Giovanni Stracquadanio

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Giovanni Stracquadanio

PROF

 https://orcid.org/0000-0001-9819-3645

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Personal profile

Current Research Interests

I am multi-disciplinary scientist interested in understanding the molecular mechanisms underpinning complex phenotypes and diseases using two of the most disruptive technologies available: synthetic biology and machine learning. Our long term goal is to reverse-engineer biological systems to create generative algorithms to design, build and test biological agents for addressing healthcare problems, such as rare metabolic diseases and cancer, and industrial biotechnology challenges, like de-novo enzyme engineering. 

Research Interests

Computational Biology

  • Variational deep learning models for de-novo enzyme engineering
  • Bayesian methods to identify genomic loci associated with cancer heritability
  • Graph neural networks for discovering cancer genes and pathways
  • Statistical methods for biological network analysis
  • Computational methods to engineer, verify and characterise synthetic chromosomes
  • Sequencing analysis of solid and liquid tumors
  • Transcriptomic analysis of solid and liquid tumors
  • Scientific software development

Synthetic Biology

  • Enzyme manufacturing
  • Whole genome synthesis
  • Pathway assembly
  • High-throughput and combinatorial screens
  • Lab automation

Administrative Roles

  • Co-director of the Edinburgh Genome Foundry (EGF) 
  • Associate Editor, BMC Genomics
  • Editorial Board, Experimental Biology and Medicine
  • Chaired scientific events:
    • International Synthetic and Systems Biology Summer School (2014, 2015, 2020).
    • Essex Synthetic Biology School (ESBS). 2018
    • Biological Systems Design 2012 (BSD). 20th Annual International Conference on Intelligent Systems for Molecular Biology (ISMB). 2012
  • Reviewer for international peer-reviewed journals
  • Reviewer for EPSRC, BBSRC, MRC
  • Member of the EPSRC Peer Review Associate College

Teaching

  • Tools for Synthetic Biology (PGBI11092)
  • Biotechnology 3 (BILG09014)

Websites

Education/Academic qualification

Computer Science, Doctor of Philosophy (PhD), Università degli Studi di Catania

Award Date: 1 Mar 2010

Computer Science, Master in Science, Università degli Studi di Catania

Award Date: 27 Jul 2006

Computer Science, Bachelor of Science, Università degli Studi di Catania

Award Date: 4 Oct 2004

External positions

Lecturer, University of Essex

1 Nov 2016 → 31 Dec 2018

Postdoctoral Fellow, Ludwig Institute for Cancer Research, University of Oxford, Oxford, United Kingdom.

18 Jul 2014 → 30 Sept 2016

Postdoctoral fellow, Johns Hopkins University

31 Aug 2010 → 14 May 2014

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  • The landscape of the heritable cancer genome

    Fanfani, V., Citi, L., Harris, A. L., Pezzella, F. & Stracquadanio, G., 17 Mar 2021, (E-pub ahead of print) In: Cancer Research.

    Research output: Contribution to journal › Article › peer-review

    Open Access
    File

  • Germline and somatic genetic variants in the p53 pathway interact to affect cancer risk, progression and drug response

    Zhang, P., Kitchen-Smith, I., Xiong, L., Stracquadanio, G., Brown, K., Richter, P., Wallace, M., Bond, E., Sahgal, N., Moore, S., Nornes, S., De Val, S., Surakhy, M., Sims, D., Wang, X., Bell, D. A., Zeron-Medina, J., Jiang, Y., Ryan, A., Selfe, J., & 18 othersShipley, J., Kar, S., Pharoah, P., Loveday, C., Jansen, R., Grochola, L. F., Palles, C., Protheroe, A., Millar, V., Ebner, D., Pagadala, M., Blagden, S. P., Maughan, T., Domingo, E., Tomlinson, I. P. M., Turnbull, C., Carter, H. & Bond, G. L., 8 Feb 2021, In: Cancer Research.

    Research output: Contribution to journal › Article › peer-review

    Open Access
    File

  • Design of a synthetic yeast genome

    Richardson, S. M., Mitchell, L. A., Stracquadanio, G., Yang, K., Dymond, J. S., DiCarlo, J. E., Lee, D., Huang, C. L. V., Chandrasegaran, S., Cai, Y., Boeke, J. D. & Bader, J. S., 10 Mar 2017, In: Science. 355, 6329, p. 1040-1044 5 p.

    Research output: Contribution to journal › Article › peer-review

  • SCRaMbLE generates designed combinatorial stochastic diversity in synthetic chromosomes

    Shen, Y., Stracquadanio, G., Wang, Y., Yang, K., Mitchell, L. A., Xue, Y., Cai, Y., Chen, T., Dymond, J. S., Kang, K., Gong, J., Zeng, X., Zhang, Y., Li, Y., Feng, Q., Xu, X., Wang, J., Wang, J., Yang, H., Boeke, J. D., & 1 othersBader, J. S., 1 Jan 2016, In: Genome Research. 26, 1, p. 36-49 14 p.

    Research output: Contribution to journal › Article › peer-review

    Open Access
    File

  • The importance of p53 pathway genetics in inherited and somatic cancer genomes

    Stracquadanio, G., Wang, X., Wallace, M. D., Grawenda, A. M., Zhang, P., Hewitt, J., Zeron-Medina, J., Castro-Giner, F., Tomlinson, I. P., Goding, C. R., Cygan, K. J., Fairbrother, W. G., Thomas, L. F., Sætrom, P., Gemignani, F., Landi, S., Schuster-Böckler, B., Bell, D. A. & Bond, G. L., 1 Apr 2016, In: Nature Reviews Cancer. 16, 4, p. 251-65 15 p.

    Research output: Contribution to journal › Review article › peer-review

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  • 4 Editorial activity
  • 4 Publication peer-review
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