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.

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).

LBM

At least 2 openings are available for the November 1st, 2020 deadline. PhD projects will be available in the following two areas of research:

  1. 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.

  1. 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.

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.

Evolutionary diversity and origin of centriolar proteins

Background:

Centrioles are small organelles that are critical for forming cilia, and which exhibit a striking 9-fold radial symmetric arrangement of microtubules, but whose evolutionary origin remains unclear. We discovered that the evolutionarily conserved SAS-6 proteins self-assemble into 9-fold radially symmetric structures thought to template the formation of the entire organelle.

Objectives:

Identify homologues of fundamental centriolar proteins such as SAS-6 across the domains of life, through protein sequence data analysis, including sequence covariation and structure prediction. Test newly identified candidates in cell free assays, including with chimeric proteins. Through the above approaches, help trace the origin of the centriole organelle.

Approaches:

Computational biology, structural prediction, cell biology

Collaboration between the Bitbol and Gönczy laboratories (EPFL, Life Sciences), as well as with the Dessimoz laboratory (UNIL and SIB).

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]).

Understanding cellular processes is crucial for making progress in medicine, biology, and biotechnology. In this context, characterizing the behavior of cells under different conditions will provide tools that improve personalized and precision medicine, green energy, or efficient chemical production. Experimental approaches are currently generating an abundant amount of biological data and further computational methods are required to perform an integrative analysis of the cellular processes.

In the Laboratory of Computational Systems Biotechnology, LCSB, we focus on modeling different cellular processes, performing large-scale computations, and data analysis. We aim to develop mathematical models and novel mathematical and computational methods that allow us to conduct research in systems medicine, systems biology, metabolic engineering, and prediction of novel bio-transformations.

We have openings for a PhD position with an expected starting time-frame of Summer 2021. The following research topic is offered:

Human metabolism data analysis and modeling

In this project, we aim to develop mathematical models that describe the metabolic state of different human cells under different conditions, such as cancer cells, retina cells and liver cells. The developed models will be used to study the alterations in metabolism that are hallmarks of a variety of human diseases, including cancer, retina degeneration, as well as various bacterial, viral, and parasitic infections. The ultimate aim of these efforts it to understand the metabolic mechanisms that underlie these alterations and guide the discovery of new drug targets and the design of new therapies.  

 The inquiries about the positions and applications including a motivation letter and the CV letters should be sent by email to: [email protected].

Neurodegenerative Disease under the Microscope: A Multimodal Imaging Approach to Decipher Aggregation Networks using Huntington Inclusion Formation as a Model System

This joint interdisciplinary PhD project exploits synergies between the Lashuel laboratory (SV-BMI-LMNN) and the Radenovic laboratory (STI-IBI-LBEN). Research in LMNN focuses on applying chemistry and biology approaches to elucidate the mechanisms of protein misfolding and aggregation and their contribution to neurodegenerative diseases. LBEN works in the research field that can be termed single molecule biophysics. They develop techniques and methodologies based on optical imaging, biosensing and single molecule manipulation with the aim to monitor the behavior of individual biological molecules and complexes in vitro and in live cells.

Neurodegenerative diseases such as Alzheimer’s or Huntington’s disease (HD) pose one of the grand challenges for our society. They severely impact the quality of life; there is no cure and therapies only alleviate the symptoms. Recent evidence suggests that phase separation and subsequent phase transitions play a key role in protein aggregation of intrinsically disordered proteins such as Huntingtin. However, very little is known about molecular and cellular determinants of these transitions. We believe that the combination of unique expertise, biochemical tools to manipulate Htt structure and PTMs, and novel imaging modalities position us well to make progress that has great potential to address this knowledge gap and develop novel approach with wide-ranging applications in basic and translational neurodegenerative research. Towards this goal, we will apply single-molecule fluorescence super-resolution (localization microscopy, single particle tracking), phase microscopy and image analysis (deep learning) to directly study Huntington’s disease in cellular and neuronal HD model systems that are well characterized at the biochemical, biophysical, omics and ultrastructural levels. The project connects the expertise of the Radenovic lab in imaging technologies with the extensive know-how of neurodegenerative disease of the Lashuel Lab.

