EDCB Open positions

This page will be updated, as the EDCB program will be informed of new positions becoming available for the Hiring Days event at EPFL. Meanwhile, do not hesitate to contact the laboratories which interest you to find out whether they have upcoming openings for PhD students.

Next Deadline for applications : April 15, 2023

In the Neuroengineering Laboratory, we are reverse-engineering cognitive and motor behaviors in the fly, Drosophila melanogaster, to better understand the mind and to design more intelligent robots. Flies are an ideal model: they generate complex behaviors, their nervous systems are small, and they are genetically malleable. Our lab develops and leverages advanced microscopy, machine learning, genetics, and computational modeling approaches to address systems-level questions.

We are always looking for talented researchers to join our team. Join us! There is much to discover!”

More [email protected] https://www.epfl.ch/labs/ramdya-lab/

https://www.epfl.ch/labs/lbm/

At least 2 openings are available. PhD projects will be available in the following two areas of research:

  1. Biological nanopores for single-molecule sensing

Nanopore sensing is a powerful single-molecule approach currently developed for the precise detection of biomolecules, as for instance in DNA and protein sequencing. Our laboratory is developing this technology exploiting the properties of biological pores. Recently, we showed that aerolysin, a pore-forming toxin, exhibits high sensitivity for single-molecule detection and can be ad hoc engineered for different sensing tasks. The goal of this project is to develop and characterize aerolysin-based nanopores as sensing devices to be applied for genome sequencing, proteomic analysis and disease diagnosis. The project is highly interdisciplinary, includes experimental and computational aspects and interactions with a diverse network of collaborators.  Students with a background in biochemistry, physics, bioengineering and computational sciences are encouraged to apply.

  1. Integrative modeling at the membrane-protein interface

Molecular interfaces are essential for the formation and regulation of all assemblies that sustain life, to define cellular boundaries and intracellular organization, and to mediate communication with the outer environment. Our laboratory has been studying the molecular mechanisms governing the association of proteins to their membrane interfaces in order to understand the functional implications of this interplay. Multiple projects are available that focus on the theoretical and computational investigation of the structural and dynamic properties of membrane protein systems. All of them are addressed in synergy with experimental collaborators to allow for an efficient integration of biochemical and biophysical data. Students with a background in biochemistry, physics, bioengineering and computational sciences are encouraged to apply.

Pluripotent stem cells (PSCs) have the potential to infinitely self-renew in vitro. This property hinges on the ability to maintain their identity through cell divisions. Cell identity maintenance requires a robust control of cell type-specific gene expression programs, which is challenged by the disruption of gene regulatory mechanisms during mitosis. How PSCs reorganize their chromatin landscape and transcriptional machinery to resume their gene expression program after mitosis is unclear.

H2A.Z is an evolutionary conserved histone variant localized at regulatory elements that central to both pluripotent cell identity (expressed genes) and plasticity (genes that are poised to become expressed during development). The absence of H2A.Z leads to defects in pluripotency maintenance and differentiation. We have recently discovered that in PSCs, H2A.Z positioning displays a specific pattern on mitotic chromosome that may reflect its role in epigenetic memory of gene expression programs through cell division.

This project aims at determining the role of H2A.Z in genome reactivation and cell identity maintenance. Specifically, you will study the role of H2A.Z chromatin occupancy on i) Pluripotency transcription factor binding during mitotic exit, ii) The kinetics and robustness of transcriptional reactivation after mitosis, and iii) The maintenance of PSC self-renewal capacity and responsiveness to differentiation cues. This will be achieved by various approaches such as genome editing of mouse embryonic stem cells, quantitative ChIP-seq, ATAC-seq,  single cell RNA-seq analysis, and stem cell differentiation assays.

If you are interested, please contact me at [email protected]

More [email protected] https://www.epfl.ch/labs/suter-lab/research/

Our lab uses computational approaches to understand inter-individual differences in immune response and susceptibility to infection. 

We are looking for a PhD student to work on multi-omic analysis of children with rare diseases, in the context of an ambitious translational project funded by the Swiss Personalized Health Network. In close partnership with clinicians in paediatric intensive care units and with machine learning researchers from the ETH domain, the student will be in charge of analyzing the genomes and transcriptomes of study participants, of developing new strategies for combined analyses of DNA and RNA data, and of designing a clinically useful diagnostic pipeline. 

Candidates should have a background in bioinformatics or computer sciences with a strong interest in applications to biomedicine. Programming skills in Python and/or R are required. 

