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Francesca Buffa

PhD


Professor of Computational Biology and Cancer Genomics

  • Full Professor of Computational Biology and Cancer Genomics
  • Principal Investigator funded by Cancer Research UK (project CBIG:23969) and the European Research Council ( project MICROC:772970)
  • Head of the cBIG Systems Biology Lab - members of the lab listed below

Research Summary

I lead a computational lab and a systems biology lab funded by the European Research Council and Cancer Research UK.

We develop and apply computational and mathematical modelling, and AI/machine learning approaches to the analysis of multi-omics and functional data from bulk and single-cell clinical and biological samples, to understand cancer as a complex system.

Some of our main projects are:

  • Machine learning methods for large clinical cohorts and biobanks to derive integrated multi-omics classifiers
  • Gene network reconstruction using bulk samples and single cells sequencing data to study transcriptional regulation and cell-cell communication
  • Integration of functional (CRISPR, phenotypic) and omics (DNA, RNA) assays to infer gene function
  • Derivation of omics 'signatures' to infer phenotype and disease outcome in clinical and biological samples
  • Development of Agent Based Modelling approaches to model disease-host interactions in complex diseases

Biography

After a Masters Degree in Theoretical Physics from the University of Turin, I completed a PhD in Physics and Mathematical Modelling at the Institute of Cancer Research, University of London. I undertook postdoctoral research in anaysis of imaging data at the ICR, and then joined the Statistics Group at the Gray Cancer Institute and the MRC Clinical Trials Unit, London, to work on biomarker research studies. Following this, I joined the Medical Sciences Division, University of Oxford, first as a postdoctoral research fellow in systems biology, and then as Principal Investigator and Head of the Computational Biology and Integrative Genomics Lab.

In addition to my research work, I teach post-graduate courses, including the new MSc in Precision Cancer Medicine, where I lead the Omics module, and the MSc in Radiation Biology, where I teach Statistics and Computational methods applied to Omics. I also teach at national and international Masters Courses and Advanced Schools, including Statistics and Bioinformatics in the MSc courses at the University of Tsukuba, Japan, and at the Advanced Courses at the Wellcome Genome Campus, University of Cambridge, UK.

I serve on several national and international committees, including funding agencies Horizon2020, the European Research Council, the Medical Research Council, the UK Research Institute and Cancer Research UK. And I am member of governative evaluation panels, including service as member of the Biological Science Panel and Interdisciplinary Advisor for the REF-2021.

I authored over 130 publications, several in high impact journals (Google Scholar, ORCID), and and I am recipient of a Cancer Research UK Programme and European Research Council Programme Award.

Group Members

Alessandro Barberis, Postdoctoral Researcher, Machine Learning (CBIG:23969)
Ryan Carter, Interdisciplinary Bioscience DTP  Student, Deep Learning, AI
Philip Charlton, Clinical Research Fellow DPhil Student, Transcriptomics, Biomarkers
Wei-Chen Cheng, Postdoctoral Researcher, Transcriptomics, Bioinformatics (CBIG:23969)
Yueachan Chi,  DPhil Student, Computational Biology
Matteo Di Giovannantonio, DPhil Student, Machine Learning (MICROC:772970)
Badran Elshenawy, DPhil Student, Transcriptomics, Bioinformatics, Computational Biology
Joachim Hagel, Immunology DTP Student, Immunology, Omics, Bioinformatics
Ben Harris, Clinical Research Fellow, Metabolism, Omics, GWAS, Bioinformatics
Fiona Hartley, DPhil Student, Hypoxia, Transcriptomics, Bioinformatics
May Sin Ke, DPhil Student, Transcriptomics, Single-Cell Sequencing
Sakura Maezono, Tsukuba University DPhil Student , Computational Biology
Ana Miar Cuervo, Postdoctoral Researcher, Hypoxia, Transcriptomics (MICROC:772970)
Dawn O'Reilly, Postdoctoral Researcher, Transcriptomics (CBIG:23969)
Jayathilake Pahala Gedara, Postdoctoral Researcher, Computational Modelling (MICROC:772970)
Clara Pavillet, Wellcome Trust DTP Student, Machine Learning, Immune Modelling
Karen Sayal, Clinical Research Fellow, Transcriptomics, Single-Cell Sequencing
Helen Sheldon, Postdoctoral Researcher, Hypoxia, CRISPR and transcriptomics (MICROC:772970)
Charalampos Triantafyllidis, Postdoctoral Researcher, Machine Learning, Network Analysis, Data Science (MICROC:772970)
Ava Van Ess, Oxford Institute DPhil Student, Hypoxia, CRISPR screens
Pedro Victori, DPhil Student, Computational Biology (MICROC:772970)