Björn A. Grüning

Publication Activity (10 Years)

Years Active: 2009-2023
Publications (10 Years): 44

Top Topics

Scientific Workflows

Teaching Practices

Top Venues

Nucleic Acids Res.

PLoS Comput. Biol.

J. Cheminformatics

Publications

Sebastian Schaaf, Anika Erxleben-Eggenhofer, Björn A. Grüning
Galaxy and RDM Being More Than a Workflow Manager: Living the Data Life Cycle. CoRDI (2023)
Aysam Guerler, Dannon Baker, Marius van den Beek, Björn A. Grüning, Dave Bouvier, Nate Coraor, Stephen D. Shank, Jordan D. Zehr, Michael C. Schatz, Anton Nekrutenko
Fast and accurate genome-wide predictions and structural modeling of protein-protein interactions using Galaxy. BMC Bioinform. 24 (1) (2023)
Nuwan Goonasekera, Catherine J. Bromhead, Simon L. Gladman, Nate Coraor, Björn A. Grüning, Enis Afgan
Right-sizing compute resource allocations for bioinformatics tools with Total Perspective Vortex. CoRR (2023)
Anup Kumar, Björn A. Grüning, Rolf Backofen
Transformer-based tool recommendation system in Galaxy. BMC Bioinform. 24 (1) (2023)
Saskia Hiltemann, Helena Rasche, Simon L. Gladman, Hans-Rudolf Hotz, Delphine Larivière, Daniel J. Blankenberg, Pratik D. Jagtap, Thomas Wollmann, Anthony Bretaudeau, Nadia Goué, Timothy J. Griffin, Coline Royaux, Yvan Le Bras, Subina P. Mehta, Anna Syme, Frederik Coppens, Bert Droesbeke, Nicola Soranzo, Wendi A. Bacon, Fotis E. Psomopoulos, Cristóbal Gallardo-Alba, John Davis, Melanie Christine Föll, Matthias Fahrner, Maria A. Doyle, Beatriz Serrano-Solano, Anne Fouilloux, Peter van Heusden, Wolfgang Maier, Dave Clements, Florian Heyl, The Galaxy Team, Björn A. Grüning, Bérénice Batut
Galaxy Training: A powerful framework for teaching! PLoS Comput. Biol. 19 (1) (2023)
Paul F. Zierep, Sanjay Kumar Srikakulam, Sebastian Schaaf, Björn A. Grüning
Conda, Container and Bots How to Build and Maintain Tool Dependencies in Workflows and Training Materials. CoRDI (2023)
Tunc Kayikcioglu, Sanjay Kumar Srikakulam, Wolfgang Maier, Björn A. Grüning
Interactive Tools (IT) in Galaxy Combining Synchronous and Asynchronous Workflows. CoRDI (2023)
Carole A. Goble, Finn Bacall, Stian Soiland-Reyes, Stuart Owen, Ignacio Eguinoa, Bert Droesbeke, Hervé Ménager, Laura Rodríguez-Navas, José María Fernández, Björn A. Grüning, Simone Leo, Luca Pireddu, Michael R. Crusoe, Johan Gustafsson, Salvador Capella-Gutiérrez, Frederik Coppens
The EOSC-Life Workflow Collaboratory for the Life Sciences. CoRDI (2023)
Enis Afgan, Anton Nekrutenko, Björn A. Grüning, Daniel J. Blankenberg, Jeremy Goecks, Michael C. Schatz, Alexander E. Ostrovsky, Alexandru Mahmoud, Andrew J. Lonie, Anna Syme, Anne Fouilloux, Anthony Bretaudeau, Anup Kumar, Arthur C. Eschenlauer, Assunta D. Desanto, Aysam Guerler, Beatriz Serrano-Solano, Bérénice Batut, Bradley W. Langhorst, Bridget Carr, Bryan A. Raubenolt, Cameron J. Hyde, Catherine J. Bromhead, Christopher B. Barnett, Coline Royaux, Cristóbal Gallardo, Daniel J. Fornika, Dannon Baker, Dave Bouvier, Dave Clements, David A. de Lima Morais, David Lopez Tabernero, Delphine Larivière, Engy Nasr, Federico Zambelli, Florian Heyl, Fotis Psomopoulos, Frederik Coppens, Gareth