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Dr Katherine James

VC Senior Fellow

Department: Applied Sciences

Dr Katherine James is Vice Chancellors Fellow in Bioinformatics.

Katherine James

Research Themes and Scholarly Interests

My research focuses on the analysis and systematic integration of largescale omics and sequence data in order to characterise highly complex cellular systems and generate novel, testable hypotheses.  My current projects involve approaches to the analysis of sequence data with a focus on wildlife transcriptomics, wildlife and environmental metagenomics, and the development of probabilistic functional integrated networks for comparative interactomics in bacteria and non-model eukaryotes.

Key Publications

  • Please visit the Pure Research Information Portal for further information
  • High intrinsic hydrolytic activity of cyanobacterial RNA polymerase compensates for the absence of transcription proofreading factors, Riaz-Bradley, A., James, K., Yuzenkova, Y. 20 Feb 2020, In: Nucleic Acids Research
  • Single-peptide DNA-dependent RNA polymerase homologous to multi-subunit RNA polymerase, Forrest, D., James, K., Yuzenkova, Y., Zenkin, N. 6 Jun 2017, In: Nature Communications
  • Deep sequencing approaches for the analysis of prokaryotic transcriptional boundaries and dynamics, James, K., Cockell, S., Zenkin, N. 1 May 2017, In: Methods
  • Misincorporation by RNA polymerase is a major source of transcription pausing in vivo, James, K., Gamba, P., Cockell, S., Zenkin, N. 1 Feb 2017, In: Nucleic Acids Research

Professional Activity

Further Information

PGR co-supervision (based at Newcastle University):

  • Aoesha Alsobhe Probabilistic functional integrated networks for drug repurposing. Start Date: September 2019
  • Hanin Alzahrani Using quality metrics for interactive visualization of biological networks. Start Date: March 2021

Latest preprinted works:

  • Katherine James, Anil Wipat, Simon J. Cockell (2021). Expanding interactome analyses beyond model eukaryotes. 
  • Katherine James, Aoesha Alsobhe, Simon J. Cockell, Anil Wipat, Matthew Pocock (2021). Integration of probabilistic functional networks without an external Gold Standard. bioRxiv:
  • Göksel Mısırlı, Bill Yang, Katherine James, Anil Wipat (2021). Virtual Parts Repository 2: Model-driven design of genetic regulatory circuits. bioRxiv:
  • Sara Luzzi, Gerald Hysenaj, Chileleko Siachisumo, Kathleen Cheung, Matthew Gazzara, Katherine James, Caroline Dalgliesh, Mahsa Kheirollahi Chadegani, Ingrid Ehrmann, Graham R Smith, Simon J Cockell, Jennifer Munkley, Yoseph Barash, David J Elliott (2020). RBMX enables productive RNA processing of ultra-long exons important for genome stability. bioRxiv: 
  • David J. Skelton, Aoesha Alsobhe, Elisa Anastasi, Christian Atallah, Jasmine E. Bird, Bradley Brown, Dwayne Didon, Phoenix Gater, Katherine James, David D. Lennon Jr, James McLaughlin, Pollyanna E. J. Moreland, Matthew Pocock, Caroline J. Whitaker, Anil Wipat (2020).  Drug repurposing prediction for COVID-19 using probabilistic networks and crowdsourced curation. arXiv: arXiv:2005.11088v2


  • Computer Science PhD July 31 2011
  • Bioinformatics MRes September 01 2006

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