Research output per year
Research output per year
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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Collaborations and top research areas from the last five years
Recent external collaboration on country/territory level. Dive into details by clicking on the dots or
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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 AccessFile -
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 others, 8 Feb 2021, In: Cancer Research.Research output: Contribution to journal › Article › peer-review
Open AccessFile -
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
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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 others, 1 Jan 2016, In: Genome Research. 26, 1, p. 36-49 14 p.Research output: Contribution to journal › Article › peer-review
Open AccessFile -
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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iScience (Journal)
Giovanni Stracquadanio (Peer reviewer)
2021 → …Activity: Publication peer-review and editorial work types › Editorial activity
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Synthetic Biology (Journal)
Giovanni Stracquadanio (Peer reviewer)
2021 → …Activity: Publication peer-review and editorial work types › Editorial activity
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SLAS Technology (Journal)
Giovanni Stracquadanio (Peer reviewer)
2018 → …Activity: Publication peer-review and editorial work types › Publication peer-review
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BMC Genomics (Journal)
Giovanni Stracquadanio (Associate editor)
2017 → …Activity: Publication peer-review and editorial work types › Editorial activity
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Experimental Biology and Medicine (Journal)
Giovanni Stracquadanio (Editorial board member)
2017 → …Activity: Publication peer-review and editorial work types › Editorial activity
Prizes
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Best Poster Award
Stracquadanio, Giovanni (Recipient), May 2015
Prize: Prize (including medals and awards)
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National Human Genome Research Institute (NHGRI) Scholarship
Stracquadanio, Giovanni (Recipient), 7 Feb 2016
Prize: Prize (including medals and awards)
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NVIDIA Data Science GPU Grant
Stracquadanio, Giovanni (Recipient), 20 Sept 2019
Prize: Prize (including medals and awards)
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21EBTA Engineering Biology for Cell and Gene Therapy Applications
Rosser, S., Calvert, J., Cobb, S., Davies, J., Menolascina, F., Pollard, S. & Stracquadanio, G.
31/01/22 → 30/01/24
Project: Research
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GREET: Generative Recombinant Enzyme Engineering for Therapeutics
Stracquadanio, G. & Rosser, S.
1/01/22 → 31/12/25
Project: Research
Datasets
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Systematic analysis of IL-17 receptor signalosome reveals a robust regulatory feedback loop
Draber, P. (Creator) & Stracquadanio, G. (Creator), National Center for Biotechnology Information (Gene Expression Omnibus), 12 May 2020
https://www.ebi.ac.uk/pride/archive/projects/PXD019020
Dataset
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PyGNA: a unified framework for geneset network analysis
Fanfani, V. (Creator), Cassano, F. (Creator) & Stracquadanio, G. (Creator), Zenodo, 13 Dec 2019
Dataset