PhD scholarship in Computational Biology – DTU Biosustain

If you are curious and proactive scientist with expertise and interest in computational biology and data science, and you are looking to make a difference working on projects that will have impact on world level challenges, this PhD position is for you! The project is a collaboration with DTU Bioengineering, Assoc. Professor Timothy P. Jenkins and we aim to develop machine learning pipelines that help process, analyse and interpret Mass spectrometry-based metaproteomics data for the study of microbial communities.

As part of DTU Biosustain, you will be an essential part of multiple initiatives towards the development of new environmentally friendly products, cleaner and more sustainable manufacturing and farming processes, new medical treatments, and richer biodiversity and ecosystems. You will collaborate with top research scientist in the field and in an international, motivating, flexible, supportive, and friendly environment at a leading research and education institution in Europe.

About the Novo Nordisk Foundation Centre for Biosustainability
Biosustainability is the discovery, production, and use of biochemicals at scale to avoid the depletion of natural resources and the harmful impact of existing ones such as fossil fuels on societies, economies, and environments. The Novo Nordisk Foundation Centre for Biosustainability (CfB) is an interdisciplinary research center at the Technical University of Denmark with 300 employees that develops new knowledge and technology to support the production of biochemicals using microbial production. The Centre comprises core facilities and academic research groups doing both basic research to determine the spectrum of chemistry that can be produced biologically and applied/translational approaches focusing on enhancing the strain design and development process. Learn more about our activities and expertise at biosustain.dtu.dk. 

About the Multi-omics Network Analytics Group
The Multi-omics Network Analytics aims to getting a holistic view of biological systems and their context to understand their complexity and provide new insights and applications that can benefit human and environmental health. We focus on Multimodal Data, processing and analyzing diverse types such as mass spectrometry (proteomics, metabolomics) and metaomics (metagenomics, metatranscriptomics, metaproteomics), tackling complex biological problems. 

A key component is integrating and interpreting multi-omics data using and developing machine learning tools. We apply these technologies to explore and understand microbial communities and their environments, unraveling assembly, interaction, adaptation, and impact, spanning ecology to biotech.

Further, we’re strong advocates of open science, adhering to open principles for our generated data, training, and software, aiming to reduce inequality and promote accessibility by democratizing data science.

Research and Development Opportunities
You will get the opportunity to learn and apply the latest algorithms/data science methods related to synthetic biotechnology and biosustainability. Further, during the selection process, you will define together with your supervisors (main and co-supervisors) the most relevant courses from the domains covered in the project (30 ECTS points of relevant PhD courses as required in Danish PhD programs). These courses will ensure that you become a bilingual scientist with deep knowledge in data science as well as biology, chemistry, computation, etc. We anticipate that by working with us, you will foster some of the following skills:

• Opportunity to work across a multi-disciplinary research program
• Access to world leading companies and initiatives within industrial biotechnology
• Transferable skills across bioengineering, process systems engineering and computer science
• Opportunity to tap into an agile innovation ecosystem
• Bioprocess development across scales in a new data-driven paradigm
• Development and application of state-of-the-art machine learning and deep learning on biotechnological problems

Responsibilities
As a PhD student embarking on a three-year journey in biotech-focused data science and machine learning, you will spearhead a pioneering project aimed at advancing enzyme optimization through Bayesian frameworks. This role not only demands scientific acumen but also leadership, project management, mentoring, and the ability to communicate complex research to the global scientific community. Here's a snapshot of the key responsibilities you will hold:

• Scientific Leadership: Lead research in Bayesian optimization, fostering interdisciplinary collaboration and innovation in enzyme engineering.
• Research Project Management: Strategically drive the project from conception through to publication, ensuring adherence to scientific and funding objectives.
• Student Supervision: Guide and support students' research, promoting their academic growth and contributions to the project's success.
• Scientific Dissemination: Actively publish and present research findings, enhancing the project's visibility and impact in the scientific community.

Requirements and qualifications
You must have a two-year master's degree (120 ECTS points) or a similar degree with an academic level equivalent to a two-year master's degree.

Ideal competencies required for the project
You are willing to work in an international environment with colleagues and partners from all over the world. The following competencies are advantageous for successful execution of these PhD projects:

• Two-year master's degree (120 ECTS points) or equivalent in computational biology, bioinformatics, data science, machine learning, or related topics
• Knowledge of Python and its scientific libraries and data stack (numpy, pandas, scipy, scikit-learn, pytorch, etc.)
• Experience using statistical techniques to analyse data, build predictive models, and evaluate their performance
• Domain knowledge about Mass spectrometry-based proteomics
• Experience processing, analysing and interpreting biological datasets
• Enjoy working with people and has good communication skills
• Curious, proactive, motivated and able to work independently

If you have these competencies and experience listed above, and you have initiative, are motivated, and eager to learn more and further improve, then you are good to go.

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.

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 . 

We offer
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.

Salary and terms of employment
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, and the position is a full-time position. The starting date for the position is 1 October 2024.

You can read more about career paths at DTU here http://www.dtu.dk/english/about/job-and-career/working-at-dtu/career-paths.

Further Information
If you have any questions, you are very welcome to contact Alberto Santos at [email protected] .

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 
Your complete online application must be submitted no later than Wednesday, 30 July 2024 (23:59 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

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

Applications 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.

There will be a competitive selection process where candidate applications will be evaluated, and the pre-selected candidates will be invited for an interview.

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 .

DTU Bioengineering
The Digital Biotechnology Lab is a research group within the Center for Antibody Technologies lead by Assoc. Prof. Timothy P. Jenkins. We are passionate about harnessing the power of modern technology to innovate the biotechnological landscape and develop real world solutions for the benefit of society. Primarily, we focus on leveraging the power ML to help identify novel protein targets and discover therapeutic, diagnostic, and reagent binding proteins. Specifically, we are interested in (1) de novo peptide sequencing, and (2) ML-guided binder discovery approaches, such as generative protein design. Our research group is highly active in numerous outreach activities and our international travel agendas are typically busy.

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.