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Dong's research interests focus on understanding the molecular mechanisms of host-pathogen interactions using high-resolution approaches coupled to bioinformatics. He is interested in 'big data' analysis, where datasets generated from multiple omics platforms are integrated for system modelling.

Trained as an experimental biologist with hands-on mass spectrometer and bioinformatics skills, his work also contributes to the understanding of proteoforms, where splice variants and post translational modifications are experimentally and bioinformatically characterised followed by functional validations. The data generated also contribute to the next round of genome annotation as solid evidence of expression to improve gene model predictions.

Latest publications can be found at Google Scholar Page ()

Wu Y, Chang YM, Stell AJ, Priestnall SL, Sharma E, Goulart MR, Gribben J, Xia D, Garden OA

Sci Rep. 2019 Sep 17;9(1):13478. doi: 10.1038/s41598-019-50065-8

Goulart, M R; Hlavaty, S I; Chang, Y-M; Polton, G; Stell, A; Perry, J; Wu, Y; Sharma, E; Broxholme, J; Lee, A C; Szladovits, B; Turmaine, M; Gribben, J; Xia, D; Garden, O A.
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Scientific Reports (Nature), 9;1:3574. 2019

Dong, X; Chaisiri, K; Xia, D; Armstrong, S D; Fang, Y; Donnelly, M J; Kadowaki, T; McGarry, J W; Darby, A C; Makepeace, B L.
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GigaScience, 7;12:33. 2018

Shukla A, Olszewski KL, Llinás M, Rommereim LM, Fox BA, Bzik DJ, Xia D, Wastling J, Beiting D, Roos DS, Shanmugam D. (2018). "Glycolysis is important for optimal asexual growth and formation of mature tissue cysts by Toxoplasma gondii." Int J Parasitol. 2018 Oct;48(12):955-968. doi: 10.1016/j.ijpara.2018.05.013.

Horcajo P, Xia D, Randle N, Collantes-Fernández E, Wastling J, Ortega-Mora LM, Regidor-Cerrillo J. (2018). "Integrative transcriptome and proteome analyses define marked differences between Neosporacaninum isolates throughout the tachyzoite lytic cycle." J Proteomics. 2018 May 30;180:108-119. doi: 10.1016/j.jprot.2017.11.007.

Dubourg A, Xia D, Winpenny JP, Naimi SA, Bouzid M, Sexton DW, Wastling JM, Hunter PR, Tyler KM. (2017). "Giardia Secretome Highlights Secreted Tenascins as a Key Component of Pathogenesis" Gigascience. 2018 Jan 29. doi: 10.1093/gigascience/giy003

Dong, X., Armstrong, S. D., Xia, D., Makepeace, B. L., Darby, A. C., Kadowaki, T. (2017). "Draft genome of the honey bee ectoparasitic mite, Tropilaelaps mercedesae, is shaped by the parasitic life history." GigaScience doi: 10.1093/gigascience/gix008

Liu, X., E. Speranza, C. Muñoz-Fontela, S. Haldenby, N. Y. Rickett, I. Garcia-Dorival, Y. Fang, Y. Hall, E.-G. Zekeng and A. Lüdtke (2017). "Transcriptomic signatures differentiate survival from fatal outcomes in humans infected with Ebola virus." Genome Biology 18(1): 4.

Armstrong, S. D., D. Xia, G. S. Bah, R. Krishna, H. F. Ngangyung, E. J. LaCourse, H. J. McSorley, J. A. Kengne-Ouafo, P. W. Chounna-Ndongmo and S. Wanji (2016). "Stage-specific proteomes from Onchocerca ochengi, sister species of the human river blindness parasite, uncover adaptations to a nodular lifestyle." Molecular & Cellular Proteomics 15(8): 2554-2575.

Borgdorff, H., S. D. Armstrong, H. L. Tytgat, D. Xia, G. F. Ndayisaba, J. M. Wastling and J. H. van de Wijgert (2016). "Unique Insights in the Cervicovaginal Lactobacillus iners and L. crispatus Proteomes and Their Associations with Microbiota Dysbiosis." PloS one 11(3): e0150767.

Dong, S., L. Liu, W. Wu, S. D. Armstrong, D. Xia, H. Nan, J. A. Hiscox and H. Chen (2016). "Determination of the interactome of non-structural protein12 from highly pathogenic porcine reproductive and respiratory syndrome virus with host cellular proteins using high throughput proteomics and identification of HSP70 as a cellular factor for virus replication." Journal of Proteomics 146: 58-69.