More [email protected] https://www.epfl.ch/labs/fellay-lab/

We have a PhD position opening on the LipoTrace project funded by European Research Council (ERC via SERI) and aimed at studying single cell lipidome dynamics in time and space. Lipids are fundamental constituents of all living beings. They participate in energy metabolism, account for the assembly of biological membranes, act as signalling molecules, and interact with proteins to influence their function and intracellular distribution. Eukaryotic cells produce thousands of different lipids each endowed with peculiar structural features and contributing to specific biological functions. With the development of lipidomics we now appreciate lipid compositional complexity of cells, and start making sense of lipidome dynamics. Lipidomes indeed vary among cell types and are reprogrammed in differentiation events. Moreover, the lipidome is subjected to remarkable cell-to-cell variation in syngeneic cell populations and specific lipid configurations associate with and influence cell states. This indicates that single-cell lipidomes participate in establishing cell identity and their remodelling assists cell differentiation, still how lipidome configurations are attained and how cells transition from one metabolic configuration to another remain unanswered questions. Here, we will develop computational tools to track single-cell lipidome dynamics in time and space to investigate the ontogenesis of lipid state heterogeneity. This information will be instrumental to address the fundamental question of how cell properties not directly determined by the transcriptome (here the lipid metabolic state) contribute to cell-fate decision-making and cell plasticity. 

More info @ https://www.epfl.ch/labs/dangelo-lab/

Our lab is developing and applying novel hybrid computational/experimental approaches for engineering classes of proteins with new functions for cell engineering, synthetic biology and therapeutic applications. Through our bottom up design approach, we also strive to better understand the molecular and physical principles that underlie the emergence, evolution and robustness of the complex functions encoded by proteins and their associated networks.

We are part of RosettaCommons (https://rosettacommons.org/), a collaborative network of academic laboratories that develop the software platform Rosetta for macromolecular modeling and design. Ultimately, we aim at developing a versatile tool to leverage the engineering of novel potent, selective therapeutic molecules and the de novo design of synthetic proteins, networks and pathways for reprogramming cellular functions.

Projects in the lab are often multidisciplinary and involve the development of novel methods (e.g. Feng et al., Nat Chem Biol 2016, Nat Chem Biol 2017) and their application involving experimental studies (e.g. Young et al., PNAS 2018; Chen et al., Nat Chem Biol 2020; Yin et al., Nature 2020). Projects involving internal collaborations between computational biologists, physicists and experimentalists in the lab are frequent. Specific research topics include the de novo design of allosteric protein biosensors, highly selective and potent mini-protein and peptide therapeutics, novel membrane receptors and signaling pathways reprogramming immune cell functions for improved cancer immunotherapies, and the development of novel algorithms for modeling & design of protein structures, interactions and motions.

Candidates should have strong programming skills in C/C++ and python. Some knowledge of bioinformatics, machine learning and/or computational biomolecular modeling are welcome.

For further information and application, please contact directly  [email protected]

The Oates lab is exploring how spatio-temporal patterns emerge at the tissue level from noisy cellular and molecular interactions using a population of genetic oscillators in the zebrafish embryo termed the segmentation clock. This multi-cellular clock governs the rhythmic, sequential, and precise formation of embryonic body segments, termed somites, and exhibits a rich set of spatial and temporal phenomena spanning from molecular to tissue scales. Defects in this clock underlie human congenital mal-segmentation disorders (hereditary scoliosis).

Although the segmentation clock has been the dominant paradigm for 20 years, this model does not account for a fascinating classical result: the heat-shock echo, in which periodic segment defects recur, like an echo, along the axis. The interval separating the defects is 5 segments, but – critically – there are no known multiple-segment periodicities in the segmentation clock. This suggests that something fundamental is still missing from our overall picture of segmentation.

Using innovative microscopy techniques, transgenic zebrafish, biochemistry, mechanical manipulation, deep sequencing, physical modeling and good old-fashioned heat-shocks, we aim to discover the mechanism underlying the repeated defects. We will characterize and investigate phenomena during the defects recently observed in our lab at multiple scales: single cell, synchronization between neighbor cells, large-scale wave patterns and mechanics of the tissue. We will also search in an unbiased way for genes that predict the echoes. If these sound to you like interesting questions and approaches to be explored in a challenging and interdisciplinary PhD, please apply to the program and contact the Oates lab via [email protected].

https://www.epfl.ch/labs/leb/

The physical properties of the mitochondrial matrix. ERC-funded project. The current dogma is that the mitochondrial interior, or matrix, behaves as a viscous fluid, albeit one with a complex shape. Interestingly, it has been reported that in vitro, different respiratory states of mitochondria correlate with differences in mitochondrial matrix viscosity, ultrastructure, and density. Fluorescence-based ratiometric, anisotropy, and recovery methods have been applied to measure its viscosity, but with results varying over two orders of magnitude. Intriguingly, motility and internal structure have been linked to metabolic states. More recently, it was reported that the internal ‘temperature’ of mitochondria is adaptive, and reaches nearly 50 °C when they are metabolically active. The field missing a comprehensive study that considers the mitochondrial matrix as a responsive complex fluid with potential for complex or non-equilibrium state behavior, the goal of this project.