Host labs

UNIL - EPFL host labs for an MD-PhD thesis

Please find below a non-exhausive list of potential UNIL-EPFL Directors of thesis/host labs able to welcome you for an MD-PhD thesis. This list will be updated once a year.

You also have the opportunity to browse the following link to see the UNIL accredited Directors of thesis.

Don't hesitate to contact one or more of them and ask for an appointment to make up your mind!

A - D

Laboratories	Thesis Directors	Subject proposed
Anaesthesiology	Suter Marc	Exploring the pathophysiology of spinal microglia in chronic pain condition
Biomedical sciences	Amati Francesca	Translational research in aging and muscle metabolism: from subcellular organelle contacts to whole organisms.
Biomedical sciences	Habib Shukry James	Wnt-bandage for Bone Repair
Biomedical sciences	Paolicelli Rosa Chiara	Microglia dysfunction in the pathogenesis of brain diseases: Studying the role of microglial TDP-43 in myelin and motor dysfunction
Biomedical sciences	Widmann Christian	Cell-penetrating peptide and homeoprotein uptake mechanisms: We have recently discovered a new endocytic pathway taken by cationic substances (see our webpage for details). This pathway needs now to be characterized in detail. An open question is whether this pathway operates from the apical or basolateral sides of epithelial cells. We therefore propose a project to address this question that will involve the use of state-of-the-art biochemical and imaging techniques.
Center for Integrative Genomics	Roignant Jean-Yves	Epitranscriptomics and neuronal diseases: Functions of RNA modifications in nervous system activity. The current lines of research of my group focus mainly on the study of chemical modifications of RNA and the function of these in the nervous system. This new field of research known as "epitranscriptomics" is fascinating because it opens up a new way of regulation hitherto unrecognized. More than 170 different modifications (methylation, acetylation and others) have been discovered on RNA, some of which are dynamically regulated upon environmental changes. Surprisingly, the loss of function of many enzymes involved in the installation of these modifications leads to neuronal deficiencies in humans, but the mechanisms involved still remain to be discovered. We offer various projects related to this theme for interested students.
Center for Integrative Genomics	Van Leeuwen Jolanda	Global analysis of suppressor mutations that rescue human genetic defects: “Monogenic” diseases often show diversity in disease severity across patients, which can be due to the presence of modifier mutations. Using genetic screens in cultured human cells, we aim to identify such modifier genes, to better understand differences in disease severity.
Centre for Integrative Physiology of Exercise (CIPE)	Malatesta Davide	Energetics and mechanics of terrestrial locomotion (walking and running): Energetic and mechanical gait analysis and training intervention: from patients to sedentary inactive healthy adults and athletes
Centre d'investigation et de recherche sur le sommeil (CIRS)	Heinzer Raphaël	Physiology of sleep and sleep disorders Epidemiology of sleep disorders in Switzerland and in developing countries. Sleep at high altitude and in extreme conditions
Clinical Neurosciences (DNC)	Allali Gilles	Research on neurodegenerative conditions
Clinical Neurosciences (DNC)	Crottaz-Herbette Sonia	Cognitive neurosciences, stroke and brain reorganization: Modulation of brain activation and structure by cognitive training in stroke patients and healthy subjects
Clinical Neurosciences (DNC)	Du Pasquier Renaud	Understanding the immunopathogenesis of demyelinating desease, primarily in the field of multiple sclerosis: To assess antigenic specificity of CNS-autoreactive antibodies in MS patients
Clinical Neurosciences (DNC)	Hegi Monika	Experimental and translational research in neuro-oncology: Targeting the cancer epigenome in glioblastoma
Clinical Neurosciences (DNC)	Serino Andrea	Understanding the neural bases of body and space representations and their role for action, perception and consciousness.
Clinical Neurosciences (DNC)	Sokolov Arseny	Cognitive neurorehabilitation & neurotechnology: Technology-assisted precision cognitive neurorehablitation in acquired brain domage
Computational Biology	Ciriello Giovanni	Cancer genomics and evolution: Exploring cancer cell plasticity in lung adenocarcinoma progression using single cell RNA-seq and spatial transcriptomics profiling of patient primary samples
Dermatology	Kuonen François	Transcriptomics study of aggressive skin cancers: Identify transcriptional changes involved in skin cancer progression; functional validation
Diagnostic Imaging and Interventional Radiology	Qanadli Salah Dine	Imaging and image guided therapies

E - F

Laboratories

Thesis Directors

Subject proposed

Education and Research

Eicher Manuela

ePRO-based Model of Care to Manage and Monitoring Symptoms of Cancer Patients Treated With Immune Checkpoint Inhibitors (IePRO)

Education and Research

Fauvel Aude

History of health and medicine (in particular: history of psychiatry, criminology, sexuality; history of women physicians). Social studies of health and medicine

Education and Research

Jox Ralph J.

