PhD Position in Computational Genomics

Job description

Are you passionate about neurodevelopment, brain diseases and the non-coding genome? Would you like to work in a highly dynamic environment at the interface of fundamental science, computational biology and applied human clinical genetics, directly benefiting patients? And all of that in a fun, young and international team at a top university? Then join our expanding research team as a PhD candidate!

Project overview

Neurodevelopmental disorders (NDDs) present a major cause of disability early in life and a significant burden to the health system. Despite improved diagnostic yield of genetic testing, our understanding of NDD disease mechanisms remains incomplete. Most currently used diagnostic modalities trying to identify genetic causes focus on protein-coding genes. The remaining 98% of the human genome has much less attention, but might harbor many hidden causes of NDDs. 

This PhD project will focus on the role of the non-coding genome in causing NDDs, focusing on advanced computational models integrating functional genomics data. 

Your research: 

We have previously used advanced massively parallel reporter assays (ChIP-STARR-seq) to characterize gene regulatory elements (enhancers) in several neural cell types. More recently, we have developed the BRAIN-MAGNET artificial intelligence algorithm (Cell 2025) that is trained on these functional genomics data. BRAIN-MAGNET allows to predict which nucleotides within an enhancer are required for their function. In the current PhD project, we aim to make the next step, developing sequence to function AI models for genomics that are trained on novel functional genomics data sets for human brain development (including single cell massively parallel reporter assays and other multi-omics data from brain organoids). This will improve our knowledge on brain gene regulation and gain novel means to interpret functionality of non-coding variants playing a role in disease. Our groups integration within the clinical genetics department will allow to test the impact of such models on real live data from NDD patients, ultimately aiming to improve their health journey.   

Our comprehensive approach to understanding NDDs and the role of the non-coding genome offers excellent opportunities for your scientific development as a PhD candidate and creates a multilayered picture of the disease that can help develop new care strategies for patients.

Work environment

The Barakat lab was established in 2017 at Erasmus MC, and focusses on deciphering molecular mechanisms leading to neurodevelopmental disorders, with a particular interest in the role of the non-coding genome and gene regulation. Using functional-genomics and computational approaches we aim to understand the gene-regulatory-landscape in cells representing neurodevelopment.

Our long-term goal is to translate our research findings to the clinic, where we aim to develop novel diagnostics and therapies focusing on the so far, so often, neglected non-coding regions of the human genome. Next to our interest in fundamental gene-regulation, we apply disease-modelling for neurodevelopmental disorders using genome-engineering, induced pluripotent stem-cells, brain-organoids, and zebrafish. We routinely use a variety of next generation sequencing based techniques in our research, including RNA-seq, ATAC-seq, ChIP-seq, Cut & Run, and chromatin conformation capture technologies, creating rich data sets that can be integrated within the project.  

Our highly international group, currently consisting of 15 members, is strongly embedded in the department of Clinical Genetics, and forms an important bridge between research and clinic, ultimately leading to advancements for patients. Since 2017, we have published >70 papers (majority in top-10 journals, including a recent paper in Cell) describing new disease entities and mechanisms. And have obtained > 7 million euro funding (including competitive grants from CURE Epilepsy, EpilepsieNL, ZonMw Veni, ZonMw Vidi) and have been awarded a number of prizes, including an KNAW Early Career Award.

Previous PhD students in the lab have successfully moved into postdoc positions both in academia as well as industry. 

Some of our more recent work includes: 

1) BRAIN-MAGNET: A functional genomics atlas for interpretation of non-coding variants.

Deng et al, Cell. 2025  doi: 10.1016/j.cell.2025.10.029.

2) Clinical utility of DNA-methylation signatures in routine diagnostics for neurodevelopmental disorders.

Smits et al  Eur J Hum Genet. 2025 doi: 10.1038/s41431-025-01919-5.

3) Mutations in the small nuclear RNA gene RNU2-2 cause a severe neurodevelopmental disorder with prominent epilepsy.

Greene et al, Nat Genet. 2025 doi: 10.1038/s41588-025-02159-5.

4) AMFR dysfunction causes autosomal recessive spastic paraplegia in human that is amenable to statin treatment in a preclinical model.

Deng et al, Acta Neuropathol. 2023 doi: 10.1007/s00401-023-02579-9.

