EDBB Open positions

This page will be updated more often as the EDBB program will be informed of new positions becoming available for the June 2022 Hiring Days event. Meanwhile, do not hesitate to contact the laboratories which interest you to find out whether they have upcoming openings for PhD students.

Ablasser Lab

Innate immunity is essential for maintaining health, and it is involved in various human diseases. A diverse range of innate immune signaling receptors enable immune cells and many other cell types of the human body to detect the presence of foreign molecules or modified self-molecules that signal infection, injury, or pathological deviations associated with diverse pathologies. This way, cells can gather information about the status and functioning of tissues and, in turn, mount robust (immune) responses to restore homeostasis.

Given these unique properties, innate immune signaling pathways provide a remarkable platform for disease intervention. On the one end of the spectrum, activation of innate immunity is an essential ingredient for triggering robust vaccine responses and successfully eradicating cancer. Conversely, abnormal activation of innate immunity can cause many complex diseases, such as cancer, autoimmunity, or neurodegeneration. Thus, there is a strong rationale to engineer “innate immune-like” behaviors in vivo, especially in light of novel advances in mRNA technologies and cell therapies, which allows for unprecedented ability to modify and design cellular functions in vivo.

Project 1: Synthetic Immunology: Development of cGAS immune-boosters for cancer immunotherapy.

The overarching goal of this Ph.D. project is to leverage the cGAS-STING innate immune signaling pathway to initiate powerful T cell responses for immune-mediated clearance of tumors. To this end, we will explore and create “synthetic” cGAS-STING variants that program designer immune activity in living T cells and innate immune cells. The project will teach aspects of structural biology, biochemistry, high-throughput cellular screens, and immune cell manipulations ex vivo. In addition, we seek to demonstrate proof-of-concept of superior antitumor immunity triggered by your designed innate immune-boosters.

Project 2: Cell therapy: Immune super-signalling cascades for re-directing T cells against tumors.

The overarching goal of this Ph.D. project is to engineer T cell-based living cell therapies that harness innate immune signaling mechanisms for improved management of solid tumors. To this end, we will engineer T cells with novel immunological properties in vitro and test their behavior in mouse cancer models in vivo. Further, aspects of unbiased profiling of triggered immune responses are part of the project.

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 evaluation of antibody responses elicited by different viral pathogens, vaccine candidates and toxins using state-of-the-art cryo-electron microscopy, immunology and bioinformatics tools. Selected candidate will then learn how to apply this information for design of novel vaccine candidates and antibody therapeutics. The primary targets of interest are human papillomavirus (HPV), non-polio enteroviruses (NP-EV), human immunodeficiency virus (HIV) and hemorrhagic fever viruses (e.g., yellow fever, dengue and hantavirus). The specific project details will be tailored according to the research interests and experience of the candidate.

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 tools that will be employed:

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., bioRxiv preprint, 2022

https://www.biorxiv.org/content/10.1101/2022.01.31.478566v1

We have several positions opening in the Aye laboratory in Swiss Federal Institute of Technology Lausanne (EPFL), Switzerland, both at PhD student and postdoctoral researcher levels. Our laboratory is a multidisciplinary laboratory focusing on small-molecule- and nucleotide-driven signaling mechanisms as they pertain to intra- and intercellular communications often conserved across evolution, and also to drug discovery. We have pioneered numerous novel and multi-award-winning interdisciplinary concepts and techniques that have been applied to important biological questions.

 The available projects will build on previously-published foundational studies, and encompass wide-ranging areas in the broader context of bioengineering and chemical biology: such as, (i) development of precision medicine targeting proteins/pathways essential in several cancer subtypes, based off two successful lead compounds that we recently discovered, and assessing their efficacies in cell culture and the best will be continued to more advanced models; (ii) projects aimed at understanding and reprogramming subcellular metabolite trafficking and signaling mechanisms; and (iii) projects targeted to advance spatial and functional omics methods in multiple living models.

