing experiments to improve and evaluate technical capabilities, the individual is expected to partner closely with cross-functional discovery programs to turn great ideas into valuable medicines that help patients. The role is based out of our Cambridge, MA facility.
We are on a quest for cures and are committed to be the world’s premier, most research-intensive biopharmaceutical company. Our teams combine leading drug discovery capabilities and world-class R&D with the purpose of turning breakthrough science into life-changing medicines.
We recognize that the diversity in our team is our strength and are committed to creating an inclusive environment for all employees. Successful candidates must demonstrate inclusive behaviors in working with a diverse group of scientists to drive our core mission.
In this role, a successful candidate will partner with computational and wet lab researchers to design experiments, identify and develop technologies, and create impactful medicines.
Key Responsibilities
  • Apply generative AI and machine learning-based protein design and engineering technologies to invent novel biologic therapeutics; including de novo design and structure-based optimization.
  • Foster a high-performance culture of collaboration, engagement, self-accountability and inclusion.
  • Effectively partner across multidisciplinary interfaces to achieve organizational objectives.
  • Actively develop talent, strategically maximizing diversity to strengthen the team.
  • Support external partnerships and collaboration opportunities.
  • Stay abreast of external advancements in the relevant scientific fields.
  • Promote the external reputation of our group.
Qualifications & Experience
  • PhD in Biochemistry, Computational Biology, Protein Engineering, Physics, or related field and minimum of 0-3 years of industry experience, or an MS and a minimum of 4 years industry experience, or B.S. and a minimum of 7 years industry experience.
  • Demonstrated success in applying GenAI/ML-based protein design methods.
  • Proven industry track record of success working with cross-functional teams.
  • Commitment to scientific excellence and rigor.
  • Excellent communication and collaboration skills.
  • Champion for diverse and inclusive culture.
  • Strong external reputation with high-impact publications, presentations, and scientific community engagement.
  • Passion for sharing knowledge and helping colleagues develop.
Required skills:
  • Experience applying generative AI methods for protein design and engineering, including de novo design and lead optimization.
  • Deep understanding of protein structure and molecular biophysics.
  • Mastery of protein structural modeling and design tools (e.g. AlphaFold, Rosetta, RFDiffusion, ProteinMPNN, or similar)
  • Strong skills in data analysis and visualization and making data-driven decisions.
  • Comprehensive scientific knowledge across workflows and domains integral to the discovery of protein therapeutics
Preferred skills
  • Experience evaluating and combining generative AI models and applying machine-learning-based methods to solve complex problems in biologics discovery and development.
  • Project leadership experience in discovery of protein therapeutics or technology development.
  • Experience in managing external collaborations.
  • Hands-on experience with NGS data.
  • Experience deploying scalable computational workflows.
#EligibleforERP
Current Employees apply HERE
Current Contingent Workers apply HERE
US and Puerto Rico Residents Only:
Our company is committed to inclusion, ensuring that candidates can engage in a hiring process that exhibits their true capabilities. Please click here if you need an accommodation during the application or hiring process.
We are an Equal Opportunity Employer, committed to fostering an inclusive and diverse workplace.  All qualified applicants will receive consideration for employment without regard to race, color, age, religion, sex, sexual orientation, gender identity, national origin, protected veteran status, or disability status, or other applicable legally protected characteristics.  For more information about personal rights under the U.S. Equal Opportunity Employment laws, visit:
We are proud to be a company that embraces the value of bringing diverse, talented, and committed people together. The fastest way to breakthrough innovation is when diverse ideas come together in an inclusive environment. We encourage our colleagues to respectfully challenge one another’s thinking and approach problems collectively.
U.S. Hybrid Work Model
Effective September 5, 2023, employees in office-based positions in the U.S. will be working a Hybrid work consisting of three total days on-site per week, Monday - Thursday, although the specific days may vary by site or organization, with Friday designated as a remote-working day, unless business critical tasks require an on-site presence.This Hybrid work model does not apply to, and daily in-person attendance is required for, field-based positions; facility-based, manufacturing-based, or research-based positions where the work to be performed is located at a Company site; positions covered by a collective-bargaining agreement (unless the agreement provides for hybrid work); or any other position for which the Company has determined the job requirements cannot be reasonably met working remotely. Please note, this Hybrid work model guidance also does not apply to roles that have been designated as “remote”.
