缅北禁地

I am currently Lecturer in Synthetic Biology in the School of Computing at 缅北禁地. I am based in the .

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

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 缅北禁地 as a Lecturer in Synthetic Biology in 2021.

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.

I am the ELIXIR-UK representative for 缅北禁地.

Current projects:

• BioIndustry 4.0: RI services to promote deep digitalization of Industrial Biotechnology - towards smart biomanufacturing (HORIZON)

PhD students:

• Mingpei Li - Design and implementation of programmable environmental response-actuator systems using bacteria
• Zhen Ou - Development of high-throughput computational and automated workflows for efficient and systematic identification and characterization of diverse enzyme sets from a protein family
• Matthew Burridge - The development of new approaches for large-scale biocatalyst panel design and characterisation
• Alex Escasinas - Comparative interactomics for synthetic bacterial systems
• Theodore Quinlan - Identification and characterisation of ‘New-to-Nature’ enzymes

Previous students:

• Dr David Markham - Investigating Metabolic Burden and Stress Responses in Prokaryotic Model Organisms through an Integrated Computational and Synthetic Biology Approach (January 2025)

Degree Programme Director:

• MSc Bioinformatics
• MSc Advanced Computer Science

Module leader:

• CSC8313 Bioinformatics Theory and Practice 2023-26
• CSC8391 Research Project for Bioinformatics 2024-26

Lecturer:

• CSC8335 Computing Environments for Digital Biology 2025-26
• CSC8334 Contemporary Topics in Bioinformatics 2024-26

