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.
Members
Evgenii Lobzaev
PhD student, 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.
PhD student, 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
PhD student, 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.
PhD student, 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.
Aidan Marnane
PhD student, 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.
PhD student, 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.
Martyna Kasprzik
Honours student, BSc Molecular Genetics, Data Science CDT, University of Edinburgh
Short bio: I am a fourth year student doing BSc Molecular Genetics at University of Edinburgh and I joined the lab to undertake my Honours Research Project. I am very interested in bioinformatics, particularly in using artificial intelligence in clinical research. My work will focus on using machine learning to assess synthetic enzymes for replacement therapies. I am currently also participating in a EuCanImage project - a European cancer imaging platform for AI in oncology. In my free time I enjoy reading and painting.
Honours student, BSc Molecular Genetics, Data Science CDT, University of Edinburgh
Short bio: I am a fourth year student doing BSc Molecular Genetics at University of Edinburgh and I joined the lab to undertake my Honours Research Project. I am very interested in bioinformatics, particularly in using artificial intelligence in clinical research. My work will focus on using machine learning to assess synthetic enzymes for replacement therapies. I am currently also participating in a EuCanImage project - a European cancer imaging platform for AI in oncology. In my free time I enjoy reading and painting.
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.