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Galaxy Freiburg

Publications by the Freiburg Galaxy Team

These are the publications by current or former members of the Freiburg Galaxy Team.

212 publications

Microbiology Galaxy Lab: a community-driven gateway for reproducible and FAIR analysis of microbiological data

Nasr, Engy MT; Pechlivanis, Nikolaos; Strepis, Nikolaos; Amato, Pierre; Bernt, Matthias; Bhardwaj, Anshu; Blankenberg, Daniel; Brites, Daniela; Cumbo, Fabio; Do, Katherine T; others

3Dtrees. earth-A platform for accessing, analyzing, and visualizing LiDAR data in forest environments

Gerberding, Kilian; Vajna-Jehle, Janusch; Kattenborn, Teja; Scharinger, Christian; Lusk, Daniel; Brede, Benjamin; Sperlich, Maximilian; Seifert, Thomas; Grüning, Björn; Puliti, Stefano; others

Right-sizing compute resource allocations for bioinformatics tools with Total Perspective Vortex

Goonasekera, Nuwan; Bromhead, Catherine; Gladman, Simon; Suderman, Keith; Coraor, Nathan; Grüning, Björn; Afgan, Enis

The Spirogyra pratensis genome illuminates the evolution of developmental programs and spiral chloroplast biology

Goldbecker, Elisa S; Varshney, Deepti; Holzhausen, Anja; Darienko, Tatyana; Zhou, Hong; Dadras, Armin; Pfeifer, Lukas; Pröschold, Thomas; Lopez-Gomez, Enrique; Woelken, Elke; Permann, Charlotte; Wollenweber, Tassilo Erik; Becker, Kerstin; König, Stefanie; Hadacek, Franz; Li, Fay-Wei; Feussner, Ivo; Fernandez-Pozo, Noe; Holzinger, Andreas; Maumus, Florian; Marques, André; Buschmann, Henrik; Schwartzenberg, Klaus; Vries, Jan; Rensing, Stefan A

Galaxy for accessible, reproducible, and collaborative data analyses: 2026 update

Community, The Galaxy; Afgan, Enis; Amoukou, Najat; Buono, Rafael Andrade; Anton, Mihail; Antoniewski, Christophe; Austin, Patrick; Awan, Ahmed Hamid; Backofen, Rolf; Bacon, Wendi Anne; Baker, Dannon; Barreau, Arthur; Batut, Bérénice; Bernt, Matthias; Blankenberg, Daniel; Bretaudeau, Anthony; Bromhead, Catherine Joan; Burhans, Richard; Burke, Melissa; Cain, Scott; Callan, Danielle; Cech, Martin; Chavero-Díez, María; Chei, Haswane; Chen, Ying; Chiang, Diana; Chilton, John M; Collins, Tyler James; Coppens, Frederik; Coraor, Nate; Coulombe, Charles; Crusoe, Michael R; Cumbo, Fabio; Cumunel, Triskell; D'Silva, Michael; Dadras, Armin; Dalle, Céline; Dang, Khai; Davis, John Y; De Geest, Paul; Koning, Willem; Defazio, Giuseppe; Depoortere, Boris; Do, Katherine; Domínguez Begines, José Manuel; Droesbeke, Bert; Duarte, Erick Nicolas; Castillo, Enol; Fix, Jeremy; Formenti, Giulio; Frey, Julian; Föll, Melanie Christine; Gauthier, Carol; Gerberding, Kilian; Giacomoni, Franck; Goecks, Jeremy; Goonasekera, Nuwan A; Goué, Nadia; Griffin, Timothy J; Grüning, Björn Andreas; Guerler, Aysam; Guitton, Yann; Gustafsson, Ove Johan Ragnar; Gömöryová, Kristína; Harakalova, Magdalena; Hecht, Helge; Heidari, Alireza; Heyl, Florian; Hillman-Jackson, Jennifer; Hiltemann, Saskia; Ansari, Mina Hojat; Hotz, Hans-Rudolf; Hyde, Cameron John; Jacques, Pierre-Étienne; Jagtap, Pratik Dilip; Joshi, Jayadev; Jossé, Marie; Jumah, Khaled Moahmmad Ahmad; Elyaderani, Arash Kadkhodaei; Kamieniecka, Katarzyna; Kattenborn, Teja; Konkol, Markus; Kostrykin, Leonid; Kucher, Natalie; Kumar, Anup; Kuntz, Mira; Langhorst, Bradley William; Lariviere, Delphine; Le Bras, Yvan; Le Corguillé, Gildas; Le Cras, Jean; Lee, Justin; Leendertse, Jan; Lefeuvre, Hugo; Leskošek, Brane; Liborio, Leandro Miguel; Libouban, Romane; Loach, Marisa; Tabernero, Jose David Lopez; Lopez-Delisle, Lucille; Lusk, Daniel; Mahmoud, Alexandru; Mahé, Molène; Maier, Wolfgang; Makunin, Igor; McCaffrey, Kirsty; Medico, Jack A; Mehta, Subina; Mei, Hailiang; Minkova, Mirela; Momin, Saim; Junior, Paulo Cilas Morais Lyra; Müller, Teresa; Nilchi, Amirhossein Naghsh; Nandi, Tannistha; Nasr, Engy Mohamed Taha; Nekrutenko, Anton; Nelson, Tiffanie; Nussbaum, Johannes; Oba, Asime James; Opioła, Łukasz; Payet, Kevin; Petera, Melanie; Polunina, Polina V; Pond, Sergei; Poterlowicz, Krzysztof; Price, Gareth Robert; Qiu, Junhao; Rasche, Helena; Raubenolt, Bryan; Reynolds, Tristan N; Rogers, Dave; Rohr, Karl; Saudade, Gabriel Ferreira; Savage, Michelle Terese; Savchenko, Volodymyr; Schatz, Michael C; Schmitz, Isabelle; Schneider, Daniela; Seguineau, Pauline; Serrano-Solano, Beatriz; Siguret, Clea; Smeds, Patrik; Sollitto, Marco; Soranzo, Nicola; Srikakulam, Sanjay Kumar; Sterck, Lieven; Strepis, Nikolaos; Stubbs, Andrew; Suderman, Keith; Syme, Anna; Tangaro, Marco Antonio; Koopaei, Reyhaneh Tavakoli; Tedds, Jonathan Andrew; Tekman, Mehmet; Thang, Wai Cheng (Mike); Thanki, Anil S; Uhl, Michael; Vajna-Jehle, Janusch; Beek, Marius; Varshney, Deepti; Vazov, Nikolay Alexandrov; Vessio, Jennifer; Videm, Pavankumar; Vondrak, Tomas; Wagner, Reid; Watson, Gregory R; Weber, Ralf J M; Whitaker-Allen, Natalie; Zambelli, Federico; Zierep, Paul; Zoabi, Rand

