EDBB Available PhD Positions

Research Groups with available PhD Positions

Next Hiring Days session: June 19-21, 2019 (this page will be updated as new positions become available). Meanwhile, do not hesitate to contact the laboratories which interest you to find out whether they have upcoming openings for PhD students.

  • Andrea ABLASSER – Laboratory of Prof. Ablasser / Global Health Institute / School of Life Sciences

The innate system is essential for maintaining health and it plays a pivotal role in several human diseases. A key element of the innate immune system are sensing receptors, also known as Pattern Recognition Receptors (PRRs), that detect foreign microbial molecules that arise during infection and, in turn, initiate defense mechanism to protect the host against pathogens. Research in my laboratory focuses on the immunorecognition of DNA. Over the past few years, we have contributed to establish new insights into the functioning and biological relevance of the innate DNA sensing. On the basis of these discoveries, our current work aims to address pertinent questions in the filed with a special emphasis on defining its function in physiological contexts that fall outside its classical, infection-associated realm. We envision that our research efforts on innate DNA sensing will eventually allow us to develop new therapeutic concepts and we are actively pursuing research into the emerging translational domain of innate immune sensing pathways. The specific PhD project will be discussed on an individual base with interested candidates.

  • Johan AUWERX – Laboratory of Integrative Systems Physiology / Interschool Institute of Bioengineering / School of Life Sciences

1. We propose to use C. elegans to elucidate how the genetic composition of the nematode renders it susceptible to dietary and pharmacological interventions. The training objective is to use molecular, biochemical, and in vivo techniques to determine how genes and environment interact, and how this affects ageing. The PhD will use dietary and pharmacological interventions in C. elegans, using either mutant strains or worms that have been fed with specific RNAi, for prototypical genes known to be involved in lifespan and ageing e.g. daf-2, daf-16, nuo-1, pme-1 and sir-2-1. Dietary interventions will consist in changing fat and carbohydrate content of the plates or liquid culture medium, caloric restriction, whereas the pharmacological interventions will be selected from benchmark compounds that are known to affect worm lifespan, e.g. resveratrol, rapamycin, nicotinamide riboside, PARP inhibitors. The PhD will explore the effect of these genetic and environmental factors on worm movement as a proxy for ageing. In follow-up experiments, the candidate will learn a variety of phenotypic and molecular/biochemical techniques, including highly specialized techniques of worm imaging e.g. using reporter strains, automated movement tracking, targeted metabolomics analysis e.g. NAD measurements, characterization of mitochondrial function (citrate synthase assays, mtDNA/nuDNA ratio, mtDNA mutation), proteomic analysis, and study of worm respiration using the Seahorse flux analyzer. The PhD will also perform lifespan studies, including Kaplan-Meier statistics, hazard ratio calculations as well as integrate the information on ageing studies in the worm with comparable information obtained in other model organisms (e.g. fly, mouse) and humans.

2. This project is based on the outcome of pre-clinical studies conducted by Amazentis, which will provide a characterization of the anti-aging effects of the lead compound UA and of a panel of naturally derived compounds. The aims of the current project will be to (1) extend our understanding of the mechanistic relationship between mitophagy and other mechanisms of ageing, followed by (2) the possible identification of novel applications for mitophagy-activating compounds. The model of choice will be C. elegans, a particularly useful tool to measure the impact of the compounds on lifespan extension and age-related phenotypes. In addition, mutant strains modeling age-related disorders (e.g. neurodegenerative disorders) or worms carrying mutations in genes of the Nucleotide Excision Repair pathway will be tested. The best compounds and conditions identified in worms will be further tested in vitro and in rodent models to validate the mechanism in a mammalian setup.