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

• Articles

  • 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 2025, 2025.08.26.672487. In Preparation.
  • 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. . eLife 2024, 12, RP89705.
  • Atallah C, James K, Ou Z, Skelton J, Markham D, Burridge MS, Finnigan J, Charnock S, Wipat A. . 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. . International Journal for Parasitology 2023, 53(2), 69-79.
  • James K, Alsobhe A, Cockell SJ, Wipat A, Pocock M. . BMC Bioinformatics 2022, 23, 302.
  • Mlslrll G, Yang B, James K, Wipat A. . ACS Synthetic Biology 2021, 10(12), 3304-3315.
  • James K, Olson P. . BMC Genomics 2020, 21(1), 346.
  • Kenny NJ, McCarthy SA, Dudchenko O, James K, Betteridge E, Corton C, Dolucan J, Mead D, Oliver K, Omer AD, Pelan S, Ryan Y, Sims Y, Skelton J, Smith M, Torrance J, Weisz D, Wipat A, Aiden EL, Howe K, Williams ST. . GigaScience 2020, 9(5).
  • Riaz-Bradley A, James K, Yuzenkova Y. . Nucleic Acids Research 2020, 48(3), 1341-1352.
  • Olson PD, Tracey A, Baillie A, James K, Doyle SR, Buddenborg SK, Rodgers FH, Holroyd N, Berriman M. . BMC Biology 2020, 18, 165.
  • Brown B, Bartley B, Beal J, Bird JE, Goni-Moreno A, McLaughlin JA, Misirli G, Roehner N, Skelton DJ, Poh CL, Ofiteru ID, James K, Wipat A. . ACS Synthetic Biology 2020, 9(9), 2410-2417.
  • Johanson Z, Martin K, Fraser G, James K. . Frontiers in Ecology and Evolution 2019, 7, 12.
  • Tarn JR, Howard-Tripp N, Lendrem DW, Mariette X, Saraux A, Devauchelle-Pensec V, Seror R, Skelton AJ, James K, McMeekin P, Al-Ali S, Hackett KL, Lendrem BC, Hargreaves B, Casement J, Mitchell S, Bowman SJ, Price E, Pease CT, Emery P, Lanyon P, Hunter J, Gupta M, Bombardieri M, Sutcliffe N, Pitzalis C, McLaren J, Cooper A, Regan M, Giles I, Isenberg D, Saravanan V, Coady D, Dasgupta B, McHugh N, Young-Min S, Moots R, Gendi N, Akil M, Griffiths B, Johnsen SJA, Norheim KB, Omdal R, Stocken D, Everett C, Fernandez C, Isaacs JD, Gottenberg J-E, Ng W-F. . The Lancet Rheumatology 2019, 1(2), e85-e94.
  • Ehrmann I, Crichton JH, Gazzara MR, James K, Liu Y, Grellscheid SN, Curk T, de Rooij D, Steyn JS, Cockell S, Adams IR, Barash Y, Elliott DJ. . eLife 2019, 8, e39304.
  • Dumusc A, Ng W-F, James K, Griffiths B, Price E, Pease CT, Emery P, Lanyon P, Jones A, Bombardieri M, Sutcliffe N, Pitzalis C, Gupta M, McLaren J, Cooper A, Giles I, Isenberg D, Saravanan V, Coady D, Dasgupta B, McHugh N, Young-Min S, Moots RJ, Gendi N, Akil M, Barone F, Fisher BA, Rauz S, Richards A, Bowman SJ, Frankland H, Mediana A, Chadravarty K, Lamabadusuriya S, Adeniba R, Hamburger J, Higham J, Poveda-Galego A, Logan J, Mulherin D, Andrews J, McManus A, Booth A, Regan M, Dimitroulas T, Kadiki L, Kaur D, Kitas G, Lloyd M, Moore L, Gordon E, Lawson C, Hunter J, Stirton L, Ortiz G, Clunie G, Rose G, Cuckow S, Knight S, Symmons D, Jones B, Carr A, Edgar S, Carrozzo M, Figueiredo F, Foggo H, Gillespie C, Hindmarsh V, Lendrem D, Macleod I, Mitchell S, Tarn J, Muir A, White P, Pugmire S, Watkins M, Field A, Kaye S, Mewar D, Medcalf P, Tomlinson P, Whiteside D, Pauling J, James J, Olaitan N, McDermott J, Godia O, Kidd E, Palmer L, Katsande V, Long P, Chandra U, MacKay K, Fedele S, Ferenkeh-Koroma A, Marconnell H, Porter S, Brailsford S, Allcoat P. . Swiss Medical Weekly 2018, 148, w14588.
  • James K, Chipeta C, Parker A, Harding S, Cockell SJ, Gillespie CS, Hallinan J, Barone F, Bowman SJ, Ng W-F, Fisher BA, for the UK Primary Sjögren's Syndrome Registry. . Rheumatology 2018, 57(7), 1222-1227.
  • Munkley J, Maia TM, Ibarluzea N, Livermore KE, Vodak D, Ehrmann I, James K, Rajan P, Barbosa-Morais NL, Elliott DJ. . F1000 Research 2018, 7(7), 1189.
  • Forrest D, James K, Yuzenkova Y, Zenkin N. . Nature Communications 2017, 8, 15774.
  • James K, Gamba P, Cockell SJ, Zenkin N. . Nucleic Acids Research 2017, 45(3), 1105-1113.
  • James K, Cockell SJ, Zenkin N. . Methods 2017, 120, 76-84.
  • Munkley J, Vodak D, Livermore KE, James K, Wilson BT, Knight B, Mccullagh P, Mcgrath J, Crundwell M, Harries LW, Leung HY, Robson CN, Mills IG, Rajan P, Elliott DJ. . eBioMedicine 2016, 8, 103-116.
  • Oni C, Mitchell S, James K, Ng WF, Griffiths B, Hindmarsh V, Prices E, Pease CT, Emery P, Lanyon P, Jones A, Bombardieri M, Sutcliffe N, Pitzalis C, Hunter J, Gupta M, McLaren J, Cooper A, Regan M, Giles I, Isenberg D, Saravanan V, Coady D, Dasgupta B, McHugh N, Young-Min S, Moots R, Gendi N, Akil M, Barone F, Fisher B, Rauz S, Richards A, Bowman SJ, UK Primary Sjogren's Syndrome. . Rheumatology 2016, 55(3), 544-552.
  • James K, Al-Ali S, Tarn J, Cockell SJ, Gillespie CS, Hindmarsh V, Locke J, Mitchell S, Lendrem D, Bowman S, Price E, Pease CT, Emery P, Lanyon P, Hunter JA, Gupta M, Bombardieri M, Sutcliffe N, Pitzalis C, McLaren J, Cooper A, Regan M, Giles I, Isenberg D, Saravanan V, Coady D, Dasgupta B, McHugh N, Young-Min S, Moots R, Gendi N, Akil M, Griffiths B, The UK Primary Sjögren’s Syndrome registry, Wipat A, Newton J, Jones DE, Isaacs J, Hallinan J, Ng W-F. . PLoS ONE 2015, 10(12), e0143970.
  • Misirli G, Wipat A, Mullen J, James K, Pocock M, Smith W, Allenby N, Hallinan J. . Journal of Integrative Bioinformatics 2013, 10(2), 224.
  • James K, Wipat A, Hallinan J. . Integrative Biology 2012, 4(7), 715-727.
  • Weile J, James K, Hallinan J, Cockell SJ, Lord P, Wipat A, Wilkinson DJ. . Bioinformatics 2012, 28(11), 1495-1500.
  • Lister AL, Charoensawan V, De S, James K, Chandra JSC, Huppert J. . Genome Biology 2009, 10(309), 3.
  • Addinall SG, Downey M, Yu M, Zubko MK, Dewar J, Leake A, Hallinan J, Shaw O, James K, Wilkinson DJ, Wipat A, Durocher D, Lydall D. A Genomewide Suppressor and Enhancer Analysis of cdc13-1 Reveals Varied Cellular Processes Influencing Telomere Capping in Saccharomyces cerevisiae . Genetics 2008, 180, 2251–2266.
  • Greenall A, Lei G, Swan DC, James K, Wang L, Peters H, Wipat A, Wilkinson DJ, Lydall D. A genome wide analysis of the response to uncapped telomeres in budding yeast reveals a novel role for the NAD⁺ biosynthetic gene BNA2in chromosome end protection. Genome Biology 2008, 9, R146.

