EDBB Open positions

This page will be updated more often as the EDBB program will be informed of new positions becoming available for the January 2023 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 as this list is non-exhaustive.

PhD Position in Optofluidic NanoBiosensors for Cancer Research

The position:

The BIOnanophotonic Systems (BIOS) Laboratory at the Institute of Bioengineering of EPFL Switzerland (led by Prof. Hatice Altug) has an open PhD position to collaborate in a Swiss National Science Foundation Sinergia project with University of Lausanne (Department of Immunobiology) and Lausanne University Hospital (Head and Neck Surgery Division and AGORA Cancer Research Center).

We are looking for a talented & motivated PhD student to work on the development of cutting-edge nanobiosensors and bioimaging systems for cancer research from understanding of lymph node metastases biology to personalized treatment strategies. Strategies will include engineering nanophotonic substrates for improved sensing performance, setting up multifunctional optical microscopy and spectroscopy systems, on-chip integration of microfluidic parts for organoid/cell analysis and biomolecule detection, establishing microarray technologies for high throughput screening experiments, handling/characterization of biological samples (including cells), optimization of surface functionalization protocols for operation in complex biological matrix, using advanced image/data analysis and demonstration of newly developed platforms for diagnostic applications. Some of the main tasks include preparing a research plan, nano/microfabrication of optimized device components (nanophotonic chips & microfluidics), reconfiguring optical set-ups, optimizing bioassays, characterizing/handling biological samples, performing optical/biological experiments, analyzing optical/biological data, reporting and disseminating research outcome.

Candidate profile:

The successful candidate is expected to hold a BSc or MSc degree in Bioengineering, Electrical

Engineering, Material Science, Biophysics, Biophotonics or a closely related discipline with outstanding academic record (indicated by grades at BS/MS courses) and involvement in research (e.g. publications in peer-reviewed scientific journals & conferences). In addition, the following qualifications are desired:

  • Hands-on experimental experience in optical microscopy, spectroscopy and optical/electronic instrumentation, & performing optical characterization.
  • Hands-on experimental experience with biosensors (not limited to optical).
  • Hand-on experience with microfluidics, BioMEMS, micro-total analysis systems and designprinciples (fluid analysis) for biomedical/clinical applications.
  • Experience in surface functionalization chemistry and bioassay development.
  • Experience with biological sample handling and characterization (e.g. cells, organoids, biomolecules).
  • Experience in cleanroom with micro/nanofabrication techniques.
  • Experience in programming user interfaces for devices/instrumentation, set-up automation, data extraction (e.g., Python, Matlab, LabVIEW).
  • Experience in data analysis using signal processing tools (also AI, DNN).
  • Fluent in English (both written and spoken) and excellent communication and interpersonal skills.
  • Independent, self-driven, creative, solution-oriented, open-minded, flexible and team-player.
  • Ability to collaborate with a wide range of interdisciplinary partners (e.g. engineers, physicists, biologists, medical doctors), well-organized, eager to learn, and able to take responsibility and define priorities quickly.

We offer:

  • Opportunity to work on multidisciplinary and cutting-edge projects using nanophotonics, spectroscopy and lab-on-chip systems for bioanalytical and biomedical applications.
  • Opportunity to access state-of-the-art research facilities and laboratory resources.
  • Opportunity to collaborate with world-leading cancer research groups and medical doctors through a multidisciplinary consortium funded by Swiss National Science Foundation Sinergia grant.
  • EPFL is an international and top ranking engineering university. It offers a young, stimulating, dynamic, interdisciplinary, international and friendly working environment, a broad range of scientific training and networking events and hosts a vibrant entrepreneurial community.
  • EPFL is an equal-opportunity employer. Candidates will be recruited based on merit.

The selected PhD student would need to enroll in an EPFL doctoral school. Minimum 4-year BS degree is necessary for acceptance by EPFL Doctoral School. Doctoral school information and employment conditions at EPFL are described in:

Keywords:

Nanophotonics, optical nanobiosensors and bioimaging systems, lab-on-a-chip systems, microarrays, microTAS, biological samples, diagnostics, cancer research.

Group website: https://www.epfl.ch/labs/bios/ – Group leader: Prof. Hatice ALTUG

Representative papers from BIOS:

1- Real-time monitoring of single-cell secretion with a high-throughput nanoplasmonic microarray. Liu et al. Biosensors and Bioelectronics, 113955 (2022).

2- Imaging-based spectrometer-less optofluidic biosensors based on dielectric metasurfaces for detecting extracellular vesicles. Jahani et al. Nature Communications. Vol. 12, No.3246 (2021).

3- Rapid and Digital Detection of Inflammatory Biomarkers Enabled by a Novel Portable Nanoplasmonic Imager. Belushkin et al. Small. Vol. 16, No.1906108 (2020).

Relevant review paper:

Advances and Applications of Nanohotonic Biosensors. Altug et al. Nature Nanotechnology. Vol. 17, p.5-16 (2022).

Start date: As soon as possible

Contact:

Please send your application with the subject line « 2023 PhD Position» to [email protected] in a single pdf file containing following information: cover letter, CV, transcript, list of publications, and contact details of at least three referees.

PBL

PhD position in differential multivalent targeting of cancer-immune signaling pathways using pattern-controlled DNA-based nanoparticles. Candidate should have a good background in (cancer) immunology and be familiar with the biophysics of multivalent interactions. The project combines protein expression, DNA nanotechnology and cell biology in a multidisciplinary effort to advance cancer diagnostics and therapy. 

https://www.epfl.ch/labs/gr-cao/

 Nanopore sensing and sequencing:

We are seeking highly motivated candidates with an interest in nanopore single-molecule sensing and sequencing to join Dr. Chan Cao’s group at the School of Life Science, EPFL (Switzerland).

