PhD positions in the Horizon Europe MSCA Doctoral Network SPACE-MEL (2)

Job description

SPACE-MEL is an EU-funded MSCA Doctoral Network advancing the next generation of spatial single-cell omics technologies for precision medicine. Bringing together leading European universities, technology providers, clinical partners and innovative companies, the programme will address key experimental and computational challenges currently limiting the clinical translation of spatial biology. By integrating multi-omics approaches, enabling the transition from 2D to 3D tissue analysis and developing advanced data interpretation methods, SPACE-MEL aims to unlock deeper insights into cellular organisation and disease mechanisms. The network will train 15 Doctoral Candidates through an interdisciplinary programme spanning spatial imaging technologies, molecular biology, computational biology, pathology and biomarker discovery. Through cross-sectoral secondments, hands-on research and comprehensive transferable-skills training, SPACE-MEL will equip a new generation of researchers with end-to-end expertise in spatial biology and strengthen Europe’s leadership in this rapidly evolving field.

What SPACE-MEL will offer

• A thorough scientific education in the frame of a doctoral training program.
• The possibility to participate in specific international courses, workshops and conferences.
• A strong involvement in a European research project with high international visibility.
• The possibility to perform research visits to internationally renowned research labs in Europe.
• A prestigious three-year MSCA Fellowship.
• A competitive salary including mobility and family allowances.

Eligibility criteria

• Supported researchers: Applicants must be doctoral candidates, i.e. not already in possession of a doctoral degree at the date of the recruitment. Researchers who have successfully defended their PhD thesis but not yet received their degree are not considered eligible.

• Mobility Rule: Researchers must not have resided or carried out their main activity (work, studies, etc.) in the country of the recruiting beneficiary for more than 12 months in the 36 months immediately before their recruitment date.

• Local requirements: Applicants must fulfil the local requirements of the recruiting institutions listed in the project descriptions below.

DC2: 3D spatial FUN-G&T-seq and/or scNMT-seq

Host institution: Erasmus University Medical Centre Rotterdam (EMC-a), Department of Molecular Genetics, Rotterdam, Netherlands

Supervisor: Dr. Miao-Ping Chien

Co-supervisors: Prof. Thierry Voet, Katholieke Universiteit Leuven, Department of Human Genetics, Belgium (Academic); Dr. Domenico Bellomo, SkylineDx B.V., Netherlands (Industry)

Project description: 

DC2 will develop a 3D spatial FUN-G&T-seq and/or scNMT-seq workflow for multimodal profiling of melanoma models and tissue samples. The project will translate the protocol developed by DC3 into 3D melanoma organoid and immune cell co-cultures, fresh 200-400 μm tissue sections or explant samples. It pursues two integrated objectives: i) establish a methodology for 3D spatial FUN-G&T-seq and/or spatial scNMT-seq; ii) apply this workflow to profile tumour and immune cells in melanoma organoid co-cultures and live tissue slices.

At Erasmus MC, the candidate will work to combine spatial FUNseq with single-cell genome and transcriptome sequencing and/or single-cell nucleosome, methylation and transcriptome sequencing. The workflow will be adapted to 3D light-sheet microscopy and thick melanoma samples, addressing challenges linked to image quality, cell selection, tissue depth and multimodal data integration. During a secondment with Dr. Chien’s group, the candidate will receive training in spatial FUNseq and image-guided single-cell isolation. A second secondment at SkylineDx will explore the possible translation of emerging signatures towards a clinically oriented assay. Expected outcomes include an established 3D spatial FUN-G&T-seq and/or scNMT-seq methodology and multimodal maps of tumour and immune cell states in 3D melanoma models.

Work environment

Host laboratory

The PhD fellow will be based at Erasmus University Medical Center Rotterdam, in the Department of Molecular Genetics, under the supervision of Dr. Miao-Ping Chien. The group specialises in the development of single-cell and spatial omics technologies for cancer biology, with particular expertise in spatially resolved functional sequencing and image-guided isolation of target cells from heterogeneous samples. Erasmus MC provides a strong biomedical research environment spanning molecular genetics, dermatology, pathology, clinical bioinformatics and skin cancer research.

The host laboratory offers access to the spatial FUNseq platform, including custom-built UFO high-throughput screening microscopes for 2D and 3D imaging, real-time image analysis and selective isolation of target cells or single cells from regions of interest. The candidate will also benefit from cell culture facilities for patient-derived primary cultures and tissue slices, histology and IHC preparation platforms, and genomics and bioinformatics infrastructure for NGS-based analysis of genomes, epigenomes and transcriptomes. These resources provide the experimental and analytical setting required to establish 3D spatial functional multi-omics workflows for melanoma precision medicine.

Secondments: This project is carried out in strong collaboration with the following groups, and visits to their laboratories are expected during the project. A willingness to travel and spend time abroad is therefore essential:

• 6 months at Katholieke Universiteit Leuven, Department of Human Genetics, Belgium (supervisor: Prof. Thierry Voet)

• 3 months at SkylineDx B.V., Netherlands (supervisor: Dr. Domenico Bellomo)

Qualifications and skills

Eligibility conditions:

• Master’s degree in a relevant discipline (biomedical sciences, bioinformatics, omics technology, bioengineering, or cancer biology etcetera).
• Applicants must be doctoral candidates; not already in possession of a doctoral degree.
• Mobility rule: researchers must not have resided or carried out their main activity in the country of the recruiting beneficiary for more than 12 months in the 36 months immediately before their recruitment date.

Required skills: 

• For the wet-lab-focused PhD position, hands-on experience with next-generation sequencing (including single-cell sequencing) is a plus.
• For the dry-lab-focused PhD position, proficiency in one or more of the following is required: R, Python, and command-line programming.
• Proficiency in the English language is required, as well as good communication skills, both oral and written. Successful candidates will need to provide an English test (e.g. IELTS, TOEFL, Cambridge English). You may be exempt if you are a national of a majority native-English speaking country, or have qualifications / degree that has been taught and assessed in English. The supervisor may also confirm that a candidate has the required level of English.

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 €3.217 and a maximum of €4.077 (scale OIO).
• Excellent fringe benefits, such as a 13th month that is already paid out in November and an 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 an incompany physiotherapist and bicycle repairer. And there is also a gym where you can work on your fitness after work. 

More information

For additional information on this project, please contact Dr. Miao-Ping Chien (m.p.chien@erasmusmc.nl).

Apply using the blue button ont his page.

Required documents:

• Statement of interest explaining why you wish to be considered for the fellowship and which qualities and experience you will bring to the role.

• Curriculum vitae et studiorum.

• A certificate of University examinations taken (with marks).

• A final degree certificate translated in English. If, at the time of application, candidates should not be yet in possession of a degree certificate, they can submit it at the time of the examination. However, if successful, the candidate will be required to provide a translated and legalised certificate as proof of eligibility for doctoral admission.

A limited number of applicants will be invited for an interview and will be required to provide contact information of up to two contact person for reference letters.

No agencies please.