Next-generation sequencing reveals novel rare fusion events with functional implication in prostate cancer von Teles Alves, I, Hartjes, T, McClellan, E, Hiltemann, S, Böttcher, R, Dits, N, Temanni, M R, Janssen, B, van Workum, W, van der Spek, P, Stubbs, A, de Klein, A, Eussen, B, Trapman, J, Jenster, G

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The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2022 update von Afgan, Enis, Nekrutenko, Anton, Grüning, Bjórn A, Blankenberg, Daniel, Goecks, Jeremy, Schatz, Michael C, Ostrovsky, Alexander E, Mahmoud, Alexandru, Lonie, Andrew J, Syme, Anna, Fouilloux, Anne, Bretaudeau, Anthony, Kumar, Anup, Eschenlauer, Arthur C, DeSanto, Assunta D, Guerler, Aysam, Serrano-Solano, Beatriz, Batut, Bérénice, Grüning, Björn A, Langhorst, Bradley W, Carr, Bridget, Raubenolt, Bryan A, Hyde, Cameron J, Bromhead, Catherine J, Barnett, Christopher B, Royaux, Coline, Gallardo, Cristóbal, Fornika, Daniel J, Baker, Dannon, Bouvier, Dave, Clements, Dave, de Lima Morais, David A, Tabernero, David Lopez, Lariviere, Delphine, Nasr, Engy, Zambelli, Federico, Heyl, Florian, Psomopoulos, Fotis, Coppens, Frederik, Price, Gareth R, Cuccuru, Gianmauro, Corguillé, Gildas Le, Von Kuster, Greg, Akbulut, Gulsum Gudukbay, Rasche, Helena, Hotz, Hans-Rudolf, Eguinoa, Ignacio, Makunin, Igor, Ranawaka, Isuru J, Taylor, James P, Joshi, Jayadev, Hillman-Jackson, Jennifer, Chilton, John M, Kamali, Kaivan, Suderman, Keith, Poterlowicz, Krzysztof, Yvan, Le Bras, Lopez-Delisle, Lucille, Sargent, Luke, Bassetti, Madeline E, Tangaro, Marco Antonio, van den Beek, Marius, Čech, Martin, Bernt, Matthias, Fahrner, Matthias, Tekman, Mehmet, Föll, Melanie C, Crusoe, Michael R, Roncoroni, Miguel, Kucher, Natalie, Coraor, Nate, Stoler, Nicholas, Rhodes, Nick, Soranzo, Nicola, Pinter, Niko, Goonasekera, Nuwan A, Moreno, Pablo A, Videm, Pavankumar, Melanie, Petera, Mandreoli, Pietro, Jagtap, Pratik D, Gu, Qiang, Weber, Ralf J M, Lazarus, Ross, Vorderman, Ruben H P, Hiltemann, Saskia, Golitsynskiy, Sergey, Garg, Shilpa, Bray, Simon A, Gladman, Simon L, Leo, Simone, Mehta, Subina P, Griffin, Timothy J, Jalili, Vahid, Yves, Vandenbrouck, Wen, Victor, Nagampalli, Vijay K, Bacon, Wendi A, de Koning, Willem, Maier, Wolfgang

