Do you want to help drive the next generation of genome-scale reconstruction? Here is the position to carry out your dream job.
No. of Position(s)
- linear programming and Matrix decomposition
According to Standard Norms
PhD degree in engineering, bioinformatics, or similar field
We are looking for a colleague with previous experience working with metabolic network reconstructions, with substantial knowledge of metabolic biochemistry. This includes familiarity with methods for computational modelling of metabolism, including constraint-based and kinetic modelling, and an understanding of the relevant methods such as linear programming and matrix decomposition.
Most of our programming is in Python/Pandas and intermediate level programming skills are essential.
Additionally, your CV will demonstrate ability to:
- communicate technical information to internal/external audiences at various levels (undergraduates to senior scientists) and from various backgrounds (technical and non-technical personnel).
- work independently and as part of a team.
- successfully work on multiple concurrent projects and meet deadlines.
Experience interfacing databases and R scripting will be an advantage
Develop genome scale models for non-model organisms
As a member of the Microbial Reconstruction Unit, you will be building organism-specific computational resources to empower microbial strain design workflows. You will work closely with the Principle Investigators (PIs) and teams to coordinate efforts within strain design projects.
Specific tasks include:
- Reconstructing metabolic networks of target organisms from genome annotations and experimental literature to enable metabolic modeling applications.
- Annotating protein structure and genome sequence information for the analysis of sequence variation.
- Construction of organism-specific databases from internal and public -omics datasets (e.g. genomics, transcriptomics, proteomics, metabolomics, and sequencing) to empower strain design projects.
- Transcription regulatory analysis of organism gene and protein expression data
- Contribution to development and implementation of computational methods and tools described above.
- Participation in a team environment as part of a large academic organization developing computational tools and workflows for strain design.
- Organization of (bi-)weekly project updates to lab management.
How to Apply?
Applications must be submitted as one PDF file containing all materials to be given consideration, fill out the online application form, and attach CV, cover letter, diploma and if relevant list of publications.
All Interested candidates irrespective of age, gender, race, disability, religion or ethnic background are encouraged to apply.
About the Project
“Microbial Reconstruction Unit”, headed by DTU Biosustain CEO Prof. Bernhard Palsson and CSO Prof. Lars Keld Nielsen. Reconstructions are collections of organism-specific knowledge, such as the set of all metabolic reactions that take place within an organism or the set of all experimentally-determined protein structures. These reconstructions are invaluable resources for rational design of microbial strains for a host of applications, but their availability outside model organisms is limited.
You will join a dynamic team developing new organism-specific reconstructions, computational tools, and databases to empower the development of microbial strains in non-model organisms for several applications, including small molecule production, bioactive compound production, and microbial foods. Half the team will work on key fermentation organisms such as Lactobacillus and Streptomyces, while the other half will work on C1 metabolism in organisms such as acetogens, methanotrophs, and cyanobacteria. Everybody will be involved in advancing reconstruction software as well as reconstructions of the model organism E. coli.
About DTU Biosustain
Recent progress in our ability to read and write genomic code, combined with advances in automation, analytics and data science, has fundamentally changed the scope and ambition of harnessing the potential of biological systems. Big data approaches and analysis of biological systems are key research instruments at the Center. DTU Biosustain utilizes these advances for microbial cell factory design to foster sustainable lifestyles in relation to three application areas: Sustainable Chemicals, Natural Products, and Microbial Foods. Learn more at biosustain.dtu.dk.