项目介绍

2024年11月27日

Function

Are you looking for a PhD position at the intersection of biology, chemistry, and computer science? Are you interested in developing new machine learning methodologies in proximity to and collaboration with experimentalists? If yes, this fully funded PhD position might be an excellent match for you.

Molecules lie at the core of both chemistry and biology. They are the basis of all life and indispensable tools in medicine and agriculture. This broad range of molecular function is enabled by a vast diversity of molecular composition, structure, as well as the interaction within and between molecules. Therefore, the computational prediction of molecular functions requires a suitable computational representation of molecules and their interactions. Developing machine learning methodologies to learn suitable molecular representations is thus essential to the computational life sciences and lies at the core of our team’s research. We aim to extend the current approach to data-driven machine learning in the life sciences, where molecules, including proteins, are commonly considered static entities, by introducing dynamics based on newly sourced data and constraints set by natural laws. Our goal is to implement machine learning techniques that have a truly beneficial impact on global health by decreasing drug development times and costs and that contribute toward making industrial chemical processes more sustainable.

As a PhD student, your work will focus on developing new biology- and chemistry-focused machine learning methodologies, enabling the computational representation of molecular composition, structure, dynamics, and associated expert knowledge and applying them to open problems in chemistry and biology. Specifically, you will adapt and implement methodologies from computer vision, such as neural radiance fields (NeRFs) or similar techniques, to our domains of interest. Furthermore, you will have the option to apply the developed methods in collaboration with experimentalists in the fields of synthetic biology/metabolism engineering, pharmacology, and agricultural chemistry.

As a PhD student embedded in a diverse group of international scientists, your responsibilities and opportunities will encompass:  

• Following, evaluating, and synthesising state-of-the-art machine learning, chemistry, and biology research;
• Connecting and collaborating with other national and international researchers in the life sciences and in computer science;
• Writing and presenting/publishing research papers at/in internationally renowned conferences/journals.

You will work here
The Probst Lab (https://probstlab.science) is embedded within the chair Bioinformatics Group (https://wur.eu/bif). You will be co-supervised by Daniel Probst and Dick de Ridder.

Function Requirements

You are a computational biologist or computational chemist with proven expertise in programming with Python. You have also taken advanced courses on machine learning and applied it as part of your master’s thesis. Alternatively, you are a computer scientist or mathematician with a proven understanding of the mathematics underlying machine learning and an interest in the life sciences. As a computational chemist or computational biologist, proven experience in molecular dynamics simulations is an advantage. As a computer scientist or mathematician, proven experience in computer vision is an advantage.

You possess:

• A successfully completed MSc degree in computer science, mathematics, biology, chemistry, or a related program;
• Proven experience in Python programming or high proficiency in another language such as C/++ or Rust. It is an advantage if you can provide a link to a code repository of a project where you were or are the main contributor;
• Experience in implementing and applying machine learning methodologies, specifically deep neural networks;
• An interest in applying state-of-the-art machine learning techniques to various fields in the life sciences;
• A collaborative attitude valuing the importance of interdisciplinarity and open science;
• The drive to present and share your work at international conferences;
• Excellent English writing skills and experience in scientific writing;

For this position your command of the English language is expected to be at C1 level. Sometimes it is necessary to submit an internationally recognised Certificate of Proficiency in the English Language. More information can be found here.

Contactinformation

For more information about this position, please contact dr. Daniel Probst , daniel.probst@wur.nl or prof. Dick de Ridder, telephone +31 317 484074 or by e-mail, dick.deridder@wur.nl.

For more information about the procedure, please contact Noorien Abbas, corporate recruiter, vacaturemeldingen.psg@wur.nl