Bioimage management and analysis in Galaxy: Tools, workflows, training, and community practices

Kostrykin, Leonid; Massei, Riccardo; Chiang, Diana; Wollmann, Thomas; Burel, Jean‐Marie; Tabernero, David Lopez; Sun, Yi; Gao, Qi; Paul, Maarten W.; Videm, Pavankumar; Watson, Cameron; Franco‐Barranco, Daniel; Kumar, Anup; Goué, Nadia; Koopaei, Reyhaneh Tavakoli; Ulman, Vladimír; Jum'ah, Khaled; Poterlowicz, Krzysztof; Etzrodt, Martin; Muñoz‐Barrutia, Arrate; Le Dévédec, Sylvia E.; Moore, Josh; Goecks, Jeremy; Gruening, Bjoern; Rohr, Karl; Serrano‐Solano, Beatriz

EISCA and EISTA: Full-Spectrum Pipelines for Single-Cell and Spatial Transcriptomics Analysis

Wu, Huihai; Lister, Ashleigh; Macaulay, Iain C; Long, Katie; Uauy, Cristobal; Lan, Yuxuan; Wickham, Gregory J; Swarbreck, David; Videm, Pavankumar; Stubbs, Andrew; others

Open-Source and FAIR Research Software for Proteomics

Perez-Riverol, Yasset; Bittremieux, Wout; Noble, William S.; Martens, Lennart; Bilbao, Aivett; Lazear, Michael R.; Grüning, 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; Käll, Lukas; Fondrie, William E.

varVAMP: degenerate primer design for tiled full genome sequencing and qPCR

Fuchs, Jonas; Kleine, Johanna; Schemmerer, Mathias; Kreibich, Julian; Maier, Wolfgang; Battur, Namuun; Krannich, Thomas; Sedaghatjoo, Somayyeh; Jaki, Lena; Maks, Anastasija; Boehm, Christina; Wilhelm, Carina; Schulze, Jessica; Mache, Christin; Berger, Elischa; Panajotov, Jessica; Arnold, Lisa; Grüning, Björn; Bauswein, Markus; Böttcher, Sindy; Johne, Reimar; Wenzel, Jürgen; Hölzer, Martin; Panning, Marcus

Guidance framework to apply best practices in ecological data analysis: lessons learned from building Galaxy-Ecology

Royaux, Coline; Mihoub, Jean-Baptiste; Jossé, Marie; Pelletier, Dominique; Norvez, Olivier; Reecht, Yves; Fouilloux, Anne; Rasche, Helena; Hiltemann, Saskia; Batut, Bérénice; Marc, Eléaume; Seguineau, Pauline; Massé, Guillaume; Amossé, Alan; Bissery, Claire; Lorrilliere, Romain; Martin, Alexis; Bas, Yves; Virgoulay, Thimothée; Chambon, Valentin; Arnaud, Elie; Michon, Elisa; Urfer, Clara; Trigodet, Eloïse; Delannoy, Marie; Loïs, Gregoire; Julliard, Romain; Grüning, Björn; Le Bras, Yvan

MaveDB 2024: a curated community database with over seven million variant effects from multiplexed functional assays

Rubin, Alan F.; Stone, Jeremy; Bianchi, Aisha Haley; Capodanno, Benjamin J.; Da, Estelle Y.; Dias, Mafalda; Esposito, Daniel; Frazer, Jonathan; Fu, Yunfan; Grindstaff, Sally B.; Harrington, Matthew R.; Li, Iris; McEwen, Abbye E.; Min, Joseph K.; Moore, Nick; Moscatelli, Olivia G.; Ong, Jesslyn; Polunina, Polina V.; Rollins, Joshua E.; Rollins, Nathan J.; Snyder, Ashley E.; Tam, Amy; Wakefield, Matthew J.; Ye, Shenyi Sunny; Starita, Lea M.; Bryant, Vanessa L.; Marks, Debora S.; Fowler, Douglas M.

Galaxy as a gateway to bioinformatics: Multi-Interface Galaxy Hands-on Training Suite (MIGHTS) for scRNA-seq

Goclowski, Camila L; Jakiela, Julia; Collins, Tyler; Hiltemann, Saskia; Howells, Morgan; Loach, Marisa; Manning, Jonathan; Moreno, Pablo; Ostrovsky, Alex; Rasche, Helena; others

Modulation of bone marrow haematopoietic stem cell activity as a therapeutic strategy after myocardial infarction: a preclinical study

Rettkowski, Jasmin; Romero-Mulero, Mari Carmen; Singh, Indranil; Wadle, Carolin; Wrobel, Jan; Chiang, Diana; Hoppe, Natalie; Mess, Julian; Schönberger, Katharina; Lalioti, Maria-Eleni; Jäcklein, Karin; SilvaRego, Beatriz; Bühler, Timon; Karabacz, Noémie; Egg, Mirijam; Demollin, Helen; Obier, Nadine; Zhang, Yu Wei; Jülicher, Claus; Hetkamp, Anne; Czerny, Martin; Jones, Michael-Jason; Seung, Hana; Jain, Ritika; Mühlen, Constantin; Maier, Alexander; Lother, Achim; Hilgendorf, Ingo; Galen, Peter; Kreso, Antonia; Westermann, Dirk; Rodriguez-Fraticelli, Alejo E.; Heidt, Timo; Cabezas-Wallscheid, Nina

CheRRI—Accurate classification of the biological relevance of putative RNA–RNA interaction sites

Müller, Teresa; Mautner, Stefan; Videm, Pavankumar; Eggenhofer, Florian; Raden, Martin; Backofen, Rolf

The Galaxy platform for accessible, reproducible, and collaborative data analyses: 2024 update

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; 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; Royaux, Coline; Sargent, Luke; Savage, Michelle T; Savchenko, Volodymyr; Savchenko, Denys; Schatz, Michael C; Seguineau, Pauline; Serrano-Solano, Beatriz; Soranzo, Nicola; Srikakulam, Sanjay Kumar; Suderman, Keith; Syme, Anna E; Tangaro, Marco Antonio; Tedds, Jonathan A; Tekman, Mehmet; Cheng (Mike) Thang, Wai; Thanki, Anil S; Uhl, Michael; Beek, Marius; Varshney, Deepti; Vessio, Jenn; Videm, Pavankumar; Von Kuster, Greg; Watson, Gregory R; Whitaker-Allen, Natalie; Winter, Uwe; Wolstencroft, Martin; Zambelli, Federico; Zierep, Paul; Zoabi, Rand

Recommendations for Uniform Variant Calling of SARS-CoV-2 Genome Sequence across Bioinformatic Workflows

Connor, Ryan; Shakya, Migun; Yarmosh, David A.; Maier, Wolfgang; Martin, Ross; Bradford, Rebecca; Brister, J. Rodney; Chain, Patrick S. G.; Copeland, Courtney A.; Iulio, Julia; Hu, Bin; Ebert, Philip; Gunti, Jonathan; Jin, Yumi; Katz, Kenneth S.; Kochergin, Andrey; LaRosa, Tré; Li, Jiani; Li, Po-E; Lo, Chien-Chi; Rashid, Sujatha; Maiorova, Evguenia S.; Xiao, Chunlin; Zalunin, Vadim; Purcell, Lisa; Pruitt, Kim D.

