PhD position in genome evolution and architecture in unicellular eukaryotes

Are you fascinated by how eukaryotic genomes evolve? Do you want to look beyond model organisms and point mutations to uncover the complexity of genome evolution? Are you excited to use computational approaches to explore how genome architecture shapes evolution in a collaborative and stimulating environment? We offer a PhD position in our diverse research team in the Laboratory of Microbiology at Wageningen University & Research. As a PhD candidate, you will investigate how 3D chromosome folding influence how the genomes of unicellular eukaryotes evolve.

What will you do?
In this PhD project, you will study the genome evolution and architecture – including 3D folding - of understudied unicellular eukaryotes, using the latest computational approaches.

As PhD candidate in our lab, you will:

• utilize cutting-edge bioinformatics tools to trace the evolution of genomes, genes and proteins, including phylogenetic analyses and reconstructions;
• use new genomic data to characterize the large-scale and small-scale genome architectures of understudied eukaryotic microbes;
• deepen our understanding of eukaryotes’ diversification and origins;
• have the opportunity to pursue your own research questions and implement your ideas;
• work independently and develop your own research questions within the project;
• contribute to teaching in our courses and supervising BSc and MSc thesis students;
• work in a stimulating environment that combines evolutionary and cellular research on eukaryotes and prokaryotes, in a team operating at the forefront of unravelling the deep origins of eukaryotic cells, and we are expanding our explorations of the understudied world of eukaryotic microbes.

Even though this is a computational project, it offers possibilities to work on eukaryotic microbes in the wet lab.

Why?
Understanding how genomes evolve is fundamental to explaining species diversity and adaptation. Compared with prokaryotes, eukaryotic genomes show a greater structural and functional plasticity, with a larger genome size, a higher proportion of non-coding regions and a more complex 3D chromosome organization. Notably, genome evolution is not only driven by small mutations, but also by larger changes, including chromosome rearrangements and horizontal gene transfer. How and why such changes occur is still an open question, in particular for eukaryotic microbes, which dominate the eukaryotic tree of life but remain poorly studied. Recent studies, conducted in model organisms, suggest that these changes are induced by how chromosomes are folded in 3D. This 3D folding of the chromosomes typically allows distant genomic regions to interact. To gain a deeper understanding of genome evolution, including in non-model organisms, taking 3D chromosome folding into account is a promising direction.

You will work here
This PhD position is embedded within the Laboratory of Microbiology, and part of the Genome Evolution and Dynamics in Eukaryotes (GEDE) group, which is led by Dr. Jolien van Hooff. You will be co-supervised by Dr. Ursula Oggenfuss. We aim to get this position filled by March 2027.

Medewerker Onderwijs Service Centrum (tijdelijk, 0,8 - 1,0 fte)

Als medewerker studentenzaken ben je een onmisbare schakel in de ondersteuning van studenten, docenten en opleidingen. Je zorgt ervoor dat onderwijsprocessen soepel verlopen en dat digitale onderwijssystemen optimaal zijn ingericht en worden beheerd. Vanuit jouw expertise help je studenten bij complexe vragen, ondersteun je onderwijscoördinatoren en programmadirecteuren en draag je bij aan een kwalitatief hoogwaardige dienstverlening. Daarbij werk je nauw samen met diverse collega's en denk je (pro)actief mee over verbeteringen in processen en dienstverlening.

Je belangrijkste werkzaamheden zijn:

• Implementeren, beheren en optimaliseren van digitale onderwijssystemen (Thesis Management Systeem, Curriculuminformatiesysteem, etc.) en ondersteunen van onderwijsprocessen, zoals aanmeldingen, roostering, inschrijvingen en digitale tentaminering.
• Adviseren en begeleiden van studenten bij complexe vraagstukken en zorgen voor heldere informatievoorziening richting studenten en docenten.
• Ondersteunen van onderwijscoördinatoren en programmadirecteuren op het gebied van onderwijs- en studentenadministratie.
• Organiseren van onderwijsgerelateerde activiteiten, waaronder introductiedagen en diploma-uitreikingen.
• Signaleren van verbeterkansen, ondersteunen van overlegstructuren en vertegenwoordigen van het Onderwijs Service Centrum in relevante overleggen.

Assistant Professor of Ethics and Political Philosophy

The Department of Philosophy at Vrije Universiteit Amsterdam invites applications for the position of Assistant Professor of Ethics and Political Philosophy.

We are looking for a philosopher with a research profile in both ethics and political philosophy. Expertise in the philosophy of economics is an advantage. The successful candidate will contribute to the Department’s interdisciplinary research and teaching profile and participate actively in its academic community.

