EDBB Open positions

This page will be updated more often as we approach the end of 2021, as the EDBB program will be informed of new positions becoming available for the January 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.

LEAGO

Laboratory of Electrophiles And Genome Operation actively seeks to recruit 1-2 PhD students keen to acquire interdisciplinary skillsets in the realms of pioneering novel bioengineering technologies and discovering druggable protein targets/pathways toward precision medicine development. Our science leverages a unique blend of models (from cultured cells to fish, worms, & mice) and cutting-edge tools at the scientific interface. For more information, please reach out to [email protected]   

Cao lab

We are seeking highly motivated candidates with an 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 applicant who is interested in this position, please send your resume to Dr. Chan Cao ([email protected])

LSBG & LBNI

The Laboratory of Systems Biology and Genetics (Deplancke Lab) together with the Laboratory for Bio and Nano Instrumentation (Fantner Lab) is looking for a motivated PhD student for an interdisciplinary research project in the field of micro-fabrication for femtoliter sampling in the context of live cell,  single cell RNA sequencing. Single cell RNA sequencing has become routine in the field of transcriptomics. Using conventional techniques, cells are killed during this process, which prevents subsequent sampling of individual cells at different time points or downstream phenotyping. The Deplancke lab (together with the Vorholt Lab (ETHZ)) has recently developed a breakthrough proof-of-concept method (Live-seq) to extract minute amounts of liquid from the cells without killing them. This liquid is then used for single cell transcriptomics. However, the throughput of this method is currently insufficientto comprehensively address many important biological questions. In this project, the Deplancke and the Fantner Labs will join forces to develop a high-throughput method based on this principle: Live-seq 2.0. 

A key component for this Live-seq 2.0 is the development of microfluidic nano-needles that can extract femtoliter cytosolic biopsies at high throughput. In this project, you will develop these nano-needles based on a hybrid MEMS process recently developed in the Fantner lab. You will work together with a team of fellow PhD students to integrate your microfluidic devices into an automated instrument and perform single cell transcriptomics experiments. 

What you will learn:

– Advanced microfabrication

– Micro- and nanofluidics

– Instrumentation

– single cell biology

– RNA sequencing. 

What we are looking for: 

– Motivation for cleanroom processing (existing experience a plus but not mandatory)

– practically oriented, independent researcher

– interest in biology and engineering

PhD student in Translational Skeletal Muscle Stem Cell Biology

Muscle Stem Cells (MuSCs) are tissue resident stem cells driving the growth, maintenance, and repair of skeletal muscle. MuSC function declines during aging and muscle wasting disorders, leading to regenerative failure and loss of muscle mass and strength. Our lab has recently identified specific nutritional solutions that stimulate MuSC activity in vitro and in vivo to accelerate muscle repair after muscle injury and has discovered a new subpopulation of MuSCs which could modulate life-long muscle plasticity in response physical activity. In this context, the PhD student will study the molecular and cellular mechanisms through which energy metabolism cross-talks with cell fate decisions to regulate stemness and regenerative potential. The project will assess stem cell metabolism at the single cell level using state of the genomics, flow cytometry and data science technologies, and will apply lineage tracing, cell fate assays and histology procedures available in the lab to study how nutrition and intracellular metabolism influence the fate of MuSCs. Through this work, the student will discover a repertoire of metabolic profiles linked to specific stem cell states, will characterize the role of a new population of MuSCs during exercise and aging, and will deliver translational solutions to enhance the regenerative capacity of skeletal muscle in health and aging.

Key words: Stem Cell Biology; Regeneration; Skeletal Muscle; Aging; Nutrition; Metabolism; Translational Research

Key responsibilities

  • Design and lead the experimental activities of the project
  • Analyze, interpret and present scientific results
  • Integrate the literature in the field & propose translational perspectives
  • Interface with team members and collaborators
  • Present at scientific conferences & publish scientific papers

Required profile

  • Masters Degree in biology or equivalent with deep understanding of muscle biology
  • Training and laboratory experience in cellular metabolism and/or molecular/cellular biology and/or stem cell biology
  • Experience with primary cell culture, flow cytometry & in-vivo work will be considered a plus
  • Passion for science with a collaborative mindset
  • Enthusiasm, curiosity and a pro-active attitude are essential
  • Good time management and organizational skills
  • Fluency in English, French would be a plus.

The student will be affiliated to the EPFL doctoral school of biotechnology and bioengineering under the supervision of Drs Pascal Stuelsatz and Jerome Feige and the position will be homed on the EPFL campus at the Nestlé Institute of Health Sciences (NIHS). NIHS is one of the four major research institutes of Nestlé Research, and delivers innovative translational research in biomedical science to maintain and improve health through nutrition. We offer a truly international working environment with an internal PhD program where the candidate will work at the interface between academia and industry and will interact with other students and post-docs. For more details, please contact Dr. Pascal Stuelsatz ([email protected]).

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

Mechanisms directing centriole fate during muscle development in zebrafish and human iPS cells.

You will monitor centrosome and centriole dynamics during muscle formation and regeneration in zebrafish embryos using high-end microscopy approaches, in collaboration with the Oates laboratory. The work will be complemented by inducing muscle formation from human iPS cells, with the goal of discovering the fate and the importance of centrioles during this differentiation program.

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

Mechanisms directing centriole fate during muscle development in zebrafish and human iPS cells.

You will monitor centrosome and centriole dynamics during muscle formation and regeneration in zebrafish embryos using high-end microscopy approaches, in collaboration with the Oates laboratory. The work will be complemented by inducing muscle formation from human iPS cells, with the goal of discovering the fate and the importance of centrioles during this differentiation program.

LCSB

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 beginning 2022. The following research topics are 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.  

Microbiome data analysis and modeling  

In this project, we aim to develop mathematical models that describe the metabolic networks of individual organisms in microbial communities and the interactions through metabolites and competition for resources. We will also develop individual agent-based representations of bacterial motility and growth using adaptive metabolic networks for each agent-cell and study how metabolic interactions can give rise to spatio-temporal arrangements in microbial communities.

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

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 info at www.p-lab.science.

We currently have three open PhD positions for candidates of all backgrounds (biology, engineering and physics):

Position 1 – Advanced microscopy methods for biophysics of pathogens
Goal: develop new hardware and software for interferometric scattering microscopy (iSCAT) and cryoEM image analysis tools to investigate bacterial pathogenicity. The ideal candidate has interests in computation, microscopy and/or biophysics.

Position 2 – Mechanobiology of the gut microbiota
Goal: investigate the role of mechanics of the intestinal mucosal surface in the stability of a healthy gut microbiota. The project combines microfluidics, tissue engineering and anaerobic biofilm formation.

Position 3 – Investigating the mechanisms of bacterial force sensing
Goal: investigate how the pathogen Pseudomonas aeruginosa senses force to regulate virulence. The project combines microbiology methodologies with single-cell level microscopy tools.

https://lpbs.epfl.ch/

The Rahi lab works 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 paper-and-pencil calculations, proving theorems, data analysis and modeling, to image analysis using neural networks. Feel free to get in touch before or after your application.

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