5) Comprehensive multi-omics integration identifies differentially active enhancers during human brain development with clinical relevance.

Yousefi et al, Genome Med. 2021 doi: 10.1186/s13073-021-00980-1

6) Expanding the mutational landscape and clinical phenotype of the YIF1B related brain disorder.

Medico Salsench et al, Brain. 2021 doi: 10.1093/brain/awab297

7) Delineating the molecular and phenotypic spectrum of the SETD1B-related syndrome.

Weerts et al, Genet Med. 2021 doi: 10.1038/s41436-021-01246-2

8) Bi-allelic variants in HOPS complex subunit VPS41 cause cerebellar ataxia and abnormal membrane trafficking.

Sanderson et al, Brain. 2021 doi: 10.1093/brain/awaa459

9) BICRA, a SWI/SNF Complex Member, Is Associated with BAF-Disorder Related Phenotypes in Humans and Model Organisms.

Barish S et al, Am J Hum Genet. 2020  doi: 10.1016/j.ajhg.2020.11.003.

10) Loss of UGP2 in brain leads to a severe epileptic encephalopathy, emphasizing that bi-allelic isoform-specific start-loss mutations of essential genes can cause genetic diseases.

Perenthaler et al, Acta Neuropathol. 2020  doi: 10.1007/s00401-019-02109-6

11) Functional Dissection of the Enhancer Repertoire in Human Embryonic Stem Cells.

Barakat et al, Cell Stem Cell. 2018. doi: 10.1016/j.stem.2018.06.014

Some of our work broadcasted in the media: 

https://amazingerasmusmc.com/genetics/discovery-of-a-new-syndrome-brings-answers-to-hundreds-of-patients-with-developmental-delay/ 

https://amazingerasmusmc.com/brain/signposts-for-genetically-unexplained-brain-disorders/

https://amazingerasmusmc.com/genetics/zebrafish-and-stem-cells-solve-medical-conundrum/

https://amazingerasmusmc.com/brain/quest-why-more-boys-than-girls-with-rare-syndrome/

https://amazingerasmusmc.com/brain/discoverers-of-very-rare-form-of-epilepsy-now-on-track-to-treatment/ 

Qualifications and skills

You are a highly motivated, curious and creative young scientist. Also you are a hardworking team player with strong problem-solving skills and broad interests. Further:

• You have successfully obtained a Master's degree (or will shortly graduate) in the field of Bioinformatics, Computer Science, Artifical intelligence, Medicine, Health Science, Life Science, Molecular Biology, or a related field.
• You have a strong computational background, and previously applied this during your training to human genomics data. You have knowledge and interest in deep learning models, especially those applied to human genomics.
• You have experience in Linux-based environments and strong programming skills in Python and/or R. Experience with machine learning or deep learning, particularly applied to genomic or biomedical data, is considered a plus.
• You have a solid understanding of neurobiology and molecular biology, with affinity for human genetics.
• You have an excellent academic track record and strong motivation to pursue a scientific career. Prior contribution to peer-reviewed scientific publications is a plus.
• You are highly communicative with good verbal and written English language skills (minimal IELTS 7.0, TOEFL 100 or equivalent) and you are willing to share your knowledge with other group members.
• You are preferably available the latest from May 1st, 2026 onwards.

Before you apply please check our conditions for employment.

Terms of employment

• You will receive a temporary position for 4 years.
• The gross monthly salary amounts a minimum of € 3.108,- and a maximum of € 3.939,- (scale OIO).
• Excellent fringe benefits, such as a 13th month that is already paid out in November and a individual travel expense package.
• An International Office which aids you in preparing for you arrival and stay.
• Pension insurance with ABP. We take care of approximately 2/3 of the monthly contribution.
• Special benefits, such as a incompany physiotherapist and bicycle repairer. And there is also a gym where you can work on your fitness after work. 

More information

Do you have questions about the role? Feel free to reach out to dr. Kristina Lanko, assistant professor, via k.lanko@erasmusmc.nl or dr. Ruizhi Deng, postdoc, via r.deng@erasmusmc.nl. 

You can also contact dr. Stefan Barakat, associate professor and head of the group, via t.barakat@erasmusmc.nl.

No agencies please.