We seek highly talented, enthusiastic and exceptionally motivated candidates with a M.Sc. degree in (bio)physics with an affinity for (neuro)biology and biophysical chemistry. We also encourage candidates with a background in (neuro)biology with an interest in advanced microscopy to apply for this position.
Good communication skills and team spirit are important. Fluency in English is an absolute requirement; the candidate must be conversant and articulate in English speaking and should have strong writing skills. An interview and a scientific presentation will be part of the selection process.

The qualified candidate will benefit from working in a collaboration of two very dynamic and multidisciplinary groups in a highly collaborative and stimulating environment and will have access to state of the art laboratories and core-facilities and a competitive salary. For more information about the labs, please visit our websites and review our recent publications at:

The Lashuel laboratory: https://www.epfl.ch/labs/lashuel-lab/

The Radenovic laboratory: https://www.epfl.ch/labs/lben/

We’re always looking for talented PhD students. with following background : optics, electronics, optical and magnetic trapping, cell and molecular biology, polymer physics, nanotechnology, and clean room experience.

LBNC

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

LBMM

Our laboratory (LBMM) develops and applies microfluidic technology with a strong translational focus. The group’s ultimate goal is to establish novel treatments against cancer.

During the past couple of years we have established powerful microfluidic platforms for cell-based and biochemical assays. We continuously develop novel microfluidic chips, detection systems and software (mainly LabVIEW) for the discovery of new drugs and antibodies, partially in collaboration with large pharma industry. Furthermore, we use microfluidic technology to predict optimal (personalised) drug cocktails for cancer therapy. The group is very interdisciplinary and includes people with various backgrounds, including biologists, engineers and programmers. However, prior knowledge in microfluidics is not mandatory for joining!

Having a comprehensive microfluidic toolbox at hand (and expanding it continuously), we are now focusing on applications in three different research fields:

Therapeutic antibodies and T-cells: Droplet based microfluidics enables to screen a large fraction of the murine and human immune repertoire in a single experiment (e.g. El Debs et al., PNAS 2012, Chaipan et al., Cell Chemical Biology 2017, Shembekar et al., Cell Reports 2018). We are actively exploiting this for novel therapeutic approaches and have founded a biotech startup company translating our results (www.velabs-therapeutics.com).

Personalised medicine: We use microfluidic devices to test drug combinations directly on solid human tumor samples and to predict optimal therapies (e.g. Eduati et al., Nature Communications 2018). Current efforts focus on genetic and imaging-based readouts. In parallel, we are constructing next generation instruments for first clinical trials. 

Genomics: We are actively developing microfluidic modules for single-cell barcoding and sequencing. This will enable the study of the mechanisms of drug resistance in great detail.

LAPD

PhD in Volumetric Bioprinting and Optogenetics

One PhD student position is available at the Laboratory of Applied Photonics Devices (LAPD) at the École Polytechnique Fédérale de Lausanne (EPFL), Switzerland.

3D bioprinting has shown to print living cells into shapes that resemble human tissues in the quest to produce lab-made human tissues for biomedical applications. However, today’s bioprinting has no means to actively steer cell behaviour and morphogenesis, leaving yet unfulfilled the potential to fully capture organ functions. It is the aim of this project to control both the form (shape) and steer cell morphogenesis.

The Project at EPFL

The LAPD has pioneered a new bioprinting method called volumetric bioprinting. This ultra-fast technique uses visible light tomography to sculpt complex 3D cell-laden bioresins, including complex vascularization, with high-resolution and centimetre-scale 3D construct in matter of seconds. The volumetric bioprinter will be tested with different light colors to target and force differentiation of optogenetic stem cells in 3D. The student will investigate light dosage schemes to induce cell differentiation directly in 3D. The objective is to fine tune the 3D light dosage to activate stable tomographic spatio-selective cell differentiation within the printer. The optogenetic stimulation is an essential component to instruct cell fate and control the function of the tissue construct.  The application is to build physiological-scale tissues and organoids that replicate human organ-level functionality. The optogenetic cells will be produced by a leading group at ETHZ.

This thesis work is part of a H2020 FET European project that includes leading academic institution and companies in Europe.

The EPFL Candidate

This research has many interdisciplinary aspects that demand a highly motivated candidate who is able to think out of the box and able to interact with different groups. The diverse aspects of the project allow a wide range of backgrounds that includes bioengineering, photonics, physics. Experience in bioprinting, optogenetics 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.

