Doctoral Candidates

Let’s meet the 11 talented PhD students that will drive the TOP-GUT research

José Pires

Starting date: 1st May 2024

Hi, I’m José Pires (23 years old) and I come from the amazing city of Porto, in Portugal.

My journey began with a bachelor’s degree in Biochemistry at the University of Porto. Over three years, I discovered my passion for cancer research, leading me to pursue a master’s degree in Medicine and Molecular Oncology at the same university. Throughout my academic journey, I engaged in workshops, courses, and even worked at a local bakery, which instilled in me the values of teamwork and perseverance.

In the dynamic “Glycobiology in Cancer” group at the Institute for Research and Innovation in Health (I3S) in Porto, under the guidance of Dr. Celso Reis and Dra. Daniela Freitas, I took my first steps in research. During my bachelor’s, I focused on characterizing the presence of truncated O-glycans in extracellular vesicles (EVs) released by gastric cancer cell lines. For my master’s thesis, I explored the role of gastric cancer-derived EVs, notably enriched in sialyl-Tn (STn), in recipient gastric cancer cells. Using a multifaceted approach, I isolated and characterized EVs from different gastric cancer cell lines and analyzed their effects on recipient cells. This included a detailed analysis of EV proteomic content to identify key proteins and signaling pathways.

My academic training provided me with hands-on experience in cell and molecular biology techniques, such as cell culture, RNA extraction, real-time PCR, western blotting, immunohistochemistry, immunofluorescence, EV isolation, and cell functional assays. A notable achievement during my master’s research was my involvement in a high-impact publication. The article, “Differential Protein and Glycan Packaging into Extracellular Vesicles in Response to 3D Gastric Cancer Cellular Organization” (Martins, Lopes et al., 2023), explored how the spatial organization of cancer cell culture influenced the composition of EVs, particularly their glycans. Additionally, I presented my work at esteemed symposiums, enhancing my presentation skills and expanding my scientific network.

Having completed my MSc, I sought to explore how science is conducted and perceived globally. I believe in the importance of a unified scientific community to progress and discover novel mechanisms or targets. This led me to apply for esteemed grants to expand my scientific network. It is crucial to address not only cancer but all gastrointestinal (GI) disorders, which pose a significant burden on individuals and healthcare systems worldwide.

Greetings! My name is Julia Mor, and I’m originally from the vibrant city of Barcelona, Spain. My academic journey has been a globetrotting adventure, exploring the wonders of biology.

I began my studies at the University of Barcelona, focusing on molecular, cellular, and systems biology. Moved by the complex interplay within living systems, I ventured to Freiburg, Germany, where I researched the development of the gut mucociliary epithelium in Xenopus frogs for my bachelor’s thesis.

Subsequently, in Vienna, I had the privilege of working in diverse labs across various fields, providing me with an immersive experience that not only deepened my scientific knowledge but also clarified my interests in biology. Finally, I started my Master’s in Molecular Microbiology, Microbial Ecology, and Immune Biology at the University of Vienna. The highlight of my studies was my research internship at Harvard Medical School, where I dove into the world of the dynamics of the gut microbiome and its impact on the immune system using murine models. At Harvard Medical School, I had the opportunity to work under very influential minds in the world of microbiology and immunology, which gave me the tools and confidence to start my PhD.

Now, as I embark on my doctoral journey, I’m thrilled to be starting my PhD position at Technische Universitat Berlin, working with Dr. Sina Bartfeld. Here I will be developing the project named “Impact of Carbohydrate Complexity on Host-Microbiome Interactions”. Our focus lies in understanding the interplay between specific elements within the gastrointestinal tract and their role in shaping interactions between probiotics and pathogens.

The aim of this project is to shed light on how interactions between specific mucins, glycans, probiotics, and pathogens within the gastrointestinal tract influence health outcomes, particularly in the context of infections, inflammatory conditions, and neoplastic diseases. By analyzing the composition of mucosal barriers we seek to understand the impact of carbohydrate complexity on maintaining gut homeostasis and responding to infections.