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The Galaxy platform for accessible, reproducible, and collaborative data analyses: 2024 update von Abueg, Linelle Ann L, Afgan, Enis, Allart, Olivier, Awan, Ahmed H, Bacon, Wendi A, Baker, Dannon, Bassetti, Madeline, Batut, Bérénice, Bernt, Matthias, Blankenberg, Daniel, Bombarely, Aureliano, Bretaudeau, Anthony, Bromhead, Catherine J, Burke, Melissa L, Capon, Patrick K, Čech, Martin, Chavero-Díez, María, Chilton, John M, Collins, Tyler J, Coppens, Frederik, Coraor, Nate, Cuccuru, Gianmauro, Cumbo, Fabio, Davis, John, De Geest, Paul F, de Koning, Willem, Demko, Martin, DeSanto, Assunta, Begines, José Manuel Domínguez, Doyle, Maria A, Droesbeke, Bert, Erxleben-Eggenhofer, Anika, Föll, Melanie C, Formenti, Giulio, Fouilloux, Anne, Gangazhe, Rendani, Genthon, Tanguy, Goecks, Jeremy, Beltran, Alejandra N Gonzalez, Goonasekera, Nuwan A, Goué, Nadia, Griffin, Timothy J, Grüning, Björn A, Guerler, Aysam, Gundersen, Sveinung, Gustafsson, Ove Johan Ragnar, Hall, Christina, Harrop, Thomas W, Hecht, Helge, Heidari, Alireza, Heisner, Tillman, Heyl, Florian, Hiltemann, Saskia, Hotz, Hans-Rudolf, Hyde, Cameron J, Jagtap, Pratik D, Jakiela, Julia, Johnson, James E, Joshi, Jayadev, Jossé, Marie, Jum’ah, Khaled, Kalaš, Matúš, Kamieniecka, Katarzyna, Kayikcioglu, Tunc, Konkol, Markus, Kostrykin, Leonid, Kucher, Natalie, Kumar, Anup, Kuntz, Mira, Lariviere, Delphine, Lazarus, Ross, Bras, Yvan Le, Corguillé, Gildas Le, Lee, Justin, Leo, Simone, Liborio, Leandro, Libouban, Romane, Tabernero, David López, Lopez-Delisle, Lucille, Los, Laila S, Mahmoud, Alexandru, Makunin, Igor, Marin, Pierre, Mehta, Subina, Mok, Winnie, Moreno, Pablo A, Morier-Genoud, François, Mosher, Stephen, Müller, Teresa, Nasr, Engy, Nekrutenko, Anton, Nelson, Tiffanie M, Oba, Asime J, Ostrovsky, Alexander, Polunina, Polina V, Poterlowicz, Krzysztof, Price, Elliott J, Price, Gareth R, Rasche, Helena, Raubenolt, Bryan

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Fostering accessible online education using Galaxy as an e-learning platform von Solano, B.S, 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

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FAIR genomes metadata schema promoting next generation sequencing data reuse in Dutch healthcare and research von Velde, K.J. van der, Singh, G., Kaliyaperumal, R., Liao, X.F., Ridder, S. de, Rebers, S., Kerstens, H.H.D., Andrade, F. de, Reeuwijk, J. van, Gruyter, F.E. de, Hiltemann, S., Ligtvoet, M., Weiss, M.M., Deutekom, H.W.M. van, Jansen, A.M.L., Stubbs, A.P., Vissers, L.E.L.M., Laros, J.F.J., Enckevort, E. van, Stemkens, D., Hoen, P.A.C.T., Belien, J.A.M., Gijn, M.E. van, Swertz, M.A.

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Galactic Circos: User-friendly Circos plots within the Galaxy platform von Rasche, Helena, Hiltemann, Saskia

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Comparison of Illumina versus Nanopore 16S rRNA Gene Sequencing of the Human Nasal Microbiota von Heikema, Astrid P, Horst-Kreft, Deborah, Boers, Stefan A, Jansen, Rick, Hiltemann, Saskia D, de Koning, Willem, Kraaij, Robert, de Ridder, Maria A J, van Houten, Chantal B, Bont, Louis J, Stubbs, Andrew P, Hays, John P

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WeFaceNano: a user-friendly pipeline for complete ONT sequence assembly and detection of antibiotic resistance in multi-plasmid bacterial isolates von Heikema, Astrid P, Jansen, Rick, Hiltemann, Saskia D, Hays, John P, Stubbs, Andrew P

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The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2018 update von Afgan, Enis, Baker, Dannon, Batut, Bérénice, van den Beek, Marius, Bouvier, Dave, Čech, Martin, Chilton, John, Clements, Dave, Coraor, Nate, Grüning, Björn A, Guerler, Aysam, Hillman-Jackson, Jennifer, Hiltemann, Saskia, Jalili, Vahid, Rasche, Helena, Soranzo, Nicola, Goecks, Jeremy, Taylor, James, Nekrutenko, Anton, Blankenberg, Daniel

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The diagnostic value of nasal microbiota and clinical parameters in a multi-parametric prediction model to differentiate bacterial versus viral infections in lower respiratory trac... von Li, Yunlei, van Houten, Chantal B, Boers, Stefan A, Jansen, Ruud, Cohen, Asi, Engelhard, Dan, Kraaij, Robert, Hiltemann, Saskia D, Ju, Jie, Fernández, David, Mankoc, Cristian, González, Eva, de Waal, Wouter J, de Winter-de Groot, Karin M, Wolfs, Tom F W, Meijers, Pieter, Luijk, Bart, Oosterheert, Jan Jelrik, Sankatsing, Sanjay U C, Bossink, Aik W J, Stein, Michal, Klein, Adi, Ashkar, Jalal, Bamberger, Ellen, Srugo, Isaac, Odeh, Majed, Dotan, Yaniv, Boico, Olga, Etshtein, Liat, Paz, Meital, Navon, Roy, Friedman, Tom, Simon, Einav, Gottlieb, Tanya M, Pri-Or, Ester, Kronenfeld, Gali, Oved, Kfir, Eden, Eran, Stubbs, Andrew P, Bont, Louis J, Hays, John P

