Postdoctoral Researcher in Quantum Computing for Bioinformatics

Uva; Amsterdam; On-site; EUR 41,000 - 64,000; Full time

Job summary

The Biosystems Data Analysis group at the University of Amsterdam is seeking a postdoctoral researcher to develop and benchmark quantum-algorithm approaches for challenging bioinformatics problems. You will work within the Q-MMD programme, contributing to reproducible studies and collaborative research across disciplines.

You will lead prototype development, compare against classical baselines, and help shape future public-private collaborations while supervising students and disseminating

Qualifications

• PhD in a relevant field.
• Strong programming and computational research skills.
• Experience building reproducible analysis or simulation workflows.
• Fluent written and spoken English.

Responsibilities

• Surveying and selecting quantum or hybrid methods with credible potential for biology problems.
• Designing reproducible proof-of-concept studies and implementing prototypes on datasets.
• Comparing accuracy, scalability and resource use with classical baselines and reporting limits.
• Collaborating with bioinformatics researchers, Lead Scientist Quantum Applications, and wider quantum ecosystem at UvA.
• Connecting prototypes to available quantum computing infrastructure and hardware partners when appropriate.
• Leading scientific publications, reusable software, and knowledge-transfer activities.
• Contributing to project valorisation strategy and follow-up proposals.
• Supervising Bachelor’s and Master’s students and fostering an inclusive research culture.

Education

PhD in bioinformatics / computational biology / quantum information / physics

Job description

Join Us!

The Biosystems Data Analysis (BDA) group at the University of Amsterdam is looking for a postdoctoral researcher to develop and rigorously benchmark quantum-computing approaches for high-impact problems in bioinformatics.

This project is part of the Faculty of Science's new Quantum Simulation for Molecular and Material Design (Q-MMD) programme. You will join a growing interdisciplinary team at the cutting edge of quantum application; four Q-MMD seed projects across the Faculty of Science, together with a Lead Scientist Quantum Applications currently being recruited. This team will explore where quantum and hybrid quantum-classical methods can make a real scientific difference, build reusable expertise and create the basis for future academic and public-private collaborations. At BDA, you will be embedded in a group whose experience is in advanced methods for biological and biomedical data.

We welcome applications from candidates with expertise in quantum computing who are motivated to cross disciplinary boundaries towards bioinformatics and computational biology. You do not need to arrive as an expert in both fields.

This is what you will do

You will develop quantum-algorithm prototypes within existing bioinformatics workflows and benchmark them transparently against state-of-the-art classical approaches. In consultation with the project leaders and collaborators, you will focus on one or both of two complementary directions:

• protein structure-based enzyme specificity and biocatalysis, including computationally demanding tasks such as pose search in high-dimensional binding landscapes, optimisation of catalytic-pocket conformations, sampling of ligand-binding modes, and improved scoring of enzyme-substrate interactions;
• DNA sequence analysis, for example sequence alignment, assembly, distance computation, or phylogenetic inference, as applicable to microbiomes and human-microbiome interactions, such as outbreak-related strain reconstruction, or phasing and assembly of complex immune-system loci.

Your tasks and responsibilities will include:

• surveying and selecting quantum or hybrid quantum-classical methods with credible potential for the chosen biological problems;
• designing reproducible proof-of-concept studies, implementing prototypes and evaluating them on suitable simulated and/or real biological datasets;
• comparing accuracy, scalability, resource requirements and scientific usefulness with strong classical baselines, and clearly identifying both opportunities and limitations;
• working closely with bioinformatics researchers, the incoming Lead Scientist Quantum Application, colleagues in the other Q-MMD seed projects as well as scientists in the wider quantum ecosystem at UvA;
• where appropriate, connecting prototypes to available quantum-computing infrastructure and hardware partners, including through the wider Amsterdam quantum ecosystem;
• taking a leading role in scientific publications, open and reusable research software, presentations and/or knowledge-transfer activities;
• helping formulate the project's valorisation strategy and develop follow-up proposals, including collaborative and public-private projects;
• contributing to the supervision of Bachelor’s and Master’s students and to an inclusive, collaborative research culture.

