Phd Position in Machine Learning to Predict Enzyme

2 weken geleden

Amsterdam, Nederland Universiteit van Amsterdam Voltijd

PhD Position in Machine Learning to Predict Enzyme Specificity

**Faculteit/Dienst**:Faculteit der Natuurw., Wiskunde & Informatica**Opleidingsniveau**:Master**Functie type**:Promotieplaats**Sluitingsdatum**:06.11.2024**Vacaturenummer**:13466-
- The position is part of the Marie Skłodowska-Curie Network program “Modelling the Biochemistry of Terpene Synthases” also called ModBioTerp. ModBioTerp aims to advance our understanding of terpene synthases using forefront modelling techniques and biochemical characterization to predict and tailor the structure and functionality of these elusive enzymes.- **What are you going to do?**
- You will work on the following research objectives:
1) Develop machine learning methodology to integrate docking results with protein sequence-and structure-features- to predict enzyme specificity.
2) Incorporate predicted protein dynamics as input for enzyme specificity prediction.- experiments and predict functionality of new enzymes.**Tasks and responsibilities**:
You will
- develop machine learning/deep learning approaches, building on recently available enzyme function prediction methodology;
- make use of available enzyme characterization data and data newly obtained by our collaborators, as input for training
- machine learning models;
- collaborate with both experimental researchers as well as with computational researchers (other PhD students working in the
- ModBioTerp project);
- be an active member of the research group and take responsibility for shared tasks; discuss your work with the group members and
- during ModBioTerp meetings; incorporate feedback and give input to others;
- take a leading role in writing manuscripts;
- complete a PhD thesis within the official appointment duration of four years;
- participate in the Faculty of Science PhD training program;
- assist in teaching and supervise Bachelor and Master theses.

**Your profile**Your experience and profile**:
You have/are
- an MSc in Data Science, Artificial Intelligence, Computational Science, Bioinformatics, Systems Biology or similar;
- interested in using machine learning/deep learning on protein sequence
- and structure-data;
- able to communicate with non-experts on computational issues;
- professional command of English.

**Our offer**
- We offer a temporary contract for 38 hours per week for the duration of 4 years (the initial contract will be for a period of 18 months and after satisfactory evaluation it will be extended for a total duration of 4 years). The preferred starting date is January 1st, 2025. This should lead to a dissertation (PhD thesis). We will draft an educational plan that includes attendance of courses and (international) meetings. We also expect you to assist in teaching undergraduates and master students.- Based on a full-time appointment (38 hours per week) the gross monthly salary will range from € 2.872 in the first year to € 3.670 (scale P) in the last year. This does not include 8% holiday allowance and 8,3% year-end allowance. The Collective Labour Agreement of Universities of the Netherlands is applicable.- Besides the salary and a vibrant and challenging environment at Science Park we offer you multiple fringe benefits:

- 232 holiday hours per year (based on fulltime);
- multiple courses to follow from our Teaching and Learning Centre;
- a complete educational program for PhD students;
- the possibility to follow courses to learn Dutch;
- help with housing for a studio or small apartment when you’re moving from abroad.

**About us**- The Faculty of Science has a student body of around 8,000, as well as 1,800 members of staff working in education, research or support services. Researchers and students at the Faculty of Science are- fascinated by every aspect of how the world works, be it elementary particles, plant molecules, the birth of the universe or the functioning of the brain.- The Swammerdam Institute for Life Sciences (SILS) is located at the vibrant Amsterdam Science Park. SILS is one of eight institutes of the University of Amsterdam's Faculty of Science (FNWI). With around 240 employees, SILS carries out internationally high-quality life science research and provides education within various university programs. Research is also carried out in close cooperation with the medical, biotech, chemical, flavor, food & agricultural, and high-tech industries, and revolves around 4 main themes, Cell & Systems biology, Neurosciences, Microbiology and Green Life Sciences.**Any questions?**
- Do you have any questions or do you require additional information? Please contact:
T: +31 20 525 5519- a detailed CV including the months (not just years) when referring to your education and work experience;
- a letter of motivation;- A knowledge security check can be part of the selection procedure.
(for details: national knowledge security guidelines)-
- The interviews will be held in the second half of November 2024.- The UvA is an equal-opportunity employer. We pri

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