Staff profile

I have worked as a bioinformatician for 21 years and have 10 years of experience of analysing next generation sequencing data. I re-joined the Department of Biosciences in 2019. I manage the Bioinformatics Facility and teach BIOL40715: Bioinformatics and Data Science and BIOL50315: Bioinformatics. I supervise students working on DATA40345: Data Science Research Project and  BIOL4121: Research Project (MBiol).

• Analysis of next generation sequencing data
• Application of bioinformatics to biological research
• Application of bioinformatics to biomedical research

• 2000: Over 100 peer-reviewed journal papers:
• 2000: h-index 45:

Journal Article

• Plant Direct MDF Regulates a Network of Auxin-Dependent and Auxin-Independent Pathways of Adventitious Root Regeneration in Arabidopsis
  
  Aldowigh, F., Matus, R., Agneessens, J., Gao, H., Wei, W., Topping, J., & Lindsey, K. (2025). Plant Direct MDF Regulates a Network of Auxin-Dependent and Auxin-Independent Pathways of Adventitious Root Regeneration in Arabidopsis. Plant Direct, 9(4), Article e70050. https://doi.org/10.1002/pld3.70050
• Evaluation of the Leishmania inositol phosphorylceramide synthase as a drug target using a chemical and genetic approach
  
  Alpizar-Sosa, E. A., Zimbres, F. M., Mantilla, B. S., Dickie, E. A., Wei, W., Burle-Caldas, G. A., Filipe, L. N., Van Bocxlaer, K., Price, H. P., Ibarra-Meneses, A. V., Beaudry, F., Fernandez-Prada, C., Whitfield, P. D., Barrett, M. P., & Denny, P. W. (2024). Evaluation of the Leishmania inositol phosphorylceramide synthase as a drug target using a chemical and genetic approach. ACS Infectious Diseases, 10(8), 2913–2928. https://doi.org/10.1021/acsinfecdis.4c00284
• The major inducible small heat shock protein HSP20-3 in the tardigrade Ramazzottius varieornatus forms filament-like structures and is an active chaperone.
  
  Al-Ansari, M., Fitzsimons, T., Wei, W., Goldberg, M. W., Kunieda, T., & Quinlan, R. A. (2024). The major inducible small heat shock protein HSP20-3 in the tardigrade Ramazzottius varieornatus forms filament-like structures and is an active chaperone. Cell Stress and Chaperones, 29(1), 51-65. https://doi.org/10.1016/j.cstres.2023.12.001
• The Oncogenic Lipid Sphingosine-1-Phosphate Impedes the Phagocytosis of Tumor Cells by M1 Macrophages in Diffuse Large B Cell Lymphoma
  
  Perry, T. A., Masand, N., Vrzalikova, K., Pugh, M., Wei, W., Hollows, R., Bouchalova, K., Nohtani, M., Fennell, E., Bouchal, J., Kearns, P., & Murray, P. G. (2024). The Oncogenic Lipid Sphingosine-1-Phosphate Impedes the Phagocytosis of Tumor Cells by M1 Macrophages in Diffuse Large B Cell Lymphoma. Cancers, 16(3), Article 574. https://doi.org/10.3390/cancers16030574
• Impact of the Physical Cellular Microenvironment on the Structure and Function of a Model Hepatocyte Cell Line for Drug Toxicity Applications
  
  Allcock, B., Wei, W., Goncalves, K., Hoyle, H., Robert, A., Quelch-Cliffe, R., Hayward, A., Cooper, J., & Przyborski, S. (2023). Impact of the Physical Cellular Microenvironment on the Structure and Function of a Model Hepatocyte Cell Line for Drug Toxicity Applications. Cells, 12(19), Article 2408. https://doi.org/10.3390/cells12192408
• Inheritance of seed weight and growth habit in 10 intercross chickpea (Cicer arietinum) nested association mapping populations
  
