EDBB Open positions

PhD Position on BioNanoPhotonic Systems Laboratory

Our laboratory (BIOS) is pioneering next-generation nanophotonic devices that can enable ultra-sensitive, quantitative, multiplexed, real-time detection of biomolecules and living systems through transformative advances in optical biosensing, imaging, and spectroscopy for making impact across a wide spectrum of applications – ranging from life science research, early disease diagnostics and point-of-care testing to environmental monitoring and safety.

Since 2018, we have been pushing the frontiers with nanophotonics to advance digital biosensing, a powerful approach that has recently emerged for ultrasensitive detection. Digital biosensing enables precise quantification of target molecules by counting individual binding events and characterizing their interaction dynamics. This approach fundamentally contrasts with conventional ensemble-averaged sensors, which generate analog signals by integrating a collective response from a large analyte population. As a result, while ensemble-averaged sensors fail to produce measurable signals at low receptor occupancy, digital sensors still offer to provide accurate counts, potentially down to single-molecule resolution.

We are looking for a new PhD student who will expand the application and the impact of our inventions on nanophotonic digital biosensing for next generation diagnostics and beyond. The student will be immersed in a research environment that empowers optical detection methods by engineered nanostructures and will be exposed to the development of bioassays, lab-on-a-chip optical systems, fabrication of biochips and microfluidic parts, and data analysis. 

To get further insight about the general concepts and the pioneering techniques that we develop in our lab please check some of our recent work on nanophotonic digital biosensing platforms for point-of-care technologies, advanced microarrays, continuous monitoring and combination of AI approaches:

https://pubs.acs.org/doi/full/10.1021/jacs.5c17838

(Kinetic Profiling in One-Step Digital Immunoassays Enables Multiplex Quantification across an Ultrabroad Dynamic Range)

https://arxiv.org/abs/2604.01182

(Digital nanophotonic biosensing empowered by silicon Mie voids)

https://onlinelibrary.wiley.com/doi/10.1002/smll.201906108

(Rapid and Digital Detection of Inflammatory Biomarkers Enabled by a Novel Portable Nanoplasmonic Imager)

https://patents.google.com/patent/US12174182B2/en?oq=US12174182B2

https://pubs.acs.org/doi/10.1021/acsnano.8b00519

(Nanoparticle-Enhanced Plasmonic Biosensor for Digital Biomarker Detection in a Microarray)

https://chemrxiv.org/doi/full/10.26434/chemrxiv-2025-mdd7v-v2

(A dynamic nanoparticle-on-film biosensor for sub-picomolar continuous monitoring in complex matrices with single-molecule resolution)

PBL

PhD in Multivalent Aptamer Design and Discovery (Skilled in organic / biochemistry, self-assembly, molecular design)

Our project develops a new technology to find short DNA molecules, called aptamers, that can accurately recognize and bind to disease-related proteins. Aptamers are powerful tools for detecting or blocking biological targets and can be used in diagnostic tests or as drug-delivery components. However, most existing methods identify aptamers that work only when acting alone, while many real-life targets, such as the spike proteins of viruses like COVID-19 or influenza, are naturally organized in groups. When single-binding aptamers are attached to nanoparticles for medical use, they often lose their effectiveness, leading to poor results or higher doses that can cause side effects. We have recently designed a new approach, named MEDUSA (Multivalent Evolved DNA-based SUpramolecular Assemblies), that mimics how these targets are arranged. By organizing candidate aptamers in geometric patterns similar to their target proteins during the selection process, we can evolve aptamers that are already optimized to work together in a multivalent setting. This innovation has already produced new aptamers against the SARS-CoV-2 spike that differ from all previously known ones.

The project will expand MEDUSA into a general platform that can be applied to many types of complex biological targets. We will explore the effect of different geometric designs, create new DNA scaffolds for diverse target shapes, integrate artificial intelligence to predict strong binders, and adapt the system for diagnostic applications. Ultimately, this technology could transform how binding molecules are developed, leading to more precise diagnostics and safer, more effective therapeutics.

