Team
Giovanni Stracquadanio, PhD FHEA - Principal Investigator
UKRI EPSRC fellow. Chair in Engineering Biology.
Co-Director of the Edinburgh Genome Foundry
School of Biological Sciences, Michael Swann Building, Room 2.35, The King's Buildings
The University of Edinburgh, Edinburgh, EH9 3BF
email: giovanni (dot) stracquadanio (at) ed (dot) ac (dot) uk
Short bio. Giovanni Stracquadanio is a Personal Chair in Engineering Biology, EPSRC fellow and
co-director of the Edinburgh Genome Foundry (EGF).
Dr Stracquadanio obtained a PhD in Informatics from the University of Catania (Italy) in 2010, and then received postdoctoral training in synthetic biology in Joel Bader and Jef Boeke labs at the Johns Hopkins University working on the synthetic yeast genome. Dr Stracquadanio was a main contributor to the Synthetic Yeast (Sc2.0) genome project, pioneering algorithms and developing software at the foundation of the first synthetic eukaryotic genome. He has also developed tools used in large-scale synthesis projects, streamlining chromosomes engineering and the assembly of biological pathways.
In 2014, he moved to the Ludwig Institute for Cancer Research (LICR) at the University of Oxford to work on cancer genetics, in Gareth Bond’s lab; here, he focused on studying how high-frequency inherited p53 mutations affect the risk of cancer and response to treatment using statistical genetics methods.
In 2016, before moving to the University of Edinburgh, Dr Stracquadanio established the first computational biology lab at the School of Computer Science and Electronic Engineering of the University of Essex, and in 2017 received the Wellcome Trust Seed Award in Science.
Dr Stracquadanio has authored more than 40 research articles published in international peer-reviewed journals, including Science, Nature Rev. Cancer, Cancer Research and PNAS. He also serves as Associate Editor for BMC Genomics and has reviewer for EPSRC, BBSRC, MRC and FLF. Since 2021, he is also a member of the EPSRC Peer Review Associate College.
Dr Stracquadanio obtained a PhD in Informatics from the University of Catania (Italy) in 2010, and then received postdoctoral training in synthetic biology in Joel Bader and Jef Boeke labs at the Johns Hopkins University working on the synthetic yeast genome. Dr Stracquadanio was a main contributor to the Synthetic Yeast (Sc2.0) genome project, pioneering algorithms and developing software at the foundation of the first synthetic eukaryotic genome. He has also developed tools used in large-scale synthesis projects, streamlining chromosomes engineering and the assembly of biological pathways.
In 2014, he moved to the Ludwig Institute for Cancer Research (LICR) at the University of Oxford to work on cancer genetics, in Gareth Bond’s lab; here, he focused on studying how high-frequency inherited p53 mutations affect the risk of cancer and response to treatment using statistical genetics methods.
In 2016, before moving to the University of Edinburgh, Dr Stracquadanio established the first computational biology lab at the School of Computer Science and Electronic Engineering of the University of Essex, and in 2017 received the Wellcome Trust Seed Award in Science.
Dr Stracquadanio has authored more than 40 research articles published in international peer-reviewed journals, including Science, Nature Rev. Cancer, Cancer Research and PNAS. He also serves as Associate Editor for BMC Genomics and has reviewer for EPSRC, BBSRC, MRC and FLF. Since 2021, he is also a member of the EPSRC Peer Review Associate College.
Postdocs and research assistants
Ginevra Camboni
University of Edinburgh
Short bio: I am a postdoctoral research associate in the Stracquadanio lab, working on developing a high-throughput screening method for AI-generated variants of alpha-galactosidases in yeast Komagataella phaffii. I obtained my BSc in biological sciences from the University of Sassari, followed by an Erasmus internship at the biophysics lab of the University of York. I then spent four years working on my PhD in Prof. Gideon Grogan laboratory at YSBL of the University of York, where I gained my expertise in working with yeasts and with high-throughput directed evolution methodologies. In my spare time I enjoy reading, socializing with friends, hiking and travelling.
