This page will be updated more often as we approach May 2021, as the EDBB program will be informed of new positions becoming available for the online EDBB Hiring Days event held from May 25 trough to June 17, 2021. Meanwhile, do not hesitate to contact any EDBB laboratories which interest you to find out whether they have upcoming openings for PhD students.
We offer the following PhD position on the ecology and evolution of bacterial pathogens. Pathogen frequently emerge due to their adaptation to natural environments or non-human hosts. Within this context, bacteria often engage in interbacterial competition and cooperation. Our laboratory studies these interbacterial interactions at the mechanistic level using microbial cell biology, genetic engineering, and basic biochemistry. Our model organisms are Vibrio cholerae (the causative agent of the ongoing 7th pandemic of cholera) and Acinetobacter baumannii (a common hospital-acquired pathogen that is frequently multi-drug resistant). We are looking for self-motivated enthusiastic PhD candidates with good organizational skills and scientific passion.
We are seeking highly motivated candidates with 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 starting time should be September 2021 at the latest.
The applicant who is interested in this position, please send your resume to Dr. Chan Cao ([email protected])
The position is part of a Swiss National Science Foundation (SNSF) PRIMA project and the student will be co-supervised by Dr. Chan Cao, Prof. Matteo Dal Peraro and/or Prof. Gisou van der Goot. The salary and benefits are very competitive.
At least 2 openings are available for the April 15th 2021 deadline. PhD projects will be available in the following two areas of research:
- 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. Recently, we showed that aerolysin, a pore-forming toxin, exhibits high sensitivity for single-molecule detection and can be ad hoc engineered for different sensing tasks. The goal of this project is to develop and characterize aerolysin-based nanopores as sensing devices to be applied for genome sequencing, proteomic analysis and disease diagnosis. The project is highly interdisciplinary, includes experimental and computational aspects and interactions with a diverse network of collaborators. Students with a background in biochemistry, physics, bioengineering and computational sciences are encouraged to apply.
2. Integrative modeling at the membrane-protein interface
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. Our laboratory has been studying the molecular mechanisms governing the association of proteins to their membrane interfaces in order to understand the functional implications of this interplay. Multiple projects are available that focus on the theoretical and computational investigation of the structural and dynamic properties of membrane protein systems. All of them are addressed in synergy with experimental collaborators to allow for an efficient integration of biochemical and biophysical data. Students with a background in biochemistry, physics, bioengineering and computational sciences are encouraged to apply.
Single cell transcriptomics (scRNA-seq) is transforming biomedical research by providing unique insights into a cell’s identity and characteristics. However, several key single cell-related technological limitations remain. As a PhD student focused on technology development, you will be expected to address one key challenge, namely our current inability to link the multi-parametric information of a cell image to a genome-wide, molecular description of that same cell. You will thereby build on technological advances that we made involving microfluids and single cell transcriptomics, as presented in Bues et al. (BioRxiv, 2020), aiming to engineer a platform that couples quantitative, high-resolution microscopy to droplet-based scRNA-seq.
Scanning Ion Conductance Microscopy for the study of neuronal wound healing
At LBNI we explore nanoscale biology through the development of novel nanocharacterization instruments. Our main area of interest is in time resolved imaging of molecular and cellular process. For this purpose, we build custom microscopes that enable experiments that are not possible with existing instruments. Recently we have developed a new scanning ion conductance microscope1 for 3D time lapse imaging of live neurons. The nanoscale resolution combined with the non-invasive nature of the instrument enables long time characterization of cell proliferation and tissue formation2. Together with collaborators in the field of neuroscience we want to apply this novel technique for the study of neuronal wound healing in networks of primary marsupial neurons. For this interdisciplinary project we are looking for a bioengineer with interest in cell biology, microscopy, and instrument development.
- Navikas, V. et al. Correlative 3D microscopy of single cells using super-resolution and scanning ion-conductance microscopy. bioRxiv (2020) doi:10.1101/2020.11.09.374157.
- Leitao, S. M. et al. Time-resolved scanning ion conductance microscopy for three-dimensional tracking of nanoscale cell surface dynamics. bioRxiv 2021.05.13.444009 (2021) doi:10.1101/2021.05.13.444009.
Gene regulation depends on transcription factors accessing DNA that packaged in chromatin.
Recently, our laboratory observed how specific transcription factors, so called pioneer factors, can access closed chromatin (Mivelaz et al., Molecular Cell 2020). Based on this study and the methods developed therein, in a new SNSF funded project we are investigating molecular mechanisms of how pTFs and chromatin remodelers collaborate activate genes. To this end we combine chemical biology, single‐molecule biophysics and genetics approaches.
Mechanisms directing centriole fate during muscle development in zebrafish and human iPS cells. The project aims at monitoring centriole and centrosome dynamics during muscle formation and regeneration in zebrafish embryos using light sheet microscopy, 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.
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 Fall 2021. 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.
Discovery of Novel Biotransformations
Living organisms utilize enzyme-catalyzed reactions to synthesize a large array of complex molecules. Enzyme catalyzed processes are characterized by mild conditions, fast reaction rates, highly stereospecific interactions, and minimal toxic byproduct formation. However, living organisms often consist of thousands of metabolites undergoing thousands of reactions. These reactions are carefully regulated through mechanisms developed over millions of years of evolution. An understanding of this complex system and regulation will enable the engineering of enzymes and pathways for the biosynthesis of industrial chemicals or novel pharmaceuticals. The objective of this project is the development of a computational framework for the discovery and the rational design of novel biosynthetic pathways for the production of useful or novel chemicals.
The inquiries about the positions and applications including a motivation letter and the CV letters should be sent by email to: [email protected].