Electron microscopy (SEM) and atomic force microscopy (AFM) are two cornerstones of nanoscale characterization in nanotechnology and bioengineering. These two instruments have complementary strengths and weaknesses. These traditionally very different techniques are normally performed in different instruments. In our recent work, we have combined these two techniques into a unique in-situ characterization tool that can be used to studdy nanoscale structures and phenomena in a completely new way. In this project, we will studdy the process of ice nucleation and the interaction with cells in 3D.

The nanoscale structure of ice has attracted increased interest in recent years due to its importance in cryo-electron microscopy as well as atmospheric ice nucleartion to understand the effect solid particle collutants have on climate change. With our new correlative AFM and SEM (AFSEM), we will studdy how ice nucleates, what it’s nanoscale mechanical properties are, and how the ice interacts with biological matter in block-face cryo-EM analysis.

What you will learn in this project:

• Use of unique, state of the art nanocharacterization instruments (atomic force microscopy, scanning electron microscopy, focussed ion beam microscopy) and develop new measurement technologies
• Working with (biological) samples at cryogenic temperatures.
• Microfabrication and instrumentation

What you can bring to the project:

• Interest in working with highly specialized custom instruments,
• Basic knowledge of electrical and mechanical engineering
• Basic knowledge of programming

Contact: [email protected]

Engineering a Microfluidic Platform for Next-Generation Live-seq

A PhD position is available in the Laboratory of Systems Biology and Genetics (LSBG) led by Prof. Bart Deplancke at EPFL (Lausanne, Switzerland). We are seeking a highly motivated candidate to contribute to the development of next-generation Live-seq, a technology that enables repeated transcriptome measurements from living single cells.

Live-seq uses Fluidic Force Microscopy (FluidFM) to extract minute quantities of cytoplasmic material from living cells without destroying them, enabling high-sensitivity transcriptomic analysis while preserving cell viability. This approach makes it possible to follow transcriptional changes in the same cell over time, opening new opportunities to study dynamic biological processes such as differentiation, infection, or drug response.

The goal of this project is to transform Live-seq from a low-throughput, operator-dependent technique into a robust and automated high-throughput platform. To achieve this, we will develop a system that integrates picoliter droplet microfluidics with MEMS nanofluidic probes used for FluidFM-based single-cell biopsies.

The PhD student will design, assemble, and optimize a microfluidic module that enables automated handling and processing of cytoplasmic biopsies extracted from living cells. The project involves microfluidic system design, integration with nanoscale probes and microscopy instrumentation, and experimental validation using high-sensitivity transcriptomic readouts.

This interdisciplinary project combines microfluidics, instrumentation engineering, nanotechnology, and single-cell genomics. It is carried out in close collaboration with the Fantner Lab at EPFL, experts in MEMS probe engineering and nanoscale instrumentation, and Cytosurge AG, developers of the FluidFM technology.

Candidate profile

We welcome highly motivated candidates with a background in:

• Bioengineering
• Mechanical or chemical engineering
• Biophysics
• Microfluidics or nanofluidics
• Biotechnology or related disciplines

Experience with microfluidic systems, pressure-driven flows, instrumentation, or microscopy is beneficial but not strictly required.

The ideal candidate enjoys hands-on experimental work, interdisciplinary collaboration, and technology development at the interface of engineering and biology.

Research environment

EPFL offers a world-class research environment with outstanding infrastructure and a vibrant international scientific community.

The successful candidate will work in an interdisciplinary setting combining instrument development, microfluidics, and single-cell transcriptomics, in close collaboration with the Deplancke Lab, the Fantner Lab at EPFL, and Cytosurge AG.

Application information

Interested candidates should apply to the EPFL Doctoral Program in Biotechnology and Bioengineering (EDBB) before the next application deadline: April 15, 2026

Start date: as soon as possible

For questions about the position, please contact:

Orane Guillaume-Gentil
EPFL, Laboratory of Systems Biology and Genetics (LSBG)
[email protected]

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.

