Francesca Buffa

Computational Biology and Integrative Genomics

We search for integrated genomic blueprints that enable us to predict how cancer will evolve and respond to treatment.


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Research Summary

High throughput technology has supported a scientific revolution both in molecular biology and clinical research. In molecular biology, and more specifically in both cancer and radiation biology, it is now possible to acquire data at the whole genome level, and to characterise a genomic blueprint for different cancer types. This has allowed us to ask questions on how the cancer genome is regulated. Most importantly we are beginning to understand how and where the blueprint of the genome is functional and what the biological and clinical implications of this function are.
In translational and clinical research it is becoming increasingly possible to acquire both genomic and disease imaging data, and this combination can provide further understanding of the molecular and clinical cancer phenotype. This revolution has enabled the accumulation of cancer genomic big data and related knowledge at a speed never experienced before in science. The knowledge generated with this big data is being increasingly organised in both specialist and general knowledge databases which can be interrogated by computational tools.
We are investigating integrative approaches to combine results from functional assays, systems level approaches and clinical knowledge with genomics (DNA) and transcriptomic (RNA) data. To achieve this we apply a wide range of sophisticated computational and statistical techniques to analyse large clinical cohorts. Our research sits at the interface between genomics, imaging and biomarkers and it is applied to molecular and radiation oncology.
Our more recent work focuses on next generation sequencing techniques and high content screening, and the development of tools to aid the translation of this big data generated knowledge into beneficial use in the clinic for treatment of patients.
The graph shows the interplay between genes regulated by hypoxia in a cancer cell. Genes are shown as circles, while their relationship with co-partners genes which help fuel progression of cancer is shown by green edges. The network demonstrates complex interplay which emerges when cancer cell undergoes hypoxia following poor blood supply, and patients with such deregulation are shown to have poorer outcome. A computational algorithm previously developed by us (Buffa et al.) was used, which aims at unravelling such interplays by starting with known key-player genes in cancer (seeds). It extends the network by finding other genes in human genome (>25,000) exhibiting similar patterns of expression, and further limiting to those genes having highest number of associates/co-partners. This way, a highly active network is identified which is shown to contain primary culprits of driving aggressive cancers.
Integrated analysis of miRNA and mRNA expression profiling as a tool to identify prognostic markers and associated pathways:
Big Data for Bioinformatics: Panel Discussion | Big Data Analytics Conference 2015:



Francesca Buffa is an Associate Professor in the Department of Oncology, University of Oxford, where she leads the Computational Biology and Integrative Genomics Group.

After a Masters Degree in Theoretical Physics from the University of Turin, Prof Buffa completed her PhD in Physics and Mathematical Modelling at the Institute of Cancer Research within the University of London. She then undertook a postdoctoral research fellowship in Mathematical Modelling and Biostatistics at the Gray Cancer Institute, London before joining the Molecular Oncology Laboratories at the Weatherall institute of Molecular Medicine, University of Oxford, first as a postdoctoral research fellow in Bioinformatics/Biostatistics then as a Group Leader.

Prof Buffa took up her current post in the Department of Oncology in 2013 where she leads a research team working at the interface between computational biology, genomics and biomarker research. In addition to her research programme, she teaches at national and international Masters Courses and Advanced Schools, and acts as bioinformatics/biostatistics advisor for genomics clinical research studies and trials. She has been invited to present her work at national and international conferences, and authored or co-authored over 100 publications, several in high impact journals.



Syed Haider, Alan McIntyre, Ruud G. P. M. van Stiphout, Laura M. Winchester, Simon Wigfield, Adrian L. Harris and Francesca M. Genomic alterations underlie a pan-cancer metabolic shift associated with tumour hypoxia. Genome Biology (2016) 17:140

Masiero M, Costa Simões F, Dong Han H, Snell C, Peterkin T, Bridges E, Mangala LS, Yen-Yao Wu S, Pradeep S, Li D, Han C, Dalton H, Lopez-Berestein G, Tuynman JB, Mortensen N, Li JL, Patient R, Sood AK, Banham AH, Harris AL and Buffa FM. A core human primary tumor angiogenesis signature identifies the endothelial orphan eceptor ELTD1 as a key regulator of angiogenesis. Cancer Cell.  2013 Aug 12;24(2):229-41. doi: 10.1016/j.ccr.2013.06.004. Epub 2013 Jul 18.

Favaro E, Bensaad K, Chong MG, Tennant DA, Ferguson DJ, Snell C, Steers G, Turley H, Li JL, Günther UL, Buffa FM, McIntyre A and Harris AL. Glucose utilization via glycogen phosphorylase sustains proliferation and prevents premature senescence in cancer cells. Cell Metab. 2012 Dec 5;16(6):751-64. doi: 10.1016/j.cmet.2012.10.017. Epub 2012 Nov 21.

Mehta S, Hughes NP, Buffa FM, Li SP, Adams RF, Adwani A, Taylor NJ, Levitt NC, Padhani AR, Makris A, Harris AL. Assessing early therapeutic response to bevacizumab in primary breast cancer using magnetic resonance imaging and gene expression profiles. J Natl Cancer Inst Monogr.  2011;2011(43):71-4. doi: 10.1093/jncimonographs/lgr027.


Google scholar: https://scholar.google.co.uk/citations?user=abd1LXcAAAAJ&hl=en&oi=ao
Research gate: https://www.researchgate.net/profile/Francesca_Buffa

Associated Researchers

Group Members

Jagat Chauhan, Postdoctoral Researcher (in collaboration with Oxford Ludwig Institute)
Wei-Chen Cheng, Postdoctoral Researcher
Pauline Robbe, DPhil Student
Dimitrios Voukantsis, Postdoctoral Researcher

About Us
We aim to enhance clinical and basic cancer research in Oxford with the ultimate goal of increasing cancer cure rates.
In Oxford, we have a great wealth of broad-ranging expertise and a powerful network of cancer researchers.
Study With Us
Our graduate training programmes for both scientists and clinicians are internationally recognised.