Team
Giovanni Stracquadanio, PhD FHEA - Principal Investigator
UKRI EPSRC fellow. Senior Lecturer in Synthetic 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 an UKRI EPSRC fellow, Senior Lecturer in Synthetic Biology 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
Michael Herrera
University of Edinburgh
Short bio: I am presently a Research Assistant within the Stracquadanio group, responsible for implementing high-throughput wetlab screens and analyses as part of the GREET (Generative Recombinant Enzyme Engineering for Therapeutics) project. Within this role, I test and validate our in-house generative deep-learning models towards the development of new enzyme therapeutics. Prior to this role, I obtained my Bachelor's degree in Medicinal Chemistry from the University of Keele (2015, first class) and worked as a Chemistry Research Assistant for Ingenza Ltd (2016-2018). I am currently completing my IBioIC/BBSRC-funded Ph.D studentship with Prof. Dominic Campopiano in biocatalysis. Outside of work, I am a multi-instrumentalist, songwriter and a keen birder.
University of Edinburgh
Short bio: I am presently a Research Assistant within the Stracquadanio group, responsible for implementing high-throughput wetlab screens and analyses as part of the GREET (Generative Recombinant Enzyme Engineering for Therapeutics) project. Within this role, I test and validate our in-house generative deep-learning models towards the development of new enzyme therapeutics. Prior to this role, I obtained my Bachelor's degree in Medicinal Chemistry from the University of Keele (2015, first class) and worked as a Chemistry Research Assistant for Ingenza Ltd (2016-2018). I am currently completing my IBioIC/BBSRC-funded Ph.D studentship with Prof. Dominic Campopiano in biocatalysis. Outside of work, I am a multi-instrumentalist, songwriter and a keen birder.
Sofija Semeniuk
University of Edinburgh
Short bio: I am a Postdoctoral Research Associate and I am working on developing a CRISPR-based screening platform for synthetic lethality (SL), aiming at engineering SL-based kill switches for CAR T-cell therapies. My previous experience includes completing a Genetics BSc at Vilnius University, and then obtaining an MSc in Synthetic Biology at the University of Edinburgh. I then continued to pursue a PhD and was developing synthetic Notch (synNotch) receptors for monitoring interactions between cancer cells and immune cells in Elise Cachat lab. Outside of work I enjoy doing sports like climbing and ice skating, and playing music.
University of Edinburgh
Short bio: I am a Postdoctoral Research Associate and I am working on developing a CRISPR-based screening platform for synthetic lethality (SL), aiming at engineering SL-based kill switches for CAR T-cell therapies. My previous experience includes completing a Genetics BSc at Vilnius University, and then obtaining an MSc in Synthetic Biology at the University of Edinburgh. I then continued to pursue a PhD and was developing synthetic Notch (synNotch) receptors for monitoring interactions between cancer cells and immune cells in Elise Cachat lab. Outside of work I enjoy doing sports like climbing and ice skating, and playing music.
PhD students
Evgenii Lobzaev
Biomedical AI CDT, University of Edinburgh
Short bio: I am a PhD student of the Biomedical AI CDT funded by UKRI. 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.
Biomedical AI CDT, University of Edinburgh
Short bio: I am a PhD student of the Biomedical AI CDT funded by UKRI. 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.
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.
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.
Sebestyen Kamp
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.
Aidan Marnane
Data Science CDT, University of Edinburgh
Short bio: I am PhD student on the UKRI EPSRC CDT in Datascience. My research work focuses on semi-supervised learning and clustering over patients' networks. Prior to this, I obtained a BSc in Mathematics from the University College Cork, and an MSc(R) in Datascience from the University of Edinburgh.
Data Science CDT, University of Edinburgh
Short bio: I am PhD student on the UKRI EPSRC CDT in Datascience. My research work focuses on semi-supervised learning and clustering over patients' networks. Prior to this, I obtained a BSc in Mathematics from the University College Cork, and an MSc(R) in Datascience from the University of Edinburgh.
Recent alumni
- 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.