Medical ethics and bioethics, in particular clinical ethics, end-of-life ethics

Endocrinology, Diabetes, Metabolism

Pitteloud Nelly

Genetics of Inherited Neuroendocrine Reproductive Disorders: The laboratory is working on deciphering genes involved in reproduction. We are using a human genetic disease model, congenital hypogonadotropic hypogonadism (CHH), where patients do not go through puberty spontaneously. We have in place a large cohort of CHH (> 500 patients). In this project, we aim (i) to discover novel genes through NGS and OMICS approaches; (ii) to study epigenetics of reproduction. Through the doctoral thesis, the candidate will determine how to phenotype CHH patients. The candidate will learn how to apply a variety of genetic analysis (i.e. high-throughput sequencing data from WES/WGS, RNA-seq, single cell data) to help discovering new genes and/or pathways involved in the pathogenesis of CHH and reproduction.

Endocrinology, Diabetes & Metabolism

Sykiotis Gerasimos

Role of the Keap1/Nrf2 antioxidant response system in the thyroid gland

EPFL-STI IBI-STI LBI

Tang Li

Multidimensional immunoengineering for enhanced cancer immunotherapy

EPFL-SV IBI

Deplancke Bart

Studying the genetic and molecular basis of complex diseases such as obesity and cancer using (single cell) omic technologies / approaches: We currently look for MD-PhD candidate researchers interested in i) studying human adipose tissue function; or ii) the heterogeneity and function of circulating tumor cells using single cell-centric technologies and analyses.

EPFL-SV ISREC

Oricchio Elisa

Cancer genomics: Understand the role of cancer genomic alterations to develop personalize therapies.

Epidemiology and Health Systems/Unisanté

Pittet Valérie

Epidemiology of inflammatory bowel diseases Interoperability of real-world data: Interoperability of IBD cohort data in Europe: a step towards personalized medicine

Experimental Therapies

Harari Alexandre

T-cell discovery

Fundamental Neurosciences

Neukomm Lukas

Molecular mechanisms that execute the degeneration of axons and neurons in the fruit fly Drosophila.

Fundamental Neurosciences

Nikoletopoulou Vassiliki

Autophagy: A new player in brain homeostasis and disease: Our work aims at characterizing the regulation and roles of degradative and secretory autophagy in the context of neuronal physiology, synaptic function and brain disease.

