Giovanni Stracquadanio

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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 internal 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 201631 Dec 2018

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

18 Jul 201430 Sep 2016

Postdoctoral fellow, Johns Hopkins University

31 Aug 201014 May 2014

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