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.
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Performing theoretical and computational research
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Developing, implementing and maintaining scientific software
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Participating in the organization of CCB and Flatiron-wide collaborative activities including seminars, workshops and meetings
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Participating in the preparation of manuscripts for publication and of presentations at scientific conferences
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Assisting in student mentorship
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Sharing expertise and providing training and guidance to CCB staff and visitors as needed.
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Ph.D. in a relevant field (applied mathematics, statistics, computational biology, biophysics, computer science, engineering, mathematical physics, or related disciplines)
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Demonstrated abilities in mathematical modeling, analysis and/or scientific computation, scientific software and algorithm development, data analysis and inference, and image analysis
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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
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Ability to work well in an interdisciplinary environment, and to collaborate with experimentalists
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Strong oral and written communication, data documentation, and presentation skills
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The full-time annual compensation for this position is $91,000.
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In addition to competitive salaries, the Simons Foundation provides employees with an outstanding benefits package.
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Cover Letter, which should include a summary of applicants’ most significant contributions in graduate school
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Curriculum vitae with publications list and, if relevant, links to software
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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
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Two (2) letters of recommendation
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Past research accomplishments
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The proposed research program
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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.
Apply by this date to ensure full consideration by the committee.
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.
Job #JPF05842
Department of Pharmaceutical Chemistry
University of California, San Francisco
Document requirements
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Cover Letter
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Curriculum Vitae - CV must clearly list current and/or pending qualifications (e.g. board eligibility/certification, medical licensure, etc.).
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Summary of Research Accomplishments (ca 1 page)
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Description of Future Research Plans (ca 2-5 pages)
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A Teaching Statement, including Formal and Informal Mentoring Activities (Optional)
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Copies of Major Publications (Optional)
3 references (contact information only)
San Francisco, CA
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Cover Letter
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Curriculum Vitae - CV must clearly list current and/or pending qualifications (e.g. board eligibility/certification, medical licensure, etc.).
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Statement of Research -
Summary of Research Accomplishments (ca 1 page)
Description of Future Research Plans (ca 2-5 pages)
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Statement of Teaching - A Teaching Statement, including Formal and Informal Mentoring Activities
(Optional)
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Copies of Major Publications (Optional) (Optional)
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3 required (contact information only)
• “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
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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.
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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
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Expertise in applying AI/ML methodologies to drug discovery, pharmacology, chemistry, bioinformatics, or computational biology.
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A commitment to teaching, mentoring, and training students and postdoctoral fellows in AI/ML-driven drug discovery.
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Interest in interdisciplinary collaboration and contributing to drug discovery and therapeutic innovation.
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Curriculum vitae.
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Statement of research interests and vision (2–3 pages).
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Statement of teaching philosophy and mentoring approach (1–2 pages).
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Names and contact information for three references.
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.
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Design, model, and computationally screen protein binders for selective binding to N-terminal amino acid motifs.
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Develop and optimize binder scaffolds using a combination of structure-based design, ML-driven design, and generative protein modeling tools.
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Collaborate with wet-lab teams to iteratively test, validate, and refine designs using experimental feedback.
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Innovate new computational pipelines for high-throughput protein binder discovery.
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Evaluate binding energetics, specificity, and structural feasibility using in silico approaches.
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Ph.D. in Computational Biology, Bioinformatics, Computer Science, Data Science, or a related computational/scientific field
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Skilled in ML model development and/or fine-tuning, especially for protein structure-function prediction and generative protein design
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Experience integrating experimental feedback loops into computational pipelines to improve design success
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Experience developing custom computational methods or ML approaches to guide protein design toward desired structural/functional properties
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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.
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Strong analytical thinking and practical problem-solving skills, including the ability to break problems into logical subproblems and devise efficient and flexible solutions
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Excellent scientific communication and documentation skills, including data summarization and visualization using Python
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Strong understanding of protein-protein and protein-peptide interactions, as well as hands-on experience conducting in silico analyses to evaluate these interactions
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Familiarity with protein structure prediction and design using cutting-edge modeling software (AlphaFold, ProteinMPNN, RFDiffusion, ESM, Rosetta, etc.)
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Experience designing binders against unstructured peptide regions, including terminal epitopes or motifs
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Familiarity with GPU-accelerated computing and scaling workflows using HPC or cloud resources
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Experience with Git
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PhD or equivalent experience in Computer Science, Machine Learning, Applied Mathematics, Computational Biology, or related field.
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Strong software engineering in Python (packaging, testing, CI), with systems thinking for data‑intensive ML.
