Open projects

Eva Kummer
Main host/supervisor
Biotech Research and Innovation Centre (BRIC), Faculty of Health and Medical Sciences, University of Copenhagen

Mads Hartvig Clausen
Interdisciplinary co-supervisor
Department of Chemistry, Technical University of Denmark

Description of the main host research group:

The Kummer group aims to uncover the molecular mechanisms that underlie genome maintenance and gene expression in non-nuclear systems. We are particularly interested in the proteins and protein complexes that mediate mitochondrial and viral DNA replication. Our main tools to study their mode of action are functional biochemical and biophysical assays combined with structural studies using single particle cryo-EM.

Description of the interdisciplinary co-supervisor group:

The Clausen research group has a special interest in chemical biology, i.e. using synthetic chemistry to provide tool compounds for answering biological questions. This overall research theme currently includes high-throughput screening (HTS) and fragment-based drug discovery (FBDD) against protein and RNA targets, medicinal chemistry related to oncology, inflammatory and infectious diseases, prodrug design and synthesis, vaccine development, plant polysaccharides, and new materials from plant cell wall components.

Fellow project opportunities:

• What?
  • The goal of the project is to identify novel inhibitory compounds for a viral helicase essential for replication and propagation of the widespread Herpes simplex viruses type 1 and type 2 (HSV-1/2). We will identify leads for such inhibitors and define their mode-of-action. Additionally, we will seek to improve their pharmacodynamic and pharmakokinetic properties in order to strengthen their potential for use in antiherpetic treatment in the future.
• How? 
  • The target protein will be recombinantly purified from insect cells. In collaboration with the DTU Screening Core HTS platform, a functional assay will be established as a read out for subsequent high-throughput compound screening. The screen will aim to identify novel inhibitors of the viral helicase. The hit compounds will then be verified in functional biochemical assays and in a cellular model. Moreover, we will assess how the compounds interact with the viral helicase to block function using single particle cryo-EM. Eventually, the compounds will be optimized in collaboration with the group of Mads H. Clausen to improve specificity, efficacy, and ADME properties.
• Why?
  • Human herpesviruses (HHVs) are one of the most widespread infections worldwide causing a range of diseases such as cold sores, mononucleosis, or even cancer. Lytic replication is a critical step in the viral life cycle and essential for viral survival in the human population. Antiherpetic medications such as the widely used nucleoside analogue acyclovir inhibit exclusively the viral DNA polymerase. However, resistance to current nucleoside analogs is emerging and alternative therapies remain scarce. In this project, we aim to identify alternative protein targets and new compounds for antiviral treatment.

Interdisciplinary aspects of the project:

This project will combine functional biochemistry and structural studies with high-throughput screening and medicinal chemistry to identify novel antiherpetic compounds and decipher their mode-of-action. The project will be carried out between the research group of Eva Kummer located in the Department of Health and Medical Sciences at the University of Copenhagen, and the group of Mads Hartvig Clausen from the Department of Chemistry at DTU. It will profit from state-of-the-art infrastructures at both sites including high-end microscopes for cryogenic electron microscopy and a fully automatic infrastructure for HTS.

Based on preliminary data in the Kummer group, the candidate will establish functional assays in the Kummer group that can be used as a read-out for high-throughput screening (HTS) to identify inhibitory compounds against the viral helicase. Training of the candidate in HTS will take place in the Clausen lab. The analysis of the HTS results as well as the verification of putative hits in biochemical and cellular assays will combine the expertise of the Clausen group in medicinal chemistry and of the Kummer group in functional biochemistry and herpesvirus research. Eventually, the binding site of the compound in the helicase will be identified by the candidate using single particle cryo-EM in the Kummer group. The structural insights will then be used to chemically optimize the compound for more effcient and specific binding to the viral helicase in collaboration with the Clausen group. Success of this project requires close collaboration between the interdisciplinary expertises present in the Kummer and Clausen labs. To be successful in this project, the candidate will therefore require a strong interdisciplinary mindset.

3 key competences required to take on the project:

To take on this project, a candidate must have prior education/experience within the following:

1. Basic experience in molecular biology
2. Basic knowledge/experience in recombinant protein production and/or purification
3. Basic knowledge/experience in biochemical, or biophysical, or structural assays to assess protein function

Cristian Bellodi
Main host/supervisor
Biotech Research and Innovation Centre (BRIC), Faculty of Health and Medical Sciences, University of Copenhagen

Mads H. Clausen
Interdisciplinary co-supervisor
Department of Chemistry, Technical University of Denmark (DTU)

Description of the main host research group:

My laboratory explores how prominent RNA modifications, including pseudouridine, regulate gene expression during development and tumorigenesis. A significant interest revolves around the role of pseudouridine-modifying proteins (PUS) in shaping molecular and cellular processes in stem and cancer cells. Using the immune system as a model, my team combines advanced genetics, sequencing, and biochemistry to uncover uncharted epitranscriptomic pathways driving normal and malignant hematopoiesis, aiming to innovate RNA-based cancer therapies.

Description of the interdisciplinary co-supervisor group:

The Clausen research group has a special interest in chemical biology, i.e. using synthetic chemistry to provide tool compounds for answering biological questions. This overall research theme currently includes HTS and FBDD against protein and RNA targets, medicinal chemistry related to oncology, inflammatory and infectious diseases, prodrug design and synthesis, vaccine development, plant polysaccharides, and new materials from plant cell wall components.

Fellow project opportunities:

• What?
  • To delineate how dysregulation RNA pseudouridylation shapes protein translation and contributes to molecular programs driving immune system aging and malignant transformation.

• How?
  • We will combine PUS-deficient genetic models and chemical screens to delineate RNA pseudouridylation-driven translational programs driving immune senesescence induced by genotoxic stress.
• Why?
  • Delineating epitranscriptomic programs that define immunosenescence may hold great promise for the treatment of various diseases common in aging population, from cardiovascular and autoimmune diseases to cancer.

Interdisciplinary aspects of the project:

The project aims to uncover how epitranscriptomic mechanisms, particularly RNA modifications, contribute to immune cell senescence and stress-induced alterations in hematopoietic stem cells (HSCs). Pseudouridine is the most abundant RNA modification in living cells and holds key roles in regulating gene expression in development and disease. Our previous work identified pseudouridine synthases (PUS) as drivers of protein translation and inflammation in HSCs through transfer RNA-derived fragments (tdRs). However, how pseudouridine reprograms gene expression to influence immune fate under stress remains unknown.

 We will use PUS-deficient models and human cell systems to define how PUS-dependent epitranscriptome and translatome remodeling triggers immune senescence and malignant transformation. By integrating cutting-edge genome editing and sequencing methods with mechanistic studies, we aim to reveal how tdR pseudouridylation shapes translational programs in response to genotoxic and metabolic stress. Furthermore, we will explore the therapeutic potential of harnessing PUS activity to modulate RNA pseudouridylation and control immune cell senescence and function. To this end, we will perform high-throughput screens (HTS) using a curated compound library of lead-like small molecules together with cell-based and biochemical assay to identify small molecule inhibitors targeting specific PUS writer complexes in dysfunctional HSC, and possibly other relevant immune cell types.

 Given that dysregulation of RNA pseudouridylation and protein synthesis underlies the etiology of autoimmune disorders and hematological cancers, these studies hold great promise for the development of innovative therapeutic strategies for modulating PUS activity in autoimmune disorders and hematological cancers.

3 key competences required to take on the project:

To take on this project, a candidate must have prior education/experience within the following:

1. Immunology
2. RNA biology
3. Proteomics

Shohreh Issazadeh-Navikas
Main host/supervisor
Biotech Research and Innovation Centre (BRIC), Faculty of Health and Medical Sciences, University of Copenhagen

Erwin Schoof
Interdisciplinary co-supervisor
Department of Biotechnology and Biomedicine, Technical University of Denmark

Description of the main host research group:

The Issazadeh-Navikas group focuses on neuronal immunity, the interaction between the immune and central nervous system (CNS), and specifically, the cross-regulation between immune genes and neurons in the CNS. The lab utilizes state-of-the-art bioinformatic analysis of unbiased next-generation sequencing (NGS), mtDNA sequencing, and single cell multi-OMICs data (transcriptomic, proteomic, lipidomic etc.) of brain and immune system of Parkinson’s disease, multiple sclerosis patients, and models, to enhance the understanding of how immune-related genes, protein and lipids influence the function and biology of neurons and other resident or infiltrating cells in the CNS.

