School of Computing Science

Staff Profiles

Dr Martin Sim

Research Associate

Background

Research Background

I am a Research Associate within the ICOS group of the School of Computing Science. I am based mainly in the Centre for Bacterial Cell Biology (CBCB) for my wet-lab work, supervised by Prof. Anil Wipat.

I was previously a PhD student of Dr. Phillip Aldridge and Dr. Colin Gilliespie (Newcastle University) for my thesis "The Abundance and Localisation of Flagella in Salmonella enterica and Escherichia coli". This combined the development of a continuous culture experimental system, fluorescence microscopy and image analysis.

I have also worked at a post-doctoral level in the medical diagnostics industry.

Research news:

April 2016 - I am an advisor for the Newcastle University 2016 iGEM team (http://2016.igem.org/Team:Newcastle/)

July 2015 - I was awarded a prize for the joint best poster presented at the Centre for Bacterial Cell Biology 2015 Symposium

Research

My current research is centred around the Newcastle University Frontiers in Engineering Biology (NUFEB) project where I am a member of the Synthetic Biology team. For this I am investigating the degradation of Estrogen by environmental microbes in municipal wastewater treatment plants. I shall be applying a synthetic biology approach to engineer model organisms and bacterial communities to improve the efficiency of synthetic Estrogen degradation.

This will involve the use of cutting edge cloning strategies, most specifically CRISPR-Cas9 genome editing. I am also carrying out evolution guided optimisation of degradation pathways, Next-Generation Sequencing, fluorescence microscopy and microfluidics. I am also expanding my knowledge of computer programming by learning the Python language. I am also involved in a trial of the MinION miniature sequencing device.

I have recently began working alongside Dr Dana Ofiteru in the School of Chemical Engineering and Advanced Materials (CEAM) examining the growth of bacterial cultures in mid-size bioreactors.

Teaching

Along with Prof. Anil Wipat and Dr Wendy Smith, I supervise students working in - or visiting - our wet-lab in the CBCB. I am currently co-supervising Computing Science MSc students within our wet-lab, working on the NUFEB research project.

Current PhD students supervised (along with Prof. Wipat):

Ms Valeria Verrone

Previous MSc students:

Mr Michael Martin (2016)

Ms Zelda Mendelowitz (2015)

Publications