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Deep learning experience (PyTorch/JAX/TensorFlow) and solid foundations in linear algebra, probability, and statistics.
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Proven experience designing robust data pipelines for large‑scale ML (HPC or cloud).
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Ability to reason about learning signal and to assess information content of real‑world scientific datasets.
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Excellent collaboration and communication in interdisciplinary teams.
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Hands‑on cryo‑EM experience (e.g., map reconstruction, refinement, or pipeline tooling).
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CUDA or C++ for performance‑critical components; experience with mixed precision and memory‑efficient training.
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Experience integrating experimental data into ML models (e.g., constraints/priors from cryo‑EM, binding assays, spectroscopy).
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Familiarity with MD data, structure prediction systems, or protein design work-flows.
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Experience with cost‑optimization for data collection and cloud utilization; clear track record of building reliable, maintainable research software at scale.
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Experience with structural biology or molecular biology data/techniques (e.g., cryo‑EM, binding assays, spectroscopy, expression, sequencing)
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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.
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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.
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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.
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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).
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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.
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Quality, governance, and reproducibility: Codify schemas/ontologies, metadata contracts, unit/integration tests, and lineage; automate validation and data drift detection; maintain documentation and examples.
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Partner across disciplines: Work closely with ML researchers, structural biologists, and drug designers; translate experimental constraints into robust computational workflows; communicate clearly and proactively.
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PhD or equivalent research experience in Chemistry, Biophysics, Physics, Computer Science, Bioinformatics or a related field.
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Demonstrated passion and proven excellence in computational molecular biology, biophysics, or bioinformatics via impactful projects, publications, or open‑source code.
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Experience with biomolecular modeling/bioinformatics (e.g., folding systems, structural analysis, MD simulation, structure/genome databases).
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Excellent technical communication for interdisciplinary work.
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Comfortable with real‑world data that lack structure/cleanliness/completeness.
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Proficiency in Python and data analysis packages (NumPy, SciPy, Pandas).
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Experience with deep learning methods and software packages (PyTorch, JAX, Tensorflow).
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Experience with structural biology or molecular biology data/techniques (e.g., cryo‑EM, binding assays, spectroscopy, expression, sequencing).
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Background or advanced training in structural biology; familiarity with structure prediction and/or MD work-flows.
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Model biomolecular structure and dynamics at scale: Use BioEmu, structure/sequence databases, and complementary tools to analyze proteins and complexes.
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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.
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Generate biological hypotheses and insights: Integrate biomolecular structure and dynamics data to generate experimentally-testable predictions and biological insights.
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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.
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Support drug‑targeting strategies: Partner with leading drug discovery experts to identify targets and propose mechanisms of action.
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Operationalize at scale: Build robust Python pipelines; automate large‑scale inference and analysis jobs on Azure with reproducible work-flows.
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Partner across disciplines: communicate clearly with ML researchers and experimental/computational biologists; present results and influence project direction.
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Work autonomously and as a team player, regularly reporting insights, risks, and next steps.
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Aim for impact: translate findings into artifacts others can use (code, datasets, internal reports, and when appropriate - papers).
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PhD or equivalent experience in Computer Science, Machine Learning, Applied Mathematics, Computational Biology, or related field.
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Strong software engineering in Python (packaging, testing, CI), with systems thinking for data‑intensive ML.
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Deep learning experience (PyTorch/JAX/TensorFlow) and solid foundations in linear algebra, probability, and statistics.
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Proven experience designing robust data pipelines for large‑scale ML (HPC or cloud).
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Ability to reason about learning signal and to assess information content of real‑world scientific datasets.
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Excellent collaboration and communication in interdisciplinary teams.
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Hands‑on cryo‑EM experience (e.g., map reconstruction, refinement, or pipeline tooling).
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CUDA or C++ for performance‑critical components; experience with mixed precision and memory‑efficient training.
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Experience integrating experimental data into ML models (e.g., constraints/priors from cryo‑EM, binding assays, spectroscopy).
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Familiarity with MD data, structure prediction systems, or protein design work-flows.
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Experience with cost‑optimization for data collection and cloud utilization; clear track record of building reliable, maintainable research software at scale.
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Experience with structural biology or molecular biology data/techniques (e.g., cryo‑EM, binding assays, spectroscopy, expression, sequencing)
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PhD or equivalent research experience in Computer Science, Machine Learning, Physics, or a related field.
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Demonstrated leadership in ML architecture and algorithm design.
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Strong expertise in deep learning (model design, large-scale training, evaluation and reproducibility), statistics and linear algebra.
