EDBB Open positions

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]

PhD Position in Next-Generation Mutagenesis Tools

The LSAM focusses on the development of synthetic microbes for the sustainable bio-production of value-added chemicals and other products. We develop molecular tools and experimental high-throughput technology that enable deep characterization and next-generation engineering of these microbes on different levels (gene regulation, proteins/enzymes and multi-protein systems). A key expertise is the combination of high-throughput experimental data generation with data-driven modelling approaches (e.g. deep learning) to allow model-guided engineering and design of microbes with new properties in a straight-forward fashion.

Project description: A critical step in the molecular engineering of synthetic biosystems is the introduction of mutations to generate libraries of genetic variants that can be screened for a desired property of interest. While there are various established in vitro and in vivo methods for targeted or random mutagenesis available, they all lack in different key aspects, most importantly the introduction of strong mutational biases that hinder efficient screening afterwards. In this project, we will build upon core expertise of our group^{[1, 2]}, and combine model-guided enzyme engineering, experimental design and next-generation sequencing to create a molecular toolbox for next-generation mutagenesis. Further, we will apply this new toolbox to impactful application cases in the context of sustainable bioproduction, diagnostics and therapeutics.

We are looking for highly motivated PhD candidates (m/w/d) with a background (MSc/diploma) in synthetic or molecular (micro-)biology, biochemistry, biotechnology or related fields. Experience with next-generation sequencing including data analysis and/or basic programming skills (R, Python) are desirable. We offer a detailed on-the-job introduction, continuous mentoring and a pleasant working environment in a young and dynamic team at the interdisciplinary interface between biology, chemistry and data science.  EPFL and LSAM’s affiliation to two schools (SV and SB) and two institutes (IBI and ISIC) represent a vibrant international and interdisciplinary environment for this project and the PhD candidate.

The position can be filled as soon as possible with a preferred start around Jan/Feb, 2026. Questions about the position and expressions of interest (CV, motivation) should be addressed to Prof. Markus Jeschek ([email protected]).

References:

[1] Höllerer, Papaxanthos, Gumpinger, Fischer, Beisel, Borgwardt, Benenson & Jeschek. Nat. Commun. 11: 3551 (2020).

[2] Huber, Kucera, Höllerer, Borgwardt, Panke, Jeschek. Nat. Commun. 16:5466 (2025).

We are excited to invite a passionate and motivated PhD student to join our lab on non-equilibrium dynamics in in-vitro cell culture systems. The Mechanics of Soft and Biological Matter Laboratory (MESOBIO) at the Institute of Mechanical Engineering, EPFL, focuses on gaining a fundamental understanding of biological and living systems as well as soft and active materials. We have one available position for a PhD student, focusing on experimental work to understand how mechanical environments lead to pattern formation and phase transition behaviors in in-vitro systems. This position will be highly complementary to ongoing theoretical and computational modeling of biological systems, advancing the fundamental principles governing tissue morphogenesis. Applications will be reviewed until the position is filled.

We welcome applications from candidates with different backgrounds. Preferred skills and qualifications for successful candidates include:
• Bachelor’s and/or Master’s degree in Bioengineering, Biology, Biophysics, Mechanical Engineering, or Materials Science and Engineering.
• Proven research experience in monolayer or organoid systems.
• Expertise in high resolution microscopy applied to biological samples.
• Prior experience with substrate patterning and/or modulation of substrate stiffness.
• Strong skills in quantitative image analysis on biological systems, including segmentation analysis.
• Excellent communication skills in English, both written and spoken.
• Self-driven and open minded with a strong willingness to explore interdisciplinary research.

We offer a highly competitive salary commensurate with previous experience, accompanied by comprehensive social benefits. All students will have access to state-of-the-art computation and experimental facilities, enabling cutting-edge research opportunities, and they will also have the opportunity to participate in collaborations within multidisciplinary projects.

Interested candidates are requested to prepare their application as a single PDF file, including a cover letter (maximum 1 page), describing research interests and demonstrating how your background and previous experiences align with the direction of our group, and a comprehensive CV, providing detailed information about your academic and professional background and skills, accompanied by contact information for three references. The application should be directly submitted to Professor Sangwoo Kim ([email protected]) with the subject line, “Name: Application for PhD Position”.

For additional information regarding the position, please feel free to reach out to Professor Sangwoo Kim.

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.

PhD Position in Biofilm Mechanics, Rheology & Antibiotic Resistance

Project: Understanding how Klebsiella pneumoniae biofilms acquire mechanical resilience and antibiotic tolerance

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

We are seeking a PhD student with a strong interest in bridging biophysics and infection biology to investigate the mechanobiology of the pathogen Klebsiella pneumoniae. Klebsiella pneumoniae has emerged as a top-priority antibiotic-resistant pathogen, driven by the rapid global spread of hypervirulent and carbapenem-resistant strains. Its unusually thick capsule and viscoelastic biofilms play central roles in immune evasion and treatment failure, yet their mechanics remain poorly understood. This project addresses this gap by uncovering how these material properties promote resilience and antibiotic tolerance.