Description of the interdisciplinary co-supervisor group

The research goal of “Cell Diversity Lab” is to develop and apply methods to understand how cell diversity, and the molecular landscapes thereof, contribute to complex biological phenotypes. As the main molecular effectors, proteins play a critical role in defining cell function, and thus the quantitative exploration of protein signaling has been a major driving force of Schoof’s laboratory. The main aim is to understand the complexity of biology and how we need to embrace the necessary integration of multiple technologies and computational analysis to truly understand biological phenomena.

Fellow project opportunities:

• What?
  • The basis of the current project is the state-of-the-art bioinformatic analysis of unbiased single cell multi-OMICs (transcriptomic, proteomic, lipidomic etc.) data of brain and immune system. Subsequently, the independent OMICs datasets are integrated and subjected to advanced machine learning and data mining techniques.
• How?
  • Data integration and analysis of various OMIC datasets is achieved adopting existing bioinformatics tools and our available HPC facilities. When necessary, novel computational tools and bioinformatics pipelines are developed (Python, R and Nextflow). The focus will be on increasing the precision and resolution in identifying novel biological pathways and molecular mechanisms. These findings will then be further validated in the lab experimentally (both in-vitro and in-vivo) in collaboration with other lab members.
• Why?
  • Neurodegenerative diseases associated with aging, such as Parkinson’s disease, are increasingly prevalent in developing societies, imposing significant personal suffering and societal burdens. Despite their high impact, no cures currently exist for these diseases, as their underlying causes remain poorly understood. The goal is to enhance the understanding of how immune-related genes, protein and lipids influence the function and biology of neurons and other resident or infiltrating cells in CNS. Defects or deficiencies in these immune genes/proteins likely contribute to neurodegeneration and the associated neuroinflammation.

Interdisciplinary aspects of the project:

This project integrates computational sciences, bioinformatics and neuroimmunology to achieve its objectives. The host lab has established leading expertise in utilizing computational tools for analyzing OMICs data in neuroscience and neuroimmunology, while the co-supervisor has a strong track record and leading position in developing different tools at single cell resolution to study the proteomic profile of cells in diverse organs and tissues.

3 key competences required to take on the project:

To take on this project, a candidate must have prior education/experience within the following:

1. Bioinformatic and computational science
2. Familiar with multiOMICs analysis
3. Cell, molecular, and/or neurobiology

Lars Henning Engelholm
Main host/supervisor
Biotech Research & Innovation Centre (BRIC), University of Copenhagen and The Finsen Laboratory/Rigshospitalet

Katrine Qvortrup
Interdisciplinary co-supervisor
Department of Chemistry, Technical University of Denmark (DTU)

Description of the main host research group:

The Engelholm Group investigates tumor–stroma interactions and receptor-mediated uptake mechanisms in cancer. We develop innovative antibody–drug conjugates (ADCs) targeting actionable receptors involved in tissue remodeling and cancer invasion, combining antibody engineering, advanced histopathology, and in vivo disease modeling. The group has generated multiple first-in-class ADCs forming the foundation of the spin-outs Adcendo and PanTarg, both advancing towards clinical translation.

Description of the interdisciplinary co-supervisor group:

The Qvortrup Group develops chemical and bioconjugation strategies for targeted drug delivery, with particular focus on site-selective antibody modification, peptide shuttles, and cleavable linkers for controlled release. The team applies modern organic synthesis and chemical biology to design precision therapeutics, including antibody–drug conjugates (ADCs) and brain-penetrating ligands. Their work bridges chemistry and translational drug design through collaborations with academia and industry.

Fellow project opportunities:

This PhD project focuses on developing antibody–drug conjugates (ADCs) with improved intracellular routing to ensure efficient payload release within lysosomes. While many ADCs are internalized after target binding, only a fraction reach the degradative compartments required for drug liberation. The fellow will work at the interface between molecular oncology and chemical biology to design ADCs that harness receptors with strong lysosomal trafficking behavior and incorporate chemical linkers tuned for enzymatic or pH-dependent cleavage.

The project will integrate antibody engineering and expression at BRIC/Finsen with the design and synthesis of site-specific linkers and payload conjugates at DTU Chemistry. Organic linker synthesis and bioconjugation will be performed by the Qvortrup Group at DTU Chemistry. The fellow will interact closely with chemists to select linker designs and evaluate their behaviour, while focusing primarily on biological characterization and trafficking analysis. The fellow will perform cellular uptake and trafficking analyses using live-cell imaging, lysosomal colocalization assays, and subcellular fractionation to map ADC fate and quantify payload release. Functional evaluation will include in vitro cytotoxicity studies, 3D tumor spheroids, and in vivo xenograft models to correlate lysosomal delivery efficiency with therapeutic outcome.

By combining molecular design and mechanistic trafficking analysis, the project addresses a central limitation in current ADCs—inefficient intracellular drug release. The results are expected to provide generalizable principles for enhancing ADC potency and selectivity. Embedded in a translational and innovation-driven environment, the fellow will also gain experience with interdisciplinary collaboration, intellectual property generation, and the full preclinical development pipeline, fully aligned with INTERACT’s mission to train researchers at the interface of chemistry and biomedicine.

Interdisciplinary aspects of the project:

The project combines biological ADC development at BRIC/Finsen with chemical linker design and conjugation strategies at DTU Chemistry, building a strong bridge between molecular oncology and synthetic chemistry. The project merges synthetic chemistry and linker engineering at DTU Chemistry with mechanistic trafficking and ADC biology at BRIC, creating a strong interdisciplinary bridge. The fellow will acquire cross-disciplinary expertise ranging from antibody molecular biology, mammalian expression, and receptor trafficking analysis to organic synthesis, linker optimization, and bioconjugation. This includes exposure to advanced microscopy, protein chemistry, and the use of fluorescent and cleavable linkers to visualize drug release in living systems.

Both research environments are highly translational and innovation-focused. The Engelholm Group has founded the spin-outs Adcendo and PanTarg, while the Qvortrup Group collaborates extensively with industry and has co-founded DISPERAZOL. Within this joint setting, the fellow will gain practical insight into innovation workflows—from discovery and validation to preclinical proof-of-concept—alongside training in entrepreneurship, patenting, and interdisciplinary project management. Together, the two groups provide an ideal framework for developing a convergence-science mindset and translating cross-disciplinary science into next-generation ADC therapeutics.

3 key competences required to take on the project:

To take on this project, a candidate must have prior education/experience within the following:

1. Basic knowledge of protein biochemistry and molecular cloning.
2. Hands-on experience with cell culture, microscopy, or biochemical assays.
3. The project includes in vivo studies; therefore, candidates should hold — or be willing to obtain — a FELASA certification and demonstrate motivation to work with animal models as part of the experimental training.

Joachim Weischenfeldt
Main host/supervisor
Biotech Research and Innovation Centre (BRIC), Faculty of Health and Medical Sciences, University of Cpenhagen

Erwin Schoof
Interdisciplinary co-supervisor
Department of Biotechnology and Biomedicine, Technical University of Denmark

Lisa Maria Riedmayr

Interdisciplinary co-supervisor

Department of Biotechnology and Biomedicine, Technical University of Denmark

Description of the main host research group:

• Mutational processes in cancer
• Impact of genomic alterations on 3D chromatin
• Mechanisms of clonal selection and evolution in cancer

Description of the interdisciplinary co-supervisor group:

The research goal of “Cell Diversity Lab” is to develop and apply methods to understand how cell diversity, and the molecular landscapes thereof, contribute to complex biological phenotypes. As the main molecular effectors, proteins play a critical role in defining cell function, and thus the quantitative exploration of protein signaling has been a major driving force of Schoof’s laboratory. The main aim is to understand the complexity of biology and how we need to embrace the necessary integration of multiple technologies and computational analysis to truly understand biological phenomena.

• Development of precision medicine technologies
• Engineering of new CRISPR tools
• Advancing iPSC-derived model systems

Fellow project opportunities:

• What:
  • 3D chromatin organisation is critical to constrain and control gene regulation. Our lab has recently identified a mechanism where somatic alterations alter 3D chromatin domains leading to dysregulation of nearby cancer gene expression. The aim of the project is to elucidate how somatic alteration can impact 3D chromatin organisation and gene regulation in cis.
• How:
  • The PhD student will pursue highly integrative and cross-disciplinary research involving CRISPR-based genome engineering and bioinformatic analysis of chromatin and genomic dataset.
• Why:
  • The non-protein coding genome has critical functions in genome maintenance and gene regulation. The project will provide novel insights into the functional consequences of chromatin changes in cancer.