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Proficiency in Python and modern ML/scientific frameworks (e.g., PyTorch, JAX, TensorFlow, NumPy, SciPy, Pandas).
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Peer-reviewed publications in leading venues (e.g., NeurIPS, ICML, ICLR or leading journals).
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Excellent technical communication for collaborating in an interdisciplinary team.
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Curiosity and drive to apply deep learning to biological problems.
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Comfort with real‑world, noisy/heterogeneous data.
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ML Engineering skills (e.g., model optimization and deployment, code design, CUDA).
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Experience with biomolecular modeling or bioinformatics (e.g., folding systems, structural analysis/visualization, MD simulation, structure/genome databases).
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Ability to work with and interpret real‑world biological data (e.g., cryo‑EM, protein binding affinities, structural/biophysical measurements).
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Invent novel deep learning techniques for models of biomolecular structure, dynamics, and function.
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Design, implement, and iterate on model architectures and training algorithms (e.g., diffusion/sequence–structure models, representation learning); run rigorous ablations and baselines.
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Define success where standards don’t exist: proposing sound benchmarks and uncertainty‑aware metrics that reflect real‑world utility.
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Build high‑quality research code (Python/PyTorch) with reproducible work-flows and robust data pipelines.
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Partner across disciplines—communicate clearly with ML researchers and experimental/computational biologists; present results and influence direction.
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Work autonomously and as a team player, reporting insights, risks, and next steps with crisp written/visual summaries.
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Thrive with imperfect, heterogeneous data, using principled curation, augmentation, and probabilistic evaluation.
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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).
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PhD in soft matter research, polymer science, or a comparable domain.
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Affinity/experience with machine learning approaches
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Ability to conduct high quality academic research, demonstrated for instance by a relevant PhD thesis and publication(s).
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Ability to teach, shown by experience or assistance in teaching and positive evaluations of these teaching efforts.
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Creative and dedicated to (multidisciplinary) collaboration.
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Excellent communication skills.
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Ability to be, or willingness to become, a good leader.
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Empathy and good listening skills.
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Flexibility and resilience.
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Excellent proficiency (written and oral) in English.
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Salary in accordance with the Collective Labour Agreement for Dutch Universities, scale 11 (min. € 4.728 max. € 6.433).
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A year-end bonus of 8.3% and annual vacation pay of 8%.
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A dedicated mentoring program to help you get to know the university and the Dutch (research) environment.
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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.
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High-quality training programs for academic leadership and teaching.
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An excellent technical infrastructure, on-campus children's day care and sports facilities.
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Partially paid parental leave and an allowance for commuting, working from home and internet costs.
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A Staff Immigration Team is available for international candidates, as are a tax compensation scheme (the 30% facility) and partner career support.
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Cover letter in which you describe your motivation and qualifications for the position.
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Curriculum vitae, including a list of your publications and the contact information of three references.
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Description of your scientific interests and plans (1-2 pages).
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Statement of your teaching goals and experience (1-2 pages).
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.
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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
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Background in protein design, computational biology or related field
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Working knowledge in at least one relevant coding language (Python, R, or C++)
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Excellent communication skills and excellent command of English, both spoken and written
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Experience in sterile cell culturing technique
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Familiarity with protein expression and purification
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Interest in protein biophysics and structural biology
Why Join Us?
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Competitive compensation + stock options
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Private health insurance
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Bi-weekly team lunches + regular socials
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The rare chance to shape the DNA of a company
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Access to cutting-edge science, a stellar team, and the chance to change the game
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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.
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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).
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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.
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Build frameworks that link molecular representations to structure–function and structure–activity relationships (SAR/QSAR), supporting candidate generation, ranking, and trade-off analysis.
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Shape strategies for computationally guided protein and small-molecule library design, ensuring broad, efficient coverage of relevant biophysical and chemical property space.
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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.
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Publish, present, and communicate findings that demonstrate measurable improvements in computational drug discovery, protein engineering, and molecular design outcomes.
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PhD or Master’s in computational biology, structural bioinformatics, biophysics, bioinformatics, computational chemistry, cheminformatics, or a related discipline.
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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).
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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).
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Solid grounding in statistics, applied mathematics, and data-driven modelling, with ability to analyse large-scale multi-omics, structural, or chemical datasets.
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Industry drug discovery / biotechnology R&D experience (3+ years) desirable, but exceptional PhD graduates will be considered.
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Evidence of research excellence (peer-reviewed publications, software packages, impactful computational analyses).
