PhD Scholarship in Spatial Transcriptomics and Bioinformatics

The Brewer group at the Bioimaging section, Department of Biochemistry and Molecular Biology, invites applications from outstanding candidates who are interested in joining our group as a PhD student. The position is available from 1 September 2023, or as soon as possible thereafter. Application deadline: 29 July 2023.

The applicant will be working in the group of Associate Professor Jonathan Brewer at the Danish Molecular Biomedical Imaging Center (DaMBIC), but will also be integrated into the Center for Functional Genomics and Tissue Plasticity (ATLAS).

We are looking for a highly motivated candidate, who will work with development and application of data analysis tools for state-of-the-art spatial transcriptomics.

The revolution in single-cell transcriptomics have shown the need for spatially resolved technologies to visualize cellular diversity and interactions in the context of intact tissues. This has led to the recent development of new technologies to acquire full transcriptome-wide data at single cell level and with high spatial resolution. These new technologies are likely to transform our understanding of biological processes and human diseases and form the basis for development of new treatments.

The Brewer group is focused on state-of-the-art imaging-based technologies for spatial transcriptomics. We have implemented MERFISH technology to elucidate tissue microenvironments in both patient and animal biopsies and in complex disease models using engineered tissues. Specifically, we are developing three MERFISH platforms for spatial transcriptomics at different scales to visualize the transcriptome from whole tissue slices, down to transcript distribution and co-localization at the sub-organellar scale. The successful candidate will join a dynamic team working on spatial transcriptomics and will help develop analysis pipelines for the data. This will include implementing and combing tools for image analysis, MERFISH decoding, data visualization, and bioinformatics analysis.

The research focus for this position is to integrate these techniques with conventional transcriptomics, to characterize cell-cell and cell-extracellular matrix interactions in healthy and diseased human tissues focusing on adipose tissues, skin biopsies, and liver biopsies. Insight from the projects will help the understanding of cell plasticity in the context of their 3D environment.

PhD scholarship qualifications/requirements:
We are looking for a highly motivated, dedicated, and ambitious candidate with:
• A Master’s degree in Life Science, preferably Molecular Biology, Biomedicine, or Computational Systems Biology. If you have not yet completed your Master programme, you can apply to be enrolled in our 4+4 PhD programme, which is a way to commence the PhD study whilst concurrently completing the Master programme.
• Molecular biology skills such as qPCR and in vitro transcription for MERFISH probe design.
• Experience with single molecule localization microscopy (STORM).
• Experience with image analysis, bioinformatics, programing languages such as Python and R. Previous experience with MERFISH data analysis would be an advantage.
• Strong communication and collaborative skills and an interest in working in an interdisciplinary environment.
• Proficiency in spoken and written English.

We offer:
• A three-year (or four-year for BSc students) PhD position in a highly stimulating, supportive, international, and interdisciplinary research environment.
• Enrolment in PhD school of Biochemistry and Molecular Biology, which allows the candidate to tailor a flexible individualized course programme.
• Training in a wide range of skills including research management, communication, networking, presentations, writing of manuscripts etc.
• Research exchange to collaborating institution, depending on the interest of the PhD student.
• Mentoring and career development.
• Access to state-of-the-art equipment, facilities, and infrastructure.
• Opportunity to interact with an extensive network of national and international collaborators.
• A competitive salary and social benefits (e.g. health coverage, parental leave, social security etc.).
• Dedicated assistance and support with various practical, social, and legal aspects (housing, visa, administration, tax etc.), especially for international candidates through our international staff office (ISO) and department.

For further information on the project and position, please contact Associate Professor Jonathan Brewer, e-mail: [email protected], tel.: +45 6550 3505.

Application, salary etc.
Appointment as a PhD Research Fellow is for three (students who have completed their MSc) or four years (students who have not yet completed their
MSc). Employment stops automatically at the end of the period. The holder of the scholarship is not allowed to have other paid employment during the period.

The successful applicant will be employed in accordance with the agreement on salaried PhD scholars between the Ministry of Finance and AC (the Danish Confederation of Professional Associations). Please check links for more information on salary and taxation.

The successful candidate will be enrolled at this university in accordance with faculty regulations and the Danish Ministerial Order on the PhD Programme at the Universities (PhD order).

The University wishes our staff to reflect the diversity of society and thus welcomes applications from all qualified candidates regardless of personal background.

Application must be in English and made in the form of a Declaration of Interest including the following:
• A research proposal/description of your approach to the above project (max one page excluding references).
• A letter stating your specific interest, motivation and qualifications for the project in question (max. two pages) (please attach this under box "Application form").
• Detailed CV, including personal contact information, education, work/research experience and skills relevant for the position, publications/manuscripts.
• Copies of diplomas, Bachelor as well as Master’s degree, including transcript of notes/grades. If awaiting Master’s diploma, provide a written statement from the supervisor.
• At least two signed reference letters. Should your referees wish to send their letters directly to us, please have them use e-mail: [email protected] mentioning your name and the title of the position in the subject line. And please note that these also need to reach us before deadline.

Shortlisting may be used in the assessment process. Applicants will be informed of their assessment by the university. Applications will be evaluated by Associate Professor Jonathan Brewer and the ATLAS Center Director Professor Susanne Mandrup.

Further information about the PhD-study can be found at the homepage of the University.

Applications must be submitted electronically using the link "Apply online". Attached files must be in Adobe PDF or Word format. Each box can only contain a single file of max. 10 Mb. We strongly recommend that you read How to apply before you apply.

Incomplete applications and applications received after the deadline will neither be considered nor evaluated. This also applies to reference letters.

Further information for international applicants about entering and working in Denmark.