San Francisco Residents Only: We will consider qualified applicants with arrest and conviction records for employment in compliance with the San Francisco Fair Chance Ordinance
Los Angeles Residents Only: We will consider for employment all qualified applicants, including those with criminal histories, in a manner consistent with the requirements of applicable state and local laws, including the City of Los Angeles’ Fair Chance Initiative for Hiring Ordinance
Search Firm Representatives Please Read Carefully 
Merck & Co., Inc., Rahway, NJ, USA, also known as Merck Sharp & Dohme LLC, Rahway, NJ, USA, does not accept unsolicited assistance from search firms for employment opportunities. All CVs / resumes submitted by search firms to any employee at our company without a valid written search agreement in place for this position will be deemed the sole property of our company.  No fee will be paid in the event a candidate is hired by our company as a result of an agency referral where no pre-existing agreement is in place. Where agency agreements are in place, introductions are position specific. Please, no phone calls or emails.
Employee Status:
Regular
Relocation:
Domestic
VISA Sponsorship:
Yes
Travel Requirements:
No Travel Required
Flexible Work Arrangements:
Not Applicable
Shift:
Not Indicated
Valid Driving License:
No
Hazardous Material(s):
n/a
Required Skills:
Data Engineering, Design Applications, Information Security, Machine Learning, Software Development, Software Development Life Cycle (SDLC), System Designs, Systems Integration, Testing
Preferred Skills:
Job Posting End Date:
04/3/2025
*A job posting is effective until 11:59:59PM on the day BEFORE the listed job posting end date. Please ensure you apply to a job posting no later than the day BEFORE the job posting end date.
Associate Principal Scientist, genAI/ML Protein Engineer
Merck
USA - Massachusetts - Cambridge (320 Bent Street)
Posted on March 31, 2025 | Posted by Tom Linsky
Job Description
Our company's Discovery Biologics Disruptive Technologies is seeking an exceptional generative AI protein engineer to drive the advancement and application of de novo design and therapeutic optimization technologies in support of our biotherapeutic portfolio. In addition to leading projects to improve technical capabilities, the individual is expected to partner closely with cross-functional discovery programs to turn great ideas into valuable medicines that help patients. The role is based out of our Cambridge, MA facility.
We are on a quest for cures and are committed to be the world’s premier, most research-intensive biopharmaceutical company. Our teams combine leading drug discovery capabilities and world-class R&D with the purpose of turning breakthrough science into life-changing medicines.
We recognize that the diversity in our team is our strength and are committed to creating an inclusive environment for all employees. Successful candidates must demonstrate inclusive behaviors in working with a diverse group of scientists to drive our core mission.
In this role, a successful candidate will partner with computational and wet lab researchers to design experiments, identify and develop technologies, and create impactful medicines.
Key Responsibilities
  • Lead the advancement and application of generative AI and machine learning-based protein design and engineering technologies to invent valuable therapeutics; including de novo, structure-based, and data-supported protein design methods.
  • Develop computational methods for therapeutic discovery efforts.
  • Foster a high-performance culture of collaboration, engagement, self-accountability and inclusion.
  • Effectively partner across multidisciplinary interfaces to achieve organizational objectives.
  • Actively develop talent, strategically maximizing diversity to strengthen the team.
  • Support external partnerships and collaboration opportunities.
  • Stay abreast of external advancements in the relevant scientific fields.
  • Promote the external reputation of our company's Discovery Biologics.
  • Qualifications & Experience
  • PhD in Biochemistry, Computational Biology, Protein Engineering, Physics, or related field and minimum of 4 years of industry experience, or an MS and a minimum of 8 years industry experience, or B.S. and a minimum of 12 years industry experience.
  • Extensive expertise applying and developing GenAI/ML-based protein design methods.
  • Experience in data-driven, ML-based protein engineering approaches.
  • Proven industry track record of success working with cross-functional teams.
  • Commitment to scientific excellence and rigor.
  • Excellent communication and collaboration skills.
  • Champion for diverse and inclusive culture.
  • Strong external reputation with high-impact publications, presentations, and scientific community engagement.
  • Passion for sharing knowledge and helping colleagues develop.