For this project, we will use genetically engineered organoids to study host-pathogen interactions in both the stomach and intestine. This includes investigating the protective effects of mucus barriers against pathogens like Helicobacter pylori and enteropathogenic Escherichia coli, as well as assessing the potential of probiotics like Lactobacillus reuteri and E. coli Nissle in counteracting pathogenic invasion.

Being a part of the TOP-gut project and the wider exTra Consortium is an exciting opportunity for me to contribute to scientific advancement alongside a diverse and dedicated group of individuals. I am confident that our collaborative efforts will not only deepen our understanding of gut-related health but also pave the way for innovative therapies and improved patient care. This journey promises to be a transformative experience, both professionally and personally, as we make meaningful contributions to the field of gastrointestinal research.

Julia Mor

Starting date: 17th June 2024

Adrian Aguilar Conde

Starting date: 1st May 2024

My name is Adrian Aguilar Conde and I come from Malaga, in the very south
of Spain. I studied Biotechnology in Madrid and decided to specialise in biomedical research near the end. Particularly, I was amazed by the complexity of our immune system and I wanted to pursue a career in research by investigating it. This prompted me to do a Master´s degree in Biomedical Sciences in Amsterdam, with a focus on infection and immunity.

During all this journey, from my BSc till the end of my MSc, I had the opportunity to join different groups, which allowed me to study different areas in translational immunology: allergy and immunotherapies, HIV infection and CRISPR-based gene therapies; cancer and antibody-based therapies. From academia in the first two internships to industry in the last one I got the chance to experience different work environments in different countries which has provided me with knowledge, structure and confidence to embark on a doctoral degree.

The TOPGUT project has provided me the opportunity to start a PhD project under the supervision of Prof. Dr. Birgit Sawitzki at the Berlin Institute of Health (BIH), which is part of Charité – Universitätsmedizin (Berlin, Germany). My research will focus on studying the immune cell composition and spatial organization of the immune system in the mucosa of stomach, small intestine and large intestine. In order to do this, we will apply cutting-edge techniques in the field of immunohistology, transcriptomics and proteomics to samples from patients with homeostatic gut and gut carcinoma.
Our findings will shed light on the implications of the immune system in determining why severe cancers develop abundantly in stomach and large intestine in comparison to the small intestine. More importantly, we will discern new approaches to integrate the respective immune cells in gut organoids for improved disease modelling and large-scale drug screening.

The more I delve into the project, the more enthusiastic I become. I feel that I am in the right place to learn about immunology and follow my dream of unravelling new important aspects our immune system and apply them to provide new therapies. At the same time, I am looking forward to learn about the complexity of stem cell biology and organ-on-chip technologies. The TOPGUT network will provide us with the needed understanding to participate in a future of preclinical studies without the involvement of animal experimentation. To me, as a person who is always ready to fight any kind of injustice in this world, animal welfare is fundamental.

Furthermore, the possibility of travelling, making science and putting altogether with all my peers makes this journey even more exciting.

Hi there,

This is Tanysha from Taipei, Taiwan. My research journey dates back to my undergraduate and graduate studies at National Yang-Ming University in Taiwan. I worked on therapeutic recombinant protein production, which utilized genetic recombination strategies to modify proteins to increase physical stability and efficiency. During that time, I experienced how exciting to establish techniques in molecular cellular biology and apply them on bench work. Apart from lab-based research, I was also a student in the Biotechnology Management Program at National Cheng-Chi University, where I gained insight into finance, management, and intellectual property rights which has helped me to bring different interdisciplinary perspectives while doing basic scientific research.

After graduation, I started my career as a research officer at the Agency for Science, Technology, and Research (A*STAR) in Singapore at Dr. Nick Barker’s lab. My studies focus on the roles of adult epithelial stem cells in the regeneration and/or cancer of various organs, including the stomach, caecum, colon, and lung. We extensively use transgenic mouse models, generating stem cell-driven cancer mouse lines to recapitulate physiologically relevant features of tumour initiation and progression. We also establish various mouse and human-derived 3D organoids to elucidate the role of dedicated tissue-resident stem cells, or to further facilitate disease amelioration.