In this project, you will develop experimental and analytical approaches to quantify the mechanics of bacterial capsules, mucoviscous aggregates, and biofilms, and link their viscoelastic properties to antibiotic response. You will:

• Combine microfluidics with single cell resolution microscopy to track real-time biofilm morphogenesis, deformation and detachment
• Characterize the rheology of capsulated and non-capsulated biofilms (oscillatory rheometry, extensional rheology, micro-indentation) and correlate with single cell dynamics within biofilms
• Map how mechanical confinement or stiffness modulate antibiotic tolerance
• Integrate mechanical datasets with transcriptomics and imaging to uncover regulatory pathways underlying mechanical resistance
• Expose the mechanical functions of the capsule in lung and gut organoid infection models.

We welcome applicants from biophysics, bioengineering, soft-matter physics, microbiology or related disciplines. A solid quantitative background (microfluidics, mechanics, imaging, data analysis) and a motivation to work at the interface of biology, physics, and engineering are both required.

You will join a dynamic, international lab specializing in bacterial mechanobiology, microfluidic organoid infection models, and high-resolution live imaging. The project is part of a broader program integrating mechanical, genetic, and infection biology approaches to understand how K. pneumoniae withstands antibiotics and interacts with host tissues.

Scanning Ion Conductance Spectroscopy for molecular diagnostics and sensing

Two positions in the field of technique development for single molecule biosensing are open in a joint project between the Laboratory of Nanoscale Biology and the Laboratory for Bio- and Nano-Instrumentation. Based on our recently invented Scanning Ion Conductance Microscopy technique (SICS), you will develop single molecule nanopore techniques to study mRNA structure or protein sequence at the single molecule level.

Nanopore-based single-molecule sensing is revolutionizing molecular diagnostics, biophysics, and sequencing. However, current techniques face critical limitations, including poor control over molecular translocation, low signal-to-noise ratios (SNR), and inefficiencies in sample delivery and in situ detection. Overcoming these challenges requires novel strategies to enhance detection precision and multiplexing capabilities. This project builds upon our recent invention of SICS,  a nanopore-based method that actively controls molecular passage, enabling high-resolution, high-fidelity measurements. Unlike traditional approaches where molecules must diffuse into the nanopore, SICS moves the nanopore sensor to the sample, drastically improving efficiency and control. The unique advantages of SICS—3D spatial multiplexing, high SNR, and the ability to reread individual molecules—position it as a powerful tool for multi-analyte diagnostic assays and next-generation sequencing technologies. By integrating computational models with advancements in instrumentation, we will refine SICS into a high-resolution, high-throughput tool for single-molecule characterization with unprecedented precision to detect target proteins for diagnostic applications, measure mRNA stability and folding dynamics, and protein amino acid composition and sequencing. This project brings together the complementary expertise of three leading groups:

The Radenovic Lab (LBEN): Specializes in nanopore fabrication, single-molecule detection, and biophysics, leading experimental development.

The Fantner Lab (LBNI): Specializes in nanocharacterization, scanning probe microscopy, microfabrication, electronics, and instrumentation

PhD students will receive co-supervision across laboratories, fostering a dynamic exchange of expertise. You will work in a team consisting of an engineering/instrumentation focussed PhD student and a biophysics/molecular biology focussed student. While each student will bring their unique expertise, each team member will work on both technique development and bio-application.

During this project you will learn:

• Use and improve advanced single molecule (scanning probe microscopy) based sensing equipment
• Design and optimize biological assays (DNA, protein, RNA) for spatial multiplexing
• Analyse large data sets including machine learning in collaboration with international project partners.
• Development of new diagnostic methods for point-of-care and pharma applications.

What you can bring:

• Willingness to work with state of the art, prototype instruments
• Interest in :
  • Position 1: Biophysics, measurement science, imaging, instrumentation, or software development, or
  • Position 2: Biochemistry, single molecule assays, protein engineering, nanopores, protein sequencing, or RNA structure
• Interest in learning from your fellow PhD student “the other side” of the project.

LPBS

Intelligent Proteins and High-Performance Cells

How can proteins be engineered to make decisions, and how can cells be pushed beyond their natural performance limits? In the Rahi lab (LPBS), we study and design the dynamic computations of life. Using a combination of optogenetics, continuous directed evolution, and AI-driven protein design, we aim to create intelligent proteins, that is, molecules that integrate multiple inputs, switch states, and perform logic-like operations. At the same time, we use light-controlled evolution to sculpt high-performance cells, probing the physical and evolutionary limits of growth, variability, and robustness.