University of Edinburgh
Short bio: I am a postdoctoral research associate in the Stracquadanio lab, working on developing a high-throughput screening method for AI-generated variants of alpha-galactosidases in yeast Komagataella phaffii. I obtained my BSc in biological sciences from the University of Sassari, followed by an Erasmus internship at the biophysics lab of the University of York. I then spent four years working on my PhD in Prof. Gideon Grogan laboratory at YSBL of the University of York, where I gained my expertise in working with yeasts and with high-throughput directed evolution methodologies. In my spare time I enjoy reading, socializing with friends, hiking and travelling.
Matthias Dierick
University of Edinburgh
Short bio: I am a postdoctoral research associate working on screening internally developed AI-engineered enzyme variants expressed by CHO cells. My current focus is on the Intelligent Deimmunization of Enzyme Replacement Therapies (IDERT) project, with the goal of spearheading a new era in enzyme replacement therapies designed for lifelong treatment. This ground-breaking approach aims to address the challenges faced by patients who currently lack viable treatment options due to strong immune response. Prior to this, I secured an FWO PhD fellowship, enabling me to study the potential of lactoferrin variants to prevent ETEC-induced diarrhoea in postweaning pig and I obtained my PhD degree in Veterinary medicine at Ghent University in 2023. Beyond the lab, I find joy in playing tennis, leisurely walks in nature and I am also a cinephile at heart.
University of Edinburgh
Short bio: I am a postdoctoral research associate working on screening internally developed AI-engineered enzyme variants expressed by CHO cells. My current focus is on the Intelligent Deimmunization of Enzyme Replacement Therapies (IDERT) project, with the goal of spearheading a new era in enzyme replacement therapies designed for lifelong treatment. This ground-breaking approach aims to address the challenges faced by patients who currently lack viable treatment options due to strong immune response. Prior to this, I secured an FWO PhD fellowship, enabling me to study the potential of lactoferrin variants to prevent ETEC-induced diarrhoea in postweaning pig and I obtained my PhD degree in Veterinary medicine at Ghent University in 2023. Beyond the lab, I find joy in playing tennis, leisurely walks in nature and I am also a cinephile at heart.
Tanya Dudnakova
University of Edinburgh
Short bio: I am a postdoctoral research associate working on the biochemical characterisation of therapeutic enzymes.
University of Edinburgh
Short bio: I am a postdoctoral research associate working on the biochemical characterisation of therapeutic enzymes.
Emmanuel Fiagbedzi
University of Edinburgh
Short bio: I am a postdoctoral research associate working on protein engineering.
University of Edinburgh
Short bio: I am a postdoctoral research associate working on protein engineering.
Louise Holyoake
University of Edinburgh
Short bio: I am a Research Technologist joining the wet lab to work towards screening protein variants for use in enzyme replacement therapies. I have worked at the University of Edinburgh since 2016, I enjoy the vibrant Engineering Biology community and working on a range of projects that include cloning and engineering proteins. I have a keen interest in how research can be transformed into real world impact through commercialisation. I continue to hone my entrepreneurial skills and I hope to put these to use in the Stracquadanio group. In my spare time I enjoy exploring the areas around Edinburgh, learning new crafts, and relaxing with our tabby cat Murray.
University of Edinburgh
Short bio: I am a Research Technologist joining the wet lab to work towards screening protein variants for use in enzyme replacement therapies. I have worked at the University of Edinburgh since 2016, I enjoy the vibrant Engineering Biology community and working on a range of projects that include cloning and engineering proteins. I have a keen interest in how research can be transformed into real world impact through commercialisation. I continue to hone my entrepreneurial skills and I hope to put these to use in the Stracquadanio group. In my spare time I enjoy exploring the areas around Edinburgh, learning new crafts, and relaxing with our tabby cat Murray.
Josh Littlefair
University of Edinburgh
Short bio: I am a postdoctoral research associate in the Stracquadanio Lab, working on machine learning approaches to engineer enzyme-replacement therapies to treat Fabry Disease, as part of the Generative Recombinant Enzyme Engineering for Therapeutics (GREET) project. I obtained my BSc in Physics with Astrophysics from Northumbria University, followed by completing my PhD in Theoretical Chemistry from Newcastle University in 2021. I spent two years as a Research Fellow in Dr Simone Meloni Laboratory of Materials Modeling and Simulations (LMMS) at the University of Ferrara as part of the H2020 Electro-Intrusion project, studying the underlying mechanisms of nanotriboelectrification to develop energy-recovering shock absorbers. My passions outside of work are learning languages, running, travelling and following Sunderland AFC.