Interdisciplinary aspects of the project:

The 3D chromatin organization plays crucial roles in genome maintenance and gene regulation. Structural variation (SV)-mediated changes of the 3D chromatin can cause profound transcriptional dysregulation, contributing to congenital diseases such as limb malformation and drive cancer gene dysregulation by enhancer hijacking. Using large mult-omic data, we have recently found several large chromatin domains to be recurrently altered in cancers, but the mechanisms and DNA-sequence contexts are poorly understood. he PhD student candidate will pursue both state-of-the art cancer genomic (main supervisor expertise) and CRISPR-based engineering approaches (co-supervisor expertise) to perturb and investigate how changes in 3D chromatin alter gene expression in cancer.

3 key competences required to take on the project:

To take on this project, a candidate must have prior education/experience within the following:

1. Molecular biology
2. Genetics and epigenetics
3. Bioinformatics

Jesper Bøje Andersen
Main host/supervisor
Biotech Research and Innovation Centre, Faculty of Health and Medical Sciences, University of Copenhagen

Sine Reker Hadrup
Interdisciplinary co-supervisor
Department of Health Technology, Technical University of Denmark

Description of the main host research group:

The Andersen group utilizes genome-wide approaches in modeling liver and bile duct cancers, stratifying patients for advancing diagnostic and prognostic biomarkers, and novel therapeutic options. Our research is focused into 3 main project themes: i) Immunogenomics, ii) metabolism, and iii) epigenomic remodeling. The outcome of our research is to significantly guide novel treatment modalities and impact the clinic to improve patients’ outcomes.

Description of the interdisciplinary co-supervisor group:

In the T cell & cancer research group we are devoted to characterize T cell recognition in the context of diseases – as such we have contributed significantly to the development of multiplex strategies for T cell detection to comprehensively evaluate T cell reactivity in both cancer and autoimmune diseases.

Fellow project opportunities:

• What?

  • All tumors evade immune destruction, but the mechanisms by which this is accomplished differ between patients. In intrahepatic cholangiocarcinoma, the Andersen group has shown that anti-tumor immunity is corrupted at the earliest point of the cancer-immunity cycle¹ in patients who rapidly progress on chemotherapy². Before treatment, these tumor tissues are characterized by myeloid enrichment, lymphocyte depletion, and suppressed cytotoxic activity. It remains unclear how some tumors (rapid progressor- or RP-like tumors) but not others (long survivor- or LS-like tumors) have autonomy to blunt initiation of the immune response from the earliest steps of antigen presentation and/or immune cell priming followed by activation. Some clues, however, might lie in the developmental origin(s) of these tumors – liver epithelia (which create the tumor) and specialized liver-resident immune cells (which patrol the tumor) possess unique immunoregulatory capabilities, as part of their physiological roles in mediating tolerance to food antigens and commensal microbes. Therefore, it is plausible (if not, likely) that some tumors have innate potential for hijacking these immunosuppressive mechanisms, creating a microenvironment that is permissive to tumor development and associated with rapid treatment failure.

 We are offering a bright and engaged PhD student an ambitious project as part of the INTERACT COFUND PhD Program that involves undertaking the challenge to identify tumor mechanisms fuelling the above phenomenon by comparing tumor antigenicity and immune cell activation between RP- and LS-like tumors.

• How?
  • If you undertake this challenging project, you will have a unique supervisor team, including an internal daily supervisor. You will have access to detailed knowledge about human biology (disease focused in liver and bile duct cancers), translational cancer genomics, and bioinformatics (Andersen group, BRIC), as well as immunology, T cell recognition, neopeptide cancer research (peptidomics), and molecular barcoding (T cells and Cancer group, xTI at DTU).

We have cell models that match the RP-like and LS-like patient tumor phenotypes. Experimental techniques are envisioned to include in vitro (co-)cultures, immunopeptidomics, immunophenotyping with high-dimensional flow cytometry, spatial transcriptomics, and multiplexed immunohistochemical staining with high degree of knowledge in bioinformatics and genomics. Accomplishing these goals will advance our biological knowledge of pathological immune tolerance in the liver microenvironment, as well as identify candidate mechanisms for modulation in the immune-oncology space.

•  Why?
  • If you undertake this collaborative project, you will be part of a team that aims to develop the next immunotherapy for one of the most deadliest malignancies, which also compared to other cancers types is on the rise with a predicted 400% the next decade. This PhD project will be the first step to undertand what happens when the early steps in the cancer immunity cycle are corrupted.  The interplay of bile duct cancer biology, genomics,  and T cell immunology is a key feature of the project.

Interdisciplinary aspects of the project:

If you undertake this collaborative project, you will take part in a team crossing two different research groups within two very different fields. You will also have a leg at two different universities – Department of Health and Medical Science, University of Copenhagen and Health Tech at the Technical University of Denmark (DTU). As such, the interdisciplinary aspects of this PhD project rest on the collaboration between the Andersen group (BRIC) and T cells and Cancer group (xTI, DTU). The project involves aspects on human cell biology (molecular biology, genomics) and immunology (immunopeptidomics, TCR-seq, T cell activation) and application of bioinformatic resources in both laboratories related to the technologies above. The workflow will integrate knowledge of cell and disease biology by MHC class I and II assessment in RP- and LS-like cell models, co-culture of cancer cell lines with PBMC-derived dendritic cells to engage antigen processing and presentation, T cell stimulation and co-stimulatory signals to prime and activate T cells, as well as T cell characterization by high-dimensional flow cytometry, CITE-seq and/or TCR-seq.

3 key competences required to take on the project:

To take on this project, a candidate must have prior education/experience within the following:

1. T cell immunology;
2. Bioinformatics is a clear advantage if you know R language;
3. Cell culture is nice to have

Bjarne Winther Kristensen
Main host/supervisor
Biotech Research and Innovation Center (BRIC), Faculty of Health and Medical Sciences, University of Copenhagen

Erwin Schoof
Interdisciplinary co-supervisor
Department of Biotechnology and Biomedicine, Technical University of Denmark

Description of the main host research group:

Glioblastoma is the most frequent and malignant type of brain cancer with poor survival outcomes for most patients. Novel therapeutic targets and strategies that overcome the efficient mechanisms of resistance are urgently needed. Our aim is to identify novel targets and to understand and overcome mechanisms of resistance in the microenvironment of glioblastomas. This is obtained by patient tissue and model systems combined with single cell and spatial mass spectrometry-based proteomics and transcriptomics. We would like to recruit for the proteomics part.

Description of the interdisciplinary co-supervisor group:

Our mission in the Cell Diversity Lab is to unravel fundamental biological concepts controlling heterogeneity within complex biological systems, especially those of the blood system and cancer. We aim to use our leading position in the field of scp-MS to identify druggable signalling mechanisms that will advance therapy and diagnostics for patients suffering from complex diseases. 
By computationally integrating several experimental approaches such as Mass Spectrometry (MS), Next-Generation Sequencing, FACS sorting and in vivo xenograft models, we aim to gain a better understanding of cellular signal processing at the single cell level.

Fellow project opportunities:

• We interrogate ecosystems and the spatial cellular organization of cells in glioblastoma. This includes (1) the tumor core, (2) the transition zone where the cancer cells start infiltrating the brain and (3) the outer regions where cancer cells have infiltrated into the brain. We focus on the interactions between tumor cells and the microenvironment. The microenvironment is heterogenous leading to potentially different mechanisms of resistance. Adding to the complexity, there is a high frequency of non-tumor cells in glioblastomas leading to potential critical cross-talk between tumor cells and microglia/macrophages and other cell types.
• We use singe-cell and spatial mass spectrometry-based proteomics to investigate cellular diversity and spatial organization of patient brain cancer tissue as well as tissue and cells in in vitro and in vivo patient-derived brain cancer models. We have existing spatial and single cell data sets (see paper examples from our groups in Nature Comm and Science (PMID: 39251578; PMID: 40839704) and we plan to generate novel comprehensive datasets based on RNA and especially proteins in this project. As the cellular workhorses, protein-level data enables us to achieve a more comprehensive understanding of the biology including cellular crosstalk compared to previous studies that are overwhelmingly relying on RNA-data alone.
• Understanding the spatial organization of glioblastoma and thereby the heterogeneity and identity of individual cell is critical in order to develop novel successful therapies.
• With the breadth of data that will be collected, advanced bioinformatics approaches will be applied to model the molecular landscapes of glioblastoma. With several workflows already established in R and Python, this project will further strengthen our spatial bioinformatics portfolio together with other senior lab members in the Kristensen and Schoof groups.