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Advantageous: experience with design algorithms (search/optimisation, active learning, generative AI for molecules) and with cloud/HPC workflows or distributed computing.
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.
Department of Data Science
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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)
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Appointable to the rank of Associate or Full Professor upon initiation of the position
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Demonstrated success in collaboratively co-organizing spaces that prioritize belonging
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Exemplary evidence of impact beyond academia through research, teaching, and/or service
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Demonstrated experience leading a productive and impactful research program aligned with the goals of the department
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Cover letter*
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Curriculum Vitae
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Research statement
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Teaching statement
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Service statement
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Three references (no actual letters, just names and email addresses)
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Cover letter
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Curriculum Vitae
120 Deschutes Hall
1202 University of Oregon
1477 E. 13th Ave.
Eugene, OR 97403-1202
Title: Computational Structural Biologist
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Predict, analyse and interpret protein structure using computational modelling tools like Boltz-2, Bindcraft, AlphaFold, RFdiffusion, RFpeptides, molecular dynamics simulations and ML/AI.
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Apply and develop Protein/peptide design methods.
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Apply and develop Free-energy calculations for molecular interactions.
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Apply molecular dynamics simulations methods to understand protein dynamics and motions.
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Generate scripts and workflows to enable automated analyses.
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Apply and develop deep learning and molecular dynamics-based approaches to biologics drug discovery.
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Be part of and contribute to multidisciplinary drug discovery project teams
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PhD in Computer Sciences applied to Biochemical systems and /or Postdoc/ biotech/industry experience.
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Demonstrated expertise in protein or peptide design.
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Demonstrated proficiency in utilizing free energy calculations for biochemical analysis and protein design using AI technologies.
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Expertise preparing and running complex molecular dynamics simulations of biochemical systems.
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Strong experience in programming with Python for molecular structures.
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Good track record of publications, strong research skills, and a history of innovation and achievements.
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Strong experience using molecular modeling packages like Biovia, MOE, Schrodinger, etc.
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Outstanding teamwork and excellent communication skills.
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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).
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Development of the best administrative framework and processes for CPD together with the Center Director and the two host departments
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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.
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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.
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Coordination of the tasks in the CPD administrative team.
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Support to the Center Director/Management in strategy development and processes.
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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.
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Coordination of employment and onboarding of researchers, many of whom may come from abroad.
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Support the planning of teaching and research for academic staff in conjunction with the Center Director to ensure equitable workloads across the Center.
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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.
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Coordination of activities with the Novo Nordisk Foundation.
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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.
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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.
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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.
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Ongoing dialogue with stakeholders, incl. researchers, funders, publics, journalists, companies, and other relevant organisations.
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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.
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Participate in Department, Faculty or University committees, working groups and new initiatives, leading these where appropriate.
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Work with the Department/Faculty technical teams on operational requirements in the CPD’s highly technical environment to support training and research.
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Advising and helping the CPD Director and Senior Leadership Group to foster and develop new internal (UCPH) and external partnerships.
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have an academic degree at Master's level or higher, ideally in a scientific discipline.
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have substantial transferable/relevant experience in a management support position gained within a large, complex organisation.
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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.
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speak and write English fluently.
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have excellent intercultural communication skills and an understanding of the world of research.
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have numerical skills and in-depth knowledge of Excel and can manage budgets.
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take responsibility for providing consistent and high-quality professional administrative and management support and follow through on tasks.
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have experience of producing detailed reports and, ideally, contributing to the development and presentation of business cases.
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have experience of working in, or managing a specialist, technical environment.
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work independently and in a structured manner and can keep an extraordinary overview of ongoing issues, challenges, and opportunities for the CPD.
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at the same time, be able to work closely and well with others, especially in the senior academic and management team of the CPD.
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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.
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are able to understand the larger context and perspective at the same time as having an eye for detail.
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possess a pioneering spirit.
https://www.eeoc.gov/sites/default/files/2023-06/22 088_EEOC_KnowYourRights6.12ScreenRdr.pdf
Company Description
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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).
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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.
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Analyze large datasets from experimental protein engineering efforts (including enzyme activity data and sequence/structure information) to refine and improve computational models.
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Develop and implement moderately complex computational methods, potentially utilizing 3D structures and/or sequences as input to enhance enzyme stability, solubility, and activity.
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Document methods and implementation methodologies, activities, sequences, and requirements in both informal and formal reports and presentations.
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Design protein libraries and datasets for high-throughput screening and hit identification.
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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.
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Design, test, deploy, and maintain high-quality pipelines on HPC and cloud infrastructures, ensuring scalable and robust solutions.
