PhD scholarship in computational biology/bioinformatics - DTU Biosustain

The Novo Nordisk Foundation for Biosustainability (DTU Biosustain) at the Technical University of Denmark is seeking highly motivated PhD candidates with an interest in deep learning and bioinformatics approaches for sustainability and human health. If your areas of interest and competence are genomic big data science and software development, and you are looking to gain experience while working on projects that will make an impact on the world, this is your chance. Your personal efforts will enable and accelerate works towards development of new environment friendly products, new medical treatments, climate friendly farming, etc by applying/developing tools /pipeline of Big Data, AI and bioinformatics for the life sciences. All code that you will develop will have a permissive open-source license (e.g., MIT), hosted on GitHub, and will be promoted at the international level via publications and conferences.  Through this, you will get the opportunity to utilize everything you know and help break new ground at the very forefront of what is possible.

Skill acquisition opportunities
At a more personal level, you will get the opportunity to learn the latest and greatest algorithms/data science methods related to personalized medicine and synthetic biotechnology. You must be open to learning new information within the biology domain, as well as be open to contributing with your software engineering expertise and ideas at our regular group meetings. You will be building the foundation for world-class scientific results. We anticipate that by working with us, you will foster the following skills:

• Programming in modern C++ (HPC languages), python and workflow language
• How to develop modern build/test/deploy infrastructure using CMAKE and continuous integration for all operating systems
• Multi-threading algorithm and logic
• Native GUI design and development
• Advanced deep learning and graph algorithms for life-science data (multi-omics)

The projects and tasks
Your mission is to develop and optimize a new software platform that can automate handling of large and heterogeneous data sets (i.e., Big Data) from biotechnology experiments (for example, long-read/Hi-C/single-cell sequencing) and their applications to sustainability and human health. You will do so by developing new or transforming traditional algorithms into high-performance multi-threading on cloud infrastructures. The core algorithms utilize state-of-the-art optimization and deep learning techniques. You will

• Develop and maintain core software business logic and GUI components written in modern C++
• Develop and maintain core software build infrastructure using CMAKE and continuous integration infrastructure scripts
• Develop and maintain scripts for deploying the software on both end-user devices and HPC infrastructure
• Develop and maintain core software algorithms and workflows for data processing and analysis
• Translate algorithms and workflows prototyped into high-performance tools
• Gain knowledge in relevant biological domain, for example, metagenomics for sustainability, medical multi-omics (cancer, diabetes), complete genomics, etc.

Your role will primarily be to perform computational modelling, write scientific publications, as well as take 30 ECTS points of relevant PhD courses as required in Danish PhD programs.

Competencies of the ideal candidate
A master's degree (120 ECTS points) or equivalent in computational biology or bioinformatics is a requirement.

We also ask that you are motivated by working in an international environment with colleagues and partners from all over the world. Added to this, the CV of the ideal candidate comprises:

• Experience programming in C++ and scripting in Python
• Workflow/pipeline development and management
• Experience in using CMAKE
• Experience using version control with e.g. GitHub
• Experience setting up and working with continuous integration tooling
• Experience within and/or motivation for working with agile methods
• Experience with clean code knowledge and Software testing knowledge
• Prototyping in Jupyter notebooks
• Familiarity with best practices for software development/large-scale genomics data analysis
• Familiarity in deep learning frameworks like pytorch
• Motivation for software development/large-scale genomic data analysis/joining our lab
• A degree in software development/data science/computational biology/bioinformatics/deep learning or related
• Ability to work independently and as part of a team.
• Ability to successfully work on multiple concurrent projects and meet deadlines.
• Knowledge of genomic problems, data types for humans and metagenomics

We offer
At DTU Biosustain we develop the next generation of sustainable biotechnologies using synthetic biology techniques. We create novel production methods and technologies as a foundation for the development of new environmentally friendly products, more energy efficient manufacturing processes, new medical treatments, climate friendly farming, etc.

You can look forward to being part of a leading research and education institution in Europe where on-going development of skills and knowledge is a part of the foundation. You will have great flexibility, as trust and respect are some of the values we build our results on. You will be supervised professionally/have your strong mentoring attention to ensure your professional training.

DTU is a leading technical university globally recognized for the excellence of its research, education, innovation and scientific advice. We offer a rewarding and challenging job in an international environment. We strive for academic excellence in an environment characterized by collegial respect and academic freedom tempered by responsibility.

Approval and Enrolment
The scholarship for the PhD degree is subject to academic approval, and the candidate will be enrolled in one of the general degree programmes at DTU. For information about our enrolment requirements and the general planning of the PhD study programme, please see DTU's rules for the PhD education .

Salary and terms of employment
The period of employment is three years. The appointment will be based on the collective agreement with the Danish Confederation of Professional Associations. The allowance will be agreed upon with the relevant union. 

The period of employment is 3 years.

Starting date is July 1st or as soon as possible hereafter. 

You can read more about career paths at DTU here .

Further information
If you would like additional information about the position, please contact Shilpa Garg at [email protected] or [email protected]. You can read more about DTU Biosustain at www.biosustain.dtu.dk .

If you are applying from abroad, you may find useful information on working in Denmark and at DTU at DTU – Moving to Denmark . Furthermore, you have the option of joining our monthly free seminar “PhD relocation to Denmark and startup “Zoom” seminar ” for all questions regarding the practical matters of moving to Denmark and working as a PhD at DTU.

Application procedure
Please submit your online application no later than 6 April 2023 (Danish time). 

Applications must be submitted as one PDF file containing all materials to be given consideration. To apply, please open the link "Apply now", fill out the online application form, and attach all your materials in English in one PDF file. The file must include:

• A letter motivating the application (cover letter)
• Curriculum vitae
• Grade transcripts and BSc/MSc diploma (in English) including official description of grading scale
• Research statement/plan
• Demonstration of coding/large-scale data analysis skills

Candidates may apply prior to obtaining their master's degree but cannot begin before having received it.

Applications and enclosures received after the deadline will not be considered.

All interested candidates irrespective of age, gender, race, disability, religion or ethnic background are encouraged to apply.

The Novo Nordisk Foundation Center for Biosustainability (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.

Technology for people
DTU develops technology for people. With our international elite research and study programmes, we are helping to create a better world and to solve the global challenges formulated in the UN’s 17 Sustainable Development Goals. Hans Christian Ørsted founded DTU in 1829 with a clear mission to develop and create value using science and engineering to benefit society. That mission lives on today. DTU has 13,500 students and 6,000 employees. We work in an international atmosphere and have an inclusive, evolving, and informal working environment. DTU has campuses in all parts of Denmark and in Greenland, and we collaborate with the best universities around the world.