Projects per year
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.
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):
Skills and expertise
- metabolic modelling
- Machine Learning
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Collaborations and top research areas from the last five years
Recent external collaboration on country/territory level. Dive into details by clicking on the dots or
Projects
- 2 Active
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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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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 AccessFile1 Citation (Scopus)8 Downloads (Pure) -
Genome-scale metabolic models reveal determinants of phenotypic differences in non-Saccharomyces yeasts
Pettersen, J. P., Castillo, S., Jouhten, P. & Almaas, E., Dec 2023, In: BMC Bioinformatics. 24, 1, 19 p., 438.Research output: Contribution to journal › Article › Scientific › peer-review
Open Access5 Citations (Scopus) -
Predictive evolution of metabolic phenotypes using model-designed environments
Jouhten, P., Konstantinidis, D., Pereira, F., Andrejev, S., Grkovska, K., Castillo, S., Ghiaci, P., Beltran, G., Almaas, E., Mas, A., Warringer, J., Gonzalez, R., Morales, P. & Patil, K. R., 1 Oct 2022, In: Molecular Systems Biology. 18, 10, e10980.Research output: Contribution to journal › Article › Scientific › peer-review
Open Access12 Citations (Scopus) -
Lager Yeast Design Through Meiotic Segregation of a Saccharomyces cerevisiae × Saccharomyces eubayanus Hybrid
Krogerus, K., Magalhães, F., Castillo, S., Peddinti, G., Vidgren, V., De Chiara, M., Yue, J.-X., Liti, G. & Gibson, B., 16 Sept 2021, In: Frontiers in Fungal Biology. 2, 17 p., 733655.Research output: Contribution to journal › Article › Scientific › peer-review
Open Access13 Citations (Scopus) -
Yeast Genome-Scale Metabolic Models for Simulating Genotype-Phenotype Relations
Castillo, S., Patil, K. R. & Jouhten, P., 2019, Yeasts in Biotechnology and Human Health. Sá-Correia, I. (ed.). Springer, Vol. 58. p. 111-133 23 p. (Progress in molecular and subcellular biology).Research output: Chapter in Book/Report/Conference proceeding › Chapter or book article › Scientific › peer-review
11 Citations (Scopus)
Datasets
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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
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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