Staff Profile

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.

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

• Articles

  • 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.
  • 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. The gene-rich genome of the scallop Pecten maximus. GigaScience 2020, 9(5).
  • Riaz-Bradley A, James K, Yuzenkova Y. High intrinsic hydrolytic activity of cyanobacterial RNA polymerase compensates for the absence of transcription proofreading factors. 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. Complete representation of a tapeworm genome reveals chromosomes capped by centromeres, necessitating a dual role in segregation and protection. 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. Capturing Multicellular System Designs Using Synthetic Biology Open Language (SBOL). ACS Synthetic Biology 2020, 9(9), 2410-2417.
  • Johanson Z, Martin K, Fraser G, James K. The synarcual of the Little Skate, Leucoraja erinacea: novel development among the vertebrates. 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. Symptom-based stratification of patients with primary Sjögren's syndrome: multi-dimensional characterisation of international observational cohorts and reanalyses of randomised clinical trials. 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. An ancient germ cell-specific RNA-binding protein protects the germline from cryptic splice site poisoning. 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. Comparison of ESSDAI and ClinESSDAI in potential optimisation of trial outcomes in primary Sjögren's syndrome: Examination of data from the UK Primary Sjögren's Syndrome Registry. 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. B-cell activity markers are associated with different disease activity domains in primary Sjögren's syndrome. 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. Androgen-dependent alternative mRNA isoform expression in prostate cancer cells. F1000 Research 2018, 7(7), 1189.
  • Forrest D, James K, Yuzenkova Y, Zenkin N. Single-peptide DNA-dependent RNA polymerase homologous to multi-subunit RNA polymerase. Nature Communications 2017, 8, 15774.
  • James K, Gamba P, Cockell SJ, Zenkin N. Misincorporation by RNA polymerase is a major source of transcription pausing in vivo. Nucleic Acids Research 2017, 45(3), 1105-1113.
  • James K, Cockell SJ, Zenkin N. Deep sequencing approaches for the analysis of prokaryotic transcriptional boundaries and dynamics. 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. Glycosylation is an Androgen-Regulated Process Essential for Prostate Cancer Cell Viability. 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. Eligibility for clinical trials in primary Sjogren's syndrome: lessons from the UK Primary Sjogren's Syndrome Registry. 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. A Transcriptional Signature of Fatigue Derived from Patients with Primary Sjögren’s Syndrome. PLoS ONE 2015, 10(12), e0143970.
  • Misirli G, Wipat A, Mullen J, James K, Pocock M, Smith W, Allenby N, Hallinan J. BacillOndex: An Integrated Data Resource for Systems and Synthetic Biology. Journal of Integrative Bioinformatics 2013, 10(2), 224.
  • James K, Wipat A, Hallinan J. Is newer better?-evaluating the effects of data curation on integrated analyses in Saccharomyces cerevisiae. Integrative Biology 2012, 4(7), 715-727.
  • Weile J, James K, Hallinan J, Cockell SJ, Lord P, Wipat A, Wilkinson DJ. Bayesian integration of networks without gold standards. Bioinformatics 2012, 28(11), 1495-1500.
  • Lister AL, Charoensawan V, De S, James K, Chandra JSC, Huppert J. Interfacing systems biology and synthetic biology. 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. Automatic Diverse Subset Selection From Enzyme Families by Solving the Maximum Diversity Problem. In: 2022 IEEE Conference on Computational Intelligence in Bioinformatics and Computational Biology (CIBCB). 2022, Ottawa, ON, Canada: IEEE.
  • 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. Eligibility for Clinical Trials in Primary Sjogren's Syndrome: Lessons from the UK Primary Sjogren's Registry. In: Rheumatology 2015. 2015, Manchester, UK: Oxford University Press.
  • James K, Wipat A, Hallinan J. Integration of full-coverage probabilistic functional networks with relevance to specific biological processes. In: Data Integration in the Life Sciences: 6th International Workshop (DILS). 2009, Manchester, UK: Springer.

• Reviews

  • James K, Wipat A, Cockell SJ. Expanding Interactome Analyses beyond Model Eukaryotes. Briefings in Functional Genomics 2022, 21(4), 243-269.
  • James K, Munoz-Munoz J. Computational Network Inference for Bacterial Interactomics. mSystems 2022, 7(2), e01456-21.
  • Gamba P, James K, Zenkin N. A link between transcription fidelity and pausing in vivo. Transcription 2017, 8(2), 99-105.
  • Best A, James K, Hysenaj G, Tyson-Capper A, Elliott DJ. Transformer2 proteins protect breast cancer cells from accumulating replication stress by ensuring productive splicing of checkpoint kinase 1. Frontiers of Chemical Science and Engineering 2016, 10(2), 186-195.
  • Hallinan JS, James K, Wipat A. Network Approaches to the Functional Analysis of Microbial Proteins. Advances in Microbial Physiology 2011, 59, 101-133.