Technologies for doctors to make better decisions faster

Leveraging theory, computation and experiments, my group and I are creating novel measurement and prediction systems for integrated cancer biology. We work in translational projects on three frontiers:

cancer genome cancer tissue network biology
Tumour evolution Tissue context Interaction networks

(1) Revealing the mutational processes acting on cancer genomes, measuring their impact on patient phenotypes, and using them for personalised therapy decisions;

(2) Improved patient stratification, early detection, and prognosis by predictive modelling of tumour imaging and genomics data;

(3) Predicting strategies to overcome resistance and reduce toxicity by comparative network analysis of transcriptional responses to combinatorial CRISPR perturbations in single cells.

 

Publications

  • Cmero et al (2020), SVclone: inferring structural variant cancer cell fraction, Nature Comms
  • Holding et al (2019), VULCAN integrates ChIP-seq with patient-derived co-expression networks to identify GRHL2 as a key co-regulator of ERa at enhancers in breast cancer, Genome Biology
  • Macintyre*, Goranova* et al (2018), Copy-number signatures and mutational processes in ovarian carcinoma, Nature Genetics
  • ... more publications

    Software

    • VULCAN - infer cofactors from ChIP-seq differential binding
    • OncoNEM - Clonal evolution trees from single cell data
    • Bitphylogeny - Bayesian framework for intra-tumour phylogenies
    • MEDICC - intra-tumor copy-number comparisons
    • nem - inferring Nested Effects Models from downstream perturbation effects
    • RedeR - statistical computing and network visualization

    ... more software

    Contact

    Florian Markowetz
    University of Cambridge CRUK Cambridge Institute
    Robinson Way
    Cambridge, CB2 0RE, UK
    e: first.last@cruk.cam.ac.uk
    p: +44 (0) 1223 769 628
    f: +44 (0) 1223 769 510 How to find us