Teaching responsibilities will focus on introductory courses in ethics and political philosophy in the bachelor’s programmes PPE, Philosophy, and other bachelor’s programmes at Vrije Universiteit Amsterdam. The successful candidate will also develop a Master course for the track Ethics, Economics and Policy, and teach in the track Philosophy, Bioethics and Health.

Note, this is an entry-level faculty position suited for early-career scholars and is not intended for senior applicants currently at or near the Associate Professor level.

Your duties
As Assistant Professor, you will:

• conduct internationally relevant research in ethics and political philosophy;
• publish your research in appropriate academic journals, books, or edited volumes;
• actively pursue external research funding, including grant opportunities for early-career researchers, individually and in collaboration with colleagues;
• teach bachelor’s and master’s courses in ethics and political philosophy;
• supervise bachelor’s and master’s theses, particularly in the Philosophy, Politics and Economics bachelor’s programme and the Ethics, Economics and Policy and Philosophy, Bioethics and Health master’s programmes;
• contribute to the development, coordination, and evaluation of courses and curricula;
• participate actively in the research and educational activities of the Ethics Group, the Department of Philosophy, and the John Stuart Mill College; and
• undertake a proportionate share of administrative and organisational responsibilities within the Department.

Postdoc Category Theory, Computer Proof Assistants and Computer Algebra Systems

Job description

Computer proof assistants and computer algebra systems have complementary strengths. A proof assistant checks each step of a mathematical argument against a formal foundation, but is not designed for computation; a computer algebra system computes efficiently with large and intricate algebraic structures, but its results depend on code that has not been formally verified. Category theory is a good place to connect the two. CAP (Categories, Algorithms, Programming) is a software system for computational category theory, implemented in GAP and part of the homalg project. Because it expresses categorical constructions directly as algorithms, it is a suitable target for formalisation. The aim of the project is to bring the two kinds of system together, so that categorical computations can be carried out with the efficiency of a computer algebra system and checked with the guarantees of a proof assistant.

The postdoctoral researcher will design and build this connection between a proof assistant — Rocq, Lean or Agda, to be decided at the start of the project — and CAP. The work is partly conceptual and partly practical: making the categorical doctrines underlying CAP precise enough to formalise, choosing a formal treatment that is faithful to the constructive content of CAP's algorithms, and implementing the result as documented, openly available software. The researcher will publish the results, present them at conferences and workshops, and contribute to the open-source libraries of both projects. There is room to shape the direction of the work according to their own interests and expertise, and to develop their own research agenda alongside it.

The position is based in the Programming Languages group, Department of Software Technology, at TU Delft, where the researcher will work with Benedikt Ahrens, and in collaboration with Mohamed Barakat at Universität Siegen, with regular exchange between the two groups. This connects the researcher to both of the relevant communities: formalisation and univalent foundations in Delft, computational category theory and the homalg/CAP ecosystem in Siegen. The role also includes contributing to the supervision of BSc and MSc students working on related projects, and possibly some classroom teaching.

Job requirements
Applications will be evaluated on the following criteria:

• PhD (awarded by the start date, or submitted with a defence scheduled) in mathematics, computer science, or a closely related field
• Research experience in at least one of: interactive theorem proving/formalisation, computer algebra, or category theory — demonstrated by publications, a thesis, or a substantial software contribution
• Demonstrable interest in the other two, and willingness to learn them to working depth
• Practical programming ability and comfort working with a substantial existing codebase
• Ability to work independently and to collaborate across the maths/CS boundary; good written and spoken English
• Experience in, and willingness to contribute to, student supervision and teaching

TU Delft (Delft University of Technology)
Delft University of Technology is built on strong foundations. As creators of the world-famous Dutch waterworks and pioneers in biotech, TU Delft is a top international university combining science, engineering and design. It delivers world class results in education, research and innovation to address challenges in the areas of energy, climate, mobility, health and digital society. For generations, our engineers have proven to be entrepreneurial problem-solvers, both in business and in a social context.

At TU Delft we embrace diversity as one of our core values and we actively engage to be a university where you feel at home and can flourish. We value different perspectives and qualities. We believe this makes our work more innovative, the TU Delft community more vibrant and the world more just. Together, we imagine, invent and create solutions using technology to have a positive impact on a global scale. That is why we invite you to apply. Your application will receive fair consideration.

Challenge. Change. Impact!

