IMSB News

For students of D-BIOL/D-HEST/D-BSSE

For students in D-BIOL/D-HEST/D-BSSE

For students of D-BIOL/D-HEST/D-BSSE

For students of D-BIOL/D-HEST/D-BSSE

For students of D-BIOL/D-HEST/D-BSSE

For students of D-BSSE/D-MATL/D-CHAB/D-BIOL

For students of D-BSSE/D-MATL/D-CHAB/D-BIOL

In this project, we will systematically characterize the function of unknown membrane proteins and their role in the cell's response to environmental conditions.

Mass spectrometry is the widely used accurate quantification of the proteome composition. However very few attempts have been made to use these techniques for the determination of the absolute stoichiometry of protein complexes. The goal of this project is to use Single Reaction Monitoring (SRM)-MS, in combination with AQUA peptides, to define the absolute stoichiometry of dynamically assembling protein complexes that are relevant in the context of inflammation and autoimmune diseases.

Mass Spectrometric Analysis of Hepatitis B Virus X Proteoforms and Interactomes.

The project lies at the intersection of genetics, psychophysics of smell, and data democracy. Students will have the opportunity to combine wet lab work, study design, and computational analysis. Students should be able to write simple scripts in R, Matlab, or Python or have the willingness to acquire and develop these skills. 

In this project, we aim at inferring functional protein-metabolite interactions in the bacterium Escherichia coli from dynamic metabolomics data.

Cryptic genetic variation (CGV) is the hidden genetic variation accumulated over time that do not contribute to the normal range of phenotypes, but may provide a source of adaptive variation to novel conditions. This project will examine if the CGV in different genetic backgrounds is influential in the evolution of circadian traits. (Keywords: Drosophila melanogaster, genetics, behavior, circadian rhythms)

How genetic variation (e.g. SNP) leads to different traits/phenotypes in natural populations is a fundamental and challenging problem in both the life and medical sciences. This project will involve several objectives to tackle this problem by first establishing an efficient in vivo CRISPR/Cas9 method and then using this method to change phenotype-associated SNPs in inbred Drosophila lines derived from a natural population.

Research project available on investigating the interplay and protein activity fine-tuning of different posttranslational modifications (PTM) sites

Research project available on investigating the regulation of metabolism in S. cerevisiae, via enzyme phosphorylation

Research project available on investigating metabolic response to mitochndrial defects in yeast

The student will learn how to process samples for mass spectrometry analysis, to analyse the resulting proteomic datasets and integrate them into a larger multi-omics framework. The work will be published in a scientific journal and the student will be involved in writing up the manuscript.

Mass Spectrometric Analysis of Hepatitis B Virus X Proteoforms and Interactomes.

Investigate the influence of amino acids on the hyperproliferative potential of PTEN mutant cell populations in Drosophila melanogaster.

Cells process external and internal biochemical signals by means of signaling cascades, which constitute complex, dynamical networks. In this project we use novel deep (machine) learning techniques to decompose such networks in their building blocks in order to elucidate the overall structure.

Discovery of genetic redundancies using a targeted genome reduction approach

Hafen Group Student Project

Two bioinformatics projects available

Master thesis or semester project

Master thesis or research projects available

Mapping cellular core functions by transposon mutagenesis and next generation sequencing

We are looking for motivated semester/master students to join our structural proteomics team at ETH to work at the interface between proteomics and structural biology.

Understanding history-dependence (hysteresis) of growth states in E. coli

We are looking for students who would like to join project for development of the new phosphopeptide enrichent for the analysis of small sample amounts. These projects are the perfect opportunity to get hands-on experience with proteomics methods and mass spectrometry instrumentation. Prior experience with mass spectrometry is not essential, although candidates with basic knowledge of proteomics methods are preferred.

A project combining wet and dry bench

A comparative study of the immediate metabolic response to oxidative stress in E. coli, Yeast and Human cells

Identifying the target of the antimicrobial peptide Sublancin

Kinetic reconstruction of E. coli central carbon metabolism with allosteric regulation

We are looking for 2 highly motivated and focussed MSc students with skills in bioinformatics for immunopeptidome analysis, who will: 1) automate a computational workflow for the analysis of immunopeptidomic SWATH MS data. 2) analyze a tissue-based map of the immunopeptidome. Contact: Dr. Etienne Caron

Epigenetic pathways are major regulators of aging and aging-associated diseases including cancer. The student will apply a recently developed mass spectrometry-based method to profile epigenetic states during aging and cancer development. Contact: Dr.Christian Feller

Causality inference from single-cell data. Inferring cause and effect, instead of mere correlative relationships between biological variables is a challenge of interest in many biological applications. This project deals with analyzing intervention experiments with single cell readout to infer causal signaling relationships.

Investigating tradeoffs between fast growth and fast switching in microorganisms

History-dependence (hysteresis) of growth states in E. coli

Proteome-scale enzyme discovery in yeast using nontargeted metabolomics.

Apply a novel framework for 13C flux analysis to co-metabolism of mycobacteria

Mapping essential core functions of microbial genomes by transposon mutagenesis and next generation sequencing

Ab initio cell type definition from high-dimensional single-cell data

Infer structure and parameters of biochemical networks through machine learning

Understanding the role of bacterial metabolism in the evolution of antibiotic resistance 

Investigate a novel protein localization factor

Investigate how a secondary messenger triggers cellular heterogeneity

Elucidate the core function of microbial genome by transposon insertion and NGS

A systems-level investigation of the stress-induced global metabolic adaptations in several organisms

Analysis of cellular cholesterol regulation using targeted mass-spectrometry