R. Price, Gianmauro Cuccuru, Gildas Le Corguillé, Gregory Von Kuster, Gulsum Gudukbay, Helena Rasche, Hans-Rudolf Hotz, Ignacio Eguinoa, Igor V. Makunin, Isuru Ranawaka, James Taylor, Jayadev Joshi, Jennifer Hillman-Jackson, John Chilton, Kaivan Kamali, Keith Suderman, Krzysztof Poterlowicz, Yvan Le Bras, Lucille Lopez-Delisle, Luke Sargent, Madeline E. Bassetti, Marco Antonio Tangaro, Marius van den Beek, Martin Cech, Matthias Bernt, Matthias Fahrner, Mehmet Tekman, Melanie Christine Föll, Michael R. Crusoe, Miguel Roncoroni, Natalie Kucher, Nate Coraor, Nicholas Stoler, Nick Rhodes, Nicola Soranzo, Niko Pinter, Nuwan Goonasekera, Pablo A. Moreno, Pavankumar Videm, Petera Melanie, Pietro Mandreoli, Pratik D. Jagtap, Qiang Gu, Ralf J. M. Weber, Ross Lazarus, Ruben H. P. Vorderman, Saskia Hiltemann, Sergey Golitsynskiy, Shilpa Garg, Simon A. Bray, Simon L. Gladman, Simone Leo, Subina P. Mehta, Timothy J. Griffin, Vahid Jalili, Yves Vandenbrouck, Victor Wen, Vijay K. Nagampalli, Wendi A. Bacon, Willem L. De Koning, Wolfgang Maier, Peter J. Briggs
The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2022 update. Nucleic Acids Res. 50 (W1) (2022)
Stian Soiland-Reyes, Peter Sefton, Mercè Crosas, Leyla Jael Castro, Frederik Coppens, José María Fernández, Daniel Garijo, Björn A. Grüning, Marco La Rosa, Simone Leo, Eoghan Ó Carragáin, Marc Portier, Ana Trisovic, RO-Crate Community, Paul Groth, Carole A. Goble
Packaging research artefacts with RO-Crate. Data Sci. 5 (2) (2022)
Beatriz Serrano-Solano, Anne Fouilloux, Ignacio Eguinoa, Matús Kalas, Björn A. Grüning, Frederik Coppens
Galaxy: A Decade of Realising CWFR Concepts. Data Intell. 4 (2) (2022)
Simon Bray, Tim Dudgeon, Rachael Skyner, Rolf Backofen, Björn A. Grüning, Frank von Delft
Galaxy workflows for fragment-based virtual screening: a case study on the SARS-CoV-2 main protease. J. Cheminformatics 14 (1) (2022)
Paul Brack, Peter Crowther, Stian Soiland-Reyes, Stuart Owen, Douglas Lowe, Alan R. Williams, Quentin Groom, Mathias Dillen, Frederik Coppens, Björn A. Grüning, Ignacio Eguinoa, Philip Ewels, Carole A. Goble
Ten simple rules for making a software tool workflow-ready. PLoS Comput. Biol. 18 (3) (2022)
Stian Soiland-Reyes, Peter Sefton, Mercè Crosas, Leyla Jael Castro, Frederik Coppens, José M. Fernández, Daniel Garijo, Björn A. Grüning, Marco La Rosa, Simone Leo, Eoghan Ó Carragáin, Marc Portier, Ana Trisovic, RO-Crate Community, Paul Groth, Carole A. Goble
Packaging research artefacts with RO-Crate. CoRR (2021)
Beatriz Serrano-Solano, Melanie Christine Föll, Cristóbal Gallardo-Alba, Anika Erxleben, Helena Rasche, Saskia Hiltemann, Matthias Fahrner, Mark J. Dunning, Marcel H. Schulz, Beáta Scholtz, Dave Clements, Anton Nekrutenko, Bérénice Batut, Björn A. Grüning
Fostering accessible online education using Galaxy as an e-learning platform. PLoS Comput. Biol. 17 (5) (2021)
Joachim Wolff, Rolf Backofen, Björn A. Grüning
Robust and efficient single-cell Hi-C clustering with approximate k-nearest neighbor graphs. Bioinform. 37 (22) (2021)
Miguel Roncoroni, Bert Droesbeke, Ignacio Eguinoa, Kim De Ruyck, Flora D'anna, Dilmurat Yusuf, Björn A. Grüning, Rolf Backofen, Frederik Coppens