Recent advent of precision and personalized medicines has highlighted the importance and prospect of human-derived microphysiological systems to offer individual therapy in a more precise and higher throughput way. Here, my PhD project will focus on the automation of patient-derived organoid models in microphysiological systems, which establish microfluidic-based two-organ platforms to allow further high throughput application and high data acquisition.

I believe the TOP-GUT program offers a great network of experienced researchers in the field, training us to bridge the gap from laboratory-based to pre-clinical and translational science research. Outside work, I enjoy spending time in nature, travelling and a little bit too much coffee. Looking forward to being part of the team!

Tanysha Chi-Ying Chen

Starting date: 1st July 2024

Faranak Heidari

Starting Date: 1st May 2024

My name is Faranak Heidari, and I am from Iran. The commencement of my scientific journey was at Sharif University of Technology (SUT) in Tehran, Iran, where I obtained my bachelor’s degree (BSc) in Chemical Engineering. As an undergraduate student, I undertook several interdisciplinary projects, one of which was my bachelor thesis: the design and simulation of a vascular-on-chip. Throughout this project, I realized that there is a severe shortage of technology for drug investigations. For instance, many developed drugs fail to obtain FDA approval due to their inability to pass animal trials. Furthermore, many people suffer from organ impairment or loss annually due to a lack of sufficient organ donors. These reasons encouraged me to pursue my master’s in the field of biomedical engineering. Therefore, I embarked on my master’s degree (MSc) in this field at SUT. During my master’s, I collaborated on projects related to the design, simulation, and fabrication of organ-on-chips. Additionally, my master’s thesis focused on “Directly Coaxial Bioprinting of 3D-Vascularized Tissue Using a Novel Bioink Based on Decellularized Human Amniotic Membrane.” Subsequently, I had the privilege of undertaking a short-term internship at the Royan Institute of Stem Cell Research in Tehran, and also served as a research assistant at Iran University of Medical Sciences.

As part of the TOPGUT project, I’ll be undertaking my PhD at Utrecht University in the Netherlands. My research will primarily focus on developing a perfusable chip that replicates both the physiological functions and topographical features of the intestinal lumen. This chip will consist of an epithelial compartment featuring crypt-villi-like patterned hydrogels seeded with intestinal PDOs, situated on top of a porous membrane. On the other side of the membrane, constituting the second compartment representing the blood side, fluid perfusion will be enabled. My investigation will center on the role of the stroma (stromal cells embedded in the hydrogels) in supporting tissue maturation and barrier function. Additionally, I’ll assess the absorption and biotransformation of various molecules (e.g., bacterial, diet-derived, and drug molecules) from the gut compartment, passing through the stroma (hydrogel), and into the blood compartment. I anticipate that my project will uncover the relationship between topography-shear stress and absorption, while also mapping the biotransformation profiles of nutrients, metabolites, and drugs originating from the gut.

I am blissful to be a part of  TOPGUT project providing me a great opportunity to do cutting edge discovery in the esteemed university while joining the international research team and diving into the work of other centers, giving rise to invaluable professional and personal experience.
I think this opportunity presents a great chance for me and fellow early-stage researchers to grow both professionally and personally. We can learn new methods, explore emerging scientific areas, and engage in cross-sector collaboration, which will enrich our research endeavors with fresh ideas.

My name is Tamara Rojas Méndez, and I am from Costa Rica, a small country famous for its high biodiversity. Naturally, growing up I was always curious about biology. I developed a more intense interest in science when I was in high school and studied how to genetically modify organisms with biotechnology. I then decided to pursue my bachelor’s degree in Biotechnology Engineering at Tecnológico de Costa Rica.

I studied and worked in parallel in a synthetic and molecular biology startup, aware that this would open my possibilities to keep learning and working in science in the global environment. I was able to move to the international sphere when I completed my bachelor’s graduation thesis project at Institut Pasteur in Paris. Subsequently, I worked in global regulatory compliance in a medical device company, where I discovered how much innovation is essential in healthtech and the relevance of improving research in medical devices.