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Enhanced sensitivity of TAPscan v4 enables comprehensive analysis of streptophyte transcription factor evolution von Petroll, Romy, Varshney, Deepti, Hiltemann, Saskia, Finke, Hermann, Schreiber, Mona, de Vries, Jan, Rensing, Stefan A

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Discriminating somatic and germline mutations in tumor DNA samples without matching normals von Hiltemann, Saskia, Jenster, Guido, Trapman, Jan, van der Spek, Peter, Stubbs, Andrew

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Development and evaluation of a culture-free microbiota profiling platform (MYcrobiota) for clinical diagnostics von Boers, Stefan A., Hiltemann, Saskia D., Stubbs, Andrew P., Jansen, Ruud, Hays, John P.

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Fostering accessible online education using Galaxy as an e-learning platform von Serrano-Solano, Beatriz, Föll, Melanie C, Gallardo-Alba, Cristóbal, Erxleben, Anika, Rasche, Helena, Hiltemann, Saskia, Fahrner, Matthias, Dunning, Mark J, Schulz, Marcel H, Scholtz, Beáta, Clements, Dave, Nekrutenko, Anton, Batut, Bérénice, Grüning, Björn A

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NanoGalaxy: Nanopore long-read sequencing data analysis in Galaxy von de Koning, Willem, Miladi, Milad, Hiltemann, Saskia, Heikema, Astrid, Hays, John P, Flemming, Stephan, van den Beek, Marius, Mustafa, Dana A, Backofen, Rolf, Grüning, Björn, Stubbs, Andrew P

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ASaiM-MT: a validated and optimized ASaiM workflow for metatranscriptomics analysis within Galaxy framework [version 2; peer review: 2 approved] von Mehta, Subina, Crane, Marie, Leith, Emma, Batut, Bérénice, Hiltemann, Saskia, Arntzen, Magnus Ø, Kunath, Benoit J, Pope, Phillip B, Delogu, Francesco, Sajulga, Ray, Kumar, Praveen, Johnson, James E, Griffin, Timothy J, Jagtap, Pratik D

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BenchAMRking: a Galaxy-based platform for illustrating the major issues associated with current antimicrobial resistance (AMR) gene prediction workflows von Strepis, Nikolaos, Dollee, Dennis, Vrins, Donny, Vanneste, Kevin, Bogaerts, Bert, Carrillo, Catherine, Bharat, Amrita, Horan, Kristy, Sherry, Norelle L, Seemann, Torsten, Howden, Benjamin P, Hiltemann, Saskia, Chindelevitch, Leonid, Stubbs, Andrew P, Hays, John P

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Galaxy Training: A powerful framework for teaching von Hiltemann, Saskia, Rasche, Helena, Gladman, Simon, Hotz, Hans-Rudolf, Larivière, Delphine, Blankenberg, Daniel, Jagtap, Pratik D, Wollmann, Thomas, Bretaudeau, Anthony, Goué, Nadia, Griffin, Timothy J, Royaux, Coline, Le Bras, Yvan, Mehta, Subina, Syme, Anna, Coppens, Frederik, Droesbeke, Bert, Soranzo, Nicola, Bacon, Wendi, Psomopoulos, Fotis, Gallardo-Alba, Cristóbal, Davis, John, Föll, Melanie Christine, Fahrner, Matthias, Doyle, Maria A, Serrano-Solano, Beatriz, Fouilloux, Anne Claire, van Heusden, Peter, Maier, Wolfgang, Clements, Dave, Heyl, Florian, Grüning, Björn, Batut, Bérénice

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Evolutionary Conserved and Divergent Responses to Copper Zinc Superoxide Dismutase Inhibition in Plants von Frohn, Stephanie, Haas, Fabian B, Chavez, Benjamin G, Dreyer, Bernd H, Reiss, Erik V, Ziplys, Anne, Weichert, Heiko, Hiltemann, Saskia, Ugalde, José M, Meyer, Andreas J, D'Auria, John C, Rensing, Stefan A, Schippers, Jos H M

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FAIR data retrieval for sensitive clinical research data in Galaxy von Ouwerkerk, Jasper, Rasche, Helena, Spalding, John D, Hiltemann, Saskia, Stubbs, Andrew P

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