What we ask of you

You are a curious and rigorous researcher who enjoys learning across disciplines. You can translate an ambitious methodological idea into a testable computational study, communicate openly about negative as well as positive results, and work effectively with collaborators who use different scientific languages.

You

• hold a PhD in bioinformatics, computational biology, computer science, quantum information/quantum computing, computational chemistry, applied mathematics, physics, or a closely related field;
• have strong programming and computational research skills, and experience building reproducible analysis or simulation workflows;
• have demonstrable expertise in one of the following domains and the motivation to acquire working knowledge of the complementary domain:
  • quantum computation;
  • bioinformatics or computational biology expertise in the project's core applications: biological sequence/structure analysis, molecular modelling, and/or optimisation and algorithms;
• have a research record appropriate to your career stage and the ability to communicate results clearly in publications, presentations and collaborative meetings;
• communicate fluently in written and spoken English and work constructively in an interdisciplinary, international team.

Experience with quantum software frameworks, high-performance computing, open-source software development, or collaboration with external partners is an advantage. We do not expect candidates to cover this entire list.

This is what we offer you

We offer a temporary employment contract for 38 hours per week for a period of 18 months, with a probationary period of three months in accordance with UvA policy. The preferred starting date is as soon as possible.

The gross monthly salary, based on 38 hours per week and dependent on relevant experience, is €3.706 to €5.760. This does not include 8% holiday allowance and 8.3% year-end allowance. The UFO profile Researcher 4 is applicable. A favourable tax agreement, the "30% ruling", may apply to non-Dutch applicants. The Collective Labour Agreement of Universities of the Netherlands is applicable.

Curious about our extensive secondary benefits package? You can read more about it here.

You will work in this team

You will be appointed in the Biosystems Data Analysis group at the Swammerdam Institute for Life Sciences (SILS). The group develops and applies computational methods to understand biological systems, with research themes that include DNA sequence analysis, microbial communities and human-microbiome interactions, protein function, enzyme specificity and computational biocatalysis.

The position is embedded in Q-MMD, the quantum-simulation programme of the Faculty's Molecular and Material Design Technology Hub. The programme connects four seed projects: quantum machine learning for molecular and material design; quantum computing for bioinformatics; quantum approaches for safe and sustainable molecular design; and benchmarking quantum simulations of materials against state-of-the-art numerical methods. Regular cross-project exchange will let you learn from different application domains while contributing bioinformatics challenges, benchmarks and software to a shared programme.

You will collaborate with the incoming Lead Scientist Quantum Applications, whose role connects the MMD programme with QuSoft and the wider quantum ecosystem. QuSoft, founded by UvA and CWI, contributes expertise ranging from quantum information theory and algorithm design to quantum simulation and implementation. The wider network also includes partners such as SURF. This wider ecosystem makes the postdoc an opportunity to help shape an emerging field at a moment when questions, methods and standards for useful quantum applications are still being defined.

The Swammerdam Institute for Life Sciences (SILS) is located at the vibrant Amsterdam Science Park. SILS is one of eight institutes of the University of Amsterdam's Faculty of Science (FNWI). With around 240 employees, SILS carries out internationally high-quality life science research and provides education within various university programs. Research is also carried out in close cooperation with the medical, biotech, chemical, flavour, food & agricultural, and high-tech industries, and revolve around 4 main themes, Cell & Systems biology, Neurosciences, Microbiology and Green Life Sciences.

The Faculty of Science has a student body of around 8,000, as well as 1,800 members of staff working in education, research or support services. Researchers and students at the Faculty of Science are fascinated by every aspect of how the world works, be it elementary particles, the birth of the universe or the functioning of the brain.

Want to know more about our organisation? Read more about working at the University of Amsterdam.

Contact

If you have any questions or do you require additional information? Please contact:

• Prof. Dr. Aalt-Jan van DIjk, [e-mail]
• Prof. Dr. Kareljan Schoutens, [e-mail]
• Dr. Anna Heintz-Buschart, [e-mail]

Applications should include the following information (all files besides your CV should be submitted in one single PDF file):

• a detailed CV including the months (not just years) when referring to your education and work experience;
• a list of publications;
• the names and email addresses of two references who can provide letters of recommendation.

A knowledge security check can be part of the selection procedure. (For details: national knowledge security guidelines)