Centre for Cancer Genomics and Computational Biology

In the Centre for Genomics and Computational Biology, we employ unbiased high-throughput sequencing, mass spectrometry and multispectral imaging of tumour samples to gain unique insights into cancer evolution, genetics and cell signalling through from premalignancy to metastatic disease. We are internationally recognised for our work on lymphoma, leukaemia and gastrointestinal cancers, and the creation of computational tools to extract maximum value from Big Data. Our ambition is to see translation of new knowledge into improvements in early cancer detection and precision medicine.

Contact us

Centre Lead: Professor Francesca Ciccarelli

Deputy Centre Lead: Professor Sarah McClelland

John Vane Science Centre,
Charterhouse Square,
London EC1M 6BQ

Recent Publications

    • Mechanistic insights into the interactions between cancer drivers and the tumour immune microenvironment. Genome Medicine (2023) in press. PMID: 37277866
    • The mutational landscape of the adult healthy parous and nulliparous human breast. Nat Commun. (2023) 6;14(1):5136 PMID: 37673861
    • Transcriptomic analysis of cutaneous squamous cell carcinoma reveals a multigene prognostic signature associated with metastasis. J Am Acad Dermatol. (2023) S0190-9622(23)02504-5. PMID: 37586461 
    • Hepatocytes undergo punctuated expansion dynamics from a periportal stem cell niche in normal human liver. J Hepatol. (2023) 79(2):417-432. PMID: 37088309
    • Targeted assembly of ectopic kinetochores to induce chromosome-specific segmental aneuploidies. EMBO J. (2023) 15;42(10):e111587. PMID: 37063065
    • Fluctuating methylation clocks for cell lineage tracing at high temporal resolution in human tissues. Nat Biotechnol (2022) Online ahead of print. PMID: 34980912
    • MultiMAP: dimensionality reduction and integration of multimodal data. Genome Biology (2021) 22(1):346. PMID: 34930412
    • Evolution via somatic genetic variation in modular species. Trends in Ecology & Evolution (2021) 36(12):1083-1092. PMID: 34538501
    • LiquidCNA: Tracking subclonal evolution from longitudinal liquid biopsies using somatic copy number alterations. iScience (2021) 24(8):102889. PMID: 34401670
    • Evolutionary dynamics in Barrett oesophagus: implications for surveillance, risk stratification and therapy. Nat Rev Gastroenterol Hepatol (2021) Online ahead of print. PMID: 34728819
    • Improving understanding of cancer in the gender diverse population. Nat Rev Cancer (2021) PMID: 34163047
    • Drug ranking using machine learning systematically predicts the efficacy of anti-cancer drugs. Nat Commun (2021) 12(1):1850. PMID: 33767176
    • KDM5 inhibition offers a novel therapeutic strategy for the treatment of KMT2D mutant lymphomas. Blood (2021) blood.2020008743. PMID: 33786580
    • Multicentre derivation and validation of a colitis-associated colorectal cancer risk prediction web tool. Gut (2021) gutjnl-2020-323546. PMID: 33990383
    • Inference of Ligand-Receptor Pairs from Single-Cell Transcriptomics Data. Methods Mol Biol (2021) 2346:1-10. PMID: 33625677
    • ACSNI: An unsupervised machine-learning tool for prediction of tissue-specific pathway components using gene expression profiles. Patterns (N Y) (2021) 2(6):100270. PMID: 34179848
    • Reconstructing single-cell karyotype alterations in colorectal cancer identifies punctuated and gradual diversification patterns. Nature Genetics (2021). PMID: 34211178
    • Chromosome Instability through the Ages: Parallels between Speciation and Somatic (Cancer) Evolution. Trends Genet (2021) S0168-9525(21)00131-1. PMID: 34083067

