EDBB Open positions

This page will be updated more often as we approach the end of 2020, as the EDBB program will be informed of new positions becoming available for the January 20-22, 2021 Hiring Days event at EPFL (or virtual event spread over January-February 2021 depending on the sanitary restrictions). Meanwhile, do not hesitate to contact any EDBB laboratories which interest you to find out whether they have upcoming openings for PhD students.

LEAGO

Laboratory of Electrophiles And Genome Operation is actively looking to recruit 1-2 PhD students keen to acquire interdisciplinary skillsets in the development and applications of novel bioengineering technologies underpinning covalent drug discovery and novel target mining, in cross-cutting projects aimed at both systems-level and individual-protein-specific-level investigations. For more information, please reach out to [email protected]   

UPBARTH

PhD project. Engineering powerful proteins with novel functions for cell engineering, synthetic biology and therapeutic applications

Protein design has made tremendous progress in recent years and is becoming central to synthetic biology applications including cell engineering approaches. For example, engineered proteins with customized signaling responses to disease-associated molecules provide promising and powerful new therapeutic agents for cancer immunotherapy, regenerative medicine and autoimmune disorders.

Our lab is developing and applying computational-experimental protein design approaches for engineering proteins with a wide range of novel functions. The technologies have been validated on several proof of concepts (e.g. Feng et al., Nat Chem Biol 2017; Arber et al., Curr Opin Biotech 2017; Keri et al., Curr Opin Struct Biol 2018; Young et al., PNAS 2018; Chen et al., Nat Chem Biol 2020; Yin et al., Nature 2020). Using these approaches, we now aim at designing innovative and powerful protein nanomachines towards engineering synthetic living cells or for improving the anti-tumor responses of engineered immune cells in cancer immunotherapies.

Specific projects typically involve some aspects of computational protein modeling and design using the techniques developed in the lab complemented by the directed evolution of desired protein functions and validation of engineered cells using a variety of cell biology approaches. Collaboration with laboratories at the CHUV/UniL/Ludwig Institute for Cancer Research (e.g. Caroline Arber, George Coukos) are in place for testing engineered molecules and cells in mouse xenograft models before potential translation to the clinic. Marrying empirical and computational protein engineering approaches has the unique potential to design a broad spectrum of cellular functions for engineering powerful cells with novel synthetic or sustained anti-tumor responses.

UPBLO & LEB

We offer the following interdisciplinary PhD (iPhD) position that will focus on bacterial shape determinants:

Despite unusual bacterial shapes and shape transitions having been documented over centuries, the underlying functionality has remained largely enigmatic. Our project will address this knowledge gap by combining quantitative shape measurements based on advanced microscopy techniques with optimal shape modeling followed by phenotypic testing of genetically engineered shape-transitional or shape-locked bacteria. Our model bacterium for this study will be Vibrio cholerae

The PhD student will be trained in both laboratories and apply his/her acquired skills to this interdisciplinary project.

PhD positions in nanopore sensing

We are seeking highly motivated candidates with interest in nanopore single-molecule sensing to join Dr. Chan Cao’s group at the School of Life Science, EPFL (Switzerland).

This newly established research group is focused on developing novel approaches to address questions in life science and diagnosis at the single-molecule level, especially specialized in nanopore technology. Nanopore measurement is an electrophoretic approach that allows the characterization of molecules of interest in real-time with sub-angstrom resolution and without the need for additional labels/amplification in aqueous solution. It has been successfully applied in sequencing long fragments of DNA and has shown great potential for single-molecule proteomics applications. The main goal of the group is to push the limits of nanopore technology and maximize its potential for as many fields of application as possible. In this position, you will join a dynamic team of computational & structure biologists, biophysicists, biochemists and analytical chemists.

The applicant should have at least one of the following backgrounds: biophysics, biochemistry, analytical chemistry, molecular biology or biomolecule synthesis. Experience in protein production and good programming skills is an advantage. The starting time should be September 2021 at the latest.

The applicant who is interested in this position, please send your resume to Dr. Chan Cao ([email protected]

The position is part of a Swiss National Science Foundation (SNSF) PRIMA project and the student will be co-supervised by Dr. Chan Cao, Prof. Matteo Dal Peraro and/or Prof. Gisou van der Goot. The salary and benefits are very competitive.

For more details please check: http://phd.epfl.ch/application

Next deadline for Doctoral program in Biotechnology and Bioengineering (EDBB), Molecular life Science (EDMS), and Computational and quantitative Biology (EDCB) is November 1st.

LPDI

De novo protein design has been successful in expanding the natural protein repertoire. However, most de novo proteins lack biological function, presenting a major methodological challenge. In vaccinology, the induction of precise antibody responses remains a cornerstone for next-generation vaccines. In the recent past we have developed a protein design algorithm, termed TopoBuilder, with which we engineered epitope-focused immunogens displaying complex structural motifs. Both in mice and non-human primates, cocktails of three de novo-designed immunogens induced robust neutralizing responses against the respiratory syncytial virus (RSV). Furthermore, the immunogens refocused pre-existing antibody responses towards defined neutralization epitopes. Overall, our design approach opens the possibility of targeting specific epitopes for vaccine and therapeutic antibody development, and more generally will be applicable to design de novo proteins displaying complex functional motifs. For this PhD project we will be extending the capabilities of our protein design approaches and further develop our vaccine concepts in the context of RSV as well as other important pathogens (Influenza).