Of course I had fallen in love with Paris and decided to pursue my master’s degree at PSL in Biomedical Engineering, specializing in Biomaterials and Biodevices during the second year. During my first year, I worked on a project to develop a chip from scratch to be able to mimic a tumor microenvironment for bioassays at Université Paris Cité. In the second year, I completed my master thesis on the development of a novel in vitro model of Annulus Fibrosus by 3D printing dense collagen/hyaluronic acid solutions at Sorbonne-Université.

Now, for my PhD project, I will focus on building a 3D platform consisting of ECM hydrogels containing gastric and intestinal organoids cultured with stromal components, fibroblasts, and engineered microvessels to emulate the in vivo microenvironment. The goal is to be able to unveil fibroblast’s role in the development of GI epithelia, using different technologies (imaging, transcriptomics, proteomics).

My expectation of the project is to be able to create an innovative model that, in the long term, can contribute to personalized patient diagnostics and assays. Moreover, I hope to gain experience in inter-sectoral collaboration skills and entrepreneurship during my secondment in industry. I also look forward to receiving useful training in project and economic management, and career planning for my endeavors after the project.

Tamara Rojas Méndez

Starting date: 15th May 2024

Catarina Antunes

Starting date: 1st of May 2024

My name is Catarina Antunes, I am 28 years old and I am from Portugal. I did my Bachelor degree in Biology at Faculdade de Ciências da Universidade de Lisboa, Portugal. Afterwards, I did my Master’s degree in Regenerative Medicine: Clinical and Industrial Delivery at the University of Edinburgh, Scotland. During my Master thesis I joined the “Mechanisms of Neurodegeneration” research group in the Center of Regenerative Medicine. The aim of my project was to investigate the oligomeric state of α-synuclein in human stem cell-derived mDA neurons and its role in Parkinson’s disease. Additionally, I did a 6-month Internship under Dr. Sebastian Jessberger at the Laboratory of Neural Plasticity at the Brain Research Institute (HiFo) from the University of Zurich, Switzerland. The project focused on the understanding of neural stem cell dynamics and adult neurogenesis. My goal was to compare the dynamics of neural stem cells with other types of stem cells (like hematopoietic stem cells) in a mouse model.

During the last 4 years, I have worked as a Senior Associate in the Translational Discovery Immunology Group at Roche pRED in Basel, Switzerland, where I had a deep focus on the development of new 3D cell culture models to apply on the characterization and treatment of Inflammatory Bowel’s Disease (IBD). To achieve this, among many other things, I have developed barrier integrity assays, migration assay and co-culture models with gut organoids in order to assess new drug target biology, perform screening and characterization of small and large molecule compounds for on- and off-target effects. Also, in my time at Roche I had the opportunity to be involved in a collaboration with MIMETAS where I started working with the organ-on-a-chip technology.

During my PhD at Mimetas BV, The Netherlands, I will focus on developing a 3D human model in the OrganoPlate to mimic intestinal architecture and the IBD environment, develop gut-on-a-chip readouts for inflammatory phenotypes suitable for high throughput screening and, validate the model with tool compounds. I think that my project could play an important role on the development of a novel patient-derived IBD model to better identify patient specific phenotypes. Additionally, I am confident that this platform will enable the testing of novel immunotherapeutic strategies which will make medicines arrive safer and faster to the patients that require so urgently a novel therapy.

I am excited to have the opportunity to integrate the TOP-GUT innovative network. A strong will, combined with a clear focus for what I am trying to achieve has kept me striving for my goals and starting this doctoral degree is the right step to take at this stage of my professional career and personal development.

Hi! My name is Eric, I was born and raised in Switzerland. After graduating highschool, I moved to the US and completed a bachelor in molecular biology at Boston University. In parallel to my studies there, I started my research journey by volunteering in the Finnerty lab where we were investigating molecular mechanisms that helped corals to resist climate change.