Mobilisation and analyses of publicly available SARS-CoV-2 data for pandemic responses

Rahman, Nadim; O’Cathail, Colman; Zyoud, Ahmad; Sokolov, Alexey; Oude Munnink, Bas; Grüning, Björn; Cummins, Carla; Amid, Clara; Nieuwenhuijse, David F.; Visontai, Dávid; Yuan, David Yu; Gupta, Dipayan; Prasad, Divyae K.; Gulyás, Gábor Máté; Rinck, Gabriele; McKinnon, Jasmine; Rajan, Jeena; Knaggs, Jeff; Skiby, Jeffrey Edward; Stéger, József; Szarvas, Judit; Gueye, Khadim; Papp, Krisztián; 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, Timothée; Maier, Wolfgang; Waheed, Zahra; Iqbal, Zamin; Aarestrup, Frank Møller; Csabai, Istvan; Koopmans, Marion; Burdett, Tony; Cochrane, Guy

Scalable, accessible and reproducible reference genome assembly and evaluation in Galaxy

Larivière, Delphine; Abueg, Linelle; Brajuka, Nadolina; Gallardo-Alba, Cristóbal; Grüning, 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; Beek, Marius; Williams, Robert W.; Waterhouse, Robert M.; Phillippy, Adam M.; Jarvis, Erich D.; Schatz, Michael C.; Nekrutenko, Anton; Formenti, Giulio

Establishing the ELIXIR Microbiome Community

Finn, RD; Balech, B; Burgin, J; Chua, P; Corre, E; Cox, CJ; Donati, C; Santos, VM; Fosso, B; Hancock, J; Heil, KF; Ishaque, N; Kale, V; Kunath, BJ; MÈdigue, C; Pafilis, E; Pesole, G; Richardson, L; Santamaria, M; Van Den Bossche, T; VizcaÌno, JA; Zafeiropoulos, H; Willassen, NP; Pelletier, E; Batut, B

Clouds, oases for airborne microbes–Differential metagenomics/metatranscriptomics analyses of cloudy and clear atmospheric situations

Péguilhan, Raphaëlle; Rossi, Florent; Joly, Muriel; Nasr, Engy; Batut, Bérénice; Enault, François; Ervens, Barbara; Amato, Pierre

“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; Grüning, Björn; Gurwitz, Kim Tamara; Hancock, John M; Harmse, Henriette; Holub, Petr; Juty, Nick; Karnbach, Geoffrey; Karoune, Emma; Keppler, Antje; Klemeier, Jessica; Lancelotti, Carla; Legras, Jean‐Luc; Lister, Allyson L; Longo, Dario Livio; Ludwig, Rebecca; Madon, Bénédicte; 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; Sánchez‐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

An international consensus on effective, inclusive, and career-spanning short-format training in the life sciences and beyond

Williams, Jason J.; Tractenberg, Rochelle E.; Batut, Bérénice; Becker, Erin A.; Brown, Anne M.; Burke, Melissa L.; Busby, Ben; Cooch, Nisha K.; Dillman, Allissa A.; Donovan, Samuel S.; Doyle, Maria A.; Gelder, Celia W. G.; Hall, Christina R.; Hertweck, Kate L.; Jordan, Kari L.; Jungck, John R.; Latour, Ainsley R.; Lindvall, Jessica M.; Lloret-Llinares, Marta; McDowell, Gary S.; Morris, Rana; Mourad, Teresa; Nisselle, Amy; Ordóñez, Patricia; Paladin, Lisanna; Palagi, Patricia M.; Sukhai, Mahadeo A.; Teal, Tracy K.; Woodley, Louise

A Galaxy of informatics resources for MS-based proteomics

Mehta, Subina; Bernt, Matthias; Chambers, Matthew; Fahrner, Matthias; Föll, Melanie Christine; Gruening, Bjoern; Horro, Carlos; Johnson, James E.; Loux, Valentin; Rajczewski, Andrew T.; Schilling, Oliver; Vandenbrouck, Yves; Gustafsson, Ove Johan Ragnar; Thang, W. C. Mike; Hyde, Cameron; Price, Gareth; Jagtap, Pratik D.; Griffin, Timothy J.

The European Reference Genome Atlas: piloting a decentralised approach to equitable biodiversity genomics

