Personal profile
Research interests
I'm passionate about AI, mainly generative AI, and all kinds of simulations of reality, including whole genome metabolic modeling and physical atomistic simulations.
I've created several tools for the automatic reconstruction of metabolic models, such as CoReCo and CarveFungi.
I've built an AI model for the generation of novel PHA synthases together with Tuula Tenkanen.
Recently, I've been working on automatic enzyme mining in the Alphafold database and enzyme annotation based on the active and binding sites.
Skills and expertise
- metabolic modelling
- Machine Learning
Expertise related to UN Sustainable Development Goals
In 2015, UN member states agreed to 17 global Sustainable Development Goals (SDGs) to end poverty, protect the planet and ensure prosperity for all. This person’s work contributes towards the following SDG(s):
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SDG 3 Good Health and Well-being -
SDG 9 Industry, Innovation, and Infrastructure -
SDG 15 Life on Land
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Collaborations and top research areas from the last five years
Projects
- 3 Active
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FoodID: NSF Food Innovation and Diversification to Advance the Bioeconomy
Honkapää, K. (Manager), Sözer, N. (Owner), Nordström, E. (Owner), Ollila, S. (Manager), Aalto, A. (Participant), Uusitalo, J. (Participant), Småros, F. (Participant), Troullier, M. (Participant), Pietiäinen, M. (Participant), Juvonen, R. (Participant), Aisala, H. (Participant), Tsitko, I. (Participant), Kortekangas, A. (Participant), Lille, M. (Participant), Alakomi, H.-L. (Participant), Castillo, S. (Participant), Alaraasakka, R.-M. (Participant), Tiainen, V. (Participant) & Nisov, A. (Participant)
Funded by Research Council of Finland, Business Finland
1/01/25 → 31/12/27
Project: Business Finland project
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FinBioFAB: Finnish BioFoundry for Advanced Biomanufacturing
Barth, D. (Manager), Nygård, Y. (PI), Koponen, T. (Participant), Girych, M. (Participant), Castillo, S. (Participant), Åkerman, M. (Participant), Lehtinen, S. (Participant), Nakari-Setälä, T. (Owner), Jäntti, J. (Participant), Healy-Rehn, M. (Participant), Laukkanen, A. (Participant), Aro, N. (Participant), Hentula, M. (Participant), Tenkanen, T. (Participant), Choo, H. (Participant) & Nguyen, T. (Participant)
1/01/25 → 31/12/29
Project: Business Finland project
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BIOINDUSTRY 4.0: RI services to promote deep digitalization of Industrial Biotechnology - towards smart biomanufacturing
Blomberg, P. (Manager), Barth, D. (Participant), Penttilä, M. (Owner), Peltonen, K. (Participant), Peddinti, G. (Participant), Castillo, S. (Participant), Mattila, H. (Participant), Jäntti, J. (Participant), Mäyrä, A. (Participant), Havisto, J. (Participant), Hietala, E. (Participant), Tenhunen, J. (Participant), Kögler, M. (Participant), Toivari, M. (Participant) & Mojzita, D. (Participant)
1/01/23 → 31/12/26
Project: EU project
Research output
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ActSeek: Fast and accurate search algorithm of active sites in Alphafold database
Castillo, S. & Ollila, O. H. S., Aug 2025, In: Bioinformatics. 41, 8, btaf424.Research output: Contribution to journal › Article › Scientific › peer-review
Open AccessFile58 Downloads (Pure) -
Discovery of Cortinarius O-methyltransferases for the heterologous production of dermolutein and physcion
Jetha, P., Mojzita, D., Maiorova, N., de Ruijter, J. C., Maaheimo, H., Hilditch, S., Peddinti, G., Castillo, S., Toivari, M., Penttilä, M. & Molnár, I., 2025, In: Biotechnology for Biofuels and Bioproducts. 18, 1, 25.Research output: Contribution to journal › Article › Scientific › peer-review
Open AccessFile3 Link opens in a new tab Citations (Scopus)105 Downloads (Pure) -
Model-guided chemical environment and metabolic network design to couple pathways with cell fitness
Kakko von Koch, N., Tenkanen, T., Castillo, S., Vidgren, V., Koponen, T., Krogerus, K., Penttilä, M. & Jouhten, P., Dec 2025, In: Metabolic Engineering Communications. 21, e00267.Research output: Contribution to journal › Article › Scientific › peer-review
Open Access -
Solid agrifood side streams as potential feedstock for microbial biomass and precision fermentation
Haajanen, E., Uusitalo, J., Juvonen, R., Hörhammer, H., Castillo, S., Ritala, A. & Nordlund, E., Dec 2025, In: Bioresource Technology Reports. 32, 102442.Research output: Contribution to journal › Article › Scientific › peer-review
Open AccessFile1 Link opens in a new tab Citation (Scopus) -
Structure-filtered search of enzyme variants
Porri, L., Castillo, S. & Jouhten, P., Jan 2025, In: Computational and Structural Biotechnology Journal. 27, p. 4226-4231 6 p.Research output: Contribution to journal › Article › Scientific › peer-review
Open Access
Datasets
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Genome wide analysis of protein production load in Trichoderma reesei
Pakula, T. (Contributor), Nygren, H. (Contributor), Barth, D. (Contributor), Heinonen, M. (Contributor), Castillo, S. (Contributor) & Arvas, M. (Contributor), Figshare, 28 Jun 2016
DOI: 10.6084/m9.figshare.c.3603251.v1
Dataset
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Inheritance of brewing-relevant phenotypes in constructed Saccharomyces cerevisiae × Saccharomyces eubayanus hybrids
Krogerus, K. (Contributor), Seppänen-Laakso, T. (Contributor), Castillo, S. (Contributor) & Gibson, B. (Contributor), Figshare, 21 Apr 2017
DOI: 10.6084/m9.figshare.c.3749447.v1
Dataset