Latest News

    • Dr Benjamin Werner and Dr Özgen Deniz (Centre for Haemato-oncology) are part of an international team shortlisted for a Cancer Grand Challenges award. Their team, decrypTEd, will receive £30,000 of seed funding to develop their ideas in the hope of being selected for the full $25m award. Read more.
    • Dr Mirjana Efremova has been awarded a Cancer Research UK Career Establishment Award of £1,043,000 to support her research into colorectal cancer, investigating the cellular state transitions mediating plasticity.
    • Professor Sarah McClelland and Molly Guscott have been awarded a CRUK City of London Centre Development fund for £25,000 for their project – “Investigating the evolution and patterns of genomic variation within single cells of ovarian cancer before and after the development of chemotherapy resistance”.
    • Dr Tanya Soliman's lab has been awarded a seed grant of £60,000 from Bart’s Charity to support their research in high-grade serous ovarian cancer in which they will be targeting a mitotic failsafe pathway.
    • Michelle Lockley is leading a clinical study to investigate a new personalised treatment approach for ovarian cancer that has returned after previous chemotherapy, with funding from Barts Charity and the Anticancer Fund. Read more about the ACTOv trial.
    • Vinaya Srirangam Nadhamuni, Clinical Research Fellow in the Centre, has been working on a project to break down language barriers to make information about bowel cancer screening & cervical screening more accessible to minority ethnic groups in the UK. Find out more.
    • Dr Sarah McClelland, awarded a research grant from the BBSRC to investigate the molecular mechanisms by which the transcription factor ZFP64 controls genomic stability.
    • Dr Benjamin Werner, awarded a UKRI Future Leader Fellowship to investigate the evolutionary dynamics of extra-chromosomal DNAs in cancer. Find out more.
    • Ms Faika Laz Banti, awarded a Commonwealth PhD Scholarship to investigate epi-therapies in Acute Myeloid Leukaemia.
    • Professor Jude Fitzgibbon with colleagues at DFCI and MSKCC was awarded a programme grant by the Lymph&Co Charity on KDM5i Therapeutics in non-Hodgkin’s lymphoma. Find out more.
    • Kinomica Ltd, a spin-out from Professor Pedro Cutillas’ group obtained Funding from Innovate UK
    • Dr Mirjana Efremova, awarded funding from the Chan Zuckerberg Initiative together with scientists from Queen Mary University of London, Newcastle University and Wellcome Sanger Institute to create a Single-Cell Multi-omic and Spatial Cell Atlas of Pediatric Skin.
    • Dr Sarah McClelland, awarded a BBSRC London Interdisciplinary Doctoral Scheme 4-year iCASE PhD studentship, in partnership with Artios Pharma.
    • Professor Trevor Graham, awarded a 5-year CRUK Programme to study colorectal cancer metastasis evolution.
    • Mr Kane Smith, awarded a Bowel Research UK PhD studentship to create a blood test to detect early signs of bowel cancer for people with inflammatory bowel disease.
    • Dr Ana Rio Machin, awarded a Junior Research Grant 2021 by the European Hematology Association to study the mechanisms & therapeutic vulnerabilities of acute myeloid leukaemia driven by the t(6;9) chromosomal translocation.

Research Teams

Areas of focus

Gastrointestinal cancers
Barrett's oesophagus 1 - McDonald lab
Haematological malignancies
FISH DLBCL - Andrew Clear 2
Barrett's oesophagus 2 - McDonald lab
Cancer cell plasticity
Cancer Cell Plasticity_Mirjana Efremova
Cancer genomics and evolution
Blue DNA structure isolated background. 3D illustration
Cell signalling and drug resistance
Mathematical and computational biology
Functional non-coding mutations in cancer
Stem cells in the evolution of metaplasia
Microscope image_crop
Ovarian cancer
Ovarian cancer image by Molly Guscott, McClelland Lab

Centre highlights

Since 2016, the BCI’s Haemato-Oncology tissue bank has released 924 vials of primary tissue to researchers from five institutions as part of a CRUK funded Programme on Poor Risk Acute Myeloid Leukaemia. The tissue collection, archiving and allied clinical information was generously supported by an award from the Medical College of St Bartholomew’s Hospital Trust. (Photo, left to right: Adrian Kontor, Tissue Bank Technician, and Ana Rio-Machin, lead lab researcher on the project).

Gabbutt, C., Schenck, R.O., Weisenberger, D.J. et al. Fluctuating methylation clocks for cell lineage tracing at high temporal resolution in human tissues. Nat Biotechnol (2022). https://doi.org/10.1038/s41587-021-01109-w. CC BY 4.0


Rio-Machin, A., Vulliamy, T., Hug, N. et al. The complex genetic landscape of familial MDS and AML reveals pathogenic germline variants. Nat Commun (2020) 11, 1044. https://doi.org/10.1038/s41467-020-14829-5. CC BY 4.0


Jackson, SS., Nambiar, KZ., O'Calloghan, S., Berner, AM. Understanding the role of sex hormones in cancer for the transgender community. Trends in Cancer (2022) DOI: https://doi.org/10.1016/j.trecan.2022.01.005