Publications on PubMed

Living systems rely on complex networks of interacting molecules to carry out all basic biological processes. Our goal is to identify interactions between proteins and map protein interaction networks that contribute to human diseases such as colorectal cancer and lung fibrosis. We apply proteomic as well as data-science techniques to define these protein interaction networks and uncover the molecular mechanisms that lead to disease. We are especially interested in defining protein interaction networks that govern oncogenic signalling pathways such as the Wnt signalling pathway, and understanding how these signalling pathways cross-talk with other oncogenic processes such as DNA methylation.

Selected / recent publications

  • Proteomic characterization of GSK3β knockout shows altered cell adhesion and metabolic pathway utilisation in colorectal cancer cells biorxiv.org, 2021 (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. 2018  (www.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 β-catenin and Dnmt1 regulates Wnt Signaling and DNA methylation in colorectal cancer cells. Molecular Cancer Research, 2015 (PubMed|pdf)
  • Structural Proteomics: Large-scale studies. In: eLS. John Wiley & Sons Ltd, Chichester. (Jun 2015) (Paper|pdf)
  • 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)


Published on  July 15th, 2020