UPNAE

Organization of cell cycle and circadian clock in patterned multicellular structures

This describes one available project in the lab that uses a combination of wet and dry approaches; other projects can be discussed directly with [email protected]. In this project we aim at continuing a longstanding interest in the lab on the interactions and dynamics of circadian oscillators and the cell cycle. To study our previous cell-based findings in a physiological context, we will use the rapidly self-renewing intestine and gut organoids. Indeed, intestine tissue turns over within 4-5 days, yet it harbors a robust clock. Thus, we will take this more complex multicellular structure to the same level of quantitative understanding as we gained in individual mouse and human cells. Owing to the spatial organization of those structure, we expected to uncover novel spatio-temporal patterning linking the two cycles. Additional analyses using single cell genomics are also possible. The project will use state-of-the art organoid culture systems , live imaging, engineering of reporters and design of genetic and chemical perturbation, signal processing (image analysis) and mathematical modeling.

Links of relevant publications form our lab, illustrating the questions and methodologies:

https://www.p-lab.science/

Position in tissue engineering/organoids:
Respiratory infections are the leading cause of death wordlwide. However, we still ignore how most pathogens dynamically infect their hosts, as most of our knowledge comes from animal experiments. This becomes particularly critical due to the rise of antibiotic resistant bacteria. To solve this, our lab is developing organoid-based systems as models of infectious disease. In these organs, we can monitor infection dynamics in real time. In the scope of a national consortium to fight antibiotic resistance, we are looking for a student who will develop lung organoids to study infections by typical airway pathogens.

LPBS

We work at the intersection of physics and systems biology. We would like a new PhD student to join us who likes theory, computation, and experiments. The experiments involve yeast, which we manipulate genetically to break their DNA to analyze the dynamics of their checkpoints, to perform directed evolution using optogenetic controls, or to analyze instabilities in their genetic networks. (Exact project to be decided.) On the theoretical side, our interests extend from image analysis using neural networks, to data analysis and modeling, to proving theorems. Feel free to get in touch before or after your application.

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

LBI

Tang lab’s research aims at developing novel strategies to engineer immunity-disease interactions, an emerging field called ‘immunoengineering’, through chemical, metabolic, and mechanical means in order to treat cancer safely and effectively with immunotherapies and vaccines. We are actively looking to recruit 1-2 PhD students who are interested in this new field and would like to work in a highly interdisciplinary environment. For more information, please see our publications (Nat. Biotech. 2018, 36, 707-716; Acc. Chem. Res. 2020, 53, 12, 2777–2790; Materials Horizons. 2020, 7, 3196-3200; ACS Central Science. 2020, 6, 3, 404–412.) and reach out to [email protected].

VDG

A major research topic of the van der Goot Lab is understanding how protein function is controlled in time and space by a major post-translational modification, S-acylation (commonly referred to as S palmitoylation). This reversible modification consists in the attachment fatty acids to proteins, thereby controlling their biogenesis, stability, localisation, and function.

Given how frequently it occurs, S-acylation influences a wide range of key physiological processes, from development, neuronal functioning to infectious diseases. We are in particular interested how pathogens (e.g. bacterial toxins and enveloped viruses) depend on S-acylation for virulence.

In this context we are looking to recruit PhD students to work the importance of S-acylation during SARS-CoV-2 infections. This project received recent funding from the Swiss National Science Foundation and preliminary experiments look extremely promising,

Since the onset of the pandemic, we have identified the cellular enzymes involved in modifying SARS structural proteins and shown that they are essential for infectivity.

The proposed project aims at further elucidating the role of S-acylation not only in infectivity but also virus biogenesis. Our approaches are always multidisciplinary, combining: cellular and biochemical studies, infection biology, structural analysis, screening of pharmacological inhibitors, high-resolution microscopy approaches, and strong collaborations with computational labs for molecular dynamics or mathematical modelling of our systems.

              Main projects

1 – Determine and characterise the S-acylation of specific SARS-CoV-2 proteins and understands its role for pathogenesis

2 – Identify S-acylated host proteins which impact SARS-CoV2 infection and characterise their role during infection

3 – Evaluate the inhibition of S-acylation cascades as a broad spectrum anti-viral strategy

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