More information about both of our research groups, including other active research themes, can be found at

https://leago.epfl.ch/ For questions or additional information, please contact [email protected]

Start date :

For all positions, they are available immediately, funding is available, and the start date is flexible. All applications should include in PDF format:
(i) Cover letter, 
(ii) CV, 
(iii) the contact information of three references. 

 

https://www.epfl.ch/labs/barth-lab/

https://lpbs.epfl.ch/

 

Title: Joint PhD position in quantitative checkpoint biology (Rahi-Barth labs)

 

Your mission

Checkpoints arrest the cell cycle when cells are damaged. However, checkpoints also ‘fail’ or

‘give up’ after long arrests. This phenomenon is thought to be critical for biology and medicine but is poorly understood. By combining novel engineered protein-based optogenetic tools, molecular biology, genetics, and microscopy, we want to understand how checkpoints tell time at the molecular level. In a collaboration between the Rahi lab, where you would be performing molecular biology centered on yeast and recording timelapse microscopy movies, and the Barth lab, where you would be designing new optogenetic allosteric switches for checkpoint proteins using computational protein design, we will explore how checkpoints read out DNA damage and decide to arrest for specific amounts of time before ‘letting go’.

 

Your profile

Candidates should have a Msc in biophysics, bioengineering, or related disciplines and be

experienced in molecular and/or cell biology, and computer programming.

 

Contact

For further information and application, please contact directly [email protected] or [email protected].

https://www.epfl.ch/labs/barth-lab/

 PhD project. Engineering powerful proteins with novel functions for synthetic cell 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, including chemosensors, mechanosensors, signaling switches and chemogenetic probes. 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 building synthetic living cells or enhancing the anti-tumor functions 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.

Project outline – PhD position by the LPDI and PTBTG labs

Biomedical research has become a highly interdisciplinary endeavor where the tight interaction of different fields is necessary for transformative breakthroughs. Within the iPhD program, we propose an interdisciplinary collaboration to engineer novel vectors for gene therapy. Our aim is to open the path for rational design of adeno-associated virus (AAV) capsids, in order to confer novel properties to this vector which is commonly used for gene delivery in therapeutic approaches. The collaborating groups are the Bertarelli Platform for Gene Therapy (PTBTG), which is specialized in designing and generating AAV vectors for gene therapy, and the Laboratory of Protein Design and Immunoengineering (LPDI), which has deep knowledge in computational protein design and engineering.

We propose to rationally engineer novel AAV vectors to target key cell types, by designing in silico modules to functionalize AAV capsid proteins that bind specific cell-surface receptors. Rational protein design may overcome some of the limitations of the currently used approaches, mainly based on the in vivo screening of AAV libraries to identify variants converging towards specific gene transfer properties. As a proof-of-concept, we will engineer an AAV capsid to target cell types which are currently poorly transduced with AAV vectors, such as Schwann cells or T lymphocytes. Towards this end, the project will leverage the expertise of LPDI in modelling and designing novel peptides and protein elements able to interact with specific receptors at the cell surface.

The research plan will be based on the following specific Aims:

Aim 1: In silico design of AAV capsid protein to target a specific receptor [rational engineering].

Aim 2: Screening and characterization of modified AAV vector particles [phenotyping].

Aim 3: Design of an AAV-based gene therapy for genetic correction of a specific disease [application].

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.

Requirements:

Candidates should hold a Master’s Degree in Biochemistry, Bioengineering, Chemical Engineering, Chemistry, Microengineering, or related field. Exceptional candidates with a bachelor degree will also be considered. The candidate should either have prior experience in protein biochemistry, molecular engineering, synthetic biology and / or cell-free systems, or experience in developing and applying state-of-the art microfluidic technologies to biological applications, particularly devices fabricated by multilayer soft lithography.

Candidates should send their curriculum vitae and a cover letter to:

Prof. Sebastian Maerkl

Email: [email protected]

Evaluation of applications will commence immediately. The position is expected to be filled and begin in Q1/Q2 of 2022.

LBMM

Our laboratory (LBMM) develops new approaches in antibody and drug discovery, exploiting droplet-based microfluidic screening systems.