  Lakmes, A., Jhar, A., Penmetsa, R. V., Wei, W., Brennan, A. C., & Kahriman, A. (2023). Inheritance of seed weight and growth habit in 10 intercross chickpea (Cicer arietinum) nested association mapping populations. Plant Breeding, 142(1), 86-96. https://doi.org/10.1111/pbr.13065
• Transcriptome-Wide Identification of Coding and Noncoding RNA-Binding Proteins Defines the Comprehensive RNA Interactome of Leishmania mexicana
  
  Kalesh, K., Wei, W., Mantilla, B., Roumeliotis, T., Choudhary, J., & Denny, P. (2022). Transcriptome-Wide Identification of Coding and Noncoding RNA-Binding Proteins Defines the Comprehensive RNA Interactome of Leishmania mexicana. Microbiology Spectrum, 10(1), Article e0242221. https://doi.org/10.1128/spectrum.02422-21
• The Quantitative Genetics of Flowering Traits in Wide Crosses of Chickpea
  
  Lakmes, A., Jhar, A., Penmetsa, R., Wei, W., Brennan, A., & Kahriman, A. (2022). The Quantitative Genetics of Flowering Traits in Wide Crosses of Chickpea. Agriculture, 12(4), Article 486. https://doi.org/10.3390/agriculture12040486
• GCH1 Deficiency Activates Brain Innate Immune Response and Impairs Tyrosine Hydroxylase Homeostasis
  
  Larbalestier, H., Keatinge, M., Watson, L., White, E., Gowda, S., Wei, W., Koler, K., Semenova, S., Elkin, A., Rimmer, N., Sweeney, S., Mazzolini, J., Sieger, D., Hide, W., McDearmid, J., Panula, P., MacDonald, R., & Bandmann, O. (2022). GCH1 Deficiency Activates Brain Innate Immune Response and Impairs Tyrosine Hydroxylase Homeostasis. Journal of Neuroscience, 42(4), 702-716. https://doi.org/10.1523/jneurosci.0653-21.2021
• Genome deletions to overcome the directed loss of gene function in Leishmania
  
  Alpizar-Sosa, E., Kumordzi, Y., Wei, W., Whitfield, P., Barrett, M., & Denny, P. (2022). Genome deletions to overcome the directed loss of gene function in Leishmania. Frontiers in Cellular and Infection Microbiology, Section Parasite and Host, 12. https://doi.org/10.3389/fcimb.2022.988688
• Amphotericin B resistance in Leishmania mexicana: Alterations to sterol metabolism and oxidative stress response
  
  Alpizer-Sosa, E., Ithnin, N., Wei, W., Pountain, A., Weidt, A., Donachie, A., Ritchie, R., Dickie, E., Burchmore, R., Denny, P., & Barrett, M. (2022). Amphotericin B resistance in Leishmania mexicana: Alterations to sterol metabolism and oxidative stress response. PLOS Neglected Tropical Diseases, 16(9), Article e0010779. https://doi.org/10.1371/journal.pntd.0010779
• ALS-linked cytoplasmic FUS assemblies are compositionally different from physiological stress granules and sequester hnRNPA3, a novel modifier of FUS toxicity
  
  An, H., Litscher, G., Watanabe, N., Wei, W., Hashimoto, T., Iwatsubo, T., Buchman, V. L., & Shelkovnikova, T. A. (2022). ALS-linked cytoplasmic FUS assemblies are compositionally different from physiological stress granules and sequester hnRNPA3, a novel modifier of FUS toxicity. Neurobiology of Disease, 162, Article 105585. https://doi.org/10.1016/j.nbd.2021.105585
• Antileishmanial Chemotherapy through Clemastine Fumarate Mediated Inhibition of the Leishmania Inositol Phosphorylceramide Synthase
  
