Scientific Publications

Massei, R., Busch, W., Serrano-Solano, B., Bernt, M., Scholz, S., Nicolay, E. K., Bohring, H., & Bumberger, J. (2025). High-content screening (HCS) workflows for FAIR image data management with OMERO. Scientific Reports, 15(1), 16236. https://doi.org/10.1038/s41598-025-00720-0

Kostrykin, L., Depoortere, B., Chiang, D., Klumpe, S., Massei, R., Kalaš, M., Fouilloux, A., & Serrano-Solano, B. (2025). Development of FAIR image analysis workflows and training in Galaxy. https://doi.org/10.37044/osf.io/hbw6m_v1

The Galaxy Community, Abueg, L. A. L., Afgan, E., Allart, O., Awan, A. H., Bacon, W. A., Baker, D., Bassetti, M., Batut, B., Bernt, M., Blankenberg, D., Bombarely, A., Bretaudeau, A., Bromhead, C. J., Burke, M. L., Capon, P. K., Čech, M., Chavero-Díez, M., Chilton, J. M., … Zoabi, R. (2024). The Galaxy platform for accessible, reproducible, and collaborative data analyses: 2024 update. Nucleic Acids Research, 52(W1), W83–W94. https://doi.org/10.1093/nar/gkae410

Callegari, A., Kueblbeck, M., Morero, N. R., Serrano-Solano, B., & Ellenberg, J. (2024). Rapid generation of homozygous fluorescent knock-in human cells using CRISPR–Cas9 genome editing and validation by automated imaging and digital PCR screening. Nature Protocols, 1–41. https://doi.org/10.1038/s41596-024-01043-6

Kostrykin, L., Woller, T., Kalaš, M., Özdemir, B., Andrade Buono, R., Sun, Y., Kumar, A., Goué, N., Grüning, B., Serrano-Solano, B., & Fouilloux, A. (2024). Enhancing the image analysis community in Galaxy. https://doi.org/10.37044/osf.io/w8dsz

Hiltemann, S., Rasche, H., Gladman, S., Hotz, H.-R., Larivière, D., Blankenberg, D., Jagtap, P. D., Wollmann, T., Bretaudeau, A., Goué, N., Griffin, T. J., Royaux, C., Le Bras, Y., Mehta, S., Syme, A., Coppens, F., Droesbeke, B., Soranzo, N., Bacon, W., … Batut, B. (2023). Galaxy Training: A powerful framework for teaching! PLOS Computational Biology, 19(1), e1010752. https://doi.org/10.1371/journal.pcbi.1010752

Kemmer, I., Keppler, A., Serrano-Solano, B., Rybina, A., Özdemir, B., Bischof, J., El Ghadraoui, A., Eriksson, J. E., & Mathur, A. (2023). Building a FAIR image data ecosystem for microscopy communities. Histochemistry and Cell Biology, 160(3), 199–209. https://doi.org/10.1007/s00418-023-02203-7

David, R., Rybina, A., Burel, J., Heriche, J., Audergon, P., Boiten, J., Coppens, F., Crockett, S., Exter, K., Fahrner, S., Fratelli, M., Goble, C., Gormanns, P., Grantner, T., Grüning, B., Gurwitz, K. T., Hancock, J. M., Harmse, H., Holub, P., … Gribbon, P. (2023). “Be sustainable”: EOSC‐Life recommendations for implementation of FAIR principles in life science data handling. The EMBO Journal, 42(23), e115008. https://doi.org/10.15252/embj.2023115008

Zulueta-Coarasa, T., Jug, F., Mathur, A., Moore, J., Muñoz-Barrutia, A., Anita, L., Babalola, K., Bankhead, P., Gilloteaux, P., Gogoberidze, N., Jones, M., Kleywegt, G. J., Korir, P., Kreshuk, A., Yoldaş, A. K., Marconato, L., Narayan, K., Norlin, N., Oezdemir, B., … Hartley, M. (2023). MIFA: Metadata, Incentives, Formats, and Accessibility guidelines to improve the reuse of AI datasets for bioimage analysis (No. arXiv:2311.10443). arXiv. https://doi.org/10.48550/arXiv.2311.10443

Serrano-Solano, B., Fouilloux, A., Eguinoa, I., Kalaš, M., Grüning, B., & Coppens, F. (2022). Galaxy: A Decade of Realising CWFR Concepts. Data Intelligence, 4(2), 358–371. https://doi.org/10.1162/dint_a_00136

The Galaxy Community, Afgan, E., Nekrutenko, A., Grüning, B. A., Blankenberg, D., Goecks, J., Schatz, M. C., Ostrovsky, A. E., Mahmoud, A., Lonie, A. J., Syme, A., Fouilloux, A., Bretaudeau, A., Nekrutenko, A., Kumar, A., Eschenlauer, A. C., DeSanto, A. D., Guerler, A., Serrano-Solano, B., … Briggs, P. J. (2022). The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2022 update. Nucleic Acids Research, 50(W1), W345–W351. https://doi.org/10.1093/nar/gkac247

Muller, C., Serrano-Solano, B., Sun, Y., Tischer, C., & Hériché, J.-K. (2022). The Image Data Explorer: Interactive exploration of image-derived data. PLOS ONE, 17(9), e0273698. https://doi.org/10.1371/journal.pone.0273698

Rasche, H., Hyde, C., Davis, J., Gladman, S., Coraor, N., Bretaudeau, A., Cuccuru, G., Bacon, W., Serrano-Solano, B., Hillman-Jackson, J., Hiltemann, S., Zhou, M., Grüning, B., & Stubbs, A. (2022). Training Infrastructure as a Service. GigaScience, 12, giad048. https://doi.org/10.1093/gigascience/giad048

Goble, C., Soiland-Reyes, S., Bacall, F., Owen, S., Williams, A., Eguinoa, I., Droesbeke, B., Leo, S., Pireddu, L., Rodríguez-Navas, L., Fernández, J. M., Capella-Gutierrez, S., Ménager, H., Grüning, B., Serrano-Solano, B., Ewels, P., & Coppens, F. (2021). Implementing FAIR Digital Objects in the EOSC-Life Workflow Collaboratory. https://doi.org/10.5281/ZENODO.4605654

Serrano-Solano, B., Föll, M. C., Gallardo-Alba, C., Erxleben, A., Rasche, H., Hiltemann, S., Fahrner, M., Dunning, M. J., Schulz, M. H., Scholtz, B., Clements, D., Nekrutenko, A., Batut, B., & Grüning, B. A. (2021). Fostering accessible online education using Galaxy as an e-learning platform. PLOS Computational Biology, 17(5), e1008923. https://doi.org/10.1371/journal.pcbi.1008923

Gallardo-Alba, C., Grüning, B., & Serrano-Solano, B. (2021). A constructivist-based proposal for bioinformatics teaching practices during lockdown. PLOS Computational Biology, 17(5), e1008922. https://doi.org/10.1371/journal.pcbi.1008922

Serrano-Solano, B., Díaz Ramos, A., Hériché, J.-K., & Ranea, J. A. G. (2017). How can functional annotations be derived from profiles of phenotypic annotations? BMC Bioinformatics, 18(1), 96. https://doi.org/10.1186/s12859-017-1503-5