After graduating, I wanted to keep doing research but switch focus towards immunology and joined the Permar lab at Duke University, studying human cytomegalovirus. Working there as a research assistant for two years crystallized my will to pursue a career in medical research, so my compass was set and it was time to continue my studies.

I therefore moved to Sweden and completed my master in biomedicine at Lund University. For my master’s project, I wanted some experience in industry and joined the Cell Assay Development team at AstraZeneca in Gothenburg, where we investigated the use of HiBiT-CETSA to screen for transcription factor modulators. I stayed in the team as a research scientist for 8 months after graduating my master’s and worked on developing various assays for drug screening.

For this exciting new step in the TOP-GUT network, I am joining the Wandall lab at the University of Copenhagen, where my PhD project will be aimed at establishing patient-derived gastric cancer organoids as model for personalized T-cell targeted immune cell therapy. Gastrointestinal (GI) cancers are a heterogenous group of diseases with many patient-specific characteristics and therefore a high need for personalized treatments. Our group has expertise in glycomics and within the scope of this project we are particularly interested in exploiting aberrantly-expressed glycans typical of GI cancers that can serve as targets for immune therapies.

In this project, I aim to establish clinically-relevant GI cancer organoids that can be engineered to replicate specific tumor microenvironments and be used for preclinical drug testing. Through this, I hope to participate in improving the success rate of anti-cancer drug development. I look forward to collaborating with my peers in the doctoral network and to learning skills that will advance the discovery of GI cancer therapies.

Eric Rochat

Starting date: 3rd June 2024

Pimkanya Morekrong

Starting date: 1st May 2024

My name is Pimkanya Morekrong, I am from Thailand. I graduated with a Master’s in Medical Biochemistry at the Faculty of Medicine, Chulalongkorn University. My Master’s thesis project focused on the Epigenetic Regulation of Cellular Aging Induced by Calcium Oxalate Crystals and Nephrolithiasis Urine HK-2 cells. The thesis research project explores the mechanistic pathways associated with different iCOCI values in CaOx nephrolithiasis urine-induced apoptosis and cellular senescence (p16). It also examines their relationship with epigenetic markers, including histone modification markers H3K4me3 and H3K9me3, in kidney stone disease patients who are Thai. During my Master’s program, I participated in a research fellows program called ‘MSCA-RISE‘ at CICbiomaGUNE in SanSebastian, Spain, which focused on developing protein nanocarriers based on oxygenated hemoglobin for tumor oxygenation and improved photodynamic therapy.

After graduation, I worked as a research assistant with the PDOs team at the Siriraj Center of Research Excellence in Precision Medicine for Systems Pharmacology, Faculty of Medicine Siriraj Hospital Mahidol University. We established 3D models  (PDO & PDXO), and primary cell cultures from cancer patients for a biobanking database platform, covering various cancer types. We analyzed the growth curve to identify proliferation and conducted drug screening profiling for anti-cancer treatment in cancer organoids. Additionally, we applied high-throughput Multiplex Immunofluorescence to identify biomarkers and heterotropic organoid culture markers for storage at the biobank. Through my research journey, I have developed an interest in gaining a deeper understanding of biomedical sciences and fostering innovative technologies, specifically in the realm of Patient-derived- organoids as a model for personalized cancer therapy. I am confident that my passion for this field will only intensify as I witness the potential of merging different interdisciplinary aspects, technological advancement, and real-world applications. This passion of mine propels my active engagement in the field, driving me to overcome new challenges and contribute to scientific knowledge with a belief in the transformative power of new discoveries.