University of Edinburgh
Short bio: I am a postdoctoral research associate in the Stracquadanio Lab, working on machine learning approaches to engineer enzyme-replacement therapies to treat Fabry Disease, as part of the Generative Recombinant Enzyme Engineering for Therapeutics (GREET) project. I obtained my BSc in Physics with Astrophysics from Northumbria University, followed by completing my PhD in Theoretical Chemistry from Newcastle University in 2021. I spent two years as a Research Fellow in Dr Simone Meloni Laboratory of Materials Modeling and Simulations (LMMS) at the University of Ferrara as part of the H2020 Electro-Intrusion project, studying the underlying mechanisms of nanotriboelectrification to develop energy-recovering shock absorbers. My passions outside of work are learning languages, running, travelling and following Sunderland AFC.
Evgenii Lobzaev
University of Edinburgh
Short bio: I am a postdoctoral research associate and my research work focuses on developing variational methods to design human enzymes for treating rare enzymatic disorders. Prior to this, I obtained a BSc in Economics/Mathematics, St.Petersburg State University of Engineering and Economics followed by a MSc in Finance from University of Maryland. I worked for almost 4 years in World Bank in Washington,DC as a quantitative analyst before I decided to change my career path to Data Science. I obtained MSc Statistics and Data Science from the University of Edinburgh and then immediately got into Biomedical AI CDT. Outside of work I like playing tennis, reading, going to a theatre or travelling.
University of Edinburgh
Short bio: I am a postdoctoral research associate and my research work focuses on developing variational methods to design human enzymes for treating rare enzymatic disorders. Prior to this, I obtained a BSc in Economics/Mathematics, St.Petersburg State University of Engineering and Economics followed by a MSc in Finance from University of Maryland. I worked for almost 4 years in World Bank in Washington,DC as a quantitative analyst before I decided to change my career path to Data Science. I obtained MSc Statistics and Data Science from the University of Edinburgh and then immediately got into Biomedical AI CDT. Outside of work I like playing tennis, reading, going to a theatre or travelling.
PhD students
Binjie Chen
University of Edinburgh
Short bio: I am PhD student of the UKRI AI CDT for Biomedical Innovation.
University of Edinburgh
Short bio: I am PhD student of the UKRI AI CDT for Biomedical Innovation.
Martyna Kasprzik
EastBIO DTP, University of Edinburgh
Short bio: I am a PhD student working on transparent deep learning for protein engineering. I am very interested in bioinformatics, particularly in using artificial intelligence in clinical research. I have also participated in a EuCanImage project - a European cancer imaging platform for AI in oncology. In my free time I enjoy reading and painting.
EastBIO DTP, University of Edinburgh
Short bio: I am a PhD student working on transparent deep learning for protein engineering. I am very interested in bioinformatics, particularly in using artificial intelligence in clinical research. I have also participated in a EuCanImage project - a European cancer imaging platform for AI in oncology. In my free time I enjoy reading and painting.
Anima Sutradhar
EastBIO CDT, University of Edinburgh
Short bio: I am a PhD student on the EASTBIO DTP, funded jointly by BBSRC and Fujifilm Diosynth Biotechnologies. I research codon optimisation for heterologous protein expression using machine learning and NLP techniques. Broadly speaking, I am trying to teach computers to understand the language of biological sequences. Prior to this, I completed my BSc in Molecular Biology at UCL, worked as a policy officer on climate change at BEIS, and then completed my Bioinformatics MSc at QMUL. When I am not doing science, I love to star-gaze, hike, write songs and illustrate. My science communication heroes are Jacob Bronowski, Carl Sagan and Kurzgesagt.
