This page reflects PhD openings within the EDBB program to the best of our current knowledge. Please do not hesitate to contact the laboratories which interest you to find out whether they have upcoming openings for PhD students as this list is non-exhaustive.
Next Deadline for applications : November 1, 2023
The position is described here: https://www.epfl.ch/about/working/sti-phd-position-mid-ir-nanophotonics-for-biosensing/
https://www.epfl.ch/labs/antanasijevic-lab/
Antanasijevic lab at the Global Health Institute (EPFL) has an open position for a PhD student with interests in structural biology, virology, and vaccine design. The research project will focus on (i) development of tools and methods for structural analyses of antibody responses in mucosal tissues, (ii) understanding the mucosal immune responses elicited by enterovirus (EV) infections in patients and (iii) design of vaccine candidates capable of conferring protective mucosal immunity against diverse EV strains. The main research tool will be state-of-the-art cryo-electron microscopy.
We are looking for excellent candidates that are motivated, enthusiastic, and organized. Previous research experience in biochemistry, virology and/or structural biology is preferred. Selected candidate will get a chance to drive interdisciplinary research projects in a highly collaborative environment.
For more details please contact: [email protected]
See the following references to learn more about the research:
Antanasijevic et al., Nature Comm, 2021
https://www.nature.com/articles/s41467-021-25087-4
Antanasijevic, Bowman et al., Sci Adv, 2022
https://www.science.org/doi/10.1126/sciadv.abk2039
Antanasijevic et al., PNAS, 2022
https://academic.oup.com/pnasnexus/article/1/5/pgac253/6798388
Expanding the universe of protein functions for synthetic biology and biomedicine
Our lab is developing and applying hybrid AI-based computational/experimental approaches for engineering classes of proteins with novel 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 and AI-based approaches for macromolecular modeling and design. Ultimately, we aim to develop a versatile tool for designing novel potent, selective therapeutic molecules, synthetic proteins, receptor biosensors, networks and pathways for reprogramming cellular functions. We are also affiliated to the Ludwig Institute for Cancer Research in Lausanne.
Projects in the lab are often multidisciplinary and involve the development of novel methods (e.g. Feng, Nat Chem Biol 2016; Nat Chem Biol 2017; Paradis, Nat Comm 2022; Dumas, biorxiv 2023) and their application involving experimental studies (e.g. Young, PNAS 2018; Chen, Nat Chem Biol 2020; Yin, Nature 2020; Keri et al., biorxiv 2023; Jefferson, Nat Comm 2023). Projects involving external collaborations with other research groups around the world or internal collaborations between computational biologists, physicists and experimentalists in the lab are frequent. We also actively translate our findings to the clinic in collaboration with physicians (e.g. Dr. Arber, Coukos from the Ludwig Institute for Cancer Research). Specific research topics include: 1. The design of protein biosensors, mechanosensors and signaling receptors for reprogramming cell (e.g. CAR T cell) functions and enhance cell-based therapies; 2. The design of highly selective and potent protein and peptide-based therapeutics towards challenging targets such as GPCRs or ion channels; 3. The study, prediction and design of protein dynamics and allostery using AI and classic computational approaches; 4. The development of novel AI-based algorithms for modeling & design of protein structures, interactions and motions.
Dry lab candidates should have strong programming skills in python/C/C++ and expertise in the development of deep learning methods. Knowledge in structural biology, bioinformatics, computational biomolecular modeling including molecular dynamics simulations is a plus. Candidates more oriented towards the wet lab should have strong skills in molecular and cell biology including experience in protein biochemistry, mammalian cell culture, microscopy, and structural biology. Hybrid computational / experimental projects are also possible.
The position is described here: https://www.epfl.ch/about/working/sti-phd-positions-in-mechanics-of-soft-and-biological-matter-laboratory/
https://www.epfl.ch/labs/nsbl/
The PhD project will primarily focus on the spatial transcriptomics and lipidomic characterization of in vitro embryoid models, specifically human gastruloids, at different developmental stages. This will entail utilizing single-cell and spatial transcriptomics to decipher cell identities and local interactome patterns. Concurrently, lipidomics approaches will be employed to understand cellular lipotypes and their relationship to fate decisions in human gastruloids. A smaller, but essential part of the project will involve collaborating on the development and validation of a hyperspectral imaging system, particularly in training machine learning models to convert RAMAN signals into transcriptomics and lipidomics information. This multi-disciplinary approach aims to improve our current understanding of optimized in vitro models, thereby contributing to more predictive assays for drug testing.
https://www.epfl.ch/labs/mckinney-lab/
We are looking for a highly motivated PhD Student to lead a project using live-cell imaging and state-of-the-art microtissue models of urinary tract infections (UTIs) to evaluate “metabolic potentiation” as a novel therapeutic strategy, with an emphasis on hard-to-treat bacterial biofilms associated with indwelling medical devices. A background in microbiology, bioengineering, or microengineering is preferred but not required. The student will be based in the Laboratory of Microbiology & Microtechnology at EPFL but will also work closely with our clinical collaborators at the Lausanne University Hospital (CHUV).
The Laboratory for Biomedical Microfluidics (LBMM, www.epfl.ch/labs/lbmm) develops new approaches in antibody discovery and personalized cancer therapy.
The group is very interdisciplinary, including people with a primary training in biology, bioinformatics and engineering. Powerful technology platforms in the field of biomedicine and genomics have been developed over the past years, also leading to the establishment of two startup companies (www.veraxa.de and www.besttherapyforme.com).
Having a comprehensive microfluidic toolbox at hand (and expanding it continuously), we are now inviting applications for two projects:
- Highly multiplexed single-cell RNAseq-based antibody discovery. The idea behind this project is to exploit transcriptomic data sets for the discovery of new therapeutic antibodies.
- Light-sheet droplet microfluidics. Here the idea is to generate digital pathology data sets after exposing patient samples to a variety of treatment options. Ultimately this should lead to the discovery of imaging-based biomarkers for drug sensitivity.
Imaging infection
The Persat lab investigates mechanical regulation of bacterial physiology and infection in order to solve the emerging problem of antibiotic resistance. The lab is highly multidisciplinary, combining methodologies from physics, engineering and biology with a strong computational emphasis.
We are looking for a motivated student interested in implementing novel microscopy technologies for the visualization of infection and bacterial structures involved in pathogenicity. The ideal candidate has a strong technical background in engineering or physics amd problems eager to implement new methods to solve high-impact biological problems.
website: p-lab.science
During physical activities, knee cartilage will experience mechanical loading and temperature increase. These stimuli will favour chondroprotection and chondroinduction. The two PhD positions will consist in stimulating human cartilage explants in a bioreactor (already existing) and evaluate the behaviour of the tissues under different conditions (mechanical and thermal) as well as developing an in vivo study where the knee cartilage of rats can be thermomechanically stimulated and the possible effect on reversing cartilage degeneration could be evaluated.
The PhD background should be in biomechanics, bioengineering, or biomedical engineering.
The Laboratory of Computational Neuro-Oncology focuses on biomedical data science for patients with brain tumours (waszaklab.org). Our research 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 offer the following PhD positions for candidates with a background in computer science, engineering, physics, or statistics.
Project 1: Deciphering the cellular origin of brain tumours at single-cell resolution.
Project 2: Leveraging long-read whole (epi)genome sequencing in neuro-oncology.
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
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
For more details, see web pages of the EDBB program’s potential thesis directors.