Required skills:
  • Expert-level knowledge in applying generative AI methods for protein design and engineering, including de novo design and lead optimization.
  • Experience evaluating and combining generative AI models and applying machine-learning-based methods to solve complex problems in biologics discovery and development.
  • Mastery of protein structural modeling and design tools (e.g. AlphaFold, Rosetta, RFDiffusion, protein MPNN, or similar)
  • Planning and leadership of projects in discovery of protein therapeutics and/or technology development.
  • Strong skills in data analysis and visualization and making data-driven decisions.
  • Comprehensive scientific knowledge across workflows and domains integral to the discovery of protein therapeutics
Preferred skills
  • Deep understanding of protein structure and sequence representations, featurization and embeddings.
  • Project leadership experience in discovery of protein therapeutics or technology development.
  • Experience in managing external collaborations.
  • Hands-on experience with NGS data.
  • Experience deploying scalable computational workflows.
#EligibleforERP
Current Employees apply HERE
Current Contingent Workers apply HERE
US and Puerto Rico Residents Only:
Our company is committed to inclusion, ensuring that candidates can engage in a hiring process that exhibits their true capabilities. Please click here if you need an accommodation during the application or hiring process.
We are an Equal Opportunity Employer, committed to fostering an inclusive and diverse workplace.  All qualified applicants will receive consideration for employment without regard to race, color, age, religion, sex, sexual orientation, gender identity, national origin, protected veteran status, or disability status, or other applicable legally protected characteristics.  For more information about personal rights under the U.S. Equal Opportunity Employment laws, visit:
We are proud to be a company that embraces the value of bringing diverse, talented, and committed people together. The fastest way to breakthrough innovation is when diverse ideas come together in an inclusive environment. We encourage our colleagues to respectfully challenge one another’s thinking and approach problems collectively.
U.S. Hybrid Work Model
Effective September 5, 2023, employees in office-based positions in the U.S. will be working a Hybrid work consisting of three total days on-site per week, Monday - Thursday, although the specific days may vary by site or organization, with Friday designated as a remote-working day, unless business critical tasks require an on-site presence.This Hybrid work model does not apply to, and daily in-person attendance is required for, field-based positions; facility-based, manufacturing-based, or research-based positions where the work to be performed is located at a Company site; positions covered by a collective-bargaining agreement (unless the agreement provides for hybrid work); or any other position for which the Company has determined the job requirements cannot be reasonably met working remotely. Please note, this Hybrid work model guidance also does not apply to roles that have been designated as “remote”.
San Francisco Residents Only: We will consider qualified applicants with arrest and conviction records for employment in compliance with the San Francisco Fair Chance Ordinance
Los Angeles Residents Only: We will consider for employment all qualified applicants, including those with criminal histories, in a manner consistent with the requirements of applicable state and local laws, including the City of Los Angeles’ Fair Chance Initiative for Hiring Ordinance
Search Firm Representatives Please Read Carefully 
Merck & Co., Inc., Rahway, NJ, USA, also known as Merck Sharp & Dohme LLC, Rahway, NJ, USA, does not accept unsolicited assistance from search firms for employment opportunities. All CVs / resumes submitted by search firms to any employee at our company without a valid written search agreement in place for this position will be deemed the sole property of our company.  No fee will be paid in the event a candidate is hired by our company as a result of an agency referral where no pre-existing agreement is in place. Where agency agreements are in place, introductions are position specific. Please, no phone calls or emails.
Employee Status:
Regular
Relocation:
Domestic
VISA Sponsorship:
Yes
Travel Requirements:
No Travel Required
Flexible Work Arrangements:
Not Applicable
Shift:
Not Indicated
Valid Driving License:
No
Hazardous Material(s):
n/a
Required Skills:
Data Engineering, Design Applications, Information Security, Machine Learning, Software Development, Software Development Life Cycle (SDLC), System Designs, Systems Integration, Testing
Preferred Skills:
Job Posting End Date:
04/10/2025
*A job posting is effective until 11:59:59PM on the day BEFORE the listed job posting end date. Please ensure you apply to a job posting no later than the day BEFORE the job posting end date.
Group Leaders
VIB.AI
Belgium
Posted on May 3, 2025 | Posted by Sergey Ochinnikov