Project: Mitochondrial contact site dynamics, structure, physiology and function

The LEB offers a range of projects as part of a multi-lab collaboration aiming to investigate mitochondrial contact sites (MCS) using chemical biology recorders, live-cell smart microscopy, and cryo-EM. The team will study how these contacts coordinate mitochondrial function and physiology. By focusing on key interactions in mitochondrial dynamics, the project seeks to identify MCS inhibitors or stabilisers.

https://www.epfl.ch/labs/lpl/

 We are seeking outstanding and motivated PhD students to join our interdisciplinary group exploring how biological pattern and function emerge from molecular and physical interactions. Ph D projects are available in the following areas: 

Extreme Cellular Mechanics: Extreme cell shape changes observed in free-living protists are among the fastest and most dramatic motions known in living systems. These rapid deformations are driven by centrin assemblies, yet, unlike other cytoskeletal proteins, the mechanisms underlying the assembly and force generation of these networks remain poorly understood. We are looking for students interested in uncovering the molecular and biophysical principles of centrin network formation, investigating how this cytoskeletal system organizes into filaments and networks capable of generating the forces that drive extreme cellular shape changes.

 Behavioral Responses Enabled by Centrin:

The survival of free-living unicellular organisms depends on their ability to mount appropriate behavioral responses to environmental changes. We are looking for students interested in investigating how centrin networks encode and regulate these behavioral programs, thereby uncovering the molecular and mechanical basis of adaptive behavior in free-living eukaryotic cells. 

Flow Generation by Cilia Arrays:

From unicellular swimmers to human airways, biological flows are generated by the collective motion of cilia. In most organisms, cilia form dense arrays of thousands of filaments that are highly patterned both spatially and temporally. We are looking for students interested in exploring how cilia patterning, geometry, and coordination determine flow generation, uncovering the biophysical principles underlying biological fluid transport. 

The successful candidates will join a collaborative and stimulating research environment that bridges cell biology, engineering, and soft matter physics. Our projects offer opportunities to develop and apply advanced imaging and biophysical techniques, computational modeling, and theoretical frameworks to address key questions in active matter and cellular biophysics. 

We welcome applicants from diverse backgrounds, including physics, biophysics, biochemistry, cell biology, and bioengineering. Candidates should demonstrate curiosity, creativity, and a strong interest in interdisciplinary research.

LBP currently has 2 open PhD positions

The Schueder lab is interested in leveraging DNA nanotechnology to design, test, and apply smart probes that push the boundaries of fluorescence microscopy in terms of spatial resolution, throughput, quantitative imaging, and single nanometer proximity mapping (molecular connectomics). Furthermore, we aim to advance both conventional and super-resolution multiplexed imaging (DNA-PAINT, FLASH-PAINT) toward imaging-based spatial omics. We are interested in applying the technology to microbiology and microbiome research, but our focus is not limited to these areas.

We are looking for up to two passionate and driven graduate students to join the lab as early as January 1st, 2026, to contribute to interdisciplinary projects centered around the lab’s focus as described above.

The ideal candidate is passionate about multiple — ideally all — of the following areas of research:

• Nanotechnology: Design of new DNA-based imaging probes and the use of DNA origami nanotechnology to benchmark newly developed probes.
• Biochemistry: Design, construction, and validation of novel binders for labeling and imaging cellular proteins, RNA, and DNA.
• Optics & Microfluidics: Development of custom microscopy setups and microfluidic systems to leverage the full potential of smart probe microscopy.
• Computation: Development of new workflows to analyze, interpret, and model the high-dimensional spatial omics data we acquire.