Interdisciplinary aspects of the project (max half page)

The interdisciplinary aspects will cover single-cell and spatial mass spectrometry-based proteomics on patient-derived glioblastoma samples and samples from experimental glioblastoma models to understand the spatial ecosystems in glioblastoma, overcome mechanisms of resistance and identify novel targets. We expect to obtain insights into tumor cell-microenvironment interactions in the different ecosystems and uncover critical cellular interactions driving cellular differential programs and aggressiveness. We will be striving towards single-cell and spatial data-informed understanding of glioblastoma, that will increase our understanding of how we can target these tumors. We aim at being able both to discover and test targets within the project we will develop.

3 key competences required to take on the project:

To take on this project, a candidate must have prior education/experience within the following:

1. Knowledge in human biology
2. Proteomics
3. Experimental research in vitro and in vivo

Chiara Francavilla
Main host/supervisor
Section of Medical Biotechnology, DTU Bioengineering, Technical University of Denmark

Janine Erler
Interdisciplinary co-supervisor
Biotech Research & Innovation Centre, Faculty of Health and Medical Sciences, University of Copenhagen

Erwin Schoof
Interdisciplinary co-supervisor
Section of Medical Biotechnology, DTU Bioengineering, Technical University of Denmark

Description of the main host research group:

•  https://www.chiarafrancavilla.eu/

The Cell Signalling Architecture team studies the principles and the regulation of cellular signalling in a variety of mammalian cell models using a system biology approach which combines biochemistry with quantitative omics – specifically phosphoproteomics - and bioinformatics. The ambition of our research is to identify and characterize novel signalling proteins that can be targeted for personalized intervention in human diseases, particularly breast cancer.

Description of the interdisciplinary co-supervisor group:

• https://researchprofiles.ku.dk/da/persons/janine-erler/

The overall aim of the Erler Lab Group is to identify and develop novel effective therapeutic strategies against metastasis for clinical translation in order to increase cancer patient survival. The main areas of research include cancer biology, tumour microenvironment (e.g. hypoxia), and metastasis.

The Cell Diversity lab unravel fundamental biological concepts controlling heterogeneity within complex biological systems, especially those of the blood system and cancer.The group develops and applies single cell proteomics to identify druggable signalling mechanisms that will advance therapy and diagnostics for patients suffering from complex diseases. 

Fellow project opportunities: 

• What?
  • To study how changes in nutrients and oxygen affect cell signalling cascades in breast cancer cells
  • To uncover how such changes affect cell fate decisions including the balance between cell proliferation, motility, and death
• How? 
  • Mammalian cell co-culture in two and three dimensions also using hypoxic cabinet
  • Biochemistry methods
  • Quantitative proteomics and phosphoproteomics technologies
  • Single cell proteomics
  • Bioinformatics tools for data analysis
• Why? 

  • Changes in the extracellular environment determine cell fate, including formation of metastasis and response to therapies, but we do not know the molecular determinants underlying changes in signalling cascades. This project will reveal such molecular determinants by combining cutting-edge co-cultures, quantitative omics, bioinformatics for data analysis, and functional assays in vitro, ex vivo, and, possibly, in patient material.

Interdisciplinary aspects of the project:

The candidate will mainly work in the laboratory of Chiara Francavilla (CF) learning and applying biochemistry, proteomics/phosphoprotoemics, and bioinformatics methods. The project is in collaboration with a wet lab-based postdoc and a bioinformatician who will offer not only training in such methods but also an international and collaborative environment to discuss results and ideas. In the lab of Janine Erler (JE) the candiate will learn advanced cancer biology methods to grow breast cancer cells upon perturbations of the microenvironment. These cells models will be then analysed using system biology in CF’s team and by single cell proteomics in ES’s team.The novel proten targets identified by these approaches will be then validated by functional assays in CF’s and JE’s teams. Regular meetings with the main supervisors, ad hoc meetings with all the supervisor team, and participation to group lab meetings will be planned since the beginning and warmly encouraged.

3 key competences required to take on the project:

To take on this project, a candidate must have prior education/experience within the following:

1. Mammalian cell culture
2. Cell biology and biochemistry assays (including immunoblotting, cell proliferation assays, etc)
3. Knowledge of cancer biology and signalling or metabolism

Jenny Emnéus
Main host/supervisor
Department of Biotechnology and Biomedicine, Technical University of Denmark

Ala Trusina
Interdisciplinary co-supervisor
Niels Bohr Institute, Faculty os Science, University of Copenhagen

Description of the main host research group:

Our research is focused on developing optoelectrical microfluidic tools that incorporate electrodes and optical waveguides for real time studies of cells and organoids with emphasis on neurodegenerative diseases. Our current focus is on the development of compartmentalised organoid-on-chip systems, in which we connect organoids from different brain regions, forming so called connectoids, that we further use to study Parkinson´s disease (PD).

Description of the interdisciplinary co-supervisor group:

The group is interested in how populations of cells self-organize to achieve complex behaviours. One direction in our group is on understanding inter- and intra-cellular coordination to respond to stresses or pattern into appropriate cell types. Another direction is how complex forms and shapes emerge during the development of organs and organoids.

Fellow project opportunities:

• What?
  • The overall objective is to develop a Digital Twin based on our on-going research of developing an in vitro nigrostriatal pathway (NSP) connectoid model to study PD.
• How?
  • This will be achieved by connecting stem cell-derived brain organoids, representing substantia nigra and striatum of the NSP, in compartmentalised microfluidic chips. Time resolved measurement data (e.g. bioimaging, neurotransmitter detection, RNA sequencing etc) will be collected at different time points during the connectoid maturation process, which will serve as the basis for mathematical modelling to generate a Digital Twin. The typical workflow will consist of: 1) building a minimal model, consisting of e.g. a set of differential equations that describe intra- and inter-cellular regulatory networks (RN) controlling cell differentiation and neurotransmitter spatio-temporal dynamics. 2) Validate model against the collected time-resolved data. 3) Use validated model to predict the most effective interventions to the RN. 4) Test predictions experimentally, and if needed, use the intervention data to refine the model.
• Why?
• There is currently no cure for Parkinson’s disease (PD), and its underlying causes remain poorly understood. Existing animal and cell-based models fail to accurately reproduce the complexity of the human disease, limiting their translational value. To overcome these challenges, there is an urgent need for advanced human in vitro 3D models that more faithfully mimic the physiological and pathological features of the human brain. A Digital Twin model derived from a chip-based connectoid system represents a fundamentally novel approach with the potential to bridge this gap. Such a model would enable in silico studies of therapeutic intervention, such as pharmacological treatments or cell-based therapies and could ultimately support the development of personalized treatment strategies based on patient-derived cells.

Interdisciplinary aspects of the project:

This PhD project is inherently interdisciplinary, bridging the borders between biology, engineering, and computational science to advance our understanding of Parkinson’s disease. By integrating organoid-on-chip technology with digital twin modelling, the project combines cutting-edge experimental systems that mimic human neurophysiology with computational approaches capable of predicting disease dynamics and treatment responses.

The project requires collaborative expertise in stem cell research, microfluidics, biomaterials, and bioimaging, as well as expertise in data analysis, modelling, and simulation. Expertise on medical biotechnology, organoid-on-chips, and bioanalysis (provided by the Emnéus group) and mathematical modelling and computational biology (provided by the Trusina group) will be supported by external co-supervisor Gunnar Cedersund at Linköping university in Sweden, with prior expertise on developing Digital Twins based on organ-on-chip devices (https://liu.se/en/employee/gunce57). It would however be valuable that the candidate has an interest in or has prior exposure to programming and mathematical modelling of biological systems.

The candidate will operate at the intersection of these fields - translating biological insight into quantitative models, and computational predictions into experimentally testable hypotheses. Through this convergence of disciplines, the project aims to establish a novel framework for studying neurodegenerative diseases in a human-relevant and mechanistically informed manner.