Cartney, Ann M Mc; Formenti, Giulio; Mouton, Alice; Panis, Diego De; Marins, Luı́sa S; Leitão, Henrique G; Diedericks, Genevieve; Kirangwa, Joseph; Morselli, Marco; Salces-Ortiz, Judit; Escudero, Nuria; Iannucci, Alessio; Natali, Chiara; Svardal, Hannes; Fernández, Rosa; Pooter, Tim De; Joris, Geert; Strazisar, Mojca; Wood, Jo; Herron, Katie E; Seehausen, Ole; Watts, Phillip C; Shaw, Felix; Davey, Robert P; Minotto, Alice; Fernández, José M; Böhne, Astrid; Alegria, Carla; Alioto, Tyler; Alves, Paulo C; Amorim, Isabel R; Aury, Jean-Marc; Backstrom, Niclas; Baldrian, Petr; Baltrunaite, Laima; Barta, Endre; Bed’Hom, Bertrand; Belser, Caroline; Bergsten, Johannes; Bertrand, Laurie; Bilandžija, Helena; Binzer-Panchal, Mahesh; Bista, Iliana; Blaxter, Mark; Borges, Paulo AV; Dias, Guilherme Borges; Bosse, Mirte; Brown, Tom; Bruggmann, Rémy; Buena-Atienza, Elena; Burgin, Josephine; Buzan, Elena; Casadei, Nicolas; Chiara, Matteo; Chozas, Sergio; Fedor Čiampor, Jr.; Crottini, Angelica; Cruaud, Corinne; Cruz, Fernando; Dalen, Love; Biase, Alessio De; Campo, Javier; Delić, Teo; Dennis, Alice B; Derks, Martijn FL; Diroma, Maria Angela; Djan, Mihajla; Duprat, Simone; Eleftheriadi, Klara; Feulner, Philine GD; Flot, Jean-François; Forni, Giobbe; Fosso, Bruno; Fournier, Pascal; Fournier-Chambrillon, Christine; Gabaldon, Toni; Garg, Shilpa; Gissi, Carmela; Giupponi, Luca; Gómez-Garrido, Jèssica; González, Josefa; Grilo, Miguel L; Gruening, Bjoern; Guérin, Thomas; Guiglielmoni, Nadège; Gut, Marta; Haesler, Marcel P; Hahn, Christoph; Halpern, Balint; Harrison, Peter; Heintz, Julia; Hindrikson, Maris; Höglund, Jacob; Howe, Kerstin; Hughes, Graham; Istace, Benjamin; Cock, Mark J.; Jancekovic, Franc; Jónsson, Zophonı́as O; Joye-Dind, Sagane; Koskimaki, Janne J.; Krystufek, Boris; Kubacka, Justyna; Kuhl, Heiner; Kusza, Szilvia; Labadie, Karine; Lahteenaro, Meri; Lantz, Henrik; Lavrinienko, Anton; Leclère, Lucas; Lopes, Ricardo Jorge; Madsen, Ole; Magdelenat, Ghislaine; Magoga, Giulia; Manousaki, Tereza; Mappes, Tapio; Marques, João P; Redondo, Gemma I Martinez; Maumus, Florian; Megens, Hendrik-Jan; Melo-Ferreira, José; Mendes, Sofia L; Montagna, Matteo; Moreno, João; Mosbech, Mai-Britt; Moura, Monica; Musilova, Zuzana; Myers, Eugene; Nash, Will J.; Nater, Alexander; Nicholson, Pamela; Niell, Manuel; Nijland, Reindert; Noel, Benjamin; Norén, Karin; Oliveira, Pedro H; Olsen, Remi-Andre; Ometto, Lino; Ossowski, Stephan; Palinauskas, Vaidas; Pálsson, Snæbjörn; Panibe, Jerome P; Paupério, Joana; Pavlek, Martina; Payen, Emilie; Pawłowska, Julia; Pellicer, Jaume; Pesole, Graziano; Pimenta, Joao; Pippel, Martin; Pirttilä, Anna Maria; Poulakakis, Nikos; Rajan, Jeena; Rego, Ruben MC; Resendes, Roberto; Resl, Philipp; Riesgo, Ana; Rödin-Mörch, Patrik; Soares, André ER; Fernandes, Carlos Rodrı́guez; Romeiras, Maria M.; Roxo, Guilherme; Ruber, Lukas; Ruiz-López, Marı́a José; Saarma, Urmas; Silva, Luis P; Sim-Sim, Manuela; Soler, Lucile; Sousa, Vitor C; Santos, Carla Sousa; Spada, Alberto; Stefanović, Milomir; Steger, Viktor; Stiller, Josefin; Stöck, Matthias; Struck, Torsten Hugo H; Sudasinghe, Hiranya; Tapanainen, Riikka; Tellgren-Roth, Christian; Trindade, Helena; Tukalenko, Yevhen; Urso, Ilenia; Vacherie, Benoit; Belleghem, Steven M Van; Oers, Kees; Vargas-Chavez, Carlos; Velickovic, Nevena; Vella, Noel; Vella, Adriana; Vernesi, Cristiano; Vicente, Sara; Villa, Sara; Pettersson, Olga Vinnere; Volckaert, Filip AM; Vörös, Judit; Wincker, Patrick; Winkler, Sylke; Ciofi, Claudio; Waterhouse, Robert M; Mazzoni, Camila J

A comparative gene expression matrix in Apoe-deficient mice identifies unique and atherosclerotic disease stage-specific gene regulation patterns in monocytes and macrophages

Härdtner, Carmen; Kumar, Anup; Ehlert, Carolin A.; Vico, Tamara Antonela; Starz, Christopher; Ehr, Alexander; Krebs, Katja; Dufner, Bianca; Hoppe, Natalie; Stachon, Peter; Heidt, Timo; Wolf, Dennis; Mühlen, Constantin; Grüning, Björn; Robbins, Clinton S.; Maegdefessel, Lars; Westermann, Dirk; Dederichs, Tsai-Sang; Hilgendorf, Ingo

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; Grüning, Björn; Cummins, Carla; Amid, Clara; Nieuwenhuijse, David; Visontai, Dávid; Yuan, David Yu; Gupta, Dipayan; Prasad, Divyae; Gulyás, Gábor Máté; Rinck, Gabriele; McKinnon, Jasmine; Rajan, Jeena; Knaggs, Jeff; Skiby, Jeffrey Edward; Stéger, József; Szarvas, Judit; Gueye, Khadim; Papp, Krisztián; Hoek, Maarten; Kumar, Manish; Ventouratou, Marianna; 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, Timothée; Maier, Wolfgang; Waheed, Zahra; Iqbal, Zamin; Aarestrup, Frank Møller; Csabai, Istvan; Koopmans, Marion; Burdett, Tony; Cochrane, Guy

Integrative meta-omics in Galaxy and beyond

Schiml, Valerie C.; Delogu, Francesco; Kumar, Praveen; Kunath, Benoit; Batut, Bérénice; Mehta, Subina; Johnson, James E.; Grüning, Björn; Pope, Phillip B.; Jagtap, Pratik D.; Griffin, Timothy J.; Arntzen, Magnus Ø.

Galaxy Training: A powerful framework for teaching!

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; Bras, Yvan Le; 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; Heusden, Peter; Maier, Wolfgang; Clements, Dave; Heyl, Florian; Grüning, Björn; and, Bérénice Batut

Packaging research artefacts with RO-Crate

Soiland-Reyes, Stian; Sefton, Peter; Crosas, Mercè; Castro, Leyla Jael; Coppens, Frederik; Fernández, José M.; Garijo, Daniel; Grüning, Björn; La Rosa, Marco; Leo, Simone; Ó Carragáin, Eoghan; Portier, Marc; Trisovic, Ana; Community, RO-Crate; Groth, Paul; Goble, Carole

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; Grüning, Björn; Stubbs, Andrew

The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2022 update

Enis Afgan; 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; Nekrutenko, Anton; 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; Blankenberg, Daniel; Fornika, Daniel J; Baker, Dannon; Bouvier, Dave; Clements, Dave; Lima Morais, David A; Tabernero, David Lopez; Lariviere, Delphine; Nasr, Engy; Afgan, Enis; Zambelli, Federico; Heyl, Florian; Psomopoulos, Fotis; Coppens, Frederik; Price, Gareth R; Cuccuru, Gianmauro; Corguillé, Gildas Le; Kuster, Greg Von; Akbulut, Gulsum Gudukbay; Rasche, Helena; Hotz, Hans-Rudolf; 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; Beek, Marius; Čech, Martin; Bernt, Matthias; Fahrner, Matthias; Tekman, Mehmet; Föll, 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; Koning, Willem; Maier, Wolfgang; Briggs, Peter J