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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.
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Perform other duties as assigned.
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Lead projects that develop advanced computational protein design strategies to meet diverse scientific and technical challenges.
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Independently determine the appropriate technical objectives, criteria, and approaches to satisfy and execute project deliverables.
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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.
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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.
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Lead and mentor junior staff and students.
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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.
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Comprehensive knowledge of or experience in developing and implementing novel methods and algorithms for computational protein design.
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Proficiency in programming with languages such as Python, C/C++, or Java.
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Proficient written, and verbal communication skills necessary to work and collaborate effectively in a multi-disciplinary environment, and to present and explain technical information.
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Demonstrated strong record of documentation of executed work.
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Ability to prioritize, balance, and keep several parallel threads of work in simultaneous, smooth motion.
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Advanced level knowledge and significant experience in computational protein design or a related technical field.
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Ability to independently develop and execute complex analyses and to prepare and finalize tailored reports.
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Significant experience leading interdisciplinary teams, including setting clear expectations, delegating to subordinates and peers, and ensuring successful, timely completion of objectives.
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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.
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PhD in biochemistry, biophysics, bioinformatics, computational chemistry, computer science, AI/ML, or a related technical discipline focused on solving biological problems using computational approaches.
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Demonstrated understanding of fundamental biochemistry and enzyme engineering concepts including kinetics, reaction mechanisms, transition states, and rational design.
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Experience with classic computational approaches to estimating enzymatic properties such as thermodynamic stability and net charge and mathematical modeling of enzyme reaction dynamics.
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Familiarity with non-canonical amino acids and their use in protein design.
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Experience with design and modeling tools such as Rosetta, RFDiffusion, ProteinMPNN, AlphaFold, etc.
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Background in developing generative AI, structure-, or sequence-based methods for therapeutic protein design.
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Familiarity with training generative AI models, applying bioinformatics approaches to sequence analysis, and managing large databases of protein structures and sequences.
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Experience with modern deep learning frameworks (e.g., PyTorch, JAX, SageMaker) and cloud services (e.g., Git, Docker, AWS Batch, Step Functions, EKS).
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Included in 2025 Best Places to Work by Glassdoor!
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Flexible Benefits Package
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401(k)
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Relocation Assistance
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Education Reimbursement Program
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Flexible schedules (*depending on project needs)
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Our values - visit https://www.llnl.gov/inclusion/our-values
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.
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Develop, implement, and apply innovative deep learning and AI-based methods for protein structure prediction, design, and optimization.
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Evaluate and implement emerging computational tools, algorithms, and best practices in the field of machine learning-driven protein engineering.
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Integrate computational modeling and advanced analytics with experimental workflows to design and optimize antibodies and other therapeutic proteins.
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Collaborate closely with other computational and experimental scientists to support iterative design of therapeutic proteins and antibodies.
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Independently analyze scientific results, troubleshoot computational and data-driven challenges, and develop creative solutions and workflows to address challenges.
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Prepare technical documents and deliver clear, effective presentations on project progress, findings, and strategy to internal teams.
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Develop research plans and manage multiple concurrent projects or workflows.
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May include supervision and mentorship of direct reports.
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A Ph. D. or equivalent in computational biology, bioinformatics, structural biology, or a related discipline with significant and extensive experience in protein design.
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Strong foundation in deep learning, particularly as applied to protein structure modeling (e.g. AlphaFold, ProteinMPNN, RFdiffusion).
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Demonstrated experience applying machine learning to solve real-world problems in protein engineering or design.
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Familiarity with experimental approaches for protein characterization (e.g. expression, purification, biophysics, and binding assays).
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Proficient in Python and deep learning frameworks (e.g. PyTorch).
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Proficient with Linux, including experience using high performance computing environments.
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Ability to work in multi-disciplinary teams, displaying excellent interpersonal skills.
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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.
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Experience developing custom ML/AI models for biological sequence or structure generation.
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Experience using Rosetta-based methods for protein design and modeling.
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Prior experience engineering therapeutic antibodies or other biologics.
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Familiarity with cloud computing or GPU-accelerated infrastructure.
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Track record of publications in the field of computational protein design.
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curriculum vitae (including bibliography)
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description of research accomplishments (one page maximum)
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summary of future research interests (three pages maximum)
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!
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Developing, implementing and deploying programs and computational solutions employing Machine Learning/Deep learning and Cheminformatics
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Ability to implement, debug, and maintain computational tools in common programming languages (Python, etc…) and proficiency with cloud computing capabilities
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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
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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.
