Joseph Ng

Joseph Ng

All things bioinformatics, data analytics.

Publications

2023

  1. \underline+*J. C. F. Ng, Montamat Garcia, +G., Stewart, +A. T., Blair, P., Mauri, C., Dunn-Walters, D. K., & Fraternali, *F. (2023). sciCSR infers B cell state transition and predicts class-switch recombination dynamics using single-cell transcriptomic data. Nature Methods. https://doi.org/10.1038/s41592-023-02060-1
  2. Crescioli, S., Correa, I., Ng, J., Willsmore, Z. N., Laddach, R., Chenoweth, A., Chauhan, J., Di Meo, A., Stewart, A., Kalliolia, E., Alberts, E., Adams, R., Harris, R. J., Mele, S., Pellizzari, G., Black, A. B. M., Bax, H. J., Cheung, A., Nakamura, M., … Karagiannis, S. N. (2023). B cell profiles, antibody repertoire and reactivity reveal dysregulated responses with autoimmune features in melanoma. Nature Communications, 14(1), 3378. https://doi.org/10.1038/s41467-023-39042-y
  3. Mallaby, J., Mwangi, W., \underlineJ. Ng, Stewart, A., Dorey-Robinson, D., Kipling, D., Hershberg, U., Fraternali, F., Nair, V., & Dunn-Walters, D. (2023). Diversification of Immunoglobulin genes by Gene Conversion in the Domestic Chicken (Gallus gallus domesticus). Discovery Immunology. https://doi.org/10.1093/discim/kyad002

2022

  1. Stewart, +A., Sinclair, +E., +\underlineJ. Ng, O’Hare, J. S., Page, A., Serangeli, I., Margreitter, C., Kasar, N., Longman, K., Frampas, C., Costa, C., Lewis, H., Wu, B., Kipling, D., Openshaw, P., Chu, C., Baillie, J. K., Scott, J. T., Semple, M. G., … Dunn-Walters, D. (2022). Pandemic, Epidemic, Endemic: B Cell Repertoire Analysis Reveals Unique Anti-Viral Responses to SARS-CoV-2, Ebola and Respiratory Syncytial Virus. Front Immunol, 13, 807104.
  2. Guo, D., Ng, J. C. F., Dunn-Walters, D., & Fraternali, F. (2022). VCAb: An accurate and queryable database of isotype annotation for human antibody structures.
  3. Ng, J. C. F., & Fraternali, F. (2022). The “dark matter” of protein variants carries a distinct DNA signature and predicts damaging variant effects. BioRxiv. https://doi.org/10.1101/2021.05.27.445950

2021

  1. Harris, R. J., Cheung, A., Ng, J. C. F., Laddach, R., Chenoweth, A. M., Crescioli, S., Fittall, M., Dominguez Rodriguez, D., Roberts, J., Levi, D., Liu, F., Alberts, E., Quist, J., Santaolalla, A., Pinder, S. E., Gillett, C., Hammar, N., Irshad, S., Van Hemelrijck, M., … Karagiannis, S. N. (2021). Tumor-Infiltrating B Lymphocyte Profiling Identifies IgG-Biased, Clonally Expanded Prognostic Phenotypes In Triple-Negative Breast Cancer. Cancer Res.
  2. Onoufriadis, A., Cabezas, A., Ng, J. C. F., Canales, J., Costas, M. J., Ribeiro, J. M., Rodrigues, J. R., McAleer, M. A., Castelo-Soccio, L., Simpson, M. A., Fraternali, F., Irvine, A. D., Cameselle, J. C., & McGrath, J. A. (2021). Autosomal recessive hypotrichosis with loose anagen hairs associated with TKFC mutations. Br J Dermatol, 184(5), 935–943.
  3. Laddach, A., Ng, J. C. F., & Fraternali, F. (2021). Pathogenic missense protein variants affect different functional pathways and proteomic features than healthy population variants. PLoS Biol, 19(4), e3001207.
  4. Chung, S. S., Ng, J. C. F., Laddach, A., Thomas, N. S. B., & Fraternali, F. (2021). Short loop functional commonality identified in leukaemia proteome highlights crucial protein sub-networks. NAR Genom Bioinform, 3(1), lqab010.
  5. Stewart, A., Ng, J. C., Wallis, G., Tsioligka, V., Fraternali, F., & Dunn-Walters, D. K. (2021). Single-Cell Transcriptomic Analyses Define Distinct Peripheral B Cell Subsets and Discrete Development Pathways. Front Immunol, 12, 602539.

2020

  1. Nichols, C., Ng, J., Keshu, A., Kelly, G., Conte, M. R., Marber, M. S., Fraternali, F., & De Nicola, G. F. (2020). Mining the PDB for Tractable Cases Where X-ray Crystallography Combined with Fragment Screens Can Be Used to Systematically Design Protein-Protein Inhibitors: Two Test Cases Illustrated by IL1β-IL1R and p38α-TAB1 Complexes. J Med Chem, 63(14), 7559–7568.
  2. Nichols, C., Ng, J., Keshu, A., Fraternali, F., & De Nicola, G. F. (2020). A New Crystal Form of the SARS-CoV-2 Receptor Binding Domain: CR3022 Complex-An Ideal Target for In-Crystal Fragment Screening of the ACE2 Binding Site Surface. Front Pharmacol, 11, 615211.
  3. \underlineJ. C. F. Ng, & Fraternali, F. (2020). Understanding the structural details of APOBEC3-DNA interactions using graph-based representations. Current Research in Structural Biology, 2, 130–143. https://doi.org/https://doi.org/10.1016/j.crstbi.2020.07.001

2019

  1. Ng, J. C. F., Quist, J., Grigoriadis, A., Malim, M. H., & Fraternali, F. (2019). Pan-cancer transcriptomic analysis dissects immune and proliferative functions of APOBEC3 cytidine deaminases. Nucleic Acids Res, 47(3), 1178–1194.

2018

  1. Laddach, A., Ng, J. C., Chung, S. S., & Fraternali, F. (2018). Genetic variants and protein-protein interactions: a multidimensional network-centric view. Curr Opin Struct Biol, 50, 82–90.