Katherine James

About

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.

Education

• BSc Molecular Biology
• MRes Bioinformatics
• Ph.D. Computing Science, BBSRC Centre for the Integrative Systems Biology of Ageing and Nutrition (CISBAN)

Selected publications

• Burridge M, Ou Z, James K, Buldum G, Lim J, Finnigan J, Charnock S, Wipat A. ro-crate-rs: Development of a Lightweight RO-Crate Rust Library for Automated Synthetic Biology. bioRxiv 2026. Submitted.
• Crowther, M, Metcalfe, B, Suarez, C, Corrales, DC, Lagos, JAA, Wipat, A, Rudge, TJ, James, K, Koehorst, JJ. LEAF: Lightweight equipment adapter framework. Open Research Europe 2026, 6(210). Submitted.
• Ou Z, James K, Charnock S, Wipat A. Bi-level diversity optimisation for representative protein panel selection. bioRxiv 2026. Submitted.
• Thiery AP, Martin KJ, James K, Cooper RL, Standing ASI, Dillard WA, Howitt C, Nicklin EF, Cohen KE, Byrum SR, Johanson Z, Fraser GJ. Shark tooth regeneration: RNAseq reveals genes for unlimited dental renewal. bioRxiv 2026. Submitted.
• Siachisumo C, Luzzi S, Aldalaqan S, Hysenaj G, Dalgliesh C, Cheung K, Gazzara M, Yonchev ID, James K, Kheirollahi Chadegani M, Ehrmann I, Smith GR, Cockell SJ, Munkley J, Barash Y, Wilson SA, Elliott DJ. An anciently diverged family of RNA binding proteins maintain correct splicing of a class of ultra-long exons through cryptic splice site repression. eLife 2024, 12, RP89705.
• Atallah C, James K, Ou Z, Skelton J, Markham D, Burridge MS, Finnigan J, Charnock S, Wipat A. A method for the systematic selection of enzyme panel candidates by solving the maximum diversity problem. BioSystems 2024, 236, 105105.
• Papaiakovou M, Fraija-Fernández N, James K, Briscoe AG, Halla A, Jenkins TP, Dunn J, Levecke B, Mekonnen Z, Cools P, Doyle SR, Cantacessi C, Littlewood DTJ. Evaluation of genome skimming to detect and characterise human and livestock helminths. International Journal for Parasitology 2023, 53(2), 69-79.
• James K, Alsobhe A, Cockell SJ, Wipat A, Pocock M. Integration of probabilistic functional networks without an external Gold Standard. BMC Bioinformatics 2022, 23, 302.
• Mlslrll G, Yang B, James K, Wipat A. Virtual Parts Repository 2: Model-Driven Design of Genetic Regulatory Circuits. ACS Synthetic Biology 2021, 10(12), 3304-3315.
• James K, Olson P. The tapeworm interactome: inferring confidence scored protein-protein interactions from the proteome of Hymenolepis microstoma. BMC Genomics 2020, 21(1), 346.