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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.
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Expertise in AI/ML-enabled molecular generation, pose generation, sequence design, and/or affinity prediction are preferred
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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
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Excellent ability to communicate clearly and concisely with colleagues and collaborators including an ability to explain complex ideas to non-specialists
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Strong programming skills in Python and experience with data science stack including numpy, pandas, scikit-learn, and other related scientific libraries
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The level of the position will be determined by the skill set of the candidates
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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.
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We offer a comprehensive package of benefits including paid time off (vacation, holidays, sick), medical/dental/vision insurance and 401(k) to eligible employees.
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This job is eligible to participate in our short-term incentive programs.
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Utilize AI and machine learning techniques to design novel antibodies and bi/multi-specific antibodies that would be challenging to achieve from screening
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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.
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Apply deep learning and generative AI techniques to train/enhance LLM or other relevant language models using internal datasets
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Use in silico protein/antibody engineering design tools such as Rosetta to drive for structure-based design and engineering
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Leverage deep target biology from broad therapeutic areas to enable desired novel MoAs through molecular design
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Collaborate and support scientists from antibody engineering, therapeutic areas and other tech centers with biotherapeutic design
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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
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Serve as an expert in computational biologic design to keep up with the latest advancements in AI, machine learning, and protein engineering fields
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Maintain data analysis and records in well-organized fashion
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Present data clearly to teams and managements
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You are a result-driven innovator and a problem solver
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You have a strong background in computational biology, programming, deep learning algorithms, structural biology and protein engineering
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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
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You have proficiency in programming languages such as Python, R and C++
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You have competence to work with large dataset and cloud computing infrastructure
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You can efficiently coordinate multiple projects in a collaborative environment
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You have strong organizational, time-management, and presentation skills
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You enjoy working in a fast-paced, innovative and cross-functional team
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.
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Apply Bayesian optimization and other active learning techniques to diverse problems.
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Develop, train, and fine-tune generative models (ex: diffusion models, transformers) for encoding and designing protein structures and sequences.
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Collaborate with diverse functions (ex: structural biologists, protein engineers) to incorporate physical, structural, or biological priors into the model.
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Deliver models and insights to guide experimental design and data generation.
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Mentor junior engineers and contribute to the direction of the ML engineering function.
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Track and present model performance, research progress, and infrastructure improvements to internal stakeholders.
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PhD or MSc in Computer Science, Machine Learning, Computational Biology, Biophysics, or a related field.
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2+ years of experience in developing and deploying machine learning models in industry or applied research settings.
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Strong background in Bayesian optimization, active learning, or experimental design for high-dimensional biological problems.
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Experience with large-scale generative models (ex: diffusion models, transformers) and distributed training (multi-GPU, multi-node).
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Proficiency in Python and modern ML frameworks such as PyTorch or TensorFlow.
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Hands-on experience with ML infrastructure, including cloud services (AWS, or Azure) and container orchestration (Kubernetes, Docker).
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:
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 .
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Design, model, and computationally screen protein binders for selective binding to N-terminal amino acid motifs.
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Develop and optimize binder scaffolds using a combination of structure-based design, ML-driven design, and generative protein modeling tools.
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Collaborate with wet-lab teams to iteratively test, validate, and refine designs using experimental feedback.
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Innovate new computational pipelines for high-throughput protein binder discovery.
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Evaluate binding energetics, specificity, and structural feasibility using in silico approaches.
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PhD. in Computational Biology, Bioengineering, Structural Biology, or a related computational/scientific field
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Proven expertise in protein structure prediction and design using cutting-edge modeling software (AlphaFold, ProteinMPNN, RFDiffusion, ESM, Rosetta, etc.)
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Strong understanding of protein-protein and protein-peptide interactions, as well as hands-on experience conducting in silico analyses to evaluate these interactions
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Experience developing custom computational methods or ML approaches to guide design toward desired structural/functional properties
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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.
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Strong analytical thinking and practical problem-solving skills, including the ability to break problems into logical subproblems and devise efficient and flexible solutions
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Excellent scientific communication and documentation skills, including data summarization and visualization using Python
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Publications showcasing the use of advanced protein design tools (e.g., AlphaFold, RFDiffusion, ProteinMPNN) to develop proteins with targeted functions or novel structural features
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Experience designing binders against unstructured peptide regions, including terminal epitopes or motifs
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Experience with ML model development or fine-tuning, particularly for structure-function prediction or generative protein design.
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Experience integrating experimental feedback loops into computational pipelines to improve design success.