For this reason, I am strongly interested in pursuing a PhD project in “Gastric Cancer organoids model for personalized cancer therapy” at Prof. Dr.Celso Reis’s laboratory in I3S-Instituto De INVESTIGAÇÃO e INOVAÇÃO em SAÚDE da Universidade do Porto (I3S) Porto, Portugal. My current project aims to expand the existing biobank at the Glycobiology in Cancer group of gastric tumor PDOs and characterize the molecular features regarding their glycoprofile and potential therapeutic targets, such as tyrosine kinase receptors and immune checkpoints. We will then performe drug assays to evaluate the predictive value of PDOs by comparing their in vitro response with clinical patient responses. Moreover, we will glycoengineer PDOs to study the impact of glycosylation on drug treatments.  For that we will perform transcriptomic, proteomic and glycomic MS/MS approaches, as well as IHC, IF and Proximity Ligation Assay. Ultimatly, we aim to assess and validate the PDOs as models for personalized medicine and find novel therapeutic approaches for gastric cancer patients.

I am excited to join the TOP-GUT consortium, as I believe it will be a great chance to work on projects that complement strategic research priorities. This opportunity will assist me in developing and enhancing my expertise and capabilities in essential fields of Science and Technology, fostering interdisciplinary research across various scientific and technological domains.

Hi everyone,

My name is Juulia Zhou and I come from Finland. I studied law in the Netherlands, obtaining my bachelor’s at Tilburg University and my master’s at Vrije Universiteit Amsterdam. During my master’s, I specialized in international technology law, which introduced me to the fascinating field of bioethics. After working in corporate legal departments for a few years during my studies and after graduating, I decided to pursue a PhD in bioethics at the University of Oslo.

My PhD project will focus on advancing the understanding of the legal and ethical implications of organoid research, identifying areas of over and under regulation, and examining the legal and ethical status of organoids in relation to the degree of their advancement. The focus will particularly be on the legal and ethical issues arising from the transition from research to commercial and therapeutic use of organoids. The ultimate objective of the project is to ensure that future advancements in organ modelling, especially within the gastrointestinal tract, are conducted in an ethically responsible and legally compliant manner.

Juulia Zhou

Starting date: 13th  May 2024

Manuel Caro

Starting date: 1st May 2024


My name is Manuel Caro. I am 25 and from the south of Spain. My scientific journey began at University Carlos III de Madrid, where I pursued a Bachelor’s in Biomedical Engineering. I was granted the opportunity to study my third year as an exchange student at University of California, San Diego. This was my first experience abroad. Here, I learned invaluable lessons such as working in an international environment, resilience, and independence. Back in Madrid, I did my bachelor’s thesis in a laboratory at the Universidad Complutense de Madrid studying cellular differentiation on tubular thermoresponsive hydrogels where I co-cultured endothelial cells, fibroblasts, and smooth muscle cells in said tubular platforms.

I continued with a Master’s in Biomedical Sciences at Utrecht University, where I worked as an intern in the University Medical Centre of Utrecht. Here, I had the opportunity to learn about primary cell isolation and culture from rat tissue sources. I dived into the purification via colony-picking; and characterization via morphology of endothelial colony-forming cells and the subsequent confocal high-content imaging in the facilities.

I performed a second internship at Mimetas BV, and since October 2022 I was hired as a Junior Scientist to continue my research and expand on new areas. During this time, I have worked in different tissue models such as liver, kidney, and tumor microenvironment. I learned about vascularization of 3D cultures, culture of organoids and performed a wide variety of assays to study the functionality of our models.

During my PhD at Geiger’s lab in Bellinzona, I will combine all the knowledge that I have gathered during these years. I will bring my knowledge of 3D microfluidic culture systems with complex co-culture of different cell types and combine it with cancer patient-derived organoids (PDOs) in the context of replicating the interplay between cancer and immunity. Furthermore, we will colonize these cancer PDOs with engineered probiotic bacteria that either produce immunostimulatory metabolites or degrade immunosuppressive metabolites to enhance T cell responses to tumors. Then, these cancer PDOs will be exposed to tumor antigen-specific T cells.

I have been lucky enough to work with great minds that have nurtured my curious, inquisitive side. I hope to keep learning in the future from my peers and be able to act as an inspiration for them at some point. I also hope to bring all the good things about my Spanish culture into the lab, to promote as space of trust, friendship, collaboration, safety and support.