Hunt, V. L., I. J. Tsai, A. Coghlan, A. J. Reid, N. Holroyd, B. J. Foth, A. Tracey, J. A. Cotton, E. J. Stanley and H. Beasley (2016). "The genomic basis of parasitism in the Strongyloides clade of nematodes." Nature genetics. 2016 Mar;48(3):299-307.

Wang, K., E. D. Peng, A. S. Huang, D. Xia, S. J. Vermont, G. Lentini, M. Lebrun, J. M. Wastling and P. J. Bradley (2016). "Identification of Novel O-Linked Glycosylated Toxoplasma Proteins by Vicia villosa Lectin Chromatography." PloS one 11(3): e0150561.

Xiao, Y., W. Wu, J. Gao, N. Smith, C. Burkard, D. Xia, M. Zhang, C. Wang, A. Archibald and P. Digard (2016). "Characterization of the Interactome of the Porcine Reproductive and Respiratory Syndrome Virus Nonstructural Protein 2 Reveals the Hyper Variable Region as a Binding Platform for Association with 14–3–3 Proteins." Journal of proteome research 15(5): 1388-1401.

Borgdorff, H., R. Gautam, S. Armstrong, D. Xia, G. Ndayisaba, N. van Teijlingen, T. Geijtenbeek, J. Wastling and J. van de Wijgert (2015). "Cervicovaginal microbiome dysbiosis is associated with proteome changes related to alterations of the cervicovaginal mucosal barrier." Mucosal immunology. 2016 May;9(3):621-33.

Dent, S. D., D. Xia, J. M. Wastling, B. W. Neuman, P. Britton and H. J. Maier (2015). "The proteome of the infectious bronchitis virus Beau-R virion." Journal of General Virology 96(12): 3499-3506.

Jackson, A. P., S. Goyard, D. Xia, B. J. Foth, M. Sanders, J. M. Wastling, P. Minoprio and M. Berriman (2015). "Global Gene Expression Profiling through the Complete Life Cycle of Trypanosoma vivax." PLoS Negl Trop Dis 9(8): e0003975.

Krishna, R., D. Xia, S. Sanderson, A. Shanmugasundram, S. Vermont, A. Bernal, G. Daniel-Naguib, F. Ghali, B. P. Brunk and D. S. Roos (2015). "A large-scale proteogenomics study of apicomplexan pathogens—Toxoplasma gondii and Neospora caninum." Proteomics 15(15): 2618-2628.

Armstrong, S. D., S. A. Babayan, N. Lhermitte-Vallarino, N. Gray, D. Xia, C. Martin, S. Kumar, D. W. Taylor, M. L. Blaxter and J. M. Wastling (2014). "Comparative analysis of the secretome from a model filarial nematode (Litomosoides sigmodontis) reveals maximal diversity in gravid female parasites." Molecular & Cellular Proteomics 13(10): 2527-2544.

Darby, A. C., A. C. Gill, S. D. Armstrong, C. S. Hartley, D. Xia, J. M. Wastling and B. L. Makepeace (2014). "Integrated transcriptomic and proteomic analysis of the global response of Wolbachia to doxycycline-induced stress." The ISME journal 8(4): 925-937.

Ghali, F., R. Krishna, S. Perkins, A. Collins, D. Xia, J. Wastling and A. R. Jones (2014). "ProteoAnnotator–Open source proteogenomics annotation software supporting PSI standards." Proteomics 14(23-24): 2731-2741.

Jackson, A. P., T. D. Otto, A. Darby, A. Ramaprasad, D. Xia, I. E. Echaide, M. Farber, S. Gahlot, J. Gamble and D. Gupta (2014). "The evolutionary dynamics of variant antigen genes in Babesia reveal a history of genomic innovation underlying host–parasite interaction." Nucleic acids research 42(11): 7113-7131.

Wiens, O., D. Xia, C. von Schubert, J. M. Wastling, D. A. Dobbelaere, V. T. Heussler and K. L. Woods (2014). "Cell cycle-dependent phosphorylation of Theileria annulata schizont surface proteins." PloS one 9(7): e103821.

Doliwa, C., D. Xia, S. Escotte-Binet, E. L. Newsham, D. Aubert, N. Randle, J. M. Wastling and I. Villena (2013). "Identification of differentially expressed proteins in sulfadiazine resistant and sensitive strains of Toxoplasma gondii using difference-gel electrophoresis (DIGE)." International Journal for Parasitology: Drugs and Drug Resistance 3: 35-44.