Expanding the Galaxy's reference data

VijayKrishna, Nagampalli; Joshi, Jayadev; Coraor, Nate; Hillman-Jackson, Jennifer; Bouvier, Dave; Beek, Marius; Eguinoa, Ignacio; Coppens, Frederik; Davis, John; Stolarczyk, Michał; Sheffield, Nathan C; Gladman, Simon; Cuccuru, Gianmauro; Grüning, Björn; Soranzo, Nicola; Rasche, Helena; Langhorst, Bradley W; Bernt, Matthias; Fornika, Dan; Lima Morais, David Anderson; Barrette, Michel; Heusden, Peter; Petrillo, Mauro; Puertas-Gallardo, Antonio; Patak, Alex; Hotz, Hans-Rudolf; Blankenberg, Daniel

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; Grüning, Björn; 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; Nei-Hsiao; Gottberg, Anne; Klerk, Arne De; 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; Oliveira, Tulio; and, Sergei L Kosakovsky Pond

Community-driven ELIXIR activities in single-cell omics

Czarnewski, Paulo; Mahfouz, Ahmed; Calogero, Raffaele A.; Palagi, Patricia M.; Portell-Silva, Laura; Gonzalez-Uriarte, Asier; Soneson, Charlotte; Burdett, Tony; Szomolay, Barbara; Videm, Pavankumar; Hotz, Hans-Rudolf; Papatheodorou, Irene; Hancock, John M.; Grüning, Björn; Haerty, Wilfried; Krause, Roland; Capella-Gutierrez, Salvador; Leskošek, Brane; Alessandri, Luca; Arigoni, Maddalena; Rezen, Tadeja; Botzki, Alexander; Ferk, Polonca; Lindvall, Jessica; Heil, Katharina F.; Ishaque, Naveed; Korpelainen, Eija

A proteomics sample metadata representation for multiomics integration and big data analysis

Dai, Chengxin; Füllgrabe, Anja; Pfeuffer, Julianus; Solovyeva, Elizaveta M.; Deng, Jingwen; Moreno, Pablo; Kamatchinathan, Selvakumar; Kundu, Deepti Jaiswal; George, Nancy; Fexova, Silvie; Grüning, Björn; Föll, Melanie Christine; Griss, Johannes; Vaudel, Marc; Audain, Enrique; Locard-Paulet, Marie; Turewicz, Michael; Eisenacher, Martin; Uszkoreit, Julian; Bossche, Tim Van Den; Schwämmle, Veit; Webel, Henry; Schulze, Stefan; Bouyssié, David; Jayaram, Savita; Duggineni, Vinay Kumar; Samaras, Patroklos; Wilhelm, Mathias; Choi, Meena; Wang, Mingxun; Kohlbacher, Oliver; Brazma, Alvis; Papatheodorou, Irene; Bandeira, Nuno; Deutsch, Eric W.; Vizcaı́no, Juan Antonio; Bai, Mingze; Sachsenberg, Timo; Levitsky, Lev I.; Perez-Riverol, Yasset

ASaiM-MT: a validated and optimized ASaiM workflow for metatranscriptomics analysis within Galaxy framework

Mehta, Subina; Crane, Marie; Leith, Emma; Batut, Bérénice; Hiltemann, Saskia; Arntzen, Magnus Ø; Kunath, Benoit J; Pope, Phillip B; Delogu, Francesco; Sajulga, Ray; others

RNA-Seq Data Analysis in Galaxy

Batut, Bérénice; Beek, Marius van den; Doyle, Maria A; Soranzo, Nicola

Ready-to-use public infrastructure for global SARS-CoV-2 monitoring

Maier, Wolfgang; Bray, Simon; Beek, Marius; Bouvier, Dave; Coraor, Nathan; Miladi, Milad; Singh, Babita; De Argila, Jordi Rambla; Baker, Dannon; Roach, Nathan; Gladman, Simon; Coppens, Frederik; Martin, Darren P.; Lonie, Andrew; Grüning, Björn; Kosakovsky Pond, Sergei L.; Nekrutenko, Anton

User-friendly, scalable tools and workflows for single-cell RNA-seq analysis

Moreno, Pablo; Huang, Ni; Manning, Jonathan R.; Mohammed, Suhaib; Solovyev, Andrey; Polanski, Krzysztof; Bacon, Wendi; Chazarra, Ruben; Talavera-López, Carlos; Doyle, Maria A.; Marnier, Guilhem; Grüning, Björn; Rasche, Helena; George, Nancy; Fexova, Silvie Korena; Alibi, Mohamed; Miao, Zhichao; Perez-Riverol, Yasset; Haeussler, Maximilian; Brazma, Alvis; Teichmann, Sarah; Meyer, Kerstin B.; Papatheodorou, Irene

Intuitive, reproducible high-throughput molecular dynamics in Galaxy: a tutorial

Bray, Simon A; Senapathi, Tharindu; Barnett, Christopher B; Grüning, Björn A

Genome Evolution: Mutation Is the Main Driver of Genome Size in Prokaryotes

Marais, Gabriel AB; Batut, Bérénice; Daubin, Vincent

Ten simple rules for making training materials FAIR

Garcia, Leyla; Batut, Bérénice; Burke, Melissa L.; Kuzak, Mateusz; Psomopoulos, Fotis; Arcila, Ricardo; Attwood, Teresa K.; Beard, Niall; Carvalho-Silva, Denise; Dimopoulos, Alexandros C.; Angel, Victoria Dominguez; Dumontier, Michel; Gurwitz, Kim T.; Krause, Roland; McQuilton, Peter; Le Pera, Loredana; Morgan, Sarah L.; Rauste, Päivi; Via, Allegra; Kahlem, Pascal; Rustici, Gabriella; Gelder, Celia W. G.; Palagi, Patricia M.