A SARS-CoV-2 sequence submission tool for the European Nucleotide Archive. Bioinform. 37 (21) (2021)
Gulsum Gudukbay, Jashwant Raj Gunasekaran, Yilin Feng, Mahmut T. Kandemir, Anton Nekrutenko, Chita R. Das, Paul Medvedev, Björn A. Grüning, Nate Coraor, Nathan Roach, Enis Afgan
GYAN: Accelerating Bioinformatics Tools in Galaxy with GPU-Aware Computation Mapping. IPDPS Workshops (2021)
Lucille Lopez-Delisle, Leily Rabbani, Joachim Wolff, Vivek Bhardwaj, Rolf Backofen, Björn A. Grüning, Fidel Ramírez, Thomas Manke
pyGenomeTracks: reproducible plots for multivariate genomic datasets. Bioinform. 37 (3) (2021)
Qiang Gu, Anup Kumar, Simon Bray, Allison Creason, Alireza Khanteymoori, Vahid Jalili, Björn A. Grüning, Jeremy Goecks
Galaxy-ML: An accessible, reproducible, and scalable machine learning toolkit for biomedicine. PLoS Comput. Biol. 17 (6) (2021)
Cristóbal Gallardo-Alba, Björn A. Grüning, Beatriz Serrano-Solano
A constructivist-based proposal for bioinformatics teaching practices during lockdown. PLoS Comput. Biol. 17 (5) (2021)
Joachim Wolff, Nezar Abdennur, Rolf Backofen, Björn A. Grüning
Scool: a new data storage format for single-cell Hi-C data. Bioinform. 37 (9) (2021)
Rafael Ferreira da Silva, Henri Casanova, Kyle Chard, Dan Laney, Dong H. Ahn, Shantenu Jha, Carole A. Goble, Lavanya Ramakrishnan, J. Luc Peterson, Bjoern Enders, Douglas Thain, Ilkay Altintas, Yadu N. Babuji, Rosa M. Badia, Vivien Bonazzi, Tainã Coleman, Michael R. Crusoe, Ewa Deelman, Frank Di Natale, Paolo Di Tommaso, Thomas Fahringer, Rosa Filgueira, Grigori Fursin, Alex Ganose, Björn A. Grüning, Daniel S. Katz, Olga Kuchar, Ana Kupresanin, Bertram Ludäscher, Ketan Maheshwari, Marta Mattoso, Kshitij Mehta, Todd S. Munson, Jonathan Ozik, Tom Peterka, Loic Pottier, Tim Randles, Stian Soiland-Reyes, Benjamín Tovar, Matteo Turilli, Thomas D. Uram, Karan Vahi, Michael Wilde, Matthew Wolf, Justin M. Wozniak
Workflows Community Summit: Bringing the Scientific Workflows Community Together. CoRR (2021)
Simon Bray, Xavier Lucas, Anup Kumar, Björn A. Grüning
The ChemicalToolbox: reproducible, user-friendly cheminformatics analysis on the Galaxy platform. J. Cheminformatics 12 (1) (2020)
Joachim Wolff, Leily Rabbani, Ralf Gilsbach, Gautier Richard, Thomas Manke, Rolf Backofen, Björn A. Grüning
Galaxy HiCExplorer 3: a web server for reproducible Hi-C, capture Hi-C and single-cell Hi-C data analysis, quality control and visualization. Nucleic Acids Res. 48 (Webserver-Issue) (2020)
Gaurhari Dass, Manh-Tu Vu, Pan Xu, Enrique Audain, Marc-Phillip Hitz, Björn A. Grüning, Henning Hermjakob, Yasset Pérez-Riverol
The omics discovery REST interface. Nucleic Acids Res. 48 (Webserver-Issue) (2020)
Richard A. Schäfer, Steffen Lott, Jens Georg, Björn A. Grüning, Wolfgang R. Hess, Björn Voß
GLASSgo in Galaxy: high-throughput, reproducible and easy-to-integrate prediction of sRNA homologs. Bioinform. 36 (15) (2020)
Simon Bray, Tharindu Senapathi, Christopher B. Barnett, Björn A. Grüning
Intuitive, reproducible high-throughput molecular dynamics in Galaxy: a tutorial. J. Cheminformatics 12 (1) (2020)