3 key competences required to take on the project:

To take on this project, a candidate must have prior education/experience within the following:

1. Degree in biotechnology, biomedical engineering, or a related field
2. Experience with mammalian culture and microscopy
3. Experience with molecular techniques

Susanne Brix Pedersen
Main host/supervisor
Department of Biotechnology and Biomedicine, Technical University of Denmark

Nikos Hatzakis
Interdisciplinary co-supervisor
Department of Chemistry, Faculty of Science, University of Copenhagen

Description of the main host research group:

The group studies host–microbe interactions with focus on immune modulation by pathogens, commensals, and diet in early life and during chronic inflammation. Using longitudinal cohorts, they apply association and mediation analyses to identify mechanistic links, and test causality through targeted interventions. Experimental models include human cell cultures, co-culture systems, and in vivo models to characterize microbe-metabolite-immune interactions of relevance in health and disease.

Description of the interdisciplinary co-supervisor group:

The vision is to understand biology one molecule at a time. They strive to provide a dynamic and quantitative understanding in structural and cell biology and to utilize this information to control aberrant biological function. This challenge is approach with an eclectic mix of quantitative single particle microscopy techniques and machine learning analysis.

Fellow project opportunities:

• What?
  • Colorectal cancer is a leading cause of cancer-related death globally. Emerging evidence suggests that microbial metabolites from fermented foods can influence colorectal cancer risk by modulating both the gut microbiota and immune responses. 

• How?
  • This project investigates the molecular mechanisms by which specific bioactive compounds produced during fermentation of e.g. medicinal herbs - particularly phenyllactic acid (PLA) and indole-3-lactic acid (ILA) - may prevent or modulate colorectal cancer. The project integrates metabolomics, microbiome analysis, transcriptomics, and advanced imaging to uncover how fermented foods can be engineered as therapeutic tools in cancer prevention. After training and in close collaboration with team members, the candidate will perform: (i) microbial fermentation assays to determine metabolite production pathways in lactic acid bacteria; (ii) metabolomics and targeted LC-MS/MS profiling to identify and quantify fermentation-derived metabolites; (iii) bioactivity screening assays using in vitro co-culture systems to identify dual-active metabolites with both anti-biofilm and immunomodulatory properties; (iv) transcriptomics and single-cell RNA sequencing to assess host cell responses; (v) advanced bioimaging (confocal, super-resolution, and single-molecule microscopy) to visualize metabolite–cell interactions; (vi) data integration for correlating metabolite profiles with functional outcomes.
• Why?
  • Ultimately, this work seeks to elucidate host–pathogen interactions and develop novel therapeutic strategies. It focuses on the discovery and mechanistic characterization of microbial metabolites that can be harnessed for colorectal cancer prevention.

Interdisciplinary aspects of the project:

This project exemplifies a highly interdisciplinary approach, integrating expertise from immunology, microbiology, metabolomics, structural biology, and advanced imaging to investigate the preventive potential of fermented foods in colorectal cancer. The host research group at DTU Bioengineering brings deep expertise in host–microbe interactions and immune modulation. Complementing this, the co-supervisor group at UCPH Chemistry, led by Prof. Nikos Hatzakis, contributes cutting-edge capabilities in single-molecule microscopy, 4D imaging, and machine learning–based analysis. This enables high-resolution visualization and quantification of molecular interactions between bioactive compounds, immune cells, and cancer-associated biofilms. Together, the teams will dissect how specific fermentation-derived metabolites such as phenyllactic acid (PLA) and indole-3-lactic acid (ILA) modulate immune responses and microbial ecology at cellular and molecular levels. The project also involves Prof Ismail Gögenur, Zealand University hospital who is an expert in colorectal cancer surgery, and provides access to clinical material from patients.

By bridging molecular immunology, microbial ecology, and biophysical imaging of clinical patient materials, the project fosters a unique synergy that allows for mechanistic insights into cancer prevention strategies. This interdisciplinary collaboration not only strengthens the scientific rigor of the project but also ensures translational relevance from compound identification to clinical application.

3 key competences required to take on the project:

To take on this project, a candidate must have prior education/experience within the following:

1. Immunology and host-microbe interactions
2. Microbial fermentations
3. Data integration

Susanne Brix Pedersen
Main host/supervisor
Department of Biotechnology and Biomecine, Technological University of Denmark

Ole Lund
Interdisciplinary co-supervisor
Department of Health Technology, Technological University of Denmark

Description of the main host research group:

The group studies host–microbe interactions with focus on immune modulation by pathogens, commensals, and diet in early life and during chronic inflammation. Using longitudinal cohorts, they apply association and mediation analyses to identify mechanistic links, and test causality through targeted interventions. Experimental models include human cell cultures, co-culture systems, and in vivo models to characterize microbe-metabolite-immune interactions of relevance in health and disease.

Description of the interdisciplinary co-supervisor group:

The group develops advanced machine learning systems to decode biological patterns and predict biological responses. By integrating biological insight with data-driven algorithms, they aim to tailor medical interventions to individual patients. Their work focuses on receptor–ligand interactions and immune system dynamics, using pattern recognition to advance personalized healthcare and deepen our understanding of disease mechanisms.

Fellow project opportunities:

• What?
  • Chronic intestinal inflammation, as seen in inflammatory bowel disease (IBD), is increasingly recognized as a key disruptor of gut–brain axis homeostasis. This PhD project aims to unravel the molecular and cellular mechanisms underlying gut–brain axis dysregulation in IBD using longitudinal multi-omics profiling and advanced data integration models. 
• How?
  • Drawing on deeply phenotyped cohorts and data from the PRECISE-IBD initiative, the study will integrate genomics, transcriptomics, proteomics, and microbiome data across multiple time points. Plasma proteomics will be used to identify circulating biomarkers and protein quantitative trait loci (pQTLs) associated with systemic immune signalling. Single-cell RNA and ATAC sequencing of intestinal biopsies will enable high-resolution mapping of immune cell dysregulation and epithelial barrier alterations. Host–microbiome interactions will be explored through deep metagenomic sequencing and in silico analysis of microbial metabolites. Machine learning will be applied to construct patient-specific molecular trajectories and define novel subtypes of gut–brain axis perturbation. 
• Why?
  • Ultimately, this work seeks to provide mechanistic insights into how chronic intestinal inflammation influences systemic and neurological health.

Interdisciplinary aspects of the project:

This PhD project bridges immunology, microbiome science, and computational biology to unravel gut–brain axis dysregulation in chronic intestinal inflammation. The host group at DTU Bioengineering, led by Prof. Susanne Brix Pedersen, brings expertise in host–microbe interactions and immune modulation, using longitudinal cohorts and experimental models to uncover mechanistic links between microbial metabolites and immune responses. Complementing this, the co-supervisor group at DTU Health Tech, led by Prof. Ole Lund, specializes in developing machine learning algorithms for biological pattern recognition and personalized medicine. Their work enables predictive modeling of immune responses and receptor–ligand interactions. The project also includes collaboration with Prof, MD Johan Burisch, Copenhagen University Hospital - Amager and Hvidovre who heads the Copenhagen Center for Inflammatory Bowel Disease in Children, Adolescents and Adults, and provides advice, biomaterials and data from longitudinally patient cohorts to the project.

Together, the project integrates multi-omics data—including genomics, transcriptomics, proteomics, and microbiome profiles—with advanced computational tools to define molecular trajectories and novel subtypes of gut–brain axis perturbation. This interdisciplinary collaboration ensures both mechanistic depth and translational relevance, advancing our understanding of how chronic intestinal inflammation impacts systemic and neurological health.

3 key competences required to take on the project:

To take on this project, a candidate must have prior education/experience within the following:

1. Computational biology and bioinformatics, including experience with multi-omics data integration and proficiency in programming (e.g., R or Python).
2. Statistical modeling and machine learning for biological data, including familiarity with dimensionality reduction, clustering, and predictive modeling.
3. Chronic inflammation biology, with a solid understanding of host–microbe interactions.

Erwin Schoof
Main host/supervisor
Department of Biotechnology and Biomedicine, Technical University of Denmark

Joachim Weischenfeldt
Interdisciplinary co-supervisor
Biotech Research and Innovation Centre (BRIC), Faculty of Health and Medical Sciences, University of Copenhagen

Lisa Maria Riedmayr
Interdisciplinary co-supervisor
Department of Biotechnology and Biomedicine, Technical University of Denmark

Description of the main host research group:

• Cellular heterogneity in complex biological systems
• Single-cell and ultra–low input multi-omics (Mass spectrometry, next-generation sequencing, FACS)
• Signal processing and druggable signalling pathways in complex diseases

Description of the interdisciplinary co-supervisor group:

Joachim Weishenfeldt:

• Mutational processes in cancer
• Impact of genomic alterations on 3D chromatin
• Mechanisms of clonal selection and evolution in cancer

Lisa Reidmayr:

In this group, we aim to develop novel tools to accelerate next-generation gene and cell therapies, making them more effective, safer, and affordable. We combine expertise in CRISPR technologies, and innovative therapeutic design to create safer and more precise treatments by engineering CRISPR tools and synthetic DNA elements. Our highly integrative approach merges computational analyses of large-scale multiomic datasets with wet lab methods, such as pooled library designs and high-throughput screening.