UPGON

Investigating centriole fate during muscle formation in zebrafish embryos
Why? Centrioles are critical for forming centrosome in animal cells. Centrosomes are reorganized during muscle formation, but the fate of centrioles during such reorganization is unclear. 
How? Generate transgenic lines and conduct live imaging (e.g. with the lattice light sheet microscope) to monitor centriole fate during muscle formation in zebrafish embryos and identify mechanisms directing centriole fate (plus importance thereof). Approaches: molecular genetics, live imaging, cell biology, mathematical modelling.  
Collaboration between the Gönczy and Oates laboratories.

Re-engineering centriole architecture with modified SAS-6 proteins
Why? Centrioles exhibit a striking 9-fold radially symmetric architecture across eukaryotic evolution, whose importance is incompletely understood. 
How? Test whether modified and chimeric SAS-6 proteins that impart distinct symmetry and architecture to the organelle can generate functional centrioles in human cells and other systems. Approaches: molecular genetics, biochemistry, cryo-EM, AFM, CRISPR/Cas9 engineering, expansion microscopy. 

LIFMET

1) Biomedical imaging of lactate neuroprotection in stroke (HP & more).

 

2) Investigating a novel approach to measure cerebral glycolysis using hyperpolarized glucose.

 

3) PhD position in magnetic resonance spectroscopy/imaging (MRS/I) at École polytechnique fédérale de Lausanne (Switzerland)

We announce one open position at EPFL (École polytechnique fédérale de Lausanne), Switzerland. The main work will be performed at the biomedical imaging center equipped with one 7T human MRI scanner and two small animal MRI scanners (9.4T and 14.1T).

The PhD candidate will develop advanced magnetic resonance spectroscopy/imaging methods on a 7T human MRI scanner and apply them to investigate the modulatory capacity of inhibitory system induced by physical activity. Applicants should have a master degree or equivalent in physics, mathematics, biomedical engineering, life science or related disciplines in neuroimaging. Excellent programming skills in C/C++, Python or MATLAB are required. Previous experience in MR sequence programming, data acquisition and processing is a plus. The candidate should have good communication skill and strong interests in research field of biomedical engineering.

All applicants are kindly requested to submit a curriculum vita, a motivation letter, master transcripts (including a list of classes and grades) and two references (contact details or reference letters) to Dr. Lijing Xin ([email protected]).

LBNC

We expect to hire 1-2 PhD students in 2020 in the area of cell-free synthetic biology / synthetic cell engineering.

Ramdya Laboratory of Neuroengineering, two positions
We use the fly, Drosophila melanogaster, microscopy, machine vision, genetics, and computational models to identify how biological neural circuits control behavior. We aim to better understand the mind and to build more versatile robotic controllers. We use flies because they produce complex behaviors, have small nervous systems with stereotyped connectivity, and are genetically tractable. We are currently excited to welcome additional PhD students to perform and analyze 2-photon optical recordings of neuronal population dynamics governing action selection and limb control. These measurements will be used to inform simulation and robotics work in the laboratory.

LBP

Interfacial Imaging of Water: New Light on Cellular Hydration

Two PhD student positions are available at the Laboratory for fundamental BioPhotonics (LBP) at the École Polytechnique Fédérale de Lausanne (EPFL), Switzerland.

Water is the liquid of life. It is intimately linked to our well-being. Without water, cell membranes cannot function. Charges and charged groups cannot be dissolved, self-assembly cannot occur, and proteins cannot fold. That water is intimately linked with life, we experience time and again when we quench our thirst, but how does this link work?

Osmosis is the flow of water across a (cell) membrane that separates two aqueous solutions with different concentrations of a solutes. Regulating osmotic pressure is a key survival strategy of cells and plays an important role in the functioning of every organism. How osmotic pressure and cell membrane tension are regulated on the molecular level is not known. It is the aim of the ERC Synergy Grant R2 tension, a collaboration between EPFL (Prof. S. Roke) and the University of Geneva (Prof. A. Roux) to work this out.

The Project at EPFL

Nonlinear optical imaging and new ultrafast spectroscopic techniques have recently been developed in the Roke lab and used to image in real time interfacial water and electrostatic potentials on membrane interfaces of model membranes and in living cells.

In the current project: two new microscopes are to be constructed that will allow us to (1) image interfacial water in real time as well as the electrostatic field lines on the interface, and (2) image in real time membrane tension in vitro and in living systems. We will also provide a molecular ruler that links molecular conformation of lipids to mechanical forces. The new technology will first be applied in a controlled manner to in-vitro assays, after which measurements on living cells will be performed.

The EPFL Candidate

This research has many interdisciplinary aspects that demand a highly motivated candidate with strong analytical abilities that is able to think out of the box. The diverse aspects of the project allow a wide range of backgrounds that includes photonics, physics, chemistry/material science, electrical or bioengineering. Experience in nonlinear optics / microscopy, either theoretical or experimental is a bonus. We offer excellent working conditions and a state-of-the-art infrastructure in a highly dynamic and international environment at the forefront of research.

The Application Procedure

Applications should include a motivation letter, detailed CV, transcripts of diplomas as well as three letters of reference. In conjunction to the application the candidate should apply to one of the doctoral schools: photonics, materials science, or bioengineering (http://phd.epfl.ch/page-19793-en.html).

More Information http://phd.epfl.ch/prospective

LHTC

Research on the effect of ageing on aortic hemodynamics. Perform a series of measurements on different age groups of healthy males and females to establish a complete data basis of the heomodynamical and biomechanical adaptation with age of the human aorta. Use the data to develop appropriate models of aortic hemodynamics as a function of gender and age. Use these models to develop noninvasive monitoring methods for all important hémodynamique,ical biomarkers.

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