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Familiarity with GPU-accelerated computing and scaling workflows using HPC or cloud resources.
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Experience with Git
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.
- Experience investigating the feasibility of applying scientific principles and concepts to business problems and products
- Experience analyzing both experimental and observational data sets
- 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.
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5% Identifies research problems and develops complex research methodologies and procedures
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45% Collects and analyzes complex research data, conducts experiments and interviews, and documents results according to established policies and procedures under general supervision
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5% Conducts literature reviews, prepares reports and materials, and disseminates information to appropriate entities
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5% Attends and assists with the facilitation of scholarly events and presentations in support of continued professional development and the dissemination of research information
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5% Writes or assists in developing grant applications and proposals to secure research funding
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25% May supervise the day-to-day activities of a research unit as needed
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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
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5% Monitors program budget and approves unit expenditures
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
Terminal Degree in Biochemistry, Biophysics, Bioengineering or other related field
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
It is anticipated this position requires work be performed in-person, onsite, at a designated campus work location.
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
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.
stefanie.lannoye@wisc.edu
608-261-1029
Relay Access (WTRS): 7-1-1. See RELAY_SERVICE for further information.
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.
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
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Developing novel physics- and ML-based approaches to peptide structure prediction and design
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Developing novel physics- and ML-based approaches to predicting molecular properties that drive membrane permeability and oral bioavailability
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Evaluating existing methods to computationally screen peptide candidates for desired properties
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Working directly with wet-lab scientists across Therapeutics Discovery to design and optimize peptides with specific properties
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Presenting work in oral or written form at conferences, internal meetings and journals
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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.
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Advanced working knowledge of computational molecular modeling including both application of existing tools and development of new tools
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Advanced fluency in Python and related data-science packages (e.g. Pandas, NumPy, sci-kit learn)
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Experience using Schrodinger, Rosetta, MOE, GROMACS, NAMD, OpenMM or other molecular simulation software.
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Proven scientific excellence as evidenced by publications, patents, and presentations.
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Excellent interpersonal, communication, and presentation skills.
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Experience with high performance computing including either on-premises and cloud computing architectures.
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Experience with ML packages for protein modeling and design such as AlphaFold, RFDiffusion, ProteinMPNN, etc.
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Familiarity with cheminformatics toolkits (e.g., rdkit, OpenEye)
Elizabeth H. Kellogg & Alexandre Zanghellini
Elizabeth H. Kellogg & Alexandre Zanghellini
Elizabeth H. Kellogg & Alexandre Zanghellini
Elizabeth H. Kellogg & Alexandre Zanghellini
Elizabeth H. Kellogg & Alexandre Zanghellini
About the job
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Develop new computational methods to accelerate the design and optimization of cyclic peptide therapeutics.
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Work alongside machine learning developers or independently contribute to machine learning projects.
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Analyze data and suggest directions for platform advancement based on scientific insights and platform performance.
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Implement existing and novel methods into Menten AI’s computational platform for utilization at production scale.
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Contribute to the maintenance of existing areas of the platform to ensure resilience, scalability, and scientific accuracy.
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Report to the team on your progress and incorporate feedback from others, including application scientists at Menten AI.
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Be a team player by identifying areas for improvement, aiming to enhance scientific results and computational efficiency to solve complex problems.
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Ph.D. in life sciences or computational disciplines.
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Experience with developing in silico methodologies for optimization of peptides, biologics, or small molecules.
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Proficiency in developing protocols with at least one of the following: Rosetta, PyRosetta, OpenMM, RDKit, GROMACS, AMBER, GAMESS
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Ability to program in Python and familiarity with common packages such as BioPython, Pandas, NumPy, SciPy, and sci-kit-learn.
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Skilled in collaborative research environments, contributing to shared repositories and adhering to best practices, including the use of git.
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Willingness and interest to pick up new skills to solve complex problems.
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Having trained new AI models for predicting properties or generation of peptides, biologics, or small molecules.
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Experience in the Biotechnology Industry
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Previous experience in method development for cyclic peptide docking, scoring, or design.
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Familiarity with Linux, SQL, and cloud computing (AWS, Google Cloud, or Azure).
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Experience developing C++ code – Particularly C++ development in Rosetta is highly valued.
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Experience in free energy calculations from molecular dynamics simulations or other QM/MM approaches.
