We work in the area of cancer systems biology. Our goal is to understand the molecular networks that drive tumour formation in cancers such as colorectal, lung and brain. We use proteomics/multi-omics and data-driven/bioinformatics approaches to define these networks and to uncover the molecular mechanisms that underlie human disease. Specific and current interests include identifying new components of the Wnt signaling network in colorectal cancer, and mapping the interactions between the Zika virus and human brain tumour cells with a view to using Zika as an oncolytic virotherapy.
Publications on PubMed
Selected / recent publications
- Knockdown Proteomics Reveals USP7 as a Regulator of Cell-Cell Adhesion in Colorectal Cancer via AJUBA, Molecular and Cellular Proteomics, 2024 (full text)
- Multi-omics analysis reveals key immunogenic signatures induced by oncolytic Zika virus infection of paediatric brain tumour cells, 2024 (biorxiv)
- Identification of natural Zika virus peptides presented on the surface of paediatric brain tumour cells by HLA class I, 2024 (biorxiv)
- Integrative transcriptomic and proteomic meta-analysis of Zika viral infection reveals potential mechanisms for oncolytic therapy in neuroblastoma, 2022 (f1000 research)
- TransformerGO: Predicting protein-protein interactions by modelling the attention between sets of gene ontology terms Bioinformatics, 2022 (PubMed)
- Proteomic characterization of GSK3β knockout shows altered cell adhesion and metabolic pathway utilisation in colorectal cancer cells PLOS ONE, 2021 (full text)
- 3-month, 6-month, 9-month, and 12-month respiratory outcomes in patients following COVID-19-related hospitalisation: a prospective study Lancet Respir Med, 2021 (PubMed)
- The USP7 protein interaction network and its roles in tumorigenesis Genes & Diseases, 2020 (full text)
- Editorial: Integrated Omics For Defining Interactomes Frontiers in Physiology, 2020 (full text)
- An evaluation of different classification algorithms for protein sequence-based reverse vaccinology prediction. PLoS One. 2019 (PubMed)
- iOmicsPASS: a novel method for integration of multi-omics data over biological networks and discovery of predictive subnetworks. npj Systems Biology and Applications, 2019 (PubMed)
- Deep proteomic analysis of Dnmt1 mutant/hypomorphic colorectal cancer cells reveals dys-regulation of Epithelial-Mesenchymal Transition and subcellular relocalization of Beta-Catenin. 2019 (PubMed)
- Proteomic Analysis of Azacitidine-Induced Degradation Profiles Identifies Multiple Chromatin and Epigenetic Regulators Including Uhrf1 and Dnmt1 as Sensitive to Azacitidine. Journal Proteome Research, 2019 (PubMed)
- Paracrine signalling during ZEB1-mediated epithelial-mesenchymal transition augments local myofibroblast differentiation in lung fibrosis Cell Death and Differentiation, 2019 (PubMed)
- ELF3 is an antagonist of oncogenic-signalling-induced expression of EMT-TF ZEB1 Cancer Biology and Therapy, 2018 (PubMed)
- The PTPRT pseudo-phosphatase domain is a denitrase 2018www.biorxiv.org
- Multi-proteomic and transcriptomic analysis of oncogenic β-catenin molecular networks Journal of Proteome Research, 2018 (PubMed)
- A Method of Integrating Spatial Proteomics and Protein-Protein Interaction Network Data Lecture Notes in Computer Science, 2017 (full text)
- Proteomics and network analyses reveal inhibition of Akt-mTOR signaling by M. tuberculosis Mannose-capped Lipoarabinomannan, Proteomics, 2017 (PubMed)
- Noise-processing by signaling networks. Scientific Reports, 2017 (PubMed)
- Single-cell pluripotency regulatory networks. Proteomics, 2016 (PubMed)
- Proteomic and bioinformatics profile of paired human alveolar macrophages and peripheral blood monocytes. Proteomics, 2015 ([PubMed])
- How do oncoprotein mutations rewire protein–protein interaction networks? Expert Review Proteomics, 2015 (pdf)
- A protein interaction between Beta-catenin and Dnmt1 regulates Wnt Signaling and DNA methylation in colorectal cancer cells. Molecular Cancer Research, 2015 (PubMed)
- The Wnt Signaling Network in Cancer. In Systems Biology of Cancer. Cambridge University Press (2015) (link to book)
- Alternate wiring of a KNOXI genetic network underlies differences in leaf development of A. thaliana and C. hirsuta. Genes & development. 2015 (PubMed)
- Regulation of protein stability of DNA methyltransferase 1 by post-translational modifications. Acta Biochim Biophys Sin, 2014 (PubMed)
- Integrated analysis of the Wnt responsive proteome in human cells reveals diverse and cell-type specific networks. Mol Biosyst. 2014 (PubMed)
- The CRAPome: a contaminant repository for affinity purification-mass spectrometry data. Nat Methods. 2013 (PubMed)
- Gain of interaction with IRS1 by p110α-helical domain mutants is crucial for their oncogenic functions. Cancer Cell. 2013 (PubMed)