Evgeny Anatskiy, Devon Patrick Ryan, Björn A. Grüning, Laura Arrigoni, Thomas Manke, Ulrike Bönisch
Parkour LIMS: high-quality sample preparation in next generation sequencing. Bioinform. 35 (8) (2019)
Tharindu Senapathi, Simon Bray, Christopher B. Barnett, Björn A. Grüning, Kevin J. Naidoo
Biomolecular Reaction and Interaction Dynamics Global Environment (BRIDGE). Bioinform. 35 (18) (2019)
Jörg Fallmann, Pavankumar Videm, Andrea Bagnacani, Bérénice Batut, Maria A. Doyle, Tomas Klingström, Florian Eggenhofer, Peter F. Stadler, Rolf Backofen, Björn A. Grüning
The RNA workbench 2.0: next generation RNA data analysis. Nucleic Acids Res. 47 (Webserver-Issue) (2019)
Daniel Wibberg, Bérénice Batut, Peter Belmann, Jochen Blom, Frank Oliver Glöckner, Björn A. Grüning, Nils Hoffmann, Nils Kleinbölting, René Rahn, Maja Rey, Uwe Scholz, Malvika Sharan, Andreas Tauch, Ulrike Trojahn, Björn Usadel, Oliver Kohlbacher
The de.NBI / ELIXIR-DE training platform - Bioinformatics training in Germany and across Europe within ELIXIR. F1000Research 8 (2019)
Björn A. Grüning, Olivier Sallou, Pablo A. Moreno, Felipe da Veiga Leprevost, Hervé Ménager, Dan Søndergaard, Hannes L. Röst, Timo Sachsenberg, Brian O'Connor, Fábio Madeira, Victoria Dominguez Del Angel, Michael R. Crusoe, Susheel Varma, Daniel J. Blankenberg, Rafael C. Jiménez, Daniel Blankenberg, Yasset Pérez-Riverol
Recommendations for the packaging and containerizing of bioinformatics software. F1000Research 7 (2018)
Joachim Wolff, Vivek Bhardwaj, Stephan Nothjunge, Gautier Richard, Gina Renschler, Ralf Gilsbach, Thomas Manke, Rolf Backofen, Fidel Ramírez, Björn A. Grüning
Galaxy HiCExplorer: a web server for reproducible Hi-C data analysis, quality control and visualization. Nucleic Acids Res. 46 (Webserver-Issue) (2018)
Enis Afgan, Dannon Baker, Bérénice Batut, Marius van den Beek, Dave Bouvier, Martin Cech, John Chilton, Dave Clements, Nate Coraor, Björn A. Grüning, Aysam Guerler, Jennifer Hillman-Jackson, Saskia D. Hiltemann, Vahid Jalili, Helena Rasche, Nicola Soranzo, Jeremy Goecks, James Taylor, Anton Nekrutenko, Daniel J. Blankenberg
The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2018 update. Nucleic Acids Res. 46 (Webserver-Issue) (2018)
Björn A. Grüning, Jörg Fallmann, Dilmurat Yusuf, Sebastian Will, Anika Erxleben, Florian Eggenhofer, Torsten Houwaart, Bérénice Batut, Pavankumar Videm, Andrea Bagnacani, Markus Wolfien, Steffen Lott, Youri Hoogstrate, Wolfgang R. Hess, Olaf Wolkenhauer, Steve Hoffmann, Altuna Akalin, Uwe Ohler, Peter F. Stadler, Rolf Backofen
The RNA workbench: best practices for RNA and high-throughput sequencing bioinformatics in Galaxy. Nucleic Acids Res. 45 (Webserver-Issue) (2017)
Felipe da Veiga Leprevost, Björn A. Grüning, Saulo Aflitos, Hannes L. Röst, Julian Uszkoreit, Harald Barsnes, Marc Vaudel, Pablo Moreno, Laurent Gatto, Jonas Weber, Mingze Bai, Rafael C. Jimenez, Timo Sachsenberg, Julianus Pfeuffer, Roberto Vera Alvarez, Johannes Griss, Alexey I. Nesvizhskii, Yasset Pérez-Riverol
BioContainers: an open-source and community-driven framework for software standardization. Bioinform. 33 (16) (2017)