Fellow project opportunities:

• What:
  • This project aims to develop a CRISPR-driven selection system that selectively eliminates cancer cells based on their RNA and protein expression profiles, while sparing healthy cells. Recent advances in CRISPR tools enable the specific detection of differentially expressed transcripts, which will serve as the basis for this system. The project will focus on glioblastoma as a model for cancer currently lacking effective treatment options.
• How:
  • The PhD student will pursue highly interdisciplinary project involving single cell RNA-Seq and mass spectrometry, patient-derived glioblastoma models and CRISPR technology.
• Why:
  • Current cancer treatments often damage healthy tissue, leading to severe side effects and reduced quality of life. A CRISPR-based selection tool that can specifically recognize and eliminate malignant cells has the potential to provide safer, more precise therapies, reduce off-target toxicity, and ultimately improve outcomes for patients.

Interdisciplinary aspects of the project:

Glioblastoma remains one of the most lethal cancers and currently lacks effective treatment options. This project addresses this unmet clinical need by developing a CRISPR-based precision cell selection system that can be administered globally while selectively eliminating glioblastoma cells based on their RNA and protein expression profiles and sparing healthy cells.

The work is highly interdisciplinary, integrating single-cell transcriptomics, quantitative proteomics, data science, cancer biology and CRISPR techology. The PhD student will combine single-cell RNA sequencing and mass spectrometry–based proteomics (main host expertise) with state-of-the-art patient-derived glioblastoma model systems (interdisciplinary co-supervisor expertise), multiomics data analysis and CRISPR tools (co-supervisor expertise) to identify and exploit cancer-specific expression signatures. The project builds on the work of Lisa Riedmayr, who will closely guide the PhD student as day-to-day supervisor.

The availability of suitable glioblastoma models as well as the integration of multi-omic datasets will be essential to define robust molecular markers for selective targeting, and design of the CRISPR tools. By bridging cancer biology, proteomics, CRISPR therapy, and systems-level data analysis, this project provides a genuinely cross-disciplinary training environment and aims to lay the groundwork for more precise, less toxic therapeutic strategies in glioblastoma and other hard-to-treat cancers.

3 key competences required to take on the project:

To take on this project, a candidate must have prior education/experience within the following:

1. CRISPR technology
2. Molecular biology methods
3. Large scale biological data sets

Jenny Emnéus
Main host/supervisor
Department of Biotechnology and Biomedicine, Technical University of Denmark

Eva Kummer
Interdisciplinary co-supervisor
Biotech Research and Innovation Centre (BRIC), Faculty of Health and Medical Sciences, University of Denmark

Lisa Maria Riedmayr
Interdisciplinary co-supervisor
Department of Biotechnology and Biomedicine, Technical University of Denmark

Description of the main host research group:

• Chip-based bioanalytical tools for bioelectrochemistry and biosensing
• 2D/3D organoid models of neurodegenerative disease and brain–gut axis
• Microelectrode and microfluidic fabrication and optoelectronic control for real-time monitoring of neurotransmitters and cellular behaviour

Description of the interdisciplinary co-supervisor group:

Kummer group:

The Kummer group aims to uncover the molecular mechanisms that underlie genome maintenance and gene expression in non-nuclear systems. We have developed a particular interest in the proteins and protein complexes that mediate mitochondrial and viral DNA replication. Our main tools to study their mode of action are functional biochemical and biophysical assays combined with structural studies by single particle cryo-EM.

Reidmayr group:

In this group, we aim to develop novel tools to accelerate next-generation gene and cell therapies, making them more effective, safer, and affordable. We combine expertise in CRISPR technologies, and innovative therapeutic design to create safer and more precise treatments by engineering CRISPR tools and synthetic DNA elements. Our highly integrative approach merges computational analyses of large-scale multiomic datasets with wet lab methods, such as pooled library designs and high-throughput screening.

Fellow project opportunities (please address the questions below) (max half page)

• What:
  • This project aims to harness and optimize Cas13’s innate toxicity, to selectively induce apoptosis in unwanted cells within human iPSC-derived products. The goal is to use mutagenesis and high-resolution structural analysis to dissect the mechanisms underlying Cas13-induced apoptosis and enhance its selective toxicity without compromising specificity.
• How:
  • The PhD student will characterize iPSC-differentiated cell populations in complex 2D/3D model systems and structural analysis as well as structure-guided mutagenesis of Cas13 to dissect and refine Cas13-induced apoptosis.
• Why:
  • Developing controllable Cas13-based purification systems that yield purer, well-defined iPSC-derived cell products will improve the safety, efficacy, and reproducibility of regenerative therapies. At the same time, a deeper mechanistic understanding of Cas13-mediated toxicity will provide powerful tools for precise cell selection.

Interdisciplinary aspects of the project:

Human iPSC-derived cell therapies hold enormous promise for regenerative medicine but are limited by poorly defined differentiated cell populations, which can compromise safety and efficacy. This project addresses this challenge by engineering a Cas13-based purification system that selectively induces apoptosis in unwanted cells within complex iPSC-derived products.

The work is highly interdisciplinary, integrating iPSC differentiation, structural biology, atomic models, protein engineering, and CRISPR technology. The PhD student will combine advanced 2D/3D organoid model systems (host expertise, bioengineering) with structural analysis (interdisciplinary co-supervisor expertise, structural biology/biochemistry) and CRISPR technology (co-supervisor expertise, biotechnology). The project builds on the work of Lisa Riedmayr, who will closely guide the PhD student as day-to-day supervisor. A key aspect of the project is the integration of multi-parameter cellular readouts (e.g. markers of differentiation state) to define robust molecular signatures of unwanted cell populations, which will guide the design of Cas13-based purification strategies. By bridging stem cell-derived systems, CRISPR biology and structural-analysis-driven protein engineering, this project provides a genuinely cross-disciplinary training environment and aims to lay the groundwork for safer, more reproducible iPSC-derived therapies across a range of clinical indications.

3 key competences required to take on the project:

To take on this project, a candidate must have prior education/experience within the following:

1. CRISPR technology
2. Molecular biology methods (main focus on cloning)
3. Structural biology

Katrine Qvortrup
Main host/supervisor
Department of Chemistry, Technical University of Denmark (DTU)

Lars Henning Engelholm
Interdisciplinary co-supervisor
Biotech Research & Innovation Centre (BRIC), University of Copenhagen and The Finsen Laboratory/Rigshospitalet

Description of the main host research group:

The Qvortrup Group develops chemical and bioconjugation strategies for targeted drug delivery, with particular focus on antibody design and production, site-selective antibody modification, peptide shuttles, and cleavable linkers for controlled release. The team applies modern organic synthesis, chemical biology and bioengineering to design precision therapeutics, including antibody–drug conjugates (ADCs) and brain-penetrating ligands. Their work bridges chemistry and translational drug design through collaborations with academia and industry.

Description of the interdisciplinary co-supervisor group:

The Engelholm Group investigates tumor–stroma interactions and receptor-mediated uptake mechanisms in cancer. The team develops innovative antibody–drug conjugates (ADCs) targeting actionable receptors involved in tissue remodeling and cancer invasion, combining antibody engineering, advanced histopathology, and in vivo disease modeling. The group has generated multiple first-in-class ADCs forming the foundation of the spin-outs Adcendo and PanTarg, both advancing towards clinical translation.

Fellow project opportunities:

This PhD project focuses on developing next-generation antibody–drug conjugates (ADCs) capable of penetrating the blood–brain barrier (BBB) and effectively delivering therapeutic payloads to brain tumors. The fellow will work at the interface between bioengineering, chemical biology, and molecular oncology to design bispecific ADCs that combine a tumor-targeting antibody with a BBB-shuttle arm recognizing endogenous transport receptors, such as the transferrin receptor or engineered peptide ligands.

The project will employ advanced antibody engineering and expression systems to produce bispecific constructs, which will then be site-specifically conjugated to cytotoxic payloads via a cancer cell-specific linker using chemical strategies developed at DTU Chemistry. Functional characterization will be done at BRIC/Finsen and include in vitro transcytosis assays using endothelial co-cultures and microfluidic models, complemented by in vivo imaging and efficacy studies in glioblastoma models. Quantitative histopathology, receptor mapping, and pharmacokinetic analyses will provide an integrated understanding of antibody transport, tissue targeting, and therapeutic outcomes.