Fundamental Oncology

Ho Ping-Chih

Metabolic guidance to tailor T cell antitumor responses

G - O

Laboratories	Thesis Directors	Subject proposed
Gastroenterology and Hepatology	Gouttenoire Jérôme	Molecular virology and pathogenesis of hepatitis C and E: Investigating host factors required for hepatitis E virus (HEV) productive infection
Gastroenterology and Hepatology	Moradpour Darius	Molecular virology and pathogenesis of hepatitis C and E: subject to be discussed with Jérôme Gouttenoire, PhD (Laboratory Director) and Darius Moradpour, MD
Immunobiology	Esser-von Bieren Julia	Regulation and mechanisms of type 2 immune responses: Mechanisms of inflammatory macrophage reprogramming in allergic asthma and NSAID-exacerbated respiratory disease
Immunobiology	Martinon Fabio	Mechanisms driving autoinflammation
Immunobiology	Mayer Andreas	Molecular mechanisms of intracellular phosphate homeostasis - characterisation of a novel signaling pathway that is central to cellular energy metabolism: Cells need to carefully control their internal stores of inorganic phosphate, which is both an essential nutrient and potentially toxic. They face a phosphate challenge for several reasons. Growth requires a minimal concentration of this limiting resource because intracellular inorganic phosphate (Pi) is a compound of nucleic acids and modifies most cellular proteins. At the same time, cytosolic Pi may not rise much, because elevated cytosolic Pi can stall metabolism. It reduces the free energy that nucleotide triphosphate hydrolysis can provide to drive energetically unfavorable reactions. Our group undertakes a pioneering study to elucidate how cells strike this critical balance. We characterize a novel pathway for intracellular phosphate reception (INPHORS) and signaling and explore the role of acidocalcisomes in it. These studies may identify a key function of these very poorly understood organelles, provide one reason for their evolutionary conservation and elucidate a novel homeostatic system of critical importance for cellular metabolism. Its dysregulation is lethal for lower eukaryotes, and produces pathologies in humans, such as neurodegeneration, renal dysfunction, and perturbed blood clotting.
Immunology and Allergy	Muller Yannick	Laboratory for advanced cell therapies in autoimmunity and allergies
Infectious Diseases	Bochud Pierre-Yves	Immunogenetics of infectious diseases
Infectious Diseases	Roger Thierry	Harnessing innate immune training to improve sepsis management: Sepsis is a leading cause of mortality worldwide. So far, immunotherapies tested in clinical trials have been unsuccessful. Trained immunity refers to the capacity of the innate immune system to recall and adapt to an initial challenge to mount an improved response to a secondary challenge. Contrary to adaptive immune memory, trained immunity is not antigen specific, suggestive of wide-ranging effects. We recently reported that trained immunity confers broad-spectrum protection against bacterial infections, and intergenerational transmission of trained immunity conferring heterologous resistance to infections (Ciarlo et al. J Infect Dis. 2020; Théroude et al. Front Immunol. 2021, Katzmarski et al. Nat Immunol. 2021). Deeper understanding of trained immunity could bring invaluable information in the fields of infectious diseases and sepsis. Our project aims to better delineate trained immunity assessing its persistence, the impact of age (i.e. inflammaging). We also decipher molecular and metabolic pathways involved in trained immunity. On the long-term, therapies directed at trained immunity might offer new treatment options to improve vaccine efficacy or normalize dysregulated host responses in sterile and infectious pathologies.
Institute of Sport Sciences (ISSUL)	Millet Grégoire	Physiological responses to hypoxia exposure and to hypoxia-hyperoxia conditioning
Institute of Sport Sciences (ISSUL)	Place Nicolas	Plasticity of the neuromuscular function
Internal medicine	Marques-Vidal Pedro	Cardiovascular epidemiology: Research on cardiovascular epidemiology, focusing on the associations between polygenic risk scores, metabolomics, diet, physical activity and the development of cardiovascular disease. Also research on quality of management of cardiovascular risk factors and the association between psychiatric and cardiovascular diseases. For more details contact the PIs at the website.
Laboratory Medicine and Pathology (DMPL)	Abid Karim	Diagnostic biochimique des tumeurs neuro endocrines par spectrométrie de masse.
Laboratory Medicine and Pathology (DMPL)	Ciuffi Angela	HIV-host interactions : characterization of candidate cellular factors and their role during HIV life cycle: Investigation of the role of candidate factors on HIV replication identified upon differential methylation and gene expression analysis, i.e. upon epitranscriptomic and transcripomtic charaterization of HIV-infected cells. Development of new single cell tools to assess HIV life cycle, in particular integration.
Legal medicine	Castella Vincent	Setting of new molecular tools of forensic interest.
Medical radiology	Prior John	Radiomics in nuclear medicine and molecular imaging: Radiomics extracts a large number of features from medical imaging data with the goal of uncovering patterns and characteristics failing to appear to the human observer, but able to characterize better and deeper a pathology, predict therapy response of the apparition of side effects. A specific thesis subjects will be tailored to the PhD candidate depending on her/his background.
Medicine and Surgery	Manuel Oriol	Clinical patient-oriented research: Transplant Infectious Diseases - Propective observational studies within the Swiss Transplant Cohort Study (STCS) - Interventional reserche on prevention of viral infections in transplant recipients
Microbiology	Fumeaux Coralie	Study of the cell envelope in Gram negative bacteria and the mechanisms of antibiotic resistance. Study of cell envelope remodeling in Acinetobacter baumannii.
Neonatology	Giannoni Eric	Host-pathogen interactions in group B streptococcal sepsis
Neuroheuristic Research Group	Villa Alessandro	Brain dynamics studied by frequency domain near-infrared spectroscopy (FD-fNIRS) during decision making
Obstetric, Gestational diabetes	Puder Jardena	Objectively measured eating behavior with a digital tool and brain responses to food viewing in pregnancy and postpartum nd in non-pregnant subjects: Analysing eating behavior and brain responses in obese and non-obese subjects and in women with gestational diabetes and in non-pregnant subjects
Occupational and Environmental Health	Berthet Aurélie	Environmental exposure, health and toxicology: - Environmental exposure to pollutants and health effects - Exposure to pesticides and biocides and the related health effects - New tobacco products and new cannabis inhalation methods - Skin permeation of different pollutants and skin sensitization, irritation
Occupational and Environmental Health	Guseva Canu Irina	1. Burden of occupational cancers in Switzerland: Burden of asbestos-related cancers in Switzerland (BARCS) 2. Ethiology of breast cancer: Cancer du Sein et Travail de Nuit (CaSeTraN)
Oncology	Gfeller David	Computational onco-immunology: Epitope predictions, modeling TCR specificity, analysis of single-cell genomics data
Oncology	Joyce Johanna	Exploring and Exploiting the Tumour Microenvironment
Oncology	Petrova Tatiana	Vascular and tumor biology: Understanding and targeting organ-specific and tumor microenvironments
Oto-rhino-laryngology	Tolstonog Genrich	Head and neck cancer research: Assessing clonal evolution in head and neck squamous cell carcinoma and its contribution to tumor progression and treatment resistance

