PhD Position - Bioinformatics (f/m/d) for 3 years

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Job Description

Takeda’s Gene Therapy New Technologies and Innovation team is looking for talented and highly motivated candidates for pursuing a PhD research program, in which the student will generate a current and validated reconstruction of HEK cell. Older version already exists but need to be updated with respect to the current global consensus reconstruction of human metabolism.

Genome-scale metabolic models (GSMMs) are highly curated and reliable in silico reconstruction of the biochemical capabilities of an organism. In essence a GSMM is a two-dimensional annotation of the genome that allows to predict intracellular steady-state flux distributions. Thereby computationally connecting the genotype with the phenotype. 


The candidate will use RNAseq data and global proteome data to tailor the reconstruction specifically to the different HEK cell lines used by Takeda. In addition, the student will extensively characterize the time-dependence of the medium exchange spectra to constraint and validate the mathematical models. This will allow us to better understand the energy metabolism and metabolic production processes in HEK293 cell lines and enable us to identify metabolic bottlenecks and computationally devise strategies to improve productivity and product titer. Finally, several of the most promising strategies will be validated experimentally. In particular, this includes:

  • Build and validate a genome-scale metabolic models using automated bioinformatics reconstruction tools.

  • Integrate RNAseq and multi-omics data into genome-scale models to elucidate metabolic regulation mechanisms.

  • Develop in silico methods to rationally design fit for purpose cell lines

  • Critically assess different methods for simulation of specific cell line linages

  • Perform Hands-on work in a wet lab to validate the model

  • Publication of at least two papers on selected, peer-reviewed conferences and/or journals

  • Collaboration with internal and cross-functional teams and academic researchers


  • Master’s degree in Bioinformatics, Systems Biology or related disciplines with strong Mathematical skills

  • Experience in mining and analyzing biological or genetics data

  • Strong curiosity on exploring data, simulation and visualization skills

  • Ability to clearly communicate ideas and knowledge

  • Ability to work in an interdisciplinary team and pursue goals in a focused way

  • Solid skills in RStudio® and Python®

  • Excellent command of German and English

At Takeda, we are transforming the pharmaceutical industry through our R&D-driven market leadership and being a values-led company. To do this, we empower our people to realize their potential through life-changing work. Takeda encourages and supports its employees by trainings, job rotations and mentoring. A balanced work - life ratio (recognition for work and family, company kindergarten in Vienna, free ) and numerous benefits (fitness center, cafeteria, etc.) complete our profile as a top employer. For more insights into Takeda click here.

We foster an inclusive, collaborative workplace, in which our global teams are united by an unwavering commitment to deliver Better Health and a Brighter Future to people around the world. Gender, age, skin color, background or sexual orientation play no role in this as we actively promote diversity. We equally address people with disabilities. In the course of a recruitment process which is as free of barriers as possible, we encourage you to mention all relevant information in this context in your application. The salary for this important PhD position is € 2.644,- gross per month (full time, collective wage agreement for the chemical industry). Typically, a PhD candidate works 30 hours a week.


AUT - Orth an der Donau

Worker Type


Worker Sub-Type

Fixed Term (Fixed Term)

Time Type

Part time


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