PhD Position in Neuroimaging, LLM, Genetics and Cross-species comparison

Vrije Universiteit Amsterdam; Amsterdam; On-site; EUR 36,000 - 45,000; Full time

Benefits offered by this job

ABP pension

Commuting allowance

Holiday allowance 8%

End-of-year bonus 8.3%

Personalized benefits package

Job summary

Vrije Universiteit Amsterdam invites applications for a highly motivated PhD candidate to join the Connectome Lab at CNCR. The project explores how brain variation relates to evolution using large human and cross-species datasets, with emphasis on LLM-assisted data mining.

You will work on structural, diffusion, and resting-state MRI across individuals and species. You will collaborate with interdisciplinary researchers and contribute to reproducible workflows, manuscripts and teaching

Qualifications

• Master degree in neuroscience or quantitative field.
• Hands-on experience with computational analysis is important.
• Experience with FreeSurfer, FSL and GWAS is advantageous.
• Proficiency in Python, MATLAB, R and Bash; AI/LLM familiarity is a plus.
• Experience with large neuroimaging datasets and replication of analyses.

Responsibilities

• Analyze large-scale structural MRI, diffusion MRI and resting-state fMRI datasets.
• Develop pipelines for cortical reconstruction, tractography and functional connectivity.
• Investigate individual variation and neurodiversity in brain structure and connectivity.
• Integrate genetics with neuroimaging.
• Perform cross-species analyses in context of brain evolution.
• Integrate findings across datasets and imaging modalities.
• Apply computational and statistical methods for brain networks.
• Contribute to reproducible neuroimaging workflows.
• Collaborate within CNCR and international networks.
• Present findings at national and international meetings.
• Prepare scientific manuscripts and contribute to teaching.

Skills

Computational analysis

Scientific programming

Python

MATLAB

R

Bash

AI/LLM

Education

MSc in neuroscience or related quantitative field

Tools

FreeSurfer

FSL

GWAS

High-performance computing

Job description

Job description

Do you enjoy working with complex neuroimaging data, large datasets and computational methods? Do you want to work at the intersection of genetics, neuroimaging, neuroscience, neurodiversity and cross-species analyses? We are looking for a highly motivated PhD candidate to join the Connectome Lab at Vrije Universiteit Amsterdam

The Connectome Lab at the Center for Neurogenomics and Cognitive Research (CNCR), Vrije Universiteit Amsterdam, is seeking a PhD candidate in Neuroimaging, Genetics and Cross-species comparison.

The project aims to understand how variation in brain anatomy and connectivity contributes to the remarkable diversity of the human brain, and how these features relate to principles of brain evolution. We will combine large-scale human neuroimaging datasets with comparative datasets across species to investigate variation in brain structure, connectivity and functional organization.

A central goal is to understand which aspects of brain organization are highly conserved, which show substantial variation between individuals, and which features may have emerged or expanded during human brain evolution. The project therefore brings together neuroimaging, connectomics, neurodiversity, comparative neuroscience and computational neuroscience.

You will work with large structural MRI, diffusion MRI and resting-state fMRI datasets and develop and apply computational approaches to quantify variation in brain organization across individuals, populations and species. There is particularly attention for the use of LLM in data mining.

You will be part of the computational neuroimaging Lab led by Prof. Martijn van den Heuvel and work in an interdisciplinary environment with researchers from neuroimaging, computational neuroscience, genetics, psychology, psychiatry and artificial intelligence.

Your duties

• analyse large-scale structural MRI, diffusion MRI and resting-state fMRI datasets
• develop and apply pipelines for cortical reconstruction, tractography, functional connectivity and connectome analysis
• investigate individual variation and neurodiversity in brain structure and connectivity
• integrate genetics with neuroimaging
• perform comparative analyses of human and non-human brain organization in the context of brain evolution
• integrate findings across different neuroimaging datasets and imaging modalities
• develop and apply computational and statistical approaches for analysing brain networks
• contribute to reproducible and open neuroimaging workflows
• collaborate with researchers within the Connectome Lab, CNCR and international research networks
• present your findings at national and international scientific meetings
• write scientific manuscripts
• contribute to teaching activities where appropriate

Requirements

• MSc degree in neuroscience, neuroimaging, genetics, biomedical engineering, physics, computer science, artificial intelligence, mathematics, psychology, biology, or a related quantitative discipline.
• Hands-on experience with computational analysis is important.
• Ideally, you have experience with several of the following:
• structural MRI and cortical reconstruction, including FreeSurfer
• Genetics (GWAS)
• diffusion-weighted MRI (DWI), tractography and structural connectivity
• resting-state fMRI and functional connectivity analysis
• FSL and other commonly used neuroimaging software packages
• Experience with AI / LLM
• processing and quality control of neuroimaging datasets
• connectome and network neuroscience analyses
• Strong interest in and experience with
• scientific programming
• is essential. You should have experience with
• Python, MATLAB, R, Bash and/or comparable languages
• , and be comfortable working with computational analysis pipelines.
• Experience with one or more of the following would be an advantage:
• large-scale neuroimaging datasets such as UK Biobank, HCP or comparable resources
• comparative or cross-species neuroimaging
• brain atlases, surface-based analysis and registration
• machine learning or multivariate statistics
• high-performance computing
• version control and reproducible research workflows
• network science and computational modelling