Faculty of Electrical Engineering, Mathematics and Computer Science
The Faculty of Electrical Engineering, Mathematics and Computer Science (EEMCS) brings together three scientific disciplines. Combined, they reinforce each other and are the driving force behind the technology we all use in our daily lives. Technology such as the electricity grid, which our faculty is helping to make completely sustainable and future-proof. At the same time, we are developing the chips and sensors of the future, whilst also setting the foundations for the software technologies to run on this new generation of equipment – which of course includes AI. Meanwhile we are pushing the limits of applied mathematics, for example mapping out disease processes using single cell data, and using mathematics to simulate gigantic ash plumes after a volcanic eruption. In other words: there is plenty of room at the faculty for ground-breaking research. We educate innovative engineers and have excellent labs and facilities that underline our strong international position. In total, more than 1000 employees and 4,000 students work and study in this innovative environment.

Click here to go to the website of the Faculty of Electrical Engineering, Mathematics and Computer Science.

PhD student - Traumatic Brain Injury

Team
A PhD position is available in the Neurogenesis & Neurodegeneration group at the Netherlands Institute for Neuroscience in Amsterdam. The Neurogenesis & Neurodegeneration laboratory led by Evgenia Salta employs transcriptomics and other molecular and cellular approaches to map the cellular and molecular complexity of the adult human hippocampus and dissect the biological pathways that are deregulated in dementia. The team employs primarily human postmortem brain tissue and iPSC reprogramming.

Project
The project is funded by the Dutch Research Council (NWO) Open Competition and is a collaboration between the Netherlands Institute for Neuroscience (NIN) and the Swammerdam Institute of Life Sciences (SILS) at the University of Amsterdam.
Repeated mild head injuries, the kind sustained by athletes, veterans, and victims of domestic violence, are increasingly linked to long-term memory problems and a higher risk of dementia later in life. Strikingly, these lasting effects can occur even when no visible brain damage is present. Yet, we still don't understand how repeated injury leads to memory decline, and there are currently no treatments that address these long-term cognitive consequences.

Beyond helping high-risk groups, this work may also shed light on Alzheimer's and other dementias that share similar underlying processes.

The research will be performed at the Salta lab at the Netherlands Institute for Neuroscience in Amsterdam. This is a joint project with the group of Carlos Fitzsimons at the SILS, University of Amsterdam.
This study is a follow up of our previously published work:
https://www.cell.com/cell-stem-cell/fulltext/S1934-5909(26)00142-6
https://www.nature.com/articles/s41467-024-49299-6

What you will do
In this project, you will investigate what happens in the brain after repetitive mild traumatic brain injury, focusing on the hippocampus, the brain region central to memory. We are particularly interested in long-lasting inflammatory and neurogenic alterations and the cells involved in them, including microglia, astrocytes and immature neurons. By uncovering these mechanisms, you will help us to identify cellular or molecular targets that could guide the development of future therapies.

As a PhD candidate in our group, you will use state-of-the art single-nucleus RNA sequencing pipelines to process postmortem human brain from donors with a record of traumatic brain injury. You will be in charge of sample collection and stratification and apply advanced computational pipelines to identify cellular and molecular programs involved in the hippocampal response to injury and the downstream cognitive effects. Ultimately, you will establish in vitro human cell models to probe causal relationships between candidate targets and cellular phenotypes.

What we expect from you

• A Master’s degree in biomedical sciences, neuroscience or similar
• Strong affinity and hands-on experience with coding and omics-related computational analyses are a prerequisite
• Strong affinity and hands-on experience with single-cell transcriptomics are a prerequisite
• Strong experience with (iPSC) cell culture is a plus
• Excellent communication skills, as well as proficiency in spoken and written English, are expected
• Strong organizational skills, methodical and structured approach to your work, rigor, accuracy and attention to detail
• A reliable, collaborative team player who is easy to work with and delivers on commitments
• Genuine passion for scientific research
• Drive, persistence and positive attitude to tackle difficult problems that require iterative approaches, while systematically checking results against expectations to catch issues early

What we offer

• A stimulating, innovative and dynamic international research environment
• Opportunity to work with novel, exciting datasets and develop creative concepts and pipelines
• A strong community of care, support and scientific challenge
• Access to state-of-the art infrastructure and work conditions
• Active mentoring, supervision and training
• Opportunities for personal growth
• A particularly collaborative setting between the NIN and the SILS
• Possibility to develop your own projects and apply for third-party funding

The position is for a period of 4 years in total. The first appointment is for one year with the option for an extension for the remaining period pending on evaluation.

Information
For additional information, please contact Dr. E. Salta. e.salta@nin.knaw.nl
More information about the laboratory can be found on: Salta - Netherlands Institute for Neuroscience - Master the Mind (nin.nl) & https://saltalab.github.io/

Application and deadline
You can apply before December 1, 2026 via the button Apply Now.

Please send:

• A detailed CV
• A motivation letter, including a brief description of past research experience and future interests, as well as the earliest possible starting date and the name and contact details of at least two referees

Evaluation of candidates will begin immediately, and continue until the position is filled.