Scientific Publications

2025

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

2024

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

2023

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

2022

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

2021

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

2017

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