This page reflects PhD openings within the EDBB program to the best of our current knowledge and is constantly evolving as we are being informed of new openings and as we approach the January Hiring Days. Please do not hesitate to also contact the laboratories which interest you to find out whether they have upcoming openings.

Next PhD application deadline: November 1, 2024

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.

We are looking to hire a graduate student in cell-free synthetic biology. The prospective graduate student will work on building the foundations for the development of a synthetic cell. This project will involve developing state-of-art techniques and approaches in cell-free synthetic biology combined with microfluidic technologies to push the current boundaries of in vitro synthetic biology and cell-free transcription – translation systems. The graduate student will be embedded in a highly international and dynamic research environment.

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 RNA-seq biomarker discovery for drug sensitivity in leukemia. Here we plan to combine our Combi-seq approach (Mathur et al., Nature Communications 2022) with single-cell phenotypic cell sorting for drug sensitivity.
• Library vs library screening of T-cells and antigen-presenting cells for novel immune oncology approaches”. Here we aim to set up a platform for screening cell pairs for affinity. The project is carried out in the context of a large Sinergia grant consortium, including several bioinformatics groups.

The Persat lab investigates mechanical regulation of bacterial infections in order to provide innovative solutions to the antibiotic resistance crisis. The lab is highly multidisciplinary, combining methodologies from physics, engineering, computation and biology.

We have one open PhD position at the interface between microbiology and computational biology to explore mechanosensing in problematic pathogens. The project will combine RNAseq measurements across a variety of bacteria with microscopy-based screens for regulators of mechanical sensing.

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