Wastling, J. and D. Xia (2013). Proteomics of Toxoplasma gondii, Toxoplasma gondii: The Model Apicomplexan-Perspectives and Methods: Second Edition. Amsterdam and Boston: Elsevier/Academic Press.

Witschi, M., D. Xia, S. Sanderson, M. Baumgartner, J. Wastling and D. Dobbelaere (2013). "Proteomic analysis of the Theileria annulata schizont." International journal for parasitology 43(2): 173-180.

Qi, D., P. Brownridge, D. Xia, K. Mackay, F. F. Gonzalez-Galarza, J. Kenyani, V. Harman, R. J. Beynon and A. R. Jones (2012). "A software toolkit and interface for performing stable isotope labeling and top3 quantification using Progenesis LC-MS." Omics: a journal of integrative biology 16(9): 489-495.

Wastling, J., S. Armstrong, R. Krishna and D. Xia (2012). "Parasites, proteomes and systems: has Descartes’ clock run out of time?" Parasitology 139(09): 1103-1118.

Xia, D., F. Ghali, S. J. Gaskell, R. O'Cualain, P. F. Sims and A. R. Jones (2012). "Software for analysing ion mobility mass spectrometry data to improve peptide identification." Proteomics 12(12): 1912-1916.

Sohn, C. S., T. T. Cheng, M. L. Drummond, E. D. Peng, S. J. Vermont, D. Xia, S. J. Cheng, J. M. Wastling and P. J. Bradley (2011). "Identification of novel proteins in Neospora caninum using an organelle purification and monoclonal antibody approach." PLoS One 6(4): e18383.

Wastling, J., D. Xia, A. Sohal, M. Chaussepied, A. Pain and G. Langsley (2009). "Proteomes and transcriptomes of the Apicomplexa–Where’s the message?" International journal for parasitology 39(2): 135-143.

Wu, Y., M. M. Nelson, A. Quaile, D. Xia, J. M. Wastling and A. Craig (2009). "Identification of phosphorylated proteins in erythrocytes infected by the human malaria parasite Plasmodium falciparum." Malaria journal 8(1): 105.

Sanderson, S. J., D. Xia, H. Prieto, J. Yates, M. Heiges, J. C. Kissinger, E. Bromley, K. Lal, R. E. Sinden and F. Tomley (2008). "Determining the protein repertoire of Cryptosporidium parvum sporozoites." Proteomics 8(7): 1398-1414.

Xia, D., S. J. Sanderson, A. R. Jones, J. H. Prieto, J. R. Yates, E. Bromley, F. M. Tomley, K. Lal, R. E. Sinden and B. P. Brunk (2008). "The proteome of Toxoplasma gondii: integration with the genome provides novel insights into gene expression and annotation." Genome biology 9(7): R116.

• Identification of novel druggable targets in canine insulinoma through single-cell transcriptomic analysis

  

  Insulinomas in dogs are difficult to cure by surgery. We investigate which genes are crucial for survival of insulinoma cells, allowing us to design new treatments targeted at these genes. Insulinomas are the most common pancreatic neuroendocrine tumours in dogs and humans. Current treatment options are limited to surgery and palliative medical therapy. Survival is poor with a median of 4 [range 0-18] months and 14 [range 0-51] months for medically and surgically treated dogs, respectively. Hence, new, more precise treatments are needed to improve the clinical outcome for dogs and humans with malignant insulinomas.

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• Machine learning algorithms for predicting drug resistance against tuberculosis in people

  

  Tuberculosis disease (TB), caused by Mycobacterium tuberculosis, is an important global public health issue, and its drug resistance, caused by genetic mutations in the M. tuberculosis genome, poses serious challenges for effective control. Current molecular diagnostic tests are imperfect as they do not target all resistance mechanisms and drugs, nor do they inform on transmission clusters, and are therefore unable to guide completely effective individualised therapy.

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• SweetAnimals

  

  The SweetAnimal project studies the presence of sugar-binding receptors in the genomes of a variety of farmed animals, how these differ between species, what ligands expressed on pathogens they bind, and how this information can be used to develop carbohydrate-based vaccines.

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• UK Research and Innovation (UKRI) Global Challenges Research Fund (GCRF) One Health Poultry Hub

  

  With integrated streams of social, economic, biological, mathematical and policy-led research, we are co-producing detailed knowledge on the biological, structural and socio-economic factors that shape networks of chicken production and distribution. The ºÚÁÏÉç-led UKRI GCRF One Health Poultry Hub brings together leading laboratory, clinical, veterinary and social scientists, as well as skilled communications experts, programme support staff and external stakeholders.  

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