Konrad Meier, Björn A. Grüning, Clemens Blank, Michael Janczyk, Dirk von Suchodoletz
Virtualisierte wissenschaftliche Forschungsumgebungen und die zukünftige Rolle der Rechenzentren. DFN-Forum Kommunikationstechnologien (2017)
Bérénice A. Batut, Björn A. Grüning
ENASearch: A Python library for interacting with ENA's API. J. Open Source Softw. 2 (18) (2017)
Rafael C. Jiménez, Mateusz Kuzak, Monther Alhamdoosh, Michelle Barker, Bérénice Batut, Mikael Borg, Salvador Capella-Gutiérrez, Neil P. Chue Hong, Martin Cook, Manuel Corpas, Madison Flannery, Leyla J. García, Josep Lluis Gelpí, Simon Gladman, Carole A. Goble, Montserrat González Ferreiro, Alejandra N. González-Beltrán, Philippa C. Griffin, Björn A. Grüning, Jonas Hagberg, Petr Holub, Rob W. W. Hooft, Jon C. Ison, Daniel S. Katz, Brane Leskosek, Federico López-Gómez, Luis J. Oliveira, David Mellor, Rowland Mosbergen, Nicola J. Mulder, Yasset Pérez-Riverol, Robert Pergl, Horst Pichler, Bernard J. Pope, Ferran Sanz, Maria Victoria Schneider, Victoria Stodden, Radoslaw Suchecki, Radka Svobodová Vareková, Harry-Anton Talvik, Ilian T. Todorov, Andrew E. Treloar, Sonika Tyagi, Maarten van Gompel, Daniel Vaughan, Allegra Via, Xiaochuan Wang, Nathan S. Watson-Haigh, Steve Crouch
Four simple recommendations to encourage best practices in research software. F1000Research 6 (2017)
Björn A. Grüning, Eric Rasche, Boris Rebolledo-Jaramillo, Carl Eberhard, Torsten Houwaart, John Chilton, Nate Coraor, Rolf Backofen, James Taylor, Anton Nekrutenko
Jupyter and Galaxy: Easing entry barriers into complex data analyses for biomedical researchers. PLoS Comput. Biol. 13 (5) (2017)
Fidel Ramírez, Devon Patrick Ryan, Björn A. Grüning, Vivek Bhardwaj, Fabian Kilpert, Andreas S. Richter, Steffen Heyne, Friederike Dündar, Thomas Manke
deepTools2: a next generation web server for deep-sequencing data analysis. Nucleic Acids Res. 44 (Webserver-Issue) (2016)
Jon C. Ison, Kristoffer Rapacki, Hervé Ménager, Matús Kalas, Emil Rydza, Piotr Chmura, Christian Anthon, Niall Beard, Karel Berka, Dan M. Bolser, Tim Booth, Anthony Bretaudeau, Jan Brezovsky, Rita Casadio, Gianni Cesareni, Frederik Coppens, Michael Cornell, Gianmauro Cuccuru, Kristian Davidsen, Gianluca Della Vedova, Tunca Dogan, Olivia Doppelt-Azeroual, Laura Emery, Elisabeth Gasteiger, Thomas Gatter, Tatyana Goldberg, Marie Grosjean, Björn A. Grüning, Manuela Helmer-Citterich, Hans Ienasescu, Vassilios Ioannidis, Martin Closter Jespersen, Rafael C. Jimenez, Nick S. Juty, Peter Juvan, Maximilian Koch, Camille Laibe, Jing-Woei Li, Luana Licata, Fabien Mareuil, Ivan Micetic, Rune Møllegaard Friborg, Sébastien Moretti, Chris Morris, Steffen Möller, Aleksandra Nenadic, Hedi Peterson, Giuseppe Profiti, Peter M. Rice, Paolo Romano, Paola Roncaglia, Rabie Saidi, Andrea Schafferhans, Veit Schwämmle, Callum Smith, Maria Maddalena Sperotto, Heinz Stockinger, Radka Svobodová Vareková, Silvio C. E. Tosatto, Victor de la Torre, Paolo Uva, Allegra Via, Guy Yachdav, Federico Zambelli, Gert Vriend, Burkhard Rost, Helen E. Parkinson, Peter Løngreen, Søren Brunak
Tools and data services registry: a community effort to document bioinformatics resources. Nucleic Acids Res. 44 (Database-Issue) (2016)