EastBIO CDT, University of Edinburgh
Short bio: I am a PhD student on the EASTBIO DTP, funded jointly by BBSRC and Fujifilm Diosynth Biotechnologies. I research codon optimisation for heterologous protein expression using machine learning and NLP techniques. Broadly speaking, I am trying to teach computers to understand the language of biological sequences. Prior to this, I completed my BSc in Molecular Biology at UCL, worked as a policy officer on climate change at BEIS, and then completed my Bioinformatics MSc at QMUL. When I am not doing science, I love to star-gaze, hike, write songs and illustrate. My science communication heroes are Jacob Bronowski, Carl Sagan and Kurzgesagt.
Sebestyen Kamp (2nd supervisor)
Biomedical AI CDT, University of Edinburgh
Short bio: I am a UKRI-funded PhD student in the Biomedical AI CDT programme. My project focuses on developing graph neural networks to model tumor progression in cancer using single-cell RNA sequencing data. Prior to this, I obtained a BSc in molecular bionics engineering followed by a MSc in info-bionics engineering at the PPCU in Budapest. During my master's, I spent a year at the Helmholtz Zentrum Munich as a guest researcher at the Institute of Bioinformatics and Systems Biology. I worked for 5 years at a pharmaceutical startup, Turbine.AI, first as a computational biologist, and then as the data team lead. In 2021 I started the CDT in Biomedical AI and obtained a MScR in Biomedical AI at the School of Informatics at the University of Edinburgh. In my free time, I enjoy riding my bike, running, and going to concerts.
Biomedical AI CDT, University of Edinburgh
Short bio: I am a UKRI-funded PhD student in the Biomedical AI CDT programme. My project focuses on developing graph neural networks to model tumor progression in cancer using single-cell RNA sequencing data. Prior to this, I obtained a BSc in molecular bionics engineering followed by a MSc in info-bionics engineering at the PPCU in Budapest. During my master's, I spent a year at the Helmholtz Zentrum Munich as a guest researcher at the Institute of Bioinformatics and Systems Biology. I worked for 5 years at a pharmaceutical startup, Turbine.AI, first as a computational biologist, and then as the data team lead. In 2021 I started the CDT in Biomedical AI and obtained a MScR in Biomedical AI at the School of Informatics at the University of Edinburgh. In my free time, I enjoy riding my bike, running, and going to concerts.
Affiliated members
Rennos Fragkoudis. Facility Manager
Edinburgh Genome Foundry
Edinburgh Genome Foundry
Peter Vegh. Computational Biologist
Edinburgh Genome Foundry
Edinburgh Genome Foundry
Recent alumni
- Michael Herrera, Postdoc (2022-2024). Research area: Engineering replacement therapies for Fabry disease. Now: Postdoctoral fellow, School of Chemistry, University of Edinburgh..
- Sofija Semeniuk, Postdoc (2023-2024). Research area: Synthetic lethality kill switch. Now: Quotient Therapeutics..
- Aidan Marnane, PhD student (). Research area: Graph neural networks for patients' networks. Now: .
- Viola Fanfani, PhD student (2017-2021). Research area: Cancer genetics. Now: Postdoc, Harvard University, USA.
- Angelo Gaeta, PhD student (2017-2021). Research area: Computational synthetic biology. Now: Research technologist, Illumina, UK..
- Fabio Cassano, Postdoc (2019-2020). Research area: Cancer network biology. Now: University of Bari, Italy.
- David Zihala, Visiting postdoc (2020). Research area: Cancer genomics. Now: Postdoc, University of Ostrava, CZ.
- Martina Zatopkova, PhD Student (2017-2021). Research area: Cancer genomics. Now: Scientist, DNANexus, CZ.
- Alex Ball, MSc student (2021). Research area: Deep Learning for enzyme classification. Now: .
- Daniel Biro, MInf student (2020-2021). Research area: Deep Learning for variant calling. Now: .
- Hugo Madge-Leon, Research intern (2020). Research area: eQTL analysis of Cancer SNPs. Now: MSc student, ETH Zurich, Switzerland.
- Daniele Cotton, Research Intern (2020). Research area: Breast cancer heritability. Now: Medical student, Imperial College London, UK.
- Riley Williams, MSc student (2018). Research area: Deep learning. Now: Security Engineer, Sophos, UK.
- William Miguel Rosado, MSc student (2018). Research area: Biological network analysis. Now: Developer, Kalypso Rockwell, MX.