  • Yimon AYE – Laboratory of Electrophiles and Genome Operation / Institute of Chemical Sciences and Engineering / School of Basic Sciences

In the laboratory of electrophile and genome operation (LEAGO), we aim to decode nature’s inherent reactive signaling mechanisms. Through increasing our understanding of this fluid cellular communication medium, we have uncovered new pathway intersections, novel protein/enzyme regulation mechanisms, and have designed novel drug-like molecules with predictable properties. We have established several novel principals using custom-designed chemical tools that function in engineered cells, and organisms. However, we have also developed several cross-cutting cellular and biochemical systems that help with our studies. Critically, information from these model systems is directly applicable to native systems. It is our aim to develop research that is impactful across many different scientific areas, and to train scientists that are equally skilled and competent in various scientific disciplines. As our projects straddle the intersection of chemistry, biology, engineering, and physics, they are uniquely challenging, but also incredibly rewarding. So, if you are interested in interface science, we have several interesting projects focusing on regulation of kinase signaling, ubiquitylation, genome-maintenance and immune response that are ideal for PhD students wanting to leave their inhibitions behind and enter this interdisciplinary arena. https://leago.epfl.ch/

  • Patrick BART – Laboratory of Protein and Cell Engineering / Interschool Institute of Bioengineering / School of Life Sciences

Engineering powerful proteins with novel functions for cell engineering, synthetic biology and therapeutic applications

Protein design has made tremendous progress in recent years and is becoming central to synthetic biology applications including cell engineering approaches. For example, engineered proteins with customized signaling responses to disease-associated molecules provide promising and powerful new therapeutic agents for cancer immunotherapy, regenerative medicine and autoimmune disorders.

Our lab is developing and applying computational-experimental protein design approaches for engineering proteins with a wide range of novel functions. The technologies have been validated on simple proof of concepts (e.g. Feng et al., Nat Chem Biol 2017; Arber et al., Curr Opin Biotech 2017; Young et al., PNAS 2018). Using these approaches, we now aim at designing innovative and powerful protein nanomachines towards engineering synthetic living cells or for improving the anti-tumor responses of engineered immune cells in cancer immunotherapies.

Specifically, the project will involve some aspects of computational protein modeling and design using the techniques developed in the lab complemented by the directed evolution of desired protein functions. Engineered proteins will be validated using in vitro and cell-based assays reporting selective protein cellular functions and cellular behavior.

Concerning the cancer immunotherapeutic applications, the most promising designed protein candidates will be tested in mouse xenograft models in collaboration with laboratories at the CHUV/UniL (e.g. Caroline Arber, George Coukos) before potential translation to the clinic. Marrying empirical and computational protein engineering approaches has the unique potential to design a broad spectrum of cellular functions for engineering powerful cells with novel synthetic or sustained anti-tumor responses.

  • Giovanni D’ANGELO – Lipid Cell Biology Laboratory / Interschool Institute of Bioengineering / School of Life Sciences

Lipids are fundamental constituents of nearly all living-objects as their biophysical properties account for the formation of the bilayer structure characteristic of biological membranes. This structure is conserved from prokaryotes to animal cells where it enwraps the cytosol and the different intracellular organelles allowing intracellular compartmentalization.

The different organelles of the cell are enclosed by membrane bilayers whose lipid composition varies remarkably. A considerable difference exists between membranes of the endoplasmic reticulum (ER) and those of later compartments in the biosynthetic axis such as the plasma membrane (PM). While ER membranes are, indeed, poor in sterols and sphingolipids, these lipids represent major molar fractions of the extracellular leaflet of the PM.

How eukaryotic cells manage to establish and maintain their PM lipid composition in spite of the intense inter-organelle membrane exchange has been a longstanding question in the fields of membrane trafficking and lipid biochemistry.  Work from the last 15 years suggests that the coordinated action of dedicated lipid transfer and enzymatic machineries operating at the ER-Golgi Complex interface drives the formation of the PM lipid territory.

How lipid-processing enzymes are localized to the GC and whether their localization is modified to respond to environmental challenges or developmental cues is not understood.

The PhD student involved in this project will approach the study of the regulatory mechanisms that impact the topological organization of the lipid processing enzymes that can lead to:

– quantitative changes in PM biogenesis, such occur during the transition from resting to proliferative cell states.

– qualitative changes of PM lipid composition as occur during cell differentiation and development.

By this research we aim at obtaining new information about a fundamental cell process (i.e., PM lipid remodelling) where its understanding promises to have a wide impact on the fields of cell and developmental biology and implications for human health.