By uniting biological ADC design with chemical shuttle engineering, the project addresses a major unmet challenge in targeted therapy, effective delivery of biologics across the BBB. The results are expected to establish a broadly applicable platform for CNS drug delivery and expand the therapeutic reach of ADCs to previously inaccessible indications. Embedded in a highly translational and innovation-driven environment, the fellow will also gain first-hand experience with industrial collaboration, intellectual property generation, and the translational pathway from discovery to preclinical proof-of-concept, skills fully aligned with INTERACT’s mission to train the next generation of interdisciplinary scientists.

Interdisciplinary aspects of the project:

The project brings together advanced ADC design and chemical linker and engineering at DTU Chemistry, and ADC testing and development at BRIC/Finsen forming a strong bridge between chemical drug design and molecular oncology. The fellow will receive comprehensive cross-disciplinary training, ranging from antibody molecular biology and mammalian expression to protein purification, receptor binding, internalization studies, and imaging-based trafficking assays. This will be complemented by training in organic synthesis and bioconjugation chemistry, including click chemistry, peptide coupling, linker optimization, and analytical characterization.

Both host environments are highly translational and strongly innovation-oriented. The Qvortrup Group collaborates extensively with industry and has co-founded the start-up DISPERAZOL, while the Engelholm Group has founded the spin-out companies Adcendo and PanTarg. Within this setting, the fellow will gain direct experience of the innovation pipeline, from discovery to preclinical validation, including patenting, entrepreneurship, and interdisciplinary project coordination.

Together, the two groups provide a unique framework for developing a convergence-science mindset in which molecular biology and synthetic chemistry are combined to generate tangible biomedical applications. This collaboration fully reflects INTERACT’s mission to train researchers who can translate cross-disciplinary science into innovative therapeutic strategies for cancer and neurological disease.

3 key competences required to take on the project:

To take on this project, a candidate must have prior education/experience within the following:

1. Hands-on experience with chemical synthesis, biochemistry and/or cell culture.
2. Strong interest in chemical biology, drug delivery, and translational research.
3. The project includes in vivo studies; therefore, candidates should hold — or be willing to obtain — a FELASA certification and demonstrate motivation to work with animal models as part of the experimental training.

Kristoffer Vitting-Seerup

Main host/supervisor

Section of Bioinformatics, Health Technology, Technical University of Denmark

Bo Porse

Interdisciplinary co-supervisor

The Finsen laboratory/Rigshospitalet and Biotech research and Innovation Centre (BRIC), University of Copenhagen (UCPH)

Description of the main host research group:

The Isoform Analysis Group, led by Kristoffer Vitting-Seerup, aims to inspire and enable protein isoform analysis across all the health and natural sciences. We seek to do this by developing the bioinformatic tools and databases necessary to analyze isoforms (enable) as well as use them to show the importance of isoforms in human health and disease (inspire). On our website, you can read more about the group, key papers as well as supervision philosophy (see link above).

Description of the interdisciplinary co-supervisor group:

The Porse group focuses on elucidating the mechanisms governing normal and malignant haematopoiesis with special emphasis on the behaviour of hematopoietic stem cells (HSCs) during adult haematopoiesis and leukemic stem cells (LSCs) in acute myeloid leukaemia. To this end, we employ mouse models of human AML, primary patient material and a broad range of genome-wide approaches and single cell analyses incl. cutting edge single cell proteomics.

Fellow project opportunities:

Background (aka What?): Hematopoietic diseases result from disruptions in the tightly regulated processes that govern blood cell formation and function, leading to immune imbalances, inflammation, and malignancy. Understanding their molecular mechanisms, particularly isoform- and protein-level alterations, is crucial for advancing disease understanding, diagnosis, and treatment.

 Method (aka How?): This project integrates advanced single-cell proteomics (Furtwängler et al., Science 2025) with isoform-resolved computational analysis. The fellow will work closely with both the Porse lab (BRIC), who generate state-of-the-art patient and reference datasets, and the Isoform Analysis Group (DTU), who develop and applies cutting-edge isoform-level bioinformatic tools. The fellow will receive coordinated training in both groups, learning how experimental design, assay biology, and data-generation constraints shape downstream computational analysis. Specifically, you will integrate gene- and isoform-level analyses to improve our understanding of hematopoietic diseases at the single-cell level. This project has a strong focus on both human disease biology and novel applications of existing bioinformatic tools. The student will gain hands-on experience with advanced single-cell proteomics and bioinformatic data integration, working closely with both computational and experimental experts at DTU and BRIC.

 Expected results (aka why?): The project will generate an isoform-resolved single-cell proteomic analysis comparing healthy and patient samples, providing a foundation for future biomarker and drug target discovery. Here, we expect the combination of biological insight and computational analysis to strengthen the mechanistic interpretation of isoform-level proteomic changes. In a broader perspective, it has the potential to transform patients’ lives in diseases where current treatments are absent or ineffective, while revealing fundamental insights into the disease relevance of protein isoforms.

Interdisciplinary aspects of the project:

The PhD fellow will be co-trained across two complementary environments: the Porse group, world-leading in experimental hematopoiesis and single-cell proteomics, and the Isoform Analysis Group, specializing in computational isoform analysis, multi-omics integration, and data-driven modeling. The fellow will learn to interpret proteomic and isoform-level signals in the context of human hematopoietic biology, gaining insight into experimental design, assay limitations, and the molecular underpinnings of disease. In parallel, they will receive advanced training in computational workflow development, data integration, and isoform-level analysis. By being embedded in both groups and participating in joint meetings, seminars, and co-supervision, the fellow will engage in genuine interdisciplinary research and act as a bridge between experimental and computational experts.

3 key competences required to take on the project:

To take on this project, a candidate must have prior education/experience within the following:

1. Strong R or Python programming skills
2. Applied bioinformatic analysis of omics data
3. A strong interest in molecular biology

Sunil Kumar Saini
Main host/supervisor
Department of Health Technology, Technical University of Denmark

Fran Supek
Interdisciplinary co-supervisor
Biotech Research & Innovation Centre (BRIC), Faculty of Health and Medical Sciences, University of Copenhagen

Description of the main host research group:

Our overall aim is to discover novel T-cell targets (antigens) and understand the adaptation of T-cells in different disease settings. We perform extensive evaluations of T-cells using cutting-edge technologies that we have established over the years. Identification of new T-cell targets and their details characterization in cancer, viral infections, and vaccination is key to improving ongoing T-cell therapies and identifying new avenues for therapeutic application

Description of the interdisciplinary co-supervisor group:

Supek group has expertise in studying genomic and structural variants using computational analysis and machine learning approaches. Performs large-scale bioinformatic studies of multi-omic data from human tumors (somatic mutations, epigenomes, and transcriptomes), human populations (germline variation), and metagenomes (incl. human microbiomes). 

Fellow project opportunities:

Human endogenous retroviruses (HERVs), normally silenced genomic elements, can be reactivated in tumors and generate neoantigens that elicit CD8⁺ T cell responses associated with better outcomes. Our research aims to define the landscape of tumor-specific CD8⁺ T cell responses and their regulation in hematological cancers. We will map HERV-derived antigen-specific CD8⁺ T cells, an underexplored source of tumor-specific targets, assessing their frequency, clonal structure, and functional diversity using DNA-barcoded pMHC multimers and single-cell multi-omics.

We aim to perform long-read sequencing to identify the level of HERV expression in CLL and MDS patients. Based on the genomic profilling of treatment naïve and immunotherapy treated patients a computational pipeline will be established to identify cancer-specific transcripts. A large set of candidate antigens identified in this process will be evaluated for their T-cell reactivity using our state-of-the-art DNA-barcode-based T-cell detection platform in corresponding patient samples. Furthermore, we will perform a comprehensive characterization of TCR-specificity, transcriptomics, and phenotype of HERV-specific T-cells using single-cell analysis and functional assessment will be perfromed using TCR-enginnered T-cells.

This project goes beyond conventional mutation-derived antigens and will identify new antigens for T-cells mediated cancer immunotherapy that would directly influence cancer treatment strategies (e.g. cancer vaccines) by providing new target antigens for broader coverage on their own and in combination with existing therapeutic approaches. By combining immunology, computational biology, and clinical insights, this project addresses unmet needs in cancer treatment, fostering innovation in both research methodologies and therapeutic strategies.