P - Z

Laboratories	Thesis Directors	Subject proposed
Pediatric Hematology-Oncology Unit / Division of Pediatrics	Mühlethaler-Mottet Annick	Pediatric oncology: Elucidating the molecular mechanisms driving neuroblastoma tumorigenesis, phenotypic plasticity and progression.
Psychiatry	Alameda Luis	Translational and epidemiological research in early psychosis: Undertanding the gene & environment interplay between childhood trauma and polygenic risk scores on the psychpathological profiele of patients with a first-episode of psychosis.
Psychiatry	Klauser Paul	Translational research to improve early detection and to develop novel mecanism-based interventions in youth with psychotic disorders: A novel intervention based on sensory stimuli to improve cognitive impairments in adolescents at risk for psychosis
Psychiatry	Preisig Martin	Psychiatric epidemiology: Availability of large data sets. Specific topic needs to be defined in function of the candidate's interests either on the risk of children of parents with psychiatric disorders or links between psychiatric disorders and cardiovascular risk factors in the general population.
Psychiatry	Simon Olivier	Titre Clinical implications of controled medicines legislation and regulations ; opioid agonist treatments.
Psychiatry - Psychiatric Neuroscience	Stoop Ron	Neurobiology of anxiety and fear: The role of the basolateral amygdala (BLA) - prefrontal cortex (PFC) axis in social cognition, hierarchy and collaboration: a cross-spieces approach
Psychiatry - Psychiatric Neuroscience	Toni Nicolas	Adult hippocampal neurogenesis and its role in psychiatric disorders
Radiology	Bach Cuadra Meritxell	Magnetic resonance image analysis with machine learning, image segmentation, super-resolution, deep learning, neuroimaging, multiple slcerosis, thalamus, fetal brain, eye
Radiology	Jelescu Ileana	In vivo brain microscopy using diffusion MRI and translation to neurological and psychiatric disorders: Brain microstructure alterations in early cognitive decline assessed using MRI: Potential biomarker in the prodromal stages of disease
Radiology	Murray Micah	Multisensory processes across the human lifespan: from observation to innovating rehabilitation and intervention
Radiology	Richiardi Jonas	Machine learning for image + omics: Deep Imaging Genetics: using deep learning latent representations of image-derived endophenotypes to strenghten associations with genetics
Swiss BioMotion Lab	Jolles-Haeberli Brigitte	Multidisciplinary Approach for Healthier Joints
Transplantation Immunopathology Service	Golshayan Déla	Immune determinants of graft rejection and outcome after kidney transplantation
Urology	Derré Laurent	Understanding tumor immunity in bladder cancer patients to develop new treatment: Analysis of myeloid and T cells responses in bladder cancer patients undergoing the BCG therapy.
Vascular surgery	Allagnat Florent	New avenues of research for the treatment of vascular diseases: Dietary restriction and hydrogen sulfide to protect against vascular diseases
Vulnerabilities and social medicine- Unisanté	Bodenmann Patrick Grazioli Véronique	Improving health equity among populations with vulnerabilities using community-based research
Woman-mother-child (DFME)	Tolsa Jean-François	Vascular reactivity in physiological and pathological conditions: Regulation of the human umbilical circulation in pregnancies with harmonious or restricted fetal growth