Optimization of regulatory DNA with active learning
Shena Y., Kudlab G. & Oyarzún D.A.
Computational and Structural Biotechnology Journal 27, 4384–4392, 2025
Impact
Publications
Canonical transcription termination mechanisms explain a minority of operons in cyanobacteria
Cascino J.A., Dierksheide K.J., Vishwakarma R.K., Yuzenkova Y., Babitzke P., Murakami K.S. & Li G.-W.
bioRxiv , , 2025
Emerging trends in genome integration tools for precision engineering of diverse bacterial species
Rohmat R.K., Irvine T., Joshi S.H.-N., Bailey A., Jenkins C., Ulaeto D., Buscaill P. & Gorochowski T.E.
Synthetic Biology , , 2025
SHARK: a specialized host for assembling R6K plasmids
Joshi S.H.-N., Jenkins C., Ulaeto D. & Gorochowski T.E.
bioRxiv , , 2025
Discovery of Electron Hole-hopping Redox Mutations in Myoglobin by Deep Mutational Learning
Küng C., Dalkıran A., Vanella R., Oyarzún D.A. & Nash M.A.
bioRxiv , , 2025
Data-driven inference of digital twins for high-throughput phenotyping of motile and light-responsive microorganisms
Giusti A., Salzano D., di Bernardo M. & Gorochowski T.E.
Journal of the Royal Society Interface 22, 20250780, 2025
Characterization of recombinase-based genetic parts and circuits using nanopore sequencing
Greco F.V., Cameron S.K., Joshi S.H.-N., Brophy J.A.N., Grierson C.S. & Gorochowski T.E.
bioRxiv , , 2025
The Japan-UK Synthetic Biology Conference, Spring 2025: strengthening global links to engineer biology
Gorochowski T.E., Brockhurst M.A., Ceroni F., Iwasaki Y.W. & Yachie N.
ACS Synthetic Biology 14, 1873-1878, 2025
From FAIR to CURE: Guidelines for Computational Models of Biological Systems
Sauro H.M., ..., Gorochowski T.E., ... & Moraru I.
arXiv , 2502.15597, 2025
Cas9-based enrichment for targeted long-read metabarcoding
Nikolaeva-Reynolds L., Cammies C., Crichton R. & Gorochowski T.E.
Royal Society Open Science 12, 242110, 2025
Engineering Biology Applications for Environmental Solutions: Potential and Challenges
Lea-Smith D.J., Hassard F., Coulon F., Partridge N., Horsfall L., Parker K.D.J., Smith R.D.J., McCarthy R.R., McKew B., Gutierrez T., Kumar V., Dotro G., Yang Z., EBIC partners & Krasnogor N.
Nature Communications 16, 3538, 2025
Talks
Optimising genetically engineered microorganisms using 'Ecological Wind Tunnels', Fundamental to Applied Biosciences Conference, Bristol, UK, 2025 (Joseph Pennycook)
Unravelling the role of ecology when engineering biology, UKRI Engineering Biology Mission Hubs and Mission Awards Science Showcase, Manchester, UK, 2025 (Joseph Pennycook)
Does ecological stress alter the function of genetically engineered cyanobacteria?, Molecular Microbial Ecology Conference, Birmingham, UK, 2025 (Joseph Pennycook)
Cyanobacteria engineering for restoring environment (CYBER), AlgaeCytes, Kent, UK, 2025 (Shylaja Mohandass)
Genome-wide identification of putative neutral sites for engineering biology, UKRI Engineering Biology Mission Hubs and Mission Awards Science Showcase, Manchester, UK, 2025 (Yasir Akbar)
Sequence-to-expression optimization with machine learning, UKRI Engineering Biology Mission Hubs and Mission Awards Science Showcase, Manchester, UK, 2025 (Yasir Akbar)
???, Industrial Biotechnology Innovation Catalyst (IBIC) Conference, Manchester, UK, 2025 (Thierry Le Goff, NML)
???, ASEAN-UK Regional Training & Workshop, London, UK, 2025 (Julian Braybrook, NML)
Deep mutational learning for effective enzyme engineering, Synthetic Biology UK, London, UK, 2025 (Alperen Dalkıran)
Biological design with machine learning and limited data, AI Hub in Generative Models, UCL, London, UK, 2025 (Diego Oyarzún)
Biological design with machine learning and limited data, University of Cambridge, Cambridge, UK, 2025 (Diego Oyarzún)
Sequence-to-expression prediction using mRNA secondary structure information (invited keynote), PEGS Europe, Lisbon, Portugal, 2025 (Diego Oyarzún)
Sequencing-based methods for accelerated cellular programming, Japan-UK Synthetic Biology Confrerence, Osaka, Japan, 2025 (Thomas Gorochowski)
Programming biological systems across scales using synthetic biology (invited keynote), 29th IEEE International Symposium on Asynchronous Circuits and Systems, Portland, USA, 2025 (Thomas Gorochowski)
What does the future of synthetic biology look like (invited keynote), Microbial Engineering Symposium, Cambridge, UK, 2025 (Thomas Gorochowski)
Data-centric approaches to biological design and engineering (invited keynote), Multimodal AI Conference, London, UK, 2025 (Thomas Gorochowski)
???, Interconnections and Cross-Regulation of Gene Expression Processes, Gottingen, Germany, 2025 (Yulia Yuzenkova)
Programming biological systems across scales using synthetic biology, CBS Research Seminar, Montpellier, France, 2025 (Thomas Gorochowski)
Deciphering Picosynechococcus genome to identify neutral sites for synthetic barcode integration, EBIC ECR Conference, Edinburgh, UK, 2025 (Yasir Akbar)
???, Annual International RNA Polymerase Workshop, Birmingham, UK, 2025 (Moubani Chakraborty)
Posters
???, UKRI Engineering Biology Mission Hubs and Mission Awards Science Showcase, Manchester, UK, 2025 (Moubani Chakraborty)
From parts to program – genetic toolkit for reprogramming cyanobacteria, UKRI Engineering Biology Mission Hubs and Mission Awards Science Showcase, Manchester, UK, 2025 (Shylaja Mohandass)
Genome-wide identification of putative neutral sites for engineering biology, Synthetic Biology UK, London, UK, 2025 (Yasir Akbar)
Outreach and Wider Engagement
The science of microplastics: what exactly are microplastics and why we should care, The Science Tapes Podcast, Bristol, UK, 2025 (Joseph Pennycook)
Industrial visit, AlgaeCytes, Kent, UK, 2025 (Shylaja Mohandass)
Funding
International Exchange, Royal Society, IES\R1\251443, 2025–2027 (£12,000; PI: Thomas Gorochowski, Co-I: Samuel Schaffter)
Bio-Security Prevent and Respond Programme, DSIT, , 2025–2026 (???; ???)
Travel Scholarship, AlgaeCytes, , 2025 (£200; PI: Shylaja Mohandass)
Engineering Biology Seed Corn, UKRI, BB/Y007638/1, 2025–2026 (£70,088; PI: Thomas Gorochowski, Co-Is: Christopher Clements, Diego Oyarzún, Natalio Krasnogor, Yulia Yuzenkova)
Engineering Biology Mission Award, UKRI, BB/Y007638/1, 2024–2026 (£1.9M; PI: Thomas Gorochowski, Co-Is: Christopher Clements, Diego Oyarzún, Natalio Krasnogor, Yulia Yuzenkova)