Interdisciplinary aspects of the project:

Computational analysis and antigen prediction tools: Computational methods enable a high-throughput, scalable approach to understanding expression of HERVs and generating an actionable list of potential targets for further immunological validation. Supek group has extensive expertise in machine learning and evaluating genomic alterations. These will be leveraged first by performing long-read RNA-seq analysis of cancer patient samples to idenitfy alterations in the expression of HERVs followed by computaional piepline to understand the extent and sharability of such HERVs across different patients. Potential candidate antigens will be idenitifed for experimental analysis.

Immunology and T-cell detection technologies: Immunology drives the hypothesis that derugaltion of HERV expression in human cancers is capable of eliciting a cytotoxic T-cell response, offering therapeutic avenues. The SKS group has developed high-throughput T-cell analysis technologies and has long-standing experience in identifying cancer antigens and their assessment in different therapeutic settings. Combining biological samples with computaional and immunological tools would lead to identifying previously overlooked HERV-derived antigens and their biological relevance, thus, broadening the repertoire of immunotherapy targets. The project's outputs could redefine antigen discovery pipelines and improve cancer immunotherapy precision and effectiveness.

3 key competences required to take on the project:

To take on this project, a candidate must have prior education/experience within the following:

1. Masters degree in bioinformatcis or data science or similar
2. Prior experience with genomic analysis or single-cell transcriptomic analysis
3. Cell culture and molecular biology techniques

Ala Trusina
Main host/supervisor
Niels Bohr Institute, Faculty of Science, University of Copenhagen

Jenny Emnéus
Interdisciplinary co-supervisor
Department of Biotechnology and Biomedicine, Technical University of Denmark

Description of the main host research group:

The group is interested in how populations of cells self-organize to achieve complex behaviours. One direction in our group is on understanding inter- and intra-cellular coordination to respond to stresses (unfolded proteins, reactive oxygen species, antibiotics, inflammation). Another direction is how complex forms and shapes emerge during the development of organs and organoids.

Description of the interdisciplinary co-supervisor group:

Our research is focused on developing Optoelectrical compartmentalised Organ-on-Chip (OoC) systems encompassing microfluidic tools for real time studies of cells and tissue in both 2D and 3D. For this we use 3D printing (extrusion and stereo lithography based), micromilling, and soft lithography. We also develop embedded printing of human stem cells for creating vascularised 3D tissue constructs that could be used for disease modelling.

Fellow project opportunities:

This PhD project aims to develop quantitative in silico models that capture the emergence of 3D morphologies of in vitro differentiating stem cells. 

Our lab has previously developed computational approaches capable of simulating the dynamics of up to 100,000 interacting cells. These models account for a range of cellular behaviors, such as cell division, migration, differential adhesion, and cell-cell signaling. By leveraging these approaches, we have successfully simulated complex morphological transitions, including sea urchin and drosophila gastrulation, mammalian neurulation, the emergence of branched vascular structures, and 3D patterning during early pancreas development.

The methodology we employ is based on an agent-based modeling approach that simulates both mechanical and biochemical interactions between cells. The interactions are governed by discrete, logical, or continuous rules, which can be represented by differential equations. These rules are derived from current literature or inferred from data provided by experimental collaborators. This multi-scale approach enables the modeling of intricate cell behaviors, bridging experimental observations and theoretical predictions.

The focus of this project will be to use this modeling approach to develop a digital twin of the in vitro mammalian gastrulation. The overall goal is to predict and, using 3D bioprinting and optogenetics,  experimentally validate spatio-temporal perturbations that can improve the differentiation toward specific organoids. The experimental component of the project will be performed by collaborators both in our lab (time-lapse imaging of the organoids in bio-printed environments, time-lapse imaging) and Emneus lab (e.g. optimizing bioprinting techniques). The expected workflow would be to 1. Build the model that captures key phenomena observed to date in response to global stimulation by morphogens (e.g. symmetry breaking and elongation, spatio-temporal patterning of cell-fates).  2. Use model to predict which localized configuration of morphogens (FGF, WNT, BMP) will have most impact on organoid morphology/composition of cell types 3. Validate predictions using bioprinted environments/initial cell compositions 4. If needed, fine-tune the model using data from pt. 3, otherwise return to prediction phase (2.) to refine in vitro organoids (reduce variability, off-target cell types, etc.)  

By applying our validated in silico modeling tools to organoid systems we aim to uncover the underlying mechanisms governing these processes. Ultimately, this work may inform targeted perturbations to culture conditions, such as introducing specific drugs or signaling molecules, to optimize organoid development for potential use in organ replacement therapies.

Interdisciplinary aspects of the project:

Together with Emneus lab, we aim to develop quantitative predictive models of in vitro organogenesis. We envision that these data-driven models combined with well controlled spatiotemporal environments will provide us with the better understanding of how to direct in vitro organogenesis to specific outcomes. We expect the PhD student in this project to be primarily involved in modeling and data analysis (spatial transcriptomics, image processing).

3 key competences required to take on the project:

To take on this project, a candidate must have prior education/experience within the following:

1. Strong computational skills. extensive experience with programming (preferably in Python) is required. Experience with numerical methods, image processing and analysis of other biological data is a plus. 
2. Background in physics or mathematics. Either as a major, or alternatively mixed biology and physics background (e.g. BSc in Biology, Master in Physics or other combinations where Phsyics course have been a significant part).
3. Experience with modeling biological systems.

Lisa B. Frankel
Main host/supervisor
Danish Cancer Institute

Luca Laraia
Interdisciplinary co-supervisor
Department of Chemistry, Technical University of Denmark

Description of the main host research group:

The Frankel group focuses mainly on understanding fundamental cellular quality control pathways that maintain cellular and tissue homeostasis and protect against disease. We study the molecular regulation of processes such as autophagy and protein aggregation: how they work at a mechanistic level, how their dysfunction contributes to disease including cancer and neurodegeneration, and how manipulation of these processes in vivo can alter therapeutic outcomes.

Description of the interdisciplinary co-supervisor group:

• The Laraia group focuses on chemical biology. By integrating organic synthesis, biophysics, and mass spectrometry-based proteomics, the group seeks to discover small molecules or other regulators that modulate cholesterol biosynthesis, metabolism, and protein aggregation. The work is applicable across multiple disease areas, linking fundamental chemical biology with therapeutic innovation, with applications such as anti-cancer and anti-neurodegeration agents.

Fellow project opportunities:

• What?
  • The overall aim of this project is to uncover the molecular roles and therapeutic potential of an understudied protein called DCAF15. The Frankel lab has recently uncovered exciting new biological functions of DCAF15, placing it as a key regulator of cellular proteostasis that enables the early steps of protein aggregation in response to stress. Because of this discovery, and the strong implications of protein aggregation in disease such as cancer and neurodegeneration, the project will uncover how this protein functions and how we can target it in a disease context to protect cellular health.
• How?
  • Methodological approaches applied in the Frankel lab will include advanced imaging, biochemistry, multi-omics approaches as well as analysis of mouse phenotypes, including derivation of primary mouse neurons and behavioural analysis. This groundwork will be combined with methods in the Laraia lab to study DCAF15 properties including luminescence-based assays and biophysical assays such as fluorescence polarization and mass photometry.
• Why?
  • Dysregulation of proteostasis is heavily implicated in the development of cancer and neurodegeneration. For instance, neuronal protein aggregation is a common pathological driver in neurodegerative diseases such as Alzheimers, Parkinsons, Huntingtons and ALS, and currently, there are no available therapies tackling this underlying cause of disease. The research project will open new understanding of proteostasis-driven diseases and reveal potential new targetting opportunities.

Interdisciplinary aspects of the project:

The proposed project is highly synergistic, combining the areas of medicinal chemistry and biophysics from the Laraia lab at DTU with the Frankel lab’s expertise in proteostasis, cancer biology, and in vivo models. This integration will provide the PhD candidate with complementary training environments and allow the unique opportunity to address unanswered questions on cellular proteostasis at the interface of these fields. The two labs have already established an active collaboration, including regular joint meetings and student exchanges, and this foundation will be further strengthened by the joining of the new PhD student.

3 key competences required to take on the project:

To take on this project, a candidate must have prior education/experience within the following:

1. Background in cellular and molecular biology
2. Experience in the areas of biochemistry, protein interactions and/or protein purification  
3. Strong interest in disease applications and therapeutic potential