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 : December 15, 2023
https://www.epfl.ch/labs/ramdya-lab/
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!”
At least 2 openings are available. PhD projects will be available in the following two areas of research:
- 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.
- 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.
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].
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.
https://www.epfl.ch/labs/salathelab
In the past few years, studies have begun to demonstrate the potential of personalized nutrition in controlled settings, but their generalizability to the broader population remains an open question. The Digital Epidemiology Lab is harnessing the power of the digital health approach to understand the link between dietary patterns and blood glucose response, and its mediation through the gut microbiota. Based on a novel, very large data set from the Swiss “Food & You” digital cohort, we are training algorithms to create personalized diets with the goal to lower postprandial glucose response (PPGR). In the future, we are planing intervention studies to test the validity and scalability of this approach.
The source of the data, the Food & You cohort study, is a globally unique “digital cohort” on personalized nutrition in Switzerland, developed and run by the lab. As of March 2023, the cohort has collected detailed behavioral and biological data from over 1000 people within Switzerland, and has started data collection in Germany. The data comprises detailed, high temporal resolution nutritional data (at least 14 consecutive days of detailed food tracking data with images), physical activity data, gut microbiota data, and data from continuous blood glucose sensors with over 1.5 million recordings, all collected simultaneously, in addition to demographic data. The study has created an unparalleled dietary dataset of over 300,000 human-validated dishes with a total of over 42 million kcal.
We are now interested to use this data to develop recommender systems, and to investigate various aspects about the interactions of the multimodal data collected in the Food & You study. We are also planning Food & You 2, a new, extended version of the Food & You cohort. We are looking for a talented and motivated PhD student to participate in this project on data-driven personalized nutrition.
https://www.epfl.ch/labs/fellay-lab
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 host-pathogen genomic interactions, with a special emphasis on tuberculosis in the context of a collaborative project with colleagues from Tanzania and from the Swiss Tropical and Public Health Institute in Basel. The main goal of this project is to understand the biological determinants of sub-clinical TB, an epidemiologically important disease state where patients excrete live TB bacilli without reporting any symptoms. The student will be in charge of analyzing human genomic and transcriptomic data (including single-cell data) generated from clinical samples and from in vitro granulomas, and of developing new strategies for combined analyses of DNA and RNA data. 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.
https://www.epfl.ch/labs/nsbl/
The primary objective of this interdisciplinary PhD project is to investigate the brain lipidome as a key to understanding the complex interplay between lipid distribution, lipid dysmetabolism, and alpha-synuclein (aSyn) pathology formation in Parkinson’s disease (PD) using advanced computational approaches and cutting-edge technologies. By exploring the role of regional brain lipid alterations in the development and progression of aSyn pathology formation and neurodegeneration, this project offers a unique opportunity for a PhD candidate who is deeply interested in developing computational models and excited by the rapidly evolving technologies in the field.
Leveraging cutting-edge technologies such as matrix-assisted laser desorption/ionisation (MALDI) mass spectrometry imaging (MSI), this project aims to map the lipidome in the entiremouse brain in 3D and at micrometric resolution. The main activities of the PhD candidate will focus on Specific Aim 1 and Specific Aim 2:
- Determining the role of specific lipid configurations in regulating α-synuclein pathology formation and spreading in the α-synuclein pre-formed fibrils (PFF) model of PD.
- Investigating the impact of de novo α-synuclein aggregation and seeded α-synuclein aggregate formation and propatation on regional lipid metabolism.
As part of a vibrant research team, the PhD candidate will collaborate with experts in the fields of computational biology, lipid cell biology, neurodevelopmental systems biology, and chemical biology of neurodegeneration. This project provides an excellent opportunity to develop advanced computational skills, work with large-scale datasets, and employ innovative analytical pipelines to address critical questions in PD pathology.
The interdisciplinary nature of this project will allow the PhD candidate to acquire valuable expertise in both neuroscience and computational biology, positioning them at the forefront of cutting-edge research in neurodegeneration.
This project is flexible to a certain extent, allowing the candidate to decide whether to also extend their research to experimental parts, depending on their interests and expertise.
Focus of the lab:
The human body develops from a single totipotent cell. During development, this single totipotent cell gives rise to the entire diversity of cell types of the body that ultimately make up all organs. Even though those cells are transcriptionally and functionally different, they share the same genome. Epigenetic mechanisms that regulate which set of genes will be turned on and which genes will be switched off in each cell are at work in order to maintain and generate cellular diversity.
The nervous system develops during early embryonic development and ultimately contains all different types of neurons from different regions of the body. In a series of developmental transitions, progenitors differentiate into neuron and glia lineages.
In my lab, we use neural organoids to model these developmental transitions and investigate how epigenetic processes control differentiation and cell fate. We employ single-cell genomics and imaging technologies to profile the chromatin of individual cells.
We have multiple open positions.
The successful candidates should have:
-High motivation, curiosity and a strong interest in scientific discoveries
-Drive to learn innovative technologies and perform challenging experiments
-A strong background in computational analysis of genomics data
-Good experimental skills in molecular biology (e.g. IF, IP, Western-Blot, Nuclei-Acid-Extraction, Sequencing-library preparation, Cloning)
-Ideally, experience with human iPS cell culture and curiosity to further develop in vitro culture systems
Current contact email: [email protected]
The Living patterns lab at EPFL IPHYS has three open PhD positions. We are an experimental
Biophysics group exploring a wide variety of imterdisciplinary problems at the interface
of cell and developmental biology and active matter physics. Research in the lab
is centered around understanding patterning and flow generation in multiciliated cells. Individual
projects are shaped by student’s interests, for more information visit our lab website
http://livingpatterns.group or email us directly [email protected].
How and why cells regulate centriole number.
In this project, you will generate a synthetic centriole cycle with altered organelle numbers, and address the consequences on cell physiology, in cultured cells and in organoids. In doing so, you will utilize notably cell biology, live imaging, image analysis, RNAseq and data analysis.
The Laboratory of Computational Neuro-Oncology at the École Polytechnique Fédérale de Lausanne (EPFL) focuses on biomedical data science for children and young adults with brain tumors (waszaklab.org). The group studies clinical cancer genomes and develops computational and experimental methods to advance diagnostics that are globally accessible and transformative for brain tumour patients. We have the following four PhD positions to offer:
Project 1: Deciphering the cellular origin of brain tumours at single-cell resolution
Project 2: Digital neuropathology 2.0: integration of subcellular, high-plex in situ data with histopathology
Project 3: Leveraging long-read sequencing in pediatric neuro-oncology
Project 4: Targeting oncogenic enhancers in pediatric diffuse gliomas