A single-cell RNA-sequencing training and analysis suite using the Galaxy framework

Tekman, Mehmet; Batut, Bérénice; Ostrovsky, Alexander; Antoniewski, Christophe; Clements, Dave; Ramirez, Fidel; Etherington, Graham J; Hotz, Hans-Rudolf; Scholtalbers, Jelle; Manning, Jonathan R; Bellenger, Lea; Doyle, Maria A; Heydarian, Mohammad; Huang, Ni; Soranzo, Nicola; Moreno, Pablo; Mautner, Stefan; Papatheodorou, Irene; Nekrutenko, Anton; Taylor, James; Blankenberg, Daniel; Backofen, Rolf; Grüning, Björn

The omics discovery REST interface

Dass, Gaurhari; Vu, Manh-Tu; Xu, Pan; Audain, Enrique; Hitz, Marc-Phillip; Grüning, Björn A; Hermjakob, Henning; Perez-Riverol, Yasset

The omics discovery REST interface

Dass, Gaurhari; Vu, Manh-Tu; Xu, Pan; Audain, Enrique; Hitz, Marc-Phillip; Grüning, Björn A; Hermjakob, Henning; Perez-Riverol, Yasset

The de. NBI/ELIXIR-DE training platform-Bioinformatics training in Germany and across Europe within ELIXIR

Wibberg, Daniel; Batut, Bérénice; Belmann, Peter; Blom, Jochen; Glöckner, Frank Oliver; Grüning, Björn; Hoffmann, Nils; Kleinbölting, Nils; Rahn, René; Rey, Maja; others

The bio.tools registry of software tools and data resources for the life sciences

Ison, Jon; Ienasescu, Hans; Chmura, Piotr; Rydza, Emil; Ménager, Hervé; Kalaš, Matúš; Schwämmle, Veit; Grüning, Björn; Beard, Niall; Lopez, Rodrigo; Duvaud, Severine; Stockinger, Heinz; Persson, Bengt; Vařeková, Radka Svobodová; Raček, Tomáš; Vondrášek, Jiřı́; Peterson, Hedi; Salumets, Ahto; Jonassen, Inge; Hooft, Rob; Nyrönen, Tommi; Valencia, Alfonso; Capella, Salvador; Gelpı́, Josep; Zambelli, Federico; Savakis, Babis; Leskošek, Brane; Rapacki, Kristoffer; Blanchet, Christophe; Jimenez, Rafael; Oliveira, Arlindo; Vriend, Gert; Collin, Olivier; Helden, Jacques; Løngreen, Peter; Brunak, Søren

ASaiM: a Galaxy-based framework to analyze microbiota data

Batut, Bérénice; Gravouil, Kevin; Defois, Clemence; Hiltemann, Saskia; Brugère, Jean-François; Peyretaillade, Eric; Peyret, Pierre

High-resolution TADs reveal DNA sequences underlying genome organization in flies

Ramı́rez, Fidel; Bhardwaj, Vivek; Arrigoni, Laura; Lam, Kin Chung; Grüning, Björn A; Villaveces, José; Habermann, Bianca; Akhtar, Asifa; Manke, Thomas

Distinct epigenetic programs regulate cardiac myocyte development and disease in the human heart in vivo

Gilsbach, Ralf; Schwaderer, Martin; Preissl, Sebastian; Gruening, Bjoern A; Kranzhoefer, David; Schneider, Pedro; Nuehrenberg, Thomas G; Mulero-Navarro, Sonia; Weichenhan, Dieter; Braun, Christian; others

Combinatorial omics analysis reveals perturbed lysosomal homeostasis in collagen VII-deficient keratinocytes

Thriene, Kerstin; Grüning, Björn Andreas; Bornert, Olivier; Erxleben, Anika; Leppert, Juna; Athanasiou, Ioannis; Weber, Ekkehard; Kiritsi, Dimitra; Nyström, Alexander; Reinheckel, Thomas; others

Disseminating Metaproteomic Informatics Capabilities and Knowledge Using the Galaxy-P Framework

Blank, Clemens; Easterly, Caleb; Gruening, Bjoern; Johnson, James; Kolmeder, Carolin A; Kumar, Praveen; May, Damon; Mehta, Subina; Mesuere, Bart; Brown, Zachary; others

Community-Driven Data Analysis Training for Biology

Batut, Bérénice; Hiltemann, Saskia; Bagnacani, Andrea; Baker, Dannon; Bhardwaj, Vivek; Blank, Clemens; Bretaudeau, Anthony; Brillet-Guéguen, Loraine; Čech, Martin; Chilton, John; Clements, Dave; Doppelt-Azeroual, Olivia; Erxleben, Anika; Freeberg, Mallory Ann; Gladman, Simon; Hoogstrate, Youri; Hotz, Hans-Rudolf; Houwaart, Torsten; Jagtap, Pratik; Larivière, Delphine; Corguillé, Gildas Le; Manke, Thomas; Mareuil, Fabien; Ramı́rez, Fidel; Ryan, Devon; Sigloch, Florian Christoph; Soranzo, Nicola; Wolff, Joachim; Videm, Pavankumar; Wolfien, Markus; Wubuli, Aisanjiang; Yusuf, Dilmurat; Taylor, James; Backofen, Rolf; Nekrutenko, Anton; Grüning, Björn

GRIN3B missense mutation as an inherited risk factor for schizophrenia: whole-exome sequencing in a family with a familiar history of psychotic disorders

Hornig, Tobias; Gruening, Bjoern; Kundu, Kousik; Houwaart, Torsten; Backofen, Rolf; Biber, Knut; Normann, Claus

Strategies for analyzing bisulfite sequencing data

Wreczycka, Katarzyna; Gosdschan, Alexander; Yusuf, Dilmurat; Gruening, Bjoern; Assenov, Yassen; Akalin, Altuna

BioContainers: an open-source and community-driven framework for software standardization

Veiga Leprevost, Felipe; Grüning, Björn A; Alves Aflitos, Saulo; Röst, Hannes L; Uszkoreit, Julian; Barsnes, Harald; Vaudel, Marc; Moreno, Pablo; Gatto, Laurent; Weber, Jonas; others

RNA-bioinformatics: tools, services and databases for the analysis of RNA-based regulation

Backofen, Rolf; Engelhardt, Jan; Erxleben, Anika; Fallmann, Jörg; Grüning, Björn; Ohler, Uwe; Rajewsky, Nikolaus; Stadler, Peter F

The RNA workbench: best practices for RNA and high-throughput sequencing bioinformatics in Galaxy

Grüning, Björn A; Fallmann, Jörg; Yusuf, Dilmurat; Will, Sebastian; Erxleben, Anika; Eggenhofer, Florian; Houwaart, Torsten; Batut, Bérénice; Videm, Pavankumar; Bagnacani, Andrea; others

Four simple recommendations to encourage best practices in research software

Jiménez, Rafael C; Kuzak, Mateusz; Alhamdoosh, Monther; Barker, Michelle; Batut, Bérénice; Borg, Mikael; Capella-Gutierrez, Salvador; Hong, Neil Chue; Cook, Martin; Corpas, Manuel; others

miRNA profile of human retinal endothelial cells in starvation or angiogenic stimulation with and without VEGF inhibitors