During the past couple of years we have established powerful microfluidic platforms for antibody and drug discovery, which also led to the successful establishment of a startup company and an international consortium for personalized cancer therapy (www.veraxa.de and www.besttherapyforme.com). The group is very interdisciplinary and includes people with various backgrounds, including biologists, bioinformaticians, 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 inviting applications with a particular focus on antibody and drug discovery. The aim of the proposed PhD project is to perform highly multiplexed protein-interaction studies, also involving DNA-encoded libraries technology (DELT). Ideal candidates have prior experience in display technologies (e.g. mammalian, yeast or phage), antibody engineering and discovery, or profound knowledge in DELT. Throughout the project, successful candidates will have the chance to pick up new skills in microfluidics, next generation sequencing (optionally at the single cell level) and multiplexed data analysis.

https://www.epfl.ch/labs/naef-lab/

March 2022

PhD position in single molecule imaging and omics analysis of mRNA translation

 The Naef-lab at the Ecole Polytechnique Fédérale de Lausanne (EPFL) has an opening PhD student to join the lab’s longstanding research program on gene regulatory mechanisms, and notably the regulation of translation dynamics.

This position is funded in the context of a collaborative SNSF Sinergia grant “Integrated multi-scale analysis of translation: single-molecules, omics and computation” with Jeff Chao (FMI Basel) and Pierre Vandergheynst (EPFL). We are looking for a highly motivated new team member to further develop molecular and machine learning tools for bulk and single-molecule translation experiments.

We are specifically looking for interdisciplinary profiles holding a PhD in molecular or computational biology (or a closely- related field) with a strong background in areas such as single molecule imaging, omics technologies, and computational analysis. The successful candidate will work independently to develop and drive forward his/her research project, and also collaborate on ongoing projects in the group. Quantitative and interdisciplinary training, as well as previous experience with statistics, math/physics/computation, or next-generation sequencing (NGS) genomic data analysis will be highly considered.

For more information please contact [email protected]

March 2022

PhD position in systems chronobiology, multi omics & quantitative gene regulation 

Life on earth at all scales (societies, behavior, physiology, molecular functions) is temporally organized along the 24h daily cycle. This project builds on our longstanding interest to combine computational and experimental approaches to understand gene regulatory mechanisms underlying circadian rhythms, and notably their impacts on temporal physiology.  In particular, we aim at integrating time-resolved functional genomics datasets in organs to model how the circadian clock and/or environmental cycles impinge on gene regulation across multiple levels, from transcription to translation to protein accumulation. We will focus on statistical and machine learning models combining multiple types of RNA-seq and other omics measurement to dissect the dynamics of gene expression, including the mechanisms governing RNA transcription, accumulation and its translation. The work is computational (although, depending on the interest of the student, performing validation experiments would be a plus) and highly interdisciplinary, combining concepts/tools from gene regulation, bioinformatics, statistics and machine learning.

For more information please contact [email protected] 

Links to representative recent publications form our lab, illustrating the questions and methodologies that will be further developed: 

Mermet, Genes Development 2018, http://genesdev.cshlp.org/content/32/5-6/347

Yeung, Genome Research 2018, https://genome.cshlp.org/content/28/2/182 

Wang, PNAS 2018, https://www.pnas.org/content/115/8/E1916 

Gobet, PNAS 2020, https://www.pnas.org/doi/10.1073/pnas.1918145117

Phillips, MSB 2021, https://www.embopress.org/doi/full/10.15252/msb.202010135 

We are looking for a PhD student to develop cutting-edge hardware and software for interferometric scattering microscopy (iSCAT) with application to imaging of bacterial pathogens during infection (see Tala et al., Nature Microbiology 2019 and Kühn et al., PNAS 2021). The project will likely combine microscopy and biophysics approaches, and then implementation of convolutional neural networks (U-Net).
The Persat lab investigates how mechanical forces regulate bacterial physiology and infection, in particular via mechanosensing. The lab is highly multidisciplinary, combining techniques from physics, engineering and biology.

More information on our research at:
www.p-lab.science

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