The research group is focused on developing novel approaches to address questions in life science and diagnosis at the single-molecule level, especially focusing on nanopore technology. Nanopore measurement allows the characterization of molecules of interest 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 are an advantage.

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

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. The goal of this project is to engineer and design biological nanopores as sensing devices to be applied for proteomic analysis, disease diagnosis and data storage solutions. The project is highly interdisciplinary, includes experimental and computational aspects and interactions with a diverse network of collaborators. 

2. Deep learning for molecular interfaces

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. Building on our recent development, where geometric transformers were used to predict protein interactions (see PeSTo), in this project we want to expand this approach for cryoEM data fitting and refinement, as well as drug and biomolecular design.

CIBM

Developments of innovative fast acquisition and metabolic modelling strategies for clinical and preclinical deuterium MR imaging in the brain at ultra-high field

Dr Bernard Lanz from the MRI EPFL Animal Imaging and Technology Section is looking for a highly motivated PhD candidate in the area of metabolic imaging using dynamic quantitative deuterium magnetic resonance spectroscopic imaging (2H-MRSI) and cross-validation with dynamic 13C-MRS and FDG-PET: advanced methodological 2H-MRSI developments (i.e. pulse sequence development and implementation, reconstruction, post-processing, denoising techniques), implementation and acquisition of in vivo dynamic 13C-MRS and FDG-PET, development of adapted metabolic models to analyse the different dynamic metabolic data, validate and combine the obtained metabolic fluxes and applications in a rat model of epilepsy.

The candidate will be supervised by Dr Bernard Lanz and Prof. Dimitri Van De Ville, in the framework of an SNSF Weave project.

View full description: CIBM Open Position 2H MRSI CIBM AIT EDBB

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

This interdisciplinary project is focused on using a combination of microbiology, microfluidics, microtissue models of infection, and time-lapse microscopy to study the impact of “metabolic potentiation” on the eradication of bacterial pathogens by antibiotics, with a special emphasis on hard-to-treat bacterial biofilms associated with indwelling medical devices. The student will be based in the Laboratory of Microbiology and Microtechnology at EPFL but will also work closely with our clinical collaborators in Medical Microbiology at the Lausanne University Hospital (CHUV). A background in bioengineering or microengineering is preferred but not required.

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

The Oates lab is exploring how spatio-temporal patterns emerge at the tissue level from noisy cellular and molecular interactions using a population of genetic oscillators in the zebrafish embryo termed the segmentation clock. This multi-cellular clock governs the rhythmic, sequential, and precise formation of embryonic body segments, termed somites, and exhibits a rich set of spatial and temporal phenomena spanning from molecular to tissue scales. Defects in this clock underlie human congenital mal-segmentation disorders (hereditary scoliosis).

Although the segmentation clock has been the dominant paradigm for 20 years, this model does not account for a fascinating classical result: the heat-shock echo, in which periodic segment defects recur, like an echo, along the axis. The interval separating the defects is 5 segments, but – critically – there are no known multiple-segment periodicities in the segmentation clock. This suggests that something fundamental is still missing from our overall picture of segmentation.

Using innovative microscopy techniques, transgenic zebrafish, biochemistry, mechanical manipulation, deep sequencing, physical modeling and good old-fashioned heat-shocks, we aim to discover the mechanism underlying the repeated defects. the aim of this PhD would be to characterize and investigate phenomena during the defects recently observed in our lab at multiple scales: single cell, synchronization between neighbor cells, large-scale wave patterns and mechanics of the tissue. We will also search in an unbiased way for genes that predict the echoes. If these sound to you like interesting questions and approaches to be explored in a challenging and interdisciplinary PhD, please talk to us.

The background we are looking for in a student include experience with zebrafish, microscopy, coding, molecular biology, bioengineering, and/or physics. Some or all of these are useful, but your key characteristics should be curiosity, independence and a love of science.

www.p-lab.science

Microbiota mechanobiology
Commensals from our gut microbiota colonize epithelial surfaces that are covered with loose mucus. While animal and human experiments have taught us about the species that are able to colonize this environment, we know little about the biophysical principles guiding colonization of mucus. We are looking for a PhD student who will investigate colonization of the gut mucosa by commensals in a tissue-engineered gut organoid system. 

Focus of the lab:

The human body develops from a single totipotent cell. During development, this single totipotent cell gives rise to the entire diversity of cell types of the body that ultimately make up all organs. Even though those cells are transcriptionally and functionally different, they share the same genome. Epigenetic mechanisms that regulate which set of genes will be turned on and which genes will be switched off in each cell are at work in order to maintain and generate cellular diversity.

The nervous system develops during early embryonic development and ultimately contains all different types of neurons from different regions of the body. In a series of developmental transitions, progenitors differentiate into neuron and glia lineages.

In my lab, we use neural organoids to model these developmental transitions and investigate how epigenetic processes control differentiation and cell fate. We employ single-cell genomics and imaging technologies to profile the chromatin of individual cells.

 

We have multiple open positions.

 

The successful candidates should have:

-High motivation, curiosity and a strong interest in scientific discoveries

-Drive to learn innovative technologies and perform challenging experiments

-A strong background in computational analysis of genomics data

-Good experimental skills in molecular biology (e.g. IF, IP, Western-Blot, Nuclei-Acid-Extraction, Sequencing-library preparation, Cloning)

-Ideally, experience with human iPS cell culture and curiosity to further develop in vitro culture systems

Current contact email: [email protected]

 

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