Domain: computational Biology; constraint-based modelling; physiology and metabolism of prokaryotes; multi-omics integration; mathematical process optimisation

Keywords: genome-scale metabolic models; (metabolic) pathway analysis; cell factory design

Promotor: Jürgen Zanghellini

Starting date: 1st of September 2024, for a period of 3 years

Location: University of Vienna; Vienna, Austria

Funding: HORIZON-MSCA-2022-DN project PROHITS

In this Ph.D. project, you will develop, reconstruct, and curate (enzyme-constraint) genome-scale metabolic models (GEMs) of thermophilic prokaryotes for use as microbial cell factories. In close collaboration with experimental partners, you will integrate multi-omics data obtained into the GEMs and computationally derive a holistic understanding of the thermal response of the proteome of thermophiles. Equipped with this knowledge you will 1) improving our understanding of host physiology and metabolism under different cultivation conditions; and 2) computationally design, predict and optimize industrial process conditions to improve product titre, rate, and yield (TRY) of a microbial cell factory under extreme conditions.

You will be based in the group of Jürgen Zanghellini of at the Department of Analytical Chemistry, at the University of Vienna and intensively collaborate with our experimental partners at NovoArc GmbH in Vienna, a company that develops and manufactures unique lipids derived from the extremophilic Archaeon Sulfolobus acidocaldarius for applications in drug encapsulation and delivery. In addition, you will spend a 3-month secondment at the Vrije Universiteit Brussels (VUB, Brussels) linking single cell protein level data to the developed models.

The project is part of a computational/experimental EU MSCA-DN project with a total of 10 Ph.D. students, and is highly interdisciplinary. Your focus will be on the computational part. Thus, good coding skills (preferentially Python) are essential. Knowledge of machine learning/artificial intelligence as well as basic biochemical knowledge is desirable Skills in the field of -omics as well as background knowledge on archaeal biology is a bonus. Candidates must be motivated to learn about all disciplines relevant to the project.

Candidates must be fluent in English.

Applications must be submitted online in English following the instructions and respecting the conditions at https://bit.ly/prohits. The deadline for applications is 15/03/2024 at 23:59 (CET)

Further general information about the PROHITS project: http://prohits.eu