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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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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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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Galaxy mothur Toolset (GmT): a user-friendly application for 16S rRNA gene sequencing analysis using mothur von Hiltemann, Saskia D, Boers, Stefan A, van der Spek, Peter J, Jansen, Ruud, Hays, John P, Stubbs, Andrew P

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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, Fernandez, David, Mankoc, Cristian, Gonzalez, 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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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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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 Yunlei Li, Chantal B. van Houten, Stefan A. Boers, Ruud Jansen, Asi Cohen, Dan Engelhard, Robert Kraaij, Saskia D. Hiltemann, Jie Ju, David Fernández, Cristian Mankoc, Eva González, Wouter J. de Waal, Karin M. de Winter-de Groot, Tom F. W. Wolfs, Pieter Meijers, Bart Luijk, Jan Jelrik Oosterheert, Sanjay U. C. Sankatsing, Aik W. J. Bossink, Michal Stein, Adi Klein, Jalal Ashkar, Ellen Bamberger, Isaac Srugo, Majed Odeh, Yaniv Dotan, Olga Boico, Liat Etshtein, Meital Paz, Roy Navon, Tom Friedman, Einav Simon, Tanya M. Gottlieb, Ester Pri-Or, Gali Kronenfeld, Kfir Oved, Eran Eden, Andrew P. Stubbs, Louis J. Bont, John P. Hays

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Huvariome: a web server resource of whole genome next-generation sequencing allelic frequencies to aid in pathological candidate gene selection von Stubbs, Andrew, McClellan, Elizabeth A, Horsman, Sebastiaan, Hiltemann, Saskia D, Palli, Ivo, Nouwens, Stephan, Koning, Anton Hj, Hoogland, Frits, Reumers, Joke, Heijsman, Daphne, Swagemakers, Sigrid, Kremer, Andreas, Meijerink, Jules, Lambrechts, Diether, van der Spek, Peter J

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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: 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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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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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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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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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, on behalf of the Galaxy Training Network, [ missing ], Grüning, Björn, Batut, Bérénice

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FAIR Genomes metadata schema promoting Next Generation Sequencing data reuse in Dutch healthcare and research von van der Velde, K. Joeri, Singh, Gurnoor, Kaliyaperumal, Rajaram, Liao, XiaoFeng, de Ridder, Sander, Rebers, Susanne, Kerstens, Hindrik H. D., de Andrade, Fernanda, van Reeuwijk, Jeroen, De Gruyter, Fini E., Hiltemann, Saskia, Ligtvoet, Maarten, Weiss, Marjan M., van Deutekom, Hanneke W. M., Jansen, Anne M. L., Stubbs, Andrew P., Vissers, Lisenka E. L. M., Laros, Jeroen F. J., van Enckevort, Esther, Stemkens, Daphne, ‘t Hoen, Peter A. C., Beliën, Jeroen A. M., van Gijn, Mariëlle E., Swertz, Morris A.

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FAIR Genomes metadata schema promoting Next Generation Sequencing data reuse in Dutch healthcare and research von van der Velde, K Joeri, Singh, Gurnoor, Kaliyaperumal, Rajaram, Liao, XiaoFeng, de Ridder, Sander, Rebers, Susanne, Kerstens, Hindrik H D, de Andrade, Fernanda, van Reeuwijk, Jeroen, De Gruyter, Fini E, Hiltemann, Saskia, Ligtvoet, Maarten, Weiss, Marjan M, van Deutekom, Hanneke W M, Jansen, Anne M L, Stubbs, Andrew P, Vissers, Lisenka E L M, Laros, Jeroen F J, van Enckevort, Esther, Stemkens, Daphne, t Hoen, Peter A C, Beliën, Jeroen A M, van Gijn, Mariëlle E, Swertz, Morris A

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ASaiM-MT: a validated and optimized ASaiM workflow for metatranscriptomics analysis within Galaxy framework [version 1; peer review: 1 approved with reservations] von Mehta, Subina, Crane, Marie, Leith, Emma, Batut, Bérénice, Hiltemann, Saskia, Arntzen, Magnus Ø, Kunath, Benoit J, Delogu, Francesco, Sajulga, Ray, Kumar, Praveen, Johnson, James E, Griffin, Timothy J, Jagtap, Pratik D

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