• Conference Proceedings (inc. Abstracts)

  • Atallah C, James K, Ou Z, Skelton J, Markham D, Finnigan J, Charnock S, Wipat A. . In: 2022 IEEE Conference on Computational Intelligence in Bioinformatics and Computational Biology (CIBCB). 2022, Ottawa, ON, Canada: IEEE.
  • Al-Ali S, Skelton A, Cockell S, Tarn J, James K, Bowman SJ, Griffiths B, Locke J, Young D, Ng WF, UKPSSR. . In: 13th International Symposium on Sjögren's Syndrome. 2015, Bergen, Norway: Wiley-Blackwell Publishing Ltd.
  • Cartlidge C, Bowman S, Ng WF, James K, Griffiths B, Price E, Prease C, Emery P, Andrews J, Lanyon P, Hunter J, Gupta M, Bombardieri M, Sutcliffe N, Pitzalis C, McLaren J, Cooper A, Regan M, Giles I, Isenberg DA, Saravanan V, Coady D, Dasgupta B, McHugh N, Young-Min S. . In: Rheumatology 2015. 2015, Manchester, UK: Oxford University Press.
  • Tarn J, Cockell S, Gillespie C, Al-Ali S, James K, Locke J, Bowman S, Griffiths B, Young D, Ng WF. . In: ACR/ARHP Annual Meeting. 2014, Boston, MA, USA: Wiley-Blackwell Publishing.
  • James K, Lendrem D, Mitchell S, Hindmarsh V, Bowman S, Price EJ, Pease CT, Emery P, Lanyon P, Hunter J, Gupta M, Bombardieri M, Sutcliffe N, Pitzalis C, McLaren J, Cooper A, Regan M, Giles IP, Isenberg DA, Vadivelu S, Coady D, Dasgupta B, McHugh N, Griffiths B, Ng WF. . In: Rheumatology 2014. 2014, Liverpool, UK: Oxford University Press.
  • James K, Tarn JR, Al-Ali S, Hallinan J, Young DA, Ng WF. . In: Rheumatology 2014. 2014, Liverpool, UK: Oxford University Press.
  • Al-Ali S, Cockell S, Skelton A, James K, Tarn J, Young D, Griffiths B, Bowman S, Locke J, Ng WF. . In: ACR/ARHP Annual Meeting. 2014, Boston, MA, USA: Wiley-Blackwell Publishing.
  • James K, Wipat A, Hallinan J. . In: Data Integration in the Life Sciences: 6th International Workshop (DILS). 2009, Manchester, UK: Springer.

• Reviews

  • James K, Wipat A, Cockell SJ. . Briefings in Functional Genomics 2022, 21(4), 243-269.
  • James K, Munoz-Munoz J. . mSystems 2022, 7(2), e01456-21.
  • Gamba P, James K, Zenkin N. . Transcription 2017, 8(2), 99-105.
  • Best A, James K, Hysenaj G, Tyson-Capper A, Elliott DJ. . Frontiers of Chemical Science and Engineering 2016, 10(2), 186-195.
  • Hallinan JS, James K, Wipat A. . Advances in Microbial Physiology 2011, 59, 101-133.