Walz, Johanna Madeleine; Wecker, Thomas; Zhang, Pei; Cakir, Bertan; Grüning, Björn; Agostini, Hansjuergen; Faerber, Lothar; Lange, Clemens; Schlunck, Gunther R; Stahl, Andreas

Recent advances in RNA folding

Fallmann, Jörg; Will, Sebastian; Engelhardt, Jan; Grüning, Björn; Backofen, Rolf; Stadler, Peter F

Building an open, collaborative, online infrastructure for bioinformatics training

Batut, Bérénice; Network, Galaxy T; Clements, Dave; Grüning, Björn

ReGaTE, Registration of Galaxy Tools in Elixir

Doppelt-Azeroual, Olivia; Mareuil, Fabien; Deveaud, Eric; Kalaš, Matúš; Soranzo, Nicola; Beek, Marius; Gruening, Bjoern; Ison, Jon; Ménager, Hervé

EBF1 binds to EBNA2 and promotes the assembly of EBNA2 chromatin complexes in B cells

Glaser, Laura V; Rieger, Simone; Thumann, Sybille; Beer, Sophie; Kuklik-Roos, Cornelia; Martin, Dietmar E; Maier, Kerstin C; Harth-Hertle, Marie L; Grüning, Björn; Backofen, Rolf; others

Virtualisierte wissenschaftliche Forschungsumgebungen und die zukünftige Rolle der Rechenzentren

Meier, Konrad; Grüning, Björn; Blank, Clemens; Janczyk, Michael; Suchodoletz, Dirk

An Accessible Proteogenomics Informatics Resource for Cancer Researchers

Chambers, Matthew C; Jagtap, Pratik D; Johnson, James E; McGowan, Thomas; Kumar, Praveen; Onsongo, Getiria; Guerrero, Candace R; Barsnes, Harald; Vaudel, Marc; Martens, Lennart; others

ENASearch: A Python library for interacting with ENA’s API

Batut, Bérénice; Grüning, Björn

DNA methylation signatures follow preformed chromatin compartments in cardiac myocytes

Nothjunge, Stephan; Nührenberg, Thomas G; Grüning, Björn A; Doppler, Stefanie A; Preissl, Sebastian; Schwaderer, Martin; Rommel, Carolin; Krane, Markus; Hein, Lutz; Gilsbach, Ralf

DOT1L Activity Promotes Proliferation and Protects Cortical Neural Stem Cells from Activation of ATF4-DDIT3-Mediated ER Stress In Vitro

Roidl, Deborah; Hellbach, Nicole; Bovio, Patrick P; Villarreal, Alejandro; Heidrich, Stefanie; Nestel, Sigrun; Grüning, Björn A; Boenisch, Ulrike; Vogel, Tanja

MicroRNA profiling in aqueous humor of individual human eyes by next-generation sequencing

Wecker, Thomas; Hoffmeier, Klaus; Plötner, Anne; Grüning, Björn Andreas; Horres, Ralf; Backofen, Rolf; Reinhard, Thomas; Schlunck, Günther

deepTools2: a next generation web server for deep-sequencing data analysis

Ramı́rez, Fidel; Ryan, Devon P; Grüning, Björn; Bhardwaj, Vivek; Kilpert, Fabian; Richter, Andreas S; Heyne, Steffen; Dündar, Friederike; Manke, Thomas

The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2016 update

Afgan, Enis; Baker, Dannon; Beek, Marius; Blankenberg, Daniel; Bouvier, Dave; Čech, Martin; Chilton, John; Clements, Dave; Coraor, Nate; Eberhard, Carl; others

Echinocandin B biosynthesis: a biosynthetic cluster from Aspergillus nidulans NRRL 8112 and reassembly of the subclusters Ecd and Hty from Aspergillus pachycristatus NRRL 11440 reveals a single coherent gene cluster

Hüttel, Wolfgang; Youssar, Loubna; Grüning, Björn A; Günther, Stefan; Hugentobler, Katharina G

PubMedPortable: a framework for supporting the development of text mining applications

Döring, Kersten; Grüning, Björn A; Telukunta, Kiran K; Thomas, Philippe; Günther, Stefan

5'-hydroxymethylcytosine precedes loss of CpG methylation in enhancers and genes undergoing activation in cardiomyocyte maturation

Kranzhöfer, David K; Gilsbach, Ralf; Grüning, Björn A; Backofen, Rolf; Nührenberg, Thomas G; Hein, Lutz

NCBI BLAST+ integrated into Galaxy

Cock, Peter JA; Chilton, John M; Grüning, Björn; Johnson, James E; Soranzo, Nicola

The purchasable chemical space: a detailed picture

Lucas, Xavier; Grüning, Björn A; Bleher, Stefan; Günther, Stefan

Deciphering the Epigenetic Code of Cardiac Myocyte TranscriptionNovelty and Significance

Preissl, Sebastian; Schwaderer, Martin; Raulf, Alexandra; Hesse, Michael; Grüning, Björn A; Köbele, Claudia; Backofen, Rolf; Fleischmann, Bernd K; Hein, Lutz; Gilsbach, Ralf

Cutting edge: anatomy of BioJS, an open source community for the life sciences

Yachdav, Guy; Goldberg, Tatyana; Wilzbach, Sebastian; Dao, David; Shih, Iris; Choudhary, Saket; Crouch, Steve; Franz, Max; Garcı́a, Alexander; Garcı́a, Leyla J; others

Genome wide epigenetic profiling of purified cardiomyocytes enables deep insights into gene expression control

Gilsbach, R; Preissl, S; Gruening, B; Koebele, C; Schnick, T; Hein, L

Dynamics of epigenetic modifications in cardiomyocyte-specific cis-regulatory regions

Preissl, S; Gilsbach, R; Gruening, B; Koebele, C; Hein, L

Tools and data services registry: a community effort to document bioinformatics resources

Ison, Jon; Rapacki, Kristoffer; Ménager, Hervé; Kalaš, Matúš; Rydza, Emil; Chmura, Piotr; Anthon, Christian; Beard, Niall; Berka, Karel; Bolser, Dan; others

An NGS workflow blueprint for DNA sequencing data and its application in individualized molecular oncology

Li, Jian; Batcha, Aarif Mohamed Nazeer; Gaining, Björn; Mansmann, Ulrich R

Integrierte bioinformatische Methoden zur reproduzierbaren und transparenten Hochdurchsatz-Analyse von Life Science Big Data

Grüning, Björn

ChemicalToolBoX and its application on the study of the drug like and purchasable space