  • Georg FANTNER – Laboratory for Bio- and Nano-Instrumentation / Interschool Institute of Bioengineering / School of Engineering

Interdisciplinary PhD at the interface of microbiology and micro/nanotechnology.

The application of novel, cutting-edge instruments for nanoscale characterization of live cells allows unprecedented insights into the underlying molecular and mechanical mechanisms governing cell growth and division.  We are looking for a highly motivated student to lead a project using micro-/nano-fluidics, atomic force microscopy, and time-lapse optical microscopy for real-time single-cell studies of the bacterial cell cycle.  We are particularly interested in applicants with a combined background in engineering and life sciences.  What we offer is an interdisciplinary environment where you can learn diverse techniques ranging from molecular biology all the way to microfabrication and electronic circuit design. This position will be a joint appointment between the laboratories of Prof. John McKinney (School of Life Sciences) and Prof. Georg Fantner (School of Engineering).  For more information please contact us by email to [email protected] or [email protected].

Background Reading:

 Eskandarian HA, Odermatt PD, Ven J, Hannebelle M, Nievergelt AP, Dhar N, McKinney JD, Fantner GE (2017) Division site selection linked to inherited cell surface wave troughs in mycobacteria. Nature Microbiol 2:17094 PMID: 28650475.

 Nievergelt AP, Brillard C, Eskandarian HA, McKinney JD, Fantner GE (2018) Photothermal off-resonance tapping for rapid and gentle atomic force imaging of live cells. Int J Mol Sci 19(10) PMID: 30274330.

  • Diego GHEZZI – Neuro Engineering Laboratory / Interschool Institute of Bioengineering / School of Engineering

Validation of a wide-field injectable retinal prosthesis

We have designed a wide-field injectable retinal prosthesis (POLYRETINA) embedding more than 10,000 photovoltaic pixels able to provide wireless stimulation to retinal ganglion cells. The candidate will lead a project to fabricate and validate POLYRETINA in view of a early feasibility clinical trial.

  • Carlotta GUIDUCCI – Laboratory of Life Electronics / Interschool Institute of Bioengineering / School of Engineering

Single cell analysis on arrays of electrorotation microcages: A powerful platform for investigating amyloid toxicity and screening for novel drugs to treat protein aggregation diseases. https://clse.epfl.ch/openpositions/

  • Alexandre PERSAT – Microbial Mechanics Laboratory / Global Health Institute / School of Life Sciences

Through their long evolutionary history, bacteria have adapted to colonize nearly all types of environments on the surface of our planet, where they are exposed to a variety of physical phenomena. We are interested in determining how bacteria respond to the mechanics of their environments, such as fluid flow and contact with different surfaces. We try to understand how such system provides these organisms with selective advantages in the wild, be it in colonization or virulence. To achieve this, we leverage advanced microscopy techniques to simultaneously measure mechanical properties of the environment with cellular responses. In this project, we will seek to understand mechanosensory systems in different pathogens and to develop new therapeutic strategies to fight deadly infections.

  • Pavan RAMDYA – Neuroengineering Laboratory / Brain Mind Institute / School of Life Sciences

In the Neuroengineering Laboratory, we investigate the nervous system of the fly, Drosophila melanogaster, to understand how behaviors are controlled and to design more intelligent robots and prosthetics. Everyday we use custom microscopes, transgenic animals, computational models, and insect-inspired robots. Join us! There is much to discover!

  • Li TANG – Laboratory of Biomaterials for Immunoengineering / Interschool Institute of Bioengineering / School of Engineering

Highly motivated students (bachelor or master) with excellent academic achievements in a major field of Immunology, Cancer Biology, Chemistry, Polymer Science&Engineering, Bioengineering, Materials Science&Engineering, Chemical Engineering, or a closely related discipline, are encouraged to apply for EPFL doctoral programs. Preference will be given to candidates with a strong research background in immunology/chemical synthesis and published scientific papers. The candidate will utilize advanced synthetic biology techniques to create Chimeric Antigen Receptor (CAR)-T cells targeting specific chemical/physical characteristics of solid tumor and regulate the CAR-T cell trafficking and functions for cancer immunotherapy.

For more details, see web pages of the EDBB program’s potential thesis directors.