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Open-Source and FAIR Research Software for Proteomics Perez-Riverol, Yasset; Bittremieux, Wout; Noble, William S.; Martens, Lennart; Bilbao, Aivett; Lazear, Michael R.; Gruening, Bjorn; Katz, Daniel S.; MacCoss, Michael J.; Dai, Chengxin; Eng, Jimmy K.; Bouwmeester, Robbin; Shortreed, Michael R.; Audain, Enrique; Sachsenberg, Timo; Van Goey, Jeroen; Wallmann, Georg; Wen, Bo; Kall, Lukas; Fondrie, William E. Share Save
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Mobilisation and analyses of publicly available SARS- CoV-2 data for pandemic responses Rahman, Nadim; O'Cathail, Colman; Zyoud, Ahmad; Sokolov, Alexey; Munnink, Bas Oude; Gruening, Bjoern; Cummins, Carla; Amid, Clara; Nieuwenhuijse, David F.; Visontai, David; Yuan, David Yu; Gupta, Dipayan; Prasad, Divyae K.; Gulyas, Gabor Mate; Rinck, Gabriele; McKinnon, Jasmine; Rajan, Jeena; Knaggs, Jeff; Skiby, Jeffrey Edward; Steger, Jozsef; Szarvas, Judit; Gueye, Khadim; Papp, Krisztian; Hoek, Maarten; Kumar, Manish; Ventouratou, Marianna A.; Bouquieaux, Marie -Catherine; Koliba, Martin; Mansurova, Milena; Haseeb, Muhammad; Worp, Nathalie; Harrison, Peter W.; Leinonen, Rasko; Thorne, Ross; Selvakumar, Sandeep; Hunt, Sarah; Venkataraman, Sundar; Jayathilaka, Suran; Cezard, Timothee; Maier, Wolfgang; Waheed, Zahra; Iqbal, Zamin; Aarestrup, Frank Miller; Csabai, Istvan; Koopmans, Marion; Burdett, Tony; Cochrane, Guy Share Save
Scalable, accessible and reproducible reference genome assembly and evaluation in Galaxy Lariviere, Delphine; Abueg, Linelle; Brajuka, Nadolina; Gallardo-Alba, Cristobal; Gruening, Bjorn; Ko, Byung June; Ostrovsky, Alex; Palmada-Flores, Marc; Pickett, Brandon D.; Rabbani, Keon; Antunes, Agostinho; Balacco, Jennifer R.; Chaisson, Mark J. P.; Cheng, Haoyu; Collins, Joanna; Couture, Melanie; Denisova, Alexandra; Fedrigo, Olivier; Gallo, Guido Roberto; Giani, Alice Maria; Gooder, Grenville MacDonald; Horan, Kathleen; Jain, Nivesh; Johnson, Cassidy; Kim, Heebal; Lee, Chul; Marques-Bonet, Tomas; O'Toole, Brian; Rhie, Arang; Secomandi, Simona; Sozzoni, Marcella; Tilley, Tatiana; Uliano-Silva, Marcela; van den Beek, Marius; Williams, Robert W.; Waterhouse, Robert M.; Phillippy, Adam M.; Jarvis, Erich D.; Schatz, Michael C.; Nekrutenko, Anton; Formenti, Giulio Share Save
Be sustainable: EOSC-Life recommendations for implementation of FAIR principles in life science data handling David, Romain; Rybina, Arina; Burel, Jean-Marie; Heriche, Jean-Karim; Audergon, Pauline; Boiten, Jan-Willem; Coppens, Frederik; Crockett, Sara; Exter, Katrina; Fahrner, Sven; Fratelli, Maddalena; Goble, Carole; Gormanns, Philipp; Grantner, Tobias; Gruening, Bjoern; Gurwitz, Kim Tamara; Hancock, John M.; Harmse, Henriette; Holub, Petr; Juty, Nick; Karnbach, Geoffrey; Karoune, Emma; Keppler, Antje; Lancelotti, Carla; Klemeier, Jessica; Legras, Jean-Luc; Lister, Allyson L.; Longo, Dario Livio; Ludwig, Rebecca; Madon, Benedicte; Massimi, Marzia; Matser, Vera; Matteoni, Rafaele; Mayrhofer, Michaela Th; Ohmann, Christian; Panagiotopoulou, Maria; Parkinson, Helen; Perseil, Isabelle; Pfander, Claudia; Pieruschka, Roland; Raess, Michael; Rauber, Andreas; Richard, Audrey S.; Romano, Paolo; Rosato, Antonio; Sanchez-Pla, Alex; Sansone, Susanna-Assunta; Sarkans, Ugis; Serrano-Solano, Beatriz; Tang, Jing; Tanoli, Ziaurrehman; Tedds, Jonathan; Wagener, Harald; Weise, Martin; Westerhoff, Hans, V; Wittner, Rudolf; Ewbank, Jonathan; Blomberg, Niklas; Gribbon, Philip Share Save
PLANTdataHUB : a collaborative platform for continuous FAIR data sharing in plant research Weil, Heinrich Lukas; Schneider, Kevin; Tschoepe, Marcel; Bauer, Jonathan; Maus, Oliver; Frey, Kevin; Brilhaus, Dominik; Rodrigues, Cristina Martins; Doniparthi, Gajendra; Wetzels, Florian; Lukasczyk, Jonas; Kranz, Angela; Gruening, Bjoern; Zimmer, David; Dessloch, Stefan; von Suchodoletz, Dirk; Usadel, Bjoern; Garth, Christoph; Muehlhaus, Timo Share Save
Activator-blocker model of transcriptional regulation by pioneer-like factors Riesle, Aileen Julia; Gao, Meijiang; Rosenblatt, Marcus; Hermes, Jacques; Hass, Helge; Gebhard, Anna; Veil, Marina; Gruening, Bjorn; Timmer, Jens; Onichtchouk, Daria Share Save
