Centre for Synthetic Biology and the Bioeconomy

Staff Profile

Dr Katherine James

Lecturer in Synthetic Biology

Background

I am currently Lecturer in Synthetic Biology in the School of Computing at Newcastle University. I am based in the Interdisciplinary Computing and Complex BioSystems research group.


My research focuses on computational systems biology and the systematic integration of largescale data in order to characterise highly complex cellular systems and generate novel, testable hypotheses. My work involves bacterial genomics, non-model transcriptomics and metagenomics, and the development of algorithms for comparative interactomics. My main research focus is in evolutionary network re-wiring in bacterial and non-model eukaryotes.


Area of expertise: Integrative Bioinformatics, Comparative Interactomics, Systems and Synthetic Biology


Bio


I have over fifteen years’ experience in research focusing on the systematic integration of largescale omics data into networks. Originally studying BSc Molecular Biology as an undergraduate, I went on to gain an MRes in Bioinformatics, and then Ph.D. in Computing Science based at the BBSRC Centre for the Integrative Systems Biology of Ageing and Nutrition (CISBAN). My thesis involved algorithm development for probabilistic functional integrated networks (PFINs). 


I joined the BBSRC Ondex project in 2011, where I continued to work on algorithm development for network integration, as well plugin development for the BacillOndex dataset. In 2015 I joined the Centre for Bacterial Cell Biology where I developed pipelines for the analysis of advanced transcriptomic datasets, such as dRNA-seq, Ribo-seq and Net-seq, to investigate the dynamics of transcription in bacteria. At the same time I applied integrated network theory to the study of human cancers in collaboration with the Centre for Life.


In 2017 I moved to the Natural History Museum London (NHM) as Bioinformatics Manager, where my work shifted to the application of advanced bioinformatic approaches in the analysis of non-model omics data, in particular helminths, bivalves and chondrichthyes. I then spent two years as Vice Chancellors Fellow in Microbial Bioinformatics at Northumbria University, before joining Newcastle as a Lecturer in Synthetic Biology in 2021.


Teaching

I am Degree Programme Director (DPD) for MSc Bioinformatics and Co-DPD for MSc Advanced Computer Science


Module leader:

CSC8313 Bioinformatics Theory and Practice 2023-25

CSC8334 Contemporary topics in Bioinformatics 2024-25



Previous

CSC8333 Research Skills and group project for digital biology 2023-24

CSC8325 An Introduction to Bioinformatics Theory and Practice 2022-23

CSC8326 Advanced Bioinformatics Theory and Practice 2022-23




Publications