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:
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Demonstrated track record in computational protein modeling with wet-lab validation
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2+ years of experience using Rosetta, AlphaFold in protein modeling and validation
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Strong understanding of protein biochemistry or biophysics related to protein structure/function
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Fluency in one or more programming languages (Python preferred)
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Strong leadership skills with experience in managing and mentoring scientific teams
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Excellent communication, presentation, and organizational skills
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Ability to thrive in a fast-paced, innovative, and collaborative environment
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Interest in writing proposals/grants and participating in the formation of new programs to solve the nation’s most challenging problems
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Strong Research experience in Bioinformatics, Computational Biology, Biochemistry, Biophysics, or a related Biological science field.
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Preferred:
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Experience with development and application of AI/ML methods and models for protein structure analysis and modeling
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Experience with cloud computing (i.e. AWS) and software
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Expertise with experimental techniques in protein engineering and high-throughput analysis
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Demonstrated ability to communicate ideas in proposal/grant formats
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New Machine Learning-based approaches for de novo design of (bio)molecules
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Applications of generative models to biological or materials science problems
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a cover letter explaining your motivation to apply for this position
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a Curriculum Vitae including publication list
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a statement of scientific achievements (~500 words)
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a two-page summary of your future research plans (~1000 words)
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up to three of your most important papers
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names and contact details of 3 academic references
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The Max Planck Society strives for gender and diversity equality. We welcome applications from all backgrounds.
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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.
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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.
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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.
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Foster a high-performance culture of collaboration, engagement, self-accountability and inclusion.
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Effectively partner across multidisciplinary interfaces to achieve organizational objectives.
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Actively develop talent, strategically maximizing diversity to strengthen the team.
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Support external partnerships and collaboration opportunities.
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Stay abreast of external advancements in the relevant scientific fields.
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Promote the external reputation of our group.
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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.
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Demonstrated success in applying GenAI/ML-based protein design methods.
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Proven industry track record of success working with cross-functional teams.
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Commitment to scientific excellence and rigor.
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Excellent communication and collaboration skills.
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Champion for diverse and inclusive culture.
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Strong external reputation with high-impact publications, presentations, and scientific community engagement.
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Passion for sharing knowledge and helping colleagues develop.
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Experience applying generative AI methods for protein design and engineering, including de novo design and lead optimization.
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Deep understanding of protein structure and molecular biophysics.
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Mastery of protein structural modeling and design tools (e.g. AlphaFold, Rosetta, RFDiffusion, ProteinMPNN, or similar)
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Strong skills in data analysis and visualization and making data-driven decisions.
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Comprehensive scientific knowledge across workflows and domains integral to the discovery of protein therapeutics
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Experience evaluating and combining generative AI models and applying machine-learning-based methods to solve complex problems in biologics discovery and development.
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Project leadership experience in discovery of protein therapeutics or technology development.
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Experience in managing external collaborations.
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Hands-on experience with NGS data.
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Experience deploying scalable computational workflows.
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.
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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.
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Develop computational methods for therapeutic discovery efforts.
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Foster a high-performance culture of collaboration, engagement, self-accountability and inclusion.
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Effectively partner across multidisciplinary interfaces to achieve organizational objectives.
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Actively develop talent, strategically maximizing diversity to strengthen the team.
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Support external partnerships and collaboration opportunities.
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Stay abreast of external advancements in the relevant scientific fields.
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Promote the external reputation of our company's Discovery Biologics.
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Qualifications & Experience
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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.
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Extensive expertise applying and developing GenAI/ML-based protein design methods.
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Experience in data-driven, ML-based protein engineering approaches.
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Proven industry track record of success working with cross-functional teams.
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Commitment to scientific excellence and rigor.
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Excellent communication and collaboration skills.
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Champion for diverse and inclusive culture.
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Strong external reputation with high-impact publications, presentations, and scientific community engagement.
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Passion for sharing knowledge and helping colleagues develop.
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Expert-level knowledge in applying generative AI methods for protein design and engineering, including de novo design and lead optimization.
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Experience evaluating and combining generative AI models and applying machine-learning-based methods to solve complex problems in biologics discovery and development.
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Mastery of protein structural modeling and design tools (e.g. AlphaFold, Rosetta, RFDiffusion, protein MPNN, or similar)
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Planning and leadership of projects in discovery of protein therapeutics and/or technology development.
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Strong skills in data analysis and visualization and making data-driven decisions.
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Comprehensive scientific knowledge across workflows and domains integral to the discovery of protein therapeutics
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Deep understanding of protein structure and sequence representations, featurization and embeddings.
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Project leadership experience in discovery of protein therapeutics or technology development.
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Experience in managing external collaborations.
-
Hands-on experience with NGS data.
-
Experience deploying scalable computational workflows.
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.