Enis Afgan, Dannon Baker, Marius van den Beek, Daniel J. Blankenberg, Dave Bouvier, Martin Cech, John Chilton, Dave Clements, Nate Coraor, Carl Eberhard, Björn A. Grüning, Aysam Guerler, Jennifer Hillman-Jackson, Gregory Von Kuster, Eric Rasche, Nicola Soranzo, Nitesh Turaga, James Taylor, Anton Nekrutenko, Jeremy Goecks
The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2016 update. Nucleic Acids Res. 44 (Webserver-Issue) (2016)
Xavier Lucas, Björn A. Grüning, Stefan Bleher, Stefan Günther
The Purchasable Chemical Space: A Detailed Picture. J. Chem. Inf. Model. 55 (5) (2015)
Hitesh Patel, Björn A. Grüning, Stefan Günther, Irmgard Merfort
PyWATER: a PyMOL plug-in to find conserved water molecules in proteins by clustering. Bioinform. 30 (20) (2014)
Xavier Lucas, Björn A. Grüning, Stefan Günther
ChemicalToolBoX and its application on the study of the drug like and purchasable space. J. Cheminformatics 6 (S-1) (2014)
Kiran K. Telukunta, Xavier Lucas, Kersten Döring, Björn A. Grüning, Stefan Günther
Dynamic information system for small molecules. J. Cheminformatics 6 (S-1) (2014)
Fidel Ramírez, Friederike Dündar, Sarah Diehl, Björn A. Grüning, Thomas Manke
deepTools: a flexible platform for exploring deep-sequencing data. Nucleic Acids Res. 42 (Webserver-Issue) (2014)
Xavier Lucas, Christian Senger, Anika Erxleben, Björn A. Grüning, Kersten Döring, Johannes Mosch, Stephan Flemming, Stefan Günther
species. Nucleic Acids Res. 41 (Database-Issue) (2013)
Christian Senger, Björn A. Grüning, Anika Erxleben, Kersten Döring, Hitesh Patel, Stephan Flemming, Irmgard Merfort, Stefan Günther
Mining and evaluation of molecular relationships in literature. Bioinform. 28 (5) (2012)
Björn A. Grüning, Christian Senger, Anika Erxleben, Stephan Flemming, Stefan Günther
Compounds In Literature (CIL): screening for compounds and relatives in PubMed. Bioinform. 27 (9) (2011)
Peter Werner Hildebrand, Andrean Goede, Raphael A. Bauer, Björn A. Grüning, Jochen Ismer, Elke Michalsky, Robert Preissner
SuperLooper - a prediction server for the modeling of loops in globular and membrane proteins. Nucleic Acids Res. 37 (Web-Server-Issue) (2009)
Kristian Rother, Peter Werner Hildebrand, Andrean Goede, Björn A. Grüning, Robert Preissner
Voronoia: analyzing packing in protein structures. Nucleic Acids Res. 37 (Database-Issue) (2009)
Mathias Dunkel, Ulrike Schmidt, Swantje Struck, Lena Berger, Björn A. Grüning, Julia Hossbach, Ines S. Jaeger, Uta Effmert, Birgit Piechulla, Roger Eriksson, Jette Knudsen, Robert Preissner
SuperScent - a database of flavors and scents. Nucleic Acids Res. 37 (Database-Issue) (2009)
Ulrike Schmidt, Swantje Struck, Björn A. Grüning, Julia Hossbach, Ines S. Jaeger, Roza Parol, Ulrike Lindequist, Eberhard Teuscher, Robert Preissner
SuperToxic: a comprehensive database of toxic compounds. Nucleic Acids Res. 37 (Database-Issue) (2009)
Alexander S. Rose, Stephan Lorenzen, Andrean Goede, Björn A. Grüning, Peter Werner Hildebrand
RHYTHM - a server to predict the orientation of transmembrane helices in channels and membrane-coils. Nucleic Acids Res. 37 (Web-Server-Issue) (2009)