About

Hi and thanks for visiting my homepage.

My name is Nico and I currently work as a bioinformatician/chemoinformatician/ontologist at the Department of Genetics at the University of Cambridge and also at the European Bioinformatics Institute. I didn’t start out working in informatics though – for the first 10 years or so of my scientific career, I have been a practising chemist. It all started with a chemistry kit, that was given to me by my parents on my 8th birthday and got somewhat more serious when I started to study chemistry at the University of York. While at York, I took a year out to go and get some industrial experience at DSM in the Netherlands, where I was first exposed to organometallic chemistry as well as combinatorial and high-throughput experimentation in chemistry and carried out research to develop early transition metal catalysts for olefin polymerisation. After completing my degree at York and a short stint as a research chemist at Cambridge Combinatorial (now Millennium Pharmaceuticals), this theme of research continued when I joined the laboratory of Prof Philip Mountford at the University of Oxford. There the emphasis was still on transition metal catalysis, but more developing synthetic technologies to make incredibly fragile transition metal compounds, that were nevertheless amenable to being carried out in a high-throughput way. I ended up making about 120 compounds and after having spent the next two months manually analysing 300 NMR spectra and 200 mass spectra, it didn’t take much to realise that informatics tools were needed to support this type of experimentation.

As a next step, therefore, I moved to the University of Eindhoven and the laboratory or Prof Ulrich Schubert, who, at the time was developing a large high-throughput polymer synthesis, characterisation and screening laboratory and who had also recognized, that informatics would be an essential component of this. While at Eindhoven, I spent the next three years trying to make informatics solutions, originally developed for small organic molecules and medicinal chemistry purposes work for materials science and polymers, only to realise, that, for a whole number of reasons, this was a pretty futile effort and that polymers and other materials demand their own solutions.

The opportunity to start building these solutions subsequently arose at the Unilever Centre for Molecular Science Informatics in the group of Prof Peter Murray-Rust. While in Peter’s group, we developed Polymer Markup Language (PML) as an extension to CML. A further consequence of PML was the Cambridge Polymer Builder, which takes PML specifications and elaborates them into molecular representations of macromolecules. This also led to my interest on ontologies and knowledge representation: many physicochemical properties of polymers are dependent on their history and provenance and not only on their chemical structure – and ontology can help to encode relevant knowledge about this.

The best things in science happen over dinner – so when an old friend who is an immunologist and clinician specialising in Primary Immunodeficiency Diseases came to visit, we talked about each other’s work and noticed that ontologies also be of great help when attempting to diagnose patients with these diseases and to facilitate other types of research. So we started to develop ontologies and applications around several immunological questions and i particular, the ontology of Primary Immunodeficiency Diseases, together with an application leverage the ontology. This work currently takes up pretty much allof my spare and evening time, but I am really excited by it. We are gearing up to talk about this soon in greater detail, so keep checking the website. In the meantime, here’s a sneak preview of what we are doing.

Links

Research papers by Nico Adams


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