As a PhD student in our group, you will:

• Use AI-based design and simulations to generate and test candidate proteins that perform computational tasks at the molecular level.
• Develop and apply optogenetic and light-directed evolution platforms to re-engineer switchable proteins with novel functionalities.
• Explore how cellular physiology can be tuned and optimized through laboratory evolution, uncovering fundamental constraints on growth and decision-making.
• Work at the interface of machine learning, synthetic biology, biophysics, in an environment that bridges physics, biology, and engineering.

We are looking for highly motivated candidates from physics, bioengineering, and quantitative biology who are excited to combine computation and wet-lab experiments to solve fundamental and applied questions in synthetic biology.

Join us in building the next generation of programmable proteins and optimized cells, and help define what it means for biology to compute.

Contact: Prof. Sahand Rahi ([email protected])

Date: October 3, 2025

Ramdya Neuroengineering Laboratory of Neuroengineering reverse-engineers cognitive and motor behaviors in the fly, Drosophila melanogaster, to better understand the mind and to design more intelligent robots. Flies are an ideal model: they generate complex behaviors, their nervous systems are small, and they are genetically malleable. Our lab develops and leverages advanced microscopy, machine learning, genetics, and computational modeling approaches to address systems-level questions. We are always looking for talented researchers to join our team. Join us! There is much to discover!

Note: Prof. Ramyda is not participating in the Hiring Days and invites candidates to contact him directly in case of interest in his research.

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]

🚀 Join ORYL as a PhD Researcher and be part of an exclusive network of WATER enthusiasts

Help us in our quest to set a new reference in solubility and aggregation using WATER!

Are you ready to push the boundaries of science and innovation and be part of an ambitious team that aims to make a real-world impact through innovation? We’re looking for ambitious, creative, and driven PhD candidates with a background in Life Sciences and Chemistry (Pharmaceuticals, Biochemistry, Biophysics) with a strong interest in drug discovery and development to join our dynamic and innovative startup at the forefront of pharmaceutical technology, biotechnology and photonics.

At ORYL, we’re building an ultrafast instrument for automated solubility and aggregation profiling using WATER. Our team is a vibrant mix of scientists, entrepreneurs, and visionaries united by a shared passion to make an impact.

As a PhD researcher, you’ll be empowered to:

• 🔬 Conduct cutting-edge research that creates value
• 🤝 Collaborate with a multidisciplinary team of experts
• 🚀 Thrive in a startup culture that values agility, creativity, and bold ideas

We offer:

• A dynamic, supportive, and entrepreneurial environment
• Opportunities for career growth beyond academia
• Be part of a fast growing and dynamic startup company.

How do bacteria evolve new ways to communicate, and how can these mechanisms be re-engineered to build novel functions?

In the Westmann lab, we combine experimental evolution, high-throughput phenotyping, computational modeling, and evolutionary theory to investigate how bacterial communication systems evolve, diversify, and can be repurposed for new applications.

As a PhD student in our group, you will:

• Reconstruct and experimentally test ancestral bacterial communication systems to uncover how they originated and diversified
• Map large-scale sequence–function relationships to understand how molecular interactions evolve
• Apply computational and AI-based approaches to predict and design new communication circuits
• Explore how protein promiscuity, specificity, and modularity shape bacterial signaling and regulatory networks
• Work in a highly interdisciplinary, collaborative, and international environment

We are looking for curious and motivated candidates from molecular biology, bioengineering, evolutionary biology, or related fields who are excited to combine wet-lab and computational approaches to tackle fundamental and applied questions.

Join us in decoding and redesigning the molecular languages of bacteria.

Contact: Dr. Cauã A. Westmann
[email protected] or [email protected] (EPFL email from January 2026)

PhD positions—3D hydrogel droplet printing for iontronic biointerfaces

Mission

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, stimuli-responsiveness, and therapeutics delivery, enabling interactive communication with biology. The dropletronic system will be formed from three-dimensionally (3D) printed picoliter droplet networks, which use lipid bilayer, functional nanopores, and charge-selective solutes to feature sophisticated ion control.

For the PhD positions starting in January 2026, we are seeking 1–2 candidates with experience in 3D printing, microfluidics, microfabrication, stimulus-responsive soft materials, and bioengineering. Candidates should be interested in emerging, interdisciplinary fields and be motivated to address new challenges, including the development of (1) voxelated, multimaterial printing systems, (2) iontronic device and system design, and (3) organoid interfaces.

Group website: https://www.epfl.ch/labs/bion/

Group leader: Prof. Yujia Zhang

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;

Profile

• Prior experience in cleanroom manufacturing and biological experiments is a plus;
• MSc in microengineering, materials science, electronics engineering or bioengineering;
• 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);

We offer

• 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.
• International collaboration and visiting opportunities;
• 4 years to complete your PhD with a competitive remuneration;
• 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: 1st December 2025

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 program for this position: EDMI, EDBB, EDMX, or EDAM;

Contract Earliest Start Date: January 2026

Activity Rate: 100%

Contract Type: CDD

Duration: 1 year, renewable

Reference: TBC