We expect to hire 1-2 PhD students in 2020 in the area of cell-free synthetic biology / synthetic cell engineering.
- Maintenance, homeostasis and heredity of mitochondria and their genomes. HFSP-funded collaborative project (groups include Wallace Marshall (UCSF), Anjana Badrinarayanan (NCBS) and Johan Paulsson (Harvard)). Our consortium combines mathematical theory and quantitative analysis with cutting-edge experimental methods developed in our labs. Considering the mitochondrion as a living entity with its own requirements, we propose to link processes across scales. We will be able to measure fission and fusion events at the scale of single mitochondria, to understand how they accumulate to give rise to a network of a given connectivity and topology. We will be able to count nucleoids, and even individual mtDNA copies, as well as measure their spatial and temporal changes over generations. This will help us understand how numbers are homeostatically controlled and how mutants replicate and segregate to maintain genetic integrity.
- The physical properties of the mitochondrial matrix. ERC-funded project. The current dogma is that the mitochondrial interior, or matrix, behaves as a viscous fluid, albeit one with a complex shape. Interestingly, it has been reported that in vitro, different respiratory states of mitochondria correlate with differences in mitochondrial matrix viscosity, ultrastructure, and density. Fluorescence-based ratiometric, anisotropy, and recovery methods have been applied to measure its viscosity, but with results varying over two orders of magnitude. Intriguingly, motility and internal structure have been linked to metabolic states. More recently, it was reported that the internal ‘temperature’ of mitochondria is adaptive, and reaches nearly 50 °C when they are metabolically active. The field missing a comprehensive study that considers the mitochondrial matrix as a responsive complex fluid with potential for complex or non-equilibrium state behavior, the goal of this project.
PhD position for a candidate interested to:
Develop new approaches to understand transcriptional heterogeneity in tumor evolution.
PhD position in microscopy and biophysics
The lab is looking for a student interested in implementing interferrometric scattering microscopy for the visualization of bacterial extracellular filaments like flagella and pili (see Tala et al., Nature Microbiology 2019). The ideal candidate is a student interested in bioengineering or biophysical problems eager to implement new microscopy methodologies, or a microscopist interested exploring new frontiers of biophysics, all with applications to infectious diseases.
More generally, our lab investigates mechanical regulation of bacterial physiology and infection, in particular via mechanosensing. Our team is highly multidisciplinary, combining techniques from physics, engineering and biology.
Research on the effect of ageing on aortic hemodynamics. Perform a series of measurements on different age groups of healthy males and females to establish a complete data basis of the heomodynamical and biomechanical adaptation with age of the human aorta. Use the data to develop appropriate models of aortic hemodynamics as a function of gender and age. Use these models to develop noninvasive monitoring methods for all important hémodynamique,ical biomarkers.
Project title: Engineering immunity-disease interactions for enhanced cancer immunotherapy
Tang lab’s research aims at developing novel strategies to engineer immunity-disease interactions, an emerging field called ‘immunoengineering’, through chemical, metabolic, and mechanical means in order to treat cancer safely and effectively with immunotherapies. We are actively looking to recruit a PhD student who is interested in this new field and would like to work in a highly interdisciplinary environment. For more information, please see our publications below and reach out to [email protected].
Highly motivated and talented students (bachelor or master) with excellent academic achievements in a major field of Immunology, Cancer Biology, Bioengineering, or a closely related discipline, are encouraged to apply for the EPFL doctoral programs.
Guo, Y.#; Xie, Y.-Q.#; Gao, M.; Zhao, Y.; Franco, F.; Wenes, M.; Siddiqui, I.; Bevilacqua, A.; Wang, H.; Yang, H.; Feng, B.; Xie, X.; Sabatel, C.M.; Tschumi, B.; Chaiboonchoe, A.; Wang, Y.; Li, W.; Xiao, W.; Held, W.; Romero, P.; Ho, P.-C.*; Tang, L.* “Metabolic Reprogramming of Terminally Exhausted CD8+ T-cells by IL-10/Fc Enhances Anti-Tumor Immunity”, Nat. Immunol. 2021, in press.
- Lei, K.; Tang, L.* “T Cell Force-Responsive Delivery of Anticancer Drugs Using Mesoporous Silica Microparticles”, Hori. 2020, 7, 3196-3200. Cover story of Materials Horizons Issue 12, December. Highlighted: EPFL News; Materials Horizons Emerging Investigator Series.
- Lei, K.; Kurum, A.; Tang, L.* “Mechanical Immunoengineering of T-cells for Therapeutic Applications”, Chem. Res. 2020, 53, 2777–2790.
- Wei, L.; Zhao, Y.; Hu, X.; Tang, L.* “Redox-Responsive Polycondensate Neoepitope for Enhanced Personalized Cancer Vaccine”, ACS Cent. Sci. 2020, 6, 404-412.
- Guo, Y.; Lei, K.; Tang, L.* “Neoantigen Vaccine Delivery for Personalized Anticancer Immunotherapy”, Immunol. 2018, 9, 1499. 23,553 views, 5,445 downloads, >99% all Frontiers articles.
- Tang, L.*; Zheng, Y.; Melo, M.B.; Mabardi, L.; Castaño, A.P.; Xie, Y.-Q.; Li, N.; Kudchodkar, S.B.; Wong, H.C.; Jeng, E.K.; Maus, M.V. and Irvine, D.J.* “Enhancing T-cell Therapy Through TCR Signaling-Responsive Nanoparticle Drug Delivery”, Biotech. 2018, 36, 707-716. Cover story of Nature Biotechnology, Volume 36 Issue 8, August 2018.
For more details, see web pages of the EDBB program’s potential thesis directors.