Notations:

Bold: CSB group member
✢: Co-first author
†: Corresponding/Co-corresponding author

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Thomas Geddes publications as part of computational systems biology group

6. Kearney, A., Norris, D., Ghomlaghi, M., Wong, M., Humphrey, S., Carroll, L., Yang, G., Cooke, K., Yang, P., Geddes, T., Shin, S., Fazakerley, D., Nguyen, L., James, D. & Burchfield, J. (2021) Akt phosphorylates insulin receptor substrate to limit PI3K-mediated PIP3 synthesis. eLife, 10, e66942. [Full Text]

5. Norris, D.^✢, Yang, P.^✢, Shin, S.^✢, Kearney, A., Kim, H., Geddes, T., Senior A., Fazakerley, D., Nguyen, L., James, D. & Burchfield, J. (2021) Signalling heterogeneity is defined by pathway architecture and inter-cellular variability in protein expression. iScience, 24(2), 102118. [Full Text]

4. Cao, Y., Geddes, T., Yang, J. & Yang, P.^† (2020) Ensemble deep learning in bioinformatics. Nature Machine Intelligence, 2, 500-508. [Full Text] [Nature Content Sharing link]

3. Kim, H.^✢, Lin, Y.^✢, Geddes, T., Yang, J. & Yang, P.^† (2020) CiteFuse enables multi-modal analysis of CITE-seq data. Bioinformatics, 36(14), 4137-4143. [Full Text] [Biorxiv version] [BioC R package]

2. Geddes, T., Kim, T., Nan, L., Burchfield, J., Yang, J., Tao, D. & Yang, P.^† (2019) Autoencoder-based cluster ensembles for single-cell RNA-seq data analysis. BMC Bioinformatics, 20, 660. [Full Text] [Repo]

1. Kim, T., Lo, K., Geddes, T., Kim, H., Yang, J. & Yang, P.^† (2019) scReClassify: post hoc cell type classification of single-cell RNA-seq data. BMC Genomics, 20, 913. [Full Text] [Repo]