Most important publications
Galaxy-ML: An accessible, reproducible, and scalable machine learning toolkit for biomedicine
Gu, Q., Kumar, A., Bray, S., Creason, A., Khanteymoori, A., Jalili, V., Björn Grüning & Goecks, J.
PLOS Computational Biology, 17, e1009014. doi.org/10.1371/journal.pcbi.1009014 (June 2021)
Ready-to-use public infrastructure for global SARS-CoV-2 monitoring
Maier, W., Bray, S., van den Beek, M., Bouvier, D., Coraor, N., Miladi, M., Singh, B., De Argila, J. R., Baker, D., Roach, N., Gladman, S., Coppens, F., Martin, D. P., Lonie, A., Björn Grüning, Kosakovsky Pond, S. L. & Nekrutenko, A.
Nature Biotechnology, 1–2. https://www.nature.com/articles/s41587-021-01069-1 (September 2021)
User-friendly, scalable tools and workflows for single-cell RNA-seq analysis
Moreno, P., Huang, N., Manning, J. R., Mohammed, S., Solovyev, A., Polanski, K., Bacon, W., Chazarra, R., Talavera-López, C., Doyle, M. A., Marnier, G., Björn Grüning, Rasche, H., George, N., Fexova, S. K., Alibi, M., Miao, Z., Perez-Riverol, Y., Haeussler, M., Brazma, A., Teichmann, S., Meyer, K. B. & Papatheodorou, I.
Nature Methods.
https://doi.org/10.1038/s41592-021-01102-w (March 2021)
A SARS-CoV-2 sequence submission tool for the European Nucleotide Archive
Roncoroni, M., Droesbeke, B., Eguinoa, I., Ruyck, K. D., D’Anna, F., Yusuf, D., Björn Grüning, Backofen, R. & Coppens, F.
Bioinformatics. https://doi.org/10.1093/bioinformatics/btab421 (June 2021)
Fostering accessible online education using Galaxy as an e-learning platform
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. & Björn Grüning
PLOS Computational Biology, 17, 1–10. doi.org/10.1371/journal.pcbi.1008923 (May 2021)
Scool: a new data storage format for single-cell Hi-C data
Wolff, J., Abdennur, N., Backofen, R. & Björn Grüning
Bioinformatics. https://doi.org/10.1093/bioinformatics/btab243 (May 2021)
Software engineering for scientific big data analysis
Grüning, B. A., Lampa, S., Vaudel, M. & Blankenberg, D.
GigaScience, 8. doi.org/10.1093/gigascience/giz054 (May 2019)
The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2018 update
Afgan, E., Baker, D., Batut, B., van den Beek, M., Bouvier, D., Čech, M., Chilton, J., Clements, D., Coraor, N., Björn Grüning, Guerler, A., Hillman-Jackson, J., Hiltemann, S., Jalili, V., Rasche, H., Soranzo, N., Goecks, J., Taylor, J., Nekrutenko, A. & Blankenberg, D.
Nucleic Acids Research, 46, W537–W544. http://dx.doi.org/10.1093/nar/gky379 (2018)
Community-Driven Data Analysis Training for Biology
Batut, B., Hiltemann, S., Bagnacani, A., Baker, D., Bhardwaj, V., Blank, C., Bretaudeau, A., Brillet-Guéguen, L., Čech, M., Chilton, J., Clements, D., Doppelt-Azeroual, O., Erxleben, A., Freeberg, M. A., Gladman, S., Hoogstrate, Y., Hotz, H.-R., Houwaart, T., Jagtap, P., Larivière, D., Le Corguillé, G., Manke, T., Mareuil, F., Ramírez, F., Ryan, D., Sigloch, F. C., Soranzo, N., Wolff, J., Videm, P., Wolfien, M., Wubuli, A., Yusuf, D., Taylor, J., Backofen, R., Nekrutenko, A. & Björn Grüning
Cell Systems, 6, 752–758.e1. https://doi.org/10.1016/j.cels.2018.05.012 (June 2018)
Bioconda: sustainable and comprehensive software distribution for the life sciences
Björn A. Grüning, Dale, R., Sjödin, A., Chapman, B. A., Rowe, J., Tomkins-Tinch, C. H., Valieris, R. & Köster, J. Nature Methods, 15, 475–476. doi.org/10.1038/s41592-018-0046-7 (July 2018)