Lucas, Xavier; Grüning, Björn A; Günther, Stefan

Dynamic information system for small molecules

Telukunta, Kiran K; Lucas, Xavier; Döring, Kersten; Grüning, Björn A; Günther, Stefan

Regio-and stereoselective intermolecular oxidative phenol coupling in Streptomyces

Präg, Andreas; Grüning, Björn A; Häckh, Matthias; Lüdeke, Steffen; Wilde, Marcel; Luzhetskyy, Andriy; Richter, Michael; Luzhetska, Marta; Günther, Stefan; Müller, Michael

deepTools: a flexible platform for exploring deep-sequencing data

Ramı́rez, Fidel; Dündar, Friederike; Diehl, Sarah; Grüning, Björn A; Manke, Thomas

PyWATER: a PyMOL plug-in to find conserved water molecules in proteins by clustering

Patel, Hitesh; Grüning, Björn A; Günther, Stefan; Merfort, Irmgard

Dynamic DNA methylation orchestrates cardiomyocyte development, maturation and disease

Gilsbach, Ralf; Preissl, Sebastian; Grüning, Björn A; Schnick, Tilman; Burger, Lukas; Benes, Vladimir; Würch, Andreas; Bönisch, Ulrike; Günther, Stefan; Backofen, Rolf; others

Autosomal dominant immune dysregulation syndrome in humans with CTLA4 mutations

Schubert, Desirée; Bode, Claudia; Kenefeck, Rupert; Hou, Tie Zheng; Wing, James B; Kennedy, Alan; Bulashevska, Alla; Petersen, Britt-Sabina; Schäffer, Alejandro A; Grüning, Björn A; others

Autosomal-Recessive Agammaglobulinemia Due to Homozygous Mutations in Artemis: Do We Need a Modifier?

Volk, T; Reisli, I; Bjorkman, A; Pannicke, U; Fisch, P; Schaeffer, AA; Bulashevska, A; Gruening, BA; Pfeifer, D; Guner, S; others

CTLA-4 Deficiency-A Novel Autosomal-Dominant Immune Dysregulation Syndrome

Schubert, D; Bode, C; Kenefeck, R; Hou, TZ; Wing, J; Unger, S; Bulashevska, A; Gruening, BA; Petersen, BS; Schaeffer, AA; others

Bioinformatics Analysis of Exome Sequencing Data: Challenges and Solutions

Bulashevska, A; Gruening, BA; Backofen, R; Grimbacher, B

CpG-methylation characterizes cardiomyocytes in development and disease

Preissl, Sebastian; Gilsbach, Ralf; Gruening, Bjoern; Koebele, Claudia; Schnick, Tilman; Hein, Lutz

Draft genome sequence of Streptomyces viridochromogenes strain Tü57, producer of avilamycin

Grüning, Björn A; Erxleben, Anika; Hähnlein, Anna; Günther, Stefan

Galaxy tools and workflows for sequence analysis with applications in molecular plant pathology

Cock, Peter JA; Grüning, Björn A; Paszkiewicz, Konrad; Pritchard, Leighton

Characterization and phylogenetic analysis of the mitochondrial genome of Glarea lozoyensis indicates high diversity within the order Helotiales

Youssar, Loubna; Grüning, Björn Andreas; Günther, Stefan; Hüttel, Wolfgang

Genome sequence of the fungus Glarea lozoyensis: the first genome sequence of a species from the Helotiaceae family

Youssar, Loubna; Grüning, Björn Andreas; Erxleben, Anika; Günther, Stefan; Hüttel, Wolfgang

Mining and evaluation of molecular relationships in literature

Senger, Christian; Grüning, Björn A; Erxleben, Anika; Döring, Kersten; Patel, Hitesh; Flemming, Stephan; Merfort, Irmgard; Günther, Stefan

StreptomeDB: a resource for natural compounds isolated from Streptomyces species

Lucas, Xavier; Senger, Christian; Erxleben, Anika; Grüning, Björn A; Döring, Kersten; Mosch, Johannes; Flemming, Stephan; Günther, Stefan

Genome Sequence of the Fungus Glarea

Günther, Stefan; Hüttel, Wolfgang; Youssar, Loubna; Grüning, Björn Andreas; Erxleben, Anika

Genome sequence of Streptomyces sp. Tü6071

Erxleben, Anika; Wunsch-Palasis, Julia; Grüning, Björn A; Luzhetska, Marta; Bechthold, Andreas; Günther, Stefan

Compounds In Literature (CIL): screening for compounds and relatives in PubMed

Grüning, Björn A; Senger, Christian; Erxleben, Anika; Flemming, Stephan; Günther, Stefan

Small-molecule conversion of toxic oligomers to nontoxic β-sheet–rich amyloid fibrils

Bieschke, Jan; Herbst, Martin; Wiglenda, Thomas; Friedrich, Ralf P; Boeddrich, Annett; Schiele, Franziska; Kleckers, Daniela; Amo, Juan Miguel Lopez; Grüning, Björn A; Wang, Qinwen; others

SuperLooper—a prediction server for the modeling of loops in globular and membrane proteins

Hildebrand, Peter W; Goede, Andrean; Bauer, Raphael A; Gruening, Bjoern; Ismer, Jochen; Michalsky, Elke; Preissner, Robert

RHYTHM—a server to predict the orientation of transmembrane helices in channels and membrane-coils

Rose, Alexander; Lorenzen, Stephan; Goede, Andrean; Gruening, Björn; Hildebrand, Peter W

Voronoia: analyzing packing in protein structures

Rother, Kristian; Hildebrand, Peter Werner; Goede, Andrean; Gruening, Bjoern; Preissner, Robert

SuperScent—a database of flavors and scents

Dunkel, Mathias; Schmidt, Ulrike; Struck, Swantje; Berger, Lena; Gruening, Bjoern; Hossbach, Julia; Jaeger, Ines S; Effmert, Uta; Piechulla, Birgit; Eriksson, Roger; others

SuperToxic: a comprehensive database of toxic compounds

Schmidt, Ulrike; Struck, Swantje; Gruening, Bjoern; Hossbach, Julia; Jaeger, Ines S; Parol, Roza; Lindequist, Ulrike; Teuscher, Eberhard; Preissner, Robert

Toxicity versus potency: Elucidation of toxicity properties discriminating between toxins, drugs, and natural compounds

Struck, Swantje; Schmidt, Ulrike; Gruening, Bjoern; Jaeger, Ines S; Hossbach, Julia; Preissner, Robert

PROPERTIES DISCRIMINATING BETWEEN TOXINS, DRUGS

STRUCK, SWANTJE; SCHMIDT, ULRIKE; GRUENING, BJOERN; JAEGER, INES S; PREISSNER, JULIA HOSSBACH'ROBERT