High-resolution TADs reveal DNA sequences underlying genome organization in flies von Ramírez, Fidel, Bhardwaj, Vivek, Arrigoni, Laura, Lam, Kin Chung, Grüning, Björn A., Villaveces, José, Habermann, Bianca, Akhtar, Asifa, Manke, Thomas

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Galaxy HiCExplorer 3: a web server for reproducible Hi-C, capture Hi-C and single-cell Hi-C data analysis, quality control and visualization von Wolff, Joachim, Rabbani, Leily, Gilsbach, Ralf, Richard, Gautier, Manke, Thomas, Backofen, Rolf, Grüning, Björn A

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The return of metabolism: biochemistry and physiology of the pentose phosphate pathway von Stincone, Anna, Prigione, Alessandro, Cramer, Thorsten, Wamelink, Mirjam M. C., Campbell, Kate, Cheung, Eric, Olin-Sandoval, Viridiana, Grüning, Nana-Maria, Krüger, Antje, Tauqeer Alam, Mohammad, Keller, Markus A., Breitenbach, Michael, Brindle, Kevin M., Rabinowitz, Joshua D., Ralser, Markus

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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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Many-body perturbation theory calculations using the yambo code von Sangalli, D, Ferretti, A, Miranda, H, Attaccalite, C, Marri, I, Cannuccia, E, Melo, P, Marsili, M, Paleari, F, Marrazzo, A, Prandini, G, Bonfà, P, Atambo, M O, Affinito, F, Palummo, M, Molina-Sánchez, A, Hogan, C, Grüning, M, Varsano, D, Marini, A

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Bioconda: sustainable and comprehensive software distribution for the life sciences von Grüning, Björn, Dale, Ryan, Sjödin, Andreas, Chapman, Brad A., Rowe, Jillian, Tomkins-Tinch, Christopher H., Valieris, Renan, Köster, Johannes

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Galaxy HiCExplorer: a web server for reproducible Hi-C data analysis, quality control and visualization von Wolff, Joachim, Bhardwaj, Vivek, Nothjunge, Stephan, Richard, Gautier, Renschler, Gina, Gilsbach, Ralf, Manke, Thomas, Backofen, Rolf, Ramírez, Fidel, Grüning, Björn A

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BioContainers: an open-source and community-driven framework for software standardization von da Veiga Leprevost, Felipe, Grüning, Björn A, Alves Aflitos, Saulo, Röst, Hannes L, Uszkoreit, Julian, Barsnes, Harald, Vaudel, Marc, Moreno, Pablo, Gatto, Laurent, Weber, Jonas, Bai, Mingze, Jimenez, Rafael C, Sachsenberg, Timo, Pfeuffer, Julianus, Vera Alvarez, Roberto, Griss, Johannes, Nesvizhskii, Alexey I, Perez-Riverol, Yasset

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pyGenomeTracks: reproducible plots for multivariate genomic datasets von Lopez-Delisle, Lucille, Rabbani, Leily, Wolff, Joachim, Bhardwaj, Vivek, Backofen, Rolf, Gruening, Bjoern, Ramirez, Fidel, Manke, Thomas

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Advanced testing of the LoT hypothesis by social reasoning von Grüning, David J.

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Distinct epigenetic programs regulate cardiac myocyte development and disease in the human heart in vivo von Gilsbach, Ralf, Schwaderer, Martin, Preissl, Sebastian, Grüning, Björn A., Kranzhöfer, David, Schneider, Pedro, Nührenberg, Thomas G., Mulero-Navarro, Sonia, Weichenhan, Dieter, Braun, Christian, Dreßen, Martina, Jacobs, Adam R., Lahm, Harald, Doenst, Torsten, Backofen, Rolf, Krane, Markus, Gelb, Bruce D., Hein, Lutz

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Exciton-Plasmon States in Nanoscale Materials: Breakdown of the Tamm−Dancoff Approximation von Grüning, Myrta, Marini, Andrea, Gonze, Xavier

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Dynamic DNA methylation orchestrates cardiomyocyte development, maturation and disease von Gilsbach, Ralf, Preissl, Sebastian, Grüning, Björn A., Schnick, Tilman, Burger, Lukas, Benes, Vladimir, Würch, Andreas, Bönisch, Ulrike, Günther, Stefan, Backofen, Rolf, Fleischmann, Bernd K., Schübeler, Dirk, Hein, Lutz

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The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2016 update von Afgan, Enis, Baker, Dannon, van den Beek, Marius, Blankenberg, Daniel, Bouvier, Dave, Čech, Martin, Chilton, John, Clements, Dave, Coraor, Nate, Eberhard, Carl, Grüning, Björn, Guerler, Aysam, Hillman-Jackson, Jennifer, Von Kuster, Greg, Rasche, Eric, Soranzo, Nicola, Turaga, Nitesh, Taylor, James, Nekrutenko, Anton, Goecks, Jeremy

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Directing smartphone use through the self-nudge app one sec von Grüning, David J, Riedel, Frederik, Lorenz-Spreen, Philipp

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Jupyter and Galaxy: Easing entry barriers into complex data analyses for biomedical researchers von Grüning, Björn A, Rasche, Eric, Rebolledo-Jaramillo, Boris, Eberhard, Carl, Houwaart, Torsten, Chilton, John, Coraor, Nate, Backofen, Rolf, Taylor, James, Nekrutenko, Anton

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A Synthetic Sandalwood Odorant Induces Wound-Healing Processes in Human Keratinocytes via the Olfactory Receptor OR2AT4 von Busse, Daniela, Kudella, Philipp, Grüning, Nana-Maria, Gisselmann, Günter, Ständer, Sonja, Luger, Thomas, Jacobsen, Frank, Steinsträßer, Lars, Paus, Ralf, Gkogkolou, Paraskevi, Böhm, Markus, Hatt, Hanns, Benecke, Heike

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Origin of metastable oligomers and their effects on amyloid fibril self-assembly von Hasecke, Filip, Miti, Tatiana, Perez, Carlos, Barton, Jeremy, Schölzel, Daniel, Gremer, Lothar, Grüning, Clara S R, Matthews, Garrett, Meisl, Georg, Knowles, Tuomas P J, Willbold, Dieter, Neudecker, Philipp, Heise, Henrike, Ullah, Ghanim, Hoyer, Wolfgang, Muschol, Martin

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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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deepTools: a flexible platform for exploring deep-sequencing data von Ramírez, Fidel, Dündar, Friederike, Diehl, Sarah, Grüning, Björn A., Manke, Thomas

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