We are particularly interested in candidates who enjoy working with complex data, think critically about methodology, and are motivated to develop strong computational and neuroimaging expertise. You should also have a strong interest in neurodiversity and/or evolution, be able to work independently while enjoying collaboration within a multidisciplinary team, have good analytical and problem-solving skills, have a good command of written and spoken English, be motivated to learn new neuroimaging and computational techniques, support open and reproducible science and be willing to share tools and data with the wider scientific community.

As a university, we strive for equal opportunities for all, recognising that diversity takes many forms. We believe that diversity in all its complexity is invaluable for the quality of our teaching, research and service. We are always looking for talent with diverse backgrounds and experiences. This also means that we are committed to creating an inclusive community so that we can use diversity as an asset.

We realise that each individual brings a unique set of skills, expertise and mindset. Therefore we are happy to invite anyone who recognises themselves in the profile to apply, even if you do not meet all the requirements.

Conditions of employment

Fixed-term contract: 1 year.

A challenging position in a socially engaged organisation. At VU Amsterdam, you contribute to education, research and service for a better world. And that is valuable. So in return for your efforts, we offer you:

a salary of minimum € 3.204,00 (PhD year 1) and maximum € 4.051 (PhD year 4) gross per month, on a full-time basis. This is based on UFO profile PhD candidate.

a 4-year PhD position (initial 1-year contract, extended by 3 years following positive evaluation).

We also offer you attractive fringe benefits and regulations. Some examples:

• a full-time 38-hour working week comes with a holiday leave entitlement of 232 hours per year. If you choose to work 40 hours, you have 96 extra holiday leave hours on an annual basis. For part-timers, this is calculated pro rata.
• 8% holiday allowance and 8.3% end-of-year bonus
• solid pension scheme (ABP)
• contribution to commuting expenses
• optional model for designing a personalized benefits package

Employer

Vrije Universiteit Amsterdam

Research environment

You will join the Connectome Lab of prof Van den Heuvel at Vrije Universiteit Amsterdam. Our research focuses on understanding the architecture of the human brain and how its network organization relates to cognition, individual variation, brain disorders and evolution. You will work in a multidisciplinary team of PhD candidates, postdoctoral researchers and students with backgrounds spanning neuroimaging, network neuroscience, genetics, artificial intelligence, computational neuroscience and psychology. The project is embedded within the Center for Neurogenomics and Cognitive Research (CNCR), providing a highly interdisciplinary research environment and opportunities for collaboration within VU Amsterdam and with national and international research groups.

Faculty of Science

Working at the Faculty of Science means collaborating with students, lecturers and researchers who are focused on their field, yet have a broad view of the world. We are proud of a positive and inclusive workplace culture within the faculty, where we work together with great energy and a pragmatic attitude to tackle social challenges. At the Faculty of Science, scientists and students work on fundamental and complex societal issues for a sustainable, healthy and just future.

From forest fires to big data, from obesity to malnutrition, from helium to the universe and from genetics to medicine: our education and research cover the full breadth of science, from molecules to mankind.

Our academic education and research are highly experimental, technical and interdisciplinary in nature. That is why we collaborate extensively with leading scientific institutes and industry. The faculty has more than 8,000 students studying in one of the 39 programms and employs more than 1,400 staff across 10 scientific departments, making us one of the largest science faculties in the Netherlands.

Vrije Universiteit Amsterdam stands for values-driven education and research. We are open-minded experts with the ability to think freely - a broader mind. Maintaining an entrepreneurial perspective and concentrating on diversity, significance and humanity, we work on sustainable solutions with social impact. By joining forces, across the boundaries of disciplines, we work towards a better world for people and planet. Together we create a safe and respectful working and study climate, and an inspiring environment for education and research.

Learn more about our codes of conduct

We are located on one physical campus, in the heart of Amsterdam's Zuidas business district, with excellent location and accessibility. Over 6,150 staff work at the VU and over 31,000 students attend academic education.

Diversity

Diversity is the driving force of VU Amsterdam. VU wants to be accessible and receptive to diversity in disciplines, cultures, ideas, nationalities, beliefs, preferences and worldviews. We believe that trust, respect, interest and differences lead to new insights and innovation, to sharpness and clarity, to excellence and a broader understanding.

We stand for an inclusive community and believe that diversity and internationalisation contribute to the quality of education, research and our services.

Therefore, we are always searching for people whose backgrounds and experience contribute to the diversity of the VU community.