Integrative meta-omics in Galaxy and beyond Schiml, Valerie C.; Delogu, Francesco; Kumar, Praveen; Kunath, Benoit; Batut, Berenice; Mehta, Subina; Johnson, James E.; Gruening, Bjoern; Pope, Phillip B.; Jagtap, Pratik D.; Griffin, Timothy J.; Arntzen, Magnus O. Share Save
Training Infrastructure as a Service Rasche, Helena; Hyde, Cameron; Davis, John; Gladman, Simon; Coraor, Nate; Bretaudeau, Anthony; Cuccuru, Gianmauro; Bacon, Wendi; Serrano-Solano, Beatriz; Hillman-Jackson, Jennifer; Hiltemann, Saskia; Zhou, Miaomiao; Gruening, Bjoern; Stubbs, Andrew Share Save
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A comparative gene expression matrix in Apoe-deficient mice identifies unique and atherosclerotic disease stage-specific gene regulation patterns in monocytes and macrophages Haerdtner, Carmen; Kumar, Anup; Ehlert, Carolin A.; Vico, Tamara Antonela; Starz, Christopher; von Ehr, Alexander; Krebs, Katja; Dufner, Bianca; Hoppe, Natalie; Stachon, Peter; Heidt, Timo; Wolf, Dennis; von zur Muehlen, Constantin; Gruening, Bjoern; Robbins, Clinton S.; Maegdefessel, Lars; Westermann, Dirk; Dederichs, Tsai -Sang; Hilgendorf, Ingo Share Save
Catching the Wave: Detecting Strain-Specific SARS-CoV-2 Peptides in Clinical Samples Collected during Infection Waves from Diverse Geographical Locations Mehta, Subina; Carvalho, Valdemir M.; Rajczewski, Andrew T.; Pible, Olivier; Gruening, Bjoern A.; Johnson, James E.; Wagner, Reid; Armengaud, Jean; Griffin, Timothy J.; Jagtap, Pratik D. Share Save
The antileukemic activity of decitabine upon PML/RARA-negative AML blasts is supported by all-trans retinoic acid: in vitro and in vivo evidence for cooperation Meier, Ruth; Greve, Gabriele; Zimmer, Dennis; Bresser, Helena; Berberich, Bettina; Langova, Ralitsa; Stomper, Julia; Rubarth, Anne; Feuerbach, Lars; Lipka, Daniel B.; Hey, Joschka; Gruening, Bjoern; Brors, Benedikt; Duyster, Justus; Plass, Christoph; Becker, Heiko; Luebbert, Michael Share Save
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The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2022 update Ostrovsky, Alexander E.; Mahmoud, Alexandru; Lonie, Andrew J.; Syme, Anna; Fouilloux, Anne; Bretaudeau, Anthony; Nekrutenko, Anton; Kumar, Anup; Eschenlauer, Arthur C.; DeSanto, Assunta D.; Guerler, Aysam; Serrano-Solano, Beatriz; Batut, Berenice; Gruening, Bjoern A.; Langhorst, Bradley W.; Carr, Bridget; Raubenolt, Bryan A.; Hyde, Cameron J.; Bromhead, Catherine J.; Barnett, Christopher B.; Royaux, Coline; Gallardo, Cristobal; Blankenberg, Daniel; Fornika, Daniel J.; Baker, Dannon; Bouvier, Dave; Clements, Dave; Morais, David A. de Lima; Tabernero, David Lopez; Lariviere, Delphine; Nasr, Engy; Afgan, Enis; Zambelli, Federico; Heyl, Florian; Psomopoulos, Fotis; Coppens, Frederik; Price, Gareth R.; Cuccuru, Gianmauro; Le Corguille, Gildas; Von Kuster, Greg; Akbulut, Gulsum Gudukbay; Rasche, Helena; Hans-Rudolf, Hotz; Eguinoa, Ignacio; Makunin, Igor; Ranawaka, Isuru J.; Taylor, James P.; Joshi, Jayadev; Hillman-Jackson, Jennifer; Goecks, Jeremy; 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; Cech, Martin; Bernt, Matthias; Fahrner, Matthias; Tekman, Mehmet; Foell, Melanie C.; Schatz, Michael 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; Briggs, Peter J. Share Save
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Selection Analysis Identifies Clusters of Unusual Mutational Changes in Omicron Lineage BA.1 That Likely Impact Spike Function Martin, Darren P.; Lytras, Spyros; Lucaci, Alexander G.; Maier, Wolfgang; Gruening, Bjoern; Shank, Stephen D.; Weaver, Steven; MacLean, Oscar A.; Orton, Richard J.; Lemey, Philippe; Boni, Maciej F.; Tegally, Houriiyah; Harkins, Gordon W.; Scheepers, Cathrine; Bhiman, Jinal N.; Everatt, Josie; Amoako, Daniel G.; San, James Emmanuel; Giandhari, Jennifer; Sigal, Alex; Williamson, Carolyn; Hsiao, Nei-yuan; von Gottberg, Anne; De Klerk, Arne; Shafer, Robert W.; Robertson, David L.; Wilkinson, Robert J.; Sewell, B. Trevor; Lessells, Richard; Nekrutenko, Anton; Greaney, Allison J.; Starr, Tyler N.; Bloom, Jesse D.; Murrell, Ben; Wilkinson, Eduan; Gupta, Ravindra K.; de Oliveira, Tulio; Kosakovsky Pond, Sergei L. Share Save
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