If you are interested, please send your CV, a brief statement of motivation, and ideally two references to [email protected]

References:

F. Schueder, F. Rievera-Molina, M. Su., Z. Marin, P. Kidd, J. E. Rothman, D. K. Toomre, J. Bewersdorf

Unraveling cellular complexity with Transient Adapters in highly multiplexed super-resolution imaging

Cell (2024), [Co-corresponding authors]

F. Schueder, J. Lara-Gutiérrez, D. Haas, K. Sandvold Beckwith, P. Yin, J. Ellenberg, R. Jungmann

Super-resolution spatial proximity detection with proximity-PAINT

Angewandte Chemie. (2020), 2, 716-720 [Co-first authors]

F. Schueder, J. Stein, F. Stehr, A. Auer, B. Sperl, M.T. Strauss, P. Schwille, R. Jungmann

An order of magnitude faster DNA-PAINT imaging by optimized sequence design and buffer conditions.

Nature Methods. (2019). 16, 1101-1104

F. Schueder, J. Lara-Gutiérrez, B.J. Beliveau, S.K. Saka, H.M. Sasaki, J.B. Woehrstein, M.T. Strauss, H. Grabmayr, P. Yin, R. Jungmann

Multiplexed 3D super-resolution imaging of whole cells using Spinning Disk Confocal Microscopy and DNA-PAINT.

Nature Communications. (2017). 8, 2090 [Co-corresponding authors]

PhD in hydrogel acoustic metamaterials

Job description

For the 1 PhD position starting between 2026 fall and 2027 spring, we are seeking a candidate with experience in microfluidics, microfabrication, stimulus-responsive hydrogels, ultrasonics and acoustic metamaterials (acoustic crystals). The candidate should be interested in emerging, interdisciplinary fields and be motivated to address new challenges, including the development of hydrogel acoustic metamaterials.

Group leader and Research mission: Prof. Yujia Zhang

At the Laboratory for Bio-Iontronics (BION), our mission is to make bioiontronic systems for biointerfaces and hybrid intelligent systems. To that end, we are interested in developing droplet-based iontronic systems, termed dropletronics, with key functions of embodied energy, logic control, stimulus responsiveness, and therapeutic delivery, enabling interactive communication with biology.

Profile

• MSc in materials science, microengineering, or bioengineering;
• Experience with polymer characterisation and ultrasonics is required;
• More than 1 peer-reviewed publication;
• Prior experience in cleanroom manufacturing and 3D printing is a plus;
• Strong experimental skills and a practical and hands-on mindset;
• High level of motivation for interdisciplinary academic research;
• Independent, self-driven, creative, solution-oriented, open-minded, team-player, and collaborative;
• Fluency in English (French is a plus);
• Enthusiasm in sports is a plus.

Main duties and responsibilities

As a PhD Student, you will be expected to:

• Have full responsibility for your own dissertation;
• Research in close collaboration with other lab members and international collaborators;
• Experiment design and execution;
• Analyse and interpret experimental results;
• Write scientific articles for publication in peer-reviewed journals;
• Present at international conferences;
• Supervise student projects and basic administrative support;

We offer

• 4 years to complete your PhD with a competitive remuneration;
• International collaboration and visiting opportunities;
• EPFL is an international and world-class engineering institution that hosts state-of-the-art experimental facilities and a rich and vibrant scientific and entrepreneurial community.
• Term of employment: 1-year fixed-term contract (CDD), renewable for 4 years.

Information

Only applications submitted through the online platform are considered. Please apply by uploading a single PDF file that contains supporting information, including:

• Motivation Letter
• Detailed CV
• At least 2 references willing to write recommendation letters and their contact information
• Application deadline: 25 September 2026

If you are successful, you will need to enrol in one of the EPFL doctoral school programs. Please check this page for additional information. Please note that this is a separate application process necessary to be eligible to complete your PhD at EPFL. Potential doctoral programs for this position: EDMX, EDMI, or EDBB;

Contract Earliest Start Date: late 2026, flexible

Activity Rate: 100%

Contract Type: PhD Student

Reference: TBD