  Mina, J. G., Charlton, R. L., Alpizar-Sosa, E., Escrivani, D. O., Brown, C., Alqaisi, A., Borsodi, M. P. G., Figueiredo, C. P., de Lima, E. V., Dickie, E. A., Wei, W., Coutinho-Silva, R., Merritt, A., Smith, T. K., Barrett, M. P., Rossi-Bergmann, B., Denny, P. W., & Steel, P. G. (2021). Antileishmanial Chemotherapy through Clemastine Fumarate Mediated Inhibition of the Leishmania Inositol Phosphorylceramide Synthase. ACS Infectious Diseases, 7(1), 47-63. https://doi.org/10.1021/acsinfecdis.0c00546
• Meta-Analysis of the Alzheimer’s Disease Human Brain Transcriptome and Functional Dissection in Mouse Models
  
  Wan, Y.-W., Al-Ouran, R., Mangleburg, C. G., Perumal, T. M., Lee, T. V., Allison, K., Swarup, V., Funk, C. C., Gaiteri, C., Allen, M., Wang, M., Neuner, S. M., Kaczorowski, C. C., Philip, V. M., Howell, G. R., Martini-Stoica, H., Zheng, H., Mei, H., Zhong, X., … Logsdon, B. A. (2020). Meta-Analysis of the Alzheimer’s Disease Human Brain Transcriptome and Functional Dissection in Mouse Models. Cell Reports, 32(2), Article 107908. https://doi.org/10.1016/j.celrep.2020.107908
• CD40L membrane retention enhances the immunostimulatory effects of CD40 ligation
  
  Elmetwali, T., Salman, A., Wei, W., Hussain, S. A., Young, L. S., & Palmer, D. H. (2020). CD40L membrane retention enhances the immunostimulatory effects of CD40 ligation. Scientific Reports, 10(1). https://doi.org/10.1038/s41598-019-57293-y
• Long non-coding RNA Neat1 regulates adaptive behavioural response to stress in mice
  
  Kukharsky, M. S., Ninkina, N. N., An, H., Telezhkin, V., Wei, W., Meritens, C. R. de, Cooper-Knock, J., Nakagawa, S., Hirose, T., Buchman, V. L., & Shelkovnikova, T. A. (2020). Long non-coding RNA Neat1 regulates adaptive behavioural response to stress in mice. Translational Psychiatry, 10(1), Article 171. https://doi.org/10.1038/s41398-020-0854-2
• Vesicle transport in plants: A revised phylogeny of SNARE proteins
  
  Gu, X., Brennan, A., Wei, W., Guo, G., & Lindsey, K. (2020). Vesicle transport in plants: A revised phylogeny of SNARE proteins. Evolutionary Bioinformatics, 16, 1-11. https://doi.org/10.1177/1176934320956575
• Immune landscape in Burkitt lymphoma reveals M2-macrophage polarization and correlation between PD-L1 expression and non-canonical EBV latency program
  
  Granai, M., Mundo, L., Akarca, A. U., Siciliano, M. C., Rizvi, H., Mancini, V., Onyango, N., Nyagol, J., Abinya, N. O., Maha, I., Margielewska, S., Wei, W., Bibas, M., Piccaluga, P. P., Quintanilla-Martinez, L., Fend, F., Lazzi, S., Leoncini, L., & Marafioti, T. (2020). Immune landscape in Burkitt lymphoma reveals M2-macrophage polarization and correlation between PD-L1 expression and non-canonical EBV latency program. Infectious Agents and Cancer, 15(1), Article 28. https://doi.org/10.1186/s13027-020-00292-w
• Collagen Induces a More Proliferative, Migratory and Chemoresistant Phenotype in Head and Neck Cancer via DDR1
  
  Lai, S. L., Tan, M. L., Hollows, R. J., Robinson, M., Ibrahim, M., Margielewska, S., Parkinson, E. K., Ramanathan, A., Zain, R. B., Mehanna, H., Spruce, R. J., Wei, W., Chung, I., Murray, P. G., Yap, L. F., & Paterson, I. C. (2019). Collagen Induces a More Proliferative, Migratory and Chemoresistant Phenotype in Head and Neck Cancer via DDR1. Cancers, 11(11). https://doi.org/10.3390/cancers11111766