EDBB Open positions

Barth lab

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.

CIBM

Full description here.

PhD position:  spatial & functional characterization of photoreceptors lipids during retinal degeneration and neuroprotection.

The Lipid Cell Biology Laboratory, directed by Giovanni d’Angelo (https://www.epfl.ch/labs/dangelo-lab/ ) has an open position in collaboration with the Lausanne University Ophthalmology department ( https://www.ophtalmique.ch/centre-de-recherche/ ) on photoreceptors lipid characterization during retinal degeneration and retinal neuroprotection.

Project description:

Specifically, the project plans to investigate the lipid composition of the retina throughout degeneration processes and genetically-encoded neuroprotective therapy. Inherited retinal degeneration are characterized by altered phototransduction cascade and progressive death of retinal photoreceptors. Photoreceptor lipid rafts microdomains are associated with the phototransduction cascade and altered during retinal degeneration. This project will broaden our understanding of the lipid composition in photoreceptors and their role in the degeneration process, with the objective of developing a neuroprotective approach targeting cell signaling in lipid microdomains.

This project will make advantage of stem cells culture techniques, mass spectrometry (MALDI imaging), high-resolution celllular imaging, chemical biology and histochemistry techniques with the following aims:

1. Development of an iPSCD-derived organoid model for retinal and photoreceptor lipids characterization
2. Spatial & functional characterization of photoreceptor lipids in retinal organoids and mice models of retinal degeneration
3. Evaluation of a neuroprotective therapy effects on photoreceptor lipid composition and photoreceptor metabolism

The ideal candidate should have a Master’s degree (or equivalent degree) in life science, engineering, neuroscience, or biology, and be strongly motivated with a keen interest in stem cells technologies, cellular neuroscience and imaging analysis. Previous research experience with molecular biology and cell cultures techniques is an advantage.

Working environment:

The successful applicant will join the Lipid Cell Biology Laboratory – Kristian Gerhard Jebsen Chair on Metabolism research group and the Ophtalmogenetics research group of Lausanne University. The PhD candidate will be embedded in a highly international and dynamic environment in close collaboration with clinical research. The lab is based in the Jules Gonin Ophtalmic Hospital, in the city center of Lausanne. The PhD candidate will be enrolled in the EPFL Ph.D programm in Biotechnology and Bioengineering (EDBB).

Start of position:

Fall 2024

Application procedure:

Interested candidates must submit their application to the EDBB doctoral school

(https://www.epfl.ch/education/phd/edbb-biotechnology-and-bioengineering/edbb-how-to-apply)

LBNC

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:

1. 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. 
2. 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 3 positions open this round. 

1. We are looking for students interested in implementing novel human organoid-based systems, microfluidics and imaging to investigate resistant microbes and discover new drugs to combat them.
2. We are looking for students to personalize phage therapy using a human lung organoid system developed by our lab. This project is in tight collaboration with the department of infectious disease at CHUV and will immediately impact patients’ lives. 
3. We are looking for a student with strong quantitative engineering background to investigate the group behavior of resistant microbial pathogens.

Laboratory of the Physics of Biological Systems

Antibodies are key components of protein- and cell-based therapies. One tool for antibody development that laboratories around the world are focusing on is artificial intelligence (AI), leveraging structural and binding data to create prototypes of proteins that bind their targets well. However, AI tools are currently far from generating good designs with high success rates. Further, ‘smart’ proteins that switch on or off are not within the scope of AIbased tools currently. More importantly, we also need breakthroughs in experimental techniques that make it easy (and cheap) to test and improve on designs. We want a PhD student to join our lab, who is interested in developing both

1) novel experimental directed evolution techniques and

2) AI-based design methods

to make better binding, smarter, more controlled, and cheaper antibodies.

Contact Prof. Sahand Rahi ([email protected]) for more information.

Focus of the Zenk 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