We are always interested in hearing from talented and enthousiastic individuals whose research interests align with the lab’s. Please send a CV, cover letter, and contact information for three references to Prof. Heinemann.
Candidates should have conducted master (or Ph.D.) research in bioengineering, microbiology, molecular biology, synthetic biology, biophysics, chemical engineering, or a closely related field. The ideal candidate will be familiar with the following areas, with expertise in one or more of the topics: microfluidics, single-cell analysis, time-lapse microscopy, metabolic modeling or metabolism. The candidates could either have wet or dry lab experience.
Concrete open positions for PhD students and postdocs
Projects in the research line `How does metabolism control the cell cycle´?
We recently found that metabolism of budding yeast, even under constant conditions and across nutrients, oscillates in strict synchrony with the cell cycle. Remarkably, the metabolic oscillations continued when we halted the cell-cycle machinery (Papagiannakis et al, Molecular Cell, 2017), suggesting that metabolism might be an autonomous oscillator. We found that the oscillations co-coordinate the cell cycle by setting the moment for cell cycle entry and exit, in a clock-like manner (Ozsezen et al, Cell Systems, 2019). Data from our most recent work suggest (Litsios et al, Nature Cell Biol, 2019) that the metabolic oscillations might originate from biosynthesis. In the next few years, our big aim is to unravel the clockwork of cellular metabolism, working towards a novel layer of knowledge on cell cycle control.
Project 1: Unraveling the cell-cycle dynamics of the PKA pathway: In this project, we aim to map the cell-cycle-related dynamics of the PKA pathways and its contributions to the metabolic oscillations. We will used CRISPR-based cloning strategies to generate single-cell reporter constructs (including FRET sensors), which we will assess using time-lapse microscopy and microfluidics. To introduce dynamic perturbations, we will use optogenetic tools, through which we can perturb individual cells while watching them under the microscope. Keywords for this project: microscopy, image analysis, cloning, optogenetics. Suitable for someone with a background in: molecular biology, systems biology, biophysics
Project 2: Global analysis of cell-cycle-resolved multi-omics data: In this project, we aim to use cell-cycle resolved multi-layer omics data to identify sets of regulatory mechanisms that could give raise to the global metabolic/biosynthetic oscillations. We will draw on existing network data and integrate them with different computational approaches, similarly to what we had done in the past (Janssen et al, eLife, 2017), but beyond also try to come up with new approaches. Plausible candidate mechanisms we also will convert into coarse-grained kinetic models to assess feasibility to give raise to oscillations. Together with colleagues in the lab, we will test candidate mechanisms experimentally. Keywords for this project: multidimensional omics data, network analysis, computational, inference, models. Suitable for someone with a background in: systems biology, computer science, physics, engineering
Project 3: Mapping the metabolic fluxes through the cell cycle: In this project, we aim to use cell-cycle resolved experimental data on the different biosynthetic processes (which we already partly have, and partly need to generate) and will integrate these data into a recent thermodynamic/stoichiometric metabolic network model (Niebel et al, Nature Metabolism, 2019) in order to resolve the metabolic fluxes through primary metabolism during the cell cycle. The flux predictions, we will test through targeted dynamic single-cell experiments, using protein depletion and optogenetic perturbation experiments. Keywords for this project: metabolic fluxes, modeling, thermodynamic/stoichiometric model, optimization. Suitable for someone with a background in: systems biology, biophysics, engineering
We are always actively looking for Master student researchers to join the lab. Please email Dr. Heinemann for more information.