Björn A. Grüning

According to our database, Björn A. Grüning authored at least 56 papers between 2009 and 2023.

Collaborative distances:

• Dijkstra number of three.
• Erdős number of three.

2023

Transformer-based tool recommendation system in Galaxy.

Anup Kumar, Björn A. Grüning, Rolf Backofen

BMC Bioinform., December, 2023

Fast and accurate genome-wide predictions and structural modeling of protein-protein interactions using Galaxy.

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

BMC Bioinform., December, 2023

Galaxy Training: A powerful framework for teaching!

Saskia D. 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

PLoS Comput. Biol., January, 2023

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

Nuwan Goonasekera, Catherine J. Bromhead, Simon L. Gladman, Nate Coraor, Björn A. Grüning, Enis Afgan

CoRR, 2023

Conda, Container and Bots How to Build and Maintain Tool Dependencies in Workflows and Training Materials.

Paul F. Zierep, Sanjay Kumar Srikakulam, Sebastian Schaaf, Björn A. Grüning

Proceedings of the 1st Conference on Research Data Infrastructure - Connecting Communities, 2023

Galaxy and RDM Being More Than a Workflow Manager: Living the Data Life Cycle.

Sebastian Schaaf, Anika Erxleben-Eggenhofer, Björn A. Grüning

Proceedings of the 1st Conference on Research Data Infrastructure - Connecting Communities, 2023

Interactive Tools (IT) in Galaxy Combining Synchronous and Asynchronous Workflows.

Tunc Kayikcioglu, Sanjay Kumar Srikakulam, Wolfgang Maier, Björn A. Grüning

Proceedings of the 1st Conference on Research Data Infrastructure - Connecting Communities, 2023

The EOSC-Life Workflow Collaboratory for the Life Sciences.

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

Proceedings of the 1st Conference on Research Data Infrastructure - Connecting Communities, 2023

2022

Ten simple rules for making a software tool workflow-ready.

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

PLoS Comput. Biol., 2022

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

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 E. 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 D. 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

Nucleic Acids Res., 2022

Galaxy workflows for fragment-based virtual screening: a case study on the SARS-CoV-2 main protease.

Simon Bray, Tim Dudgeon, Rachael Skyner, Rolf Backofen, Björn A. Grüning, Frank von Delft

J. Cheminformatics, 2022

Galaxy: A Decade of Realising CWFR Concepts.

Beatriz Serrano-Solano, Anne Fouilloux, Ignacio Eguinoa, Matús Kalas, Björn A. Grüning, Frederik Coppens

Data Intell., 2022

Packaging research artefacts with RO-Crate.

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

Data Sci., 2022

2021

Robust and efficient single-cell Hi-C clustering with approximate k-nearest neighbor graphs.

Joachim Wolff, Rolf Backofen, Björn A. Grüning

Bioinform., November, 2021

Fostering accessible online education using Galaxy as an e-learning platform.

Beatriz Serrano-Solano, Melanie Christine Föll, Cristóbal Gallardo-Alba, Anika Erxleben, Helena Rasche, Saskia D. Hiltemann, Matthias Fahrner, Mark J. Dunning, Marcel H. Schulz, Beáta Scholtz, Dave Clements, Anton Nekrutenko, Bérénice Batut, Björn A. Grüning

PLoS Comput. Biol., 2021

Galaxy-ML: An accessible, reproducible, and scalable machine learning toolkit for biomedicine.

Qiang Gu, Anup Kumar, Simon Bray, Allison Creason, Alireza Khanteymoori, Vahid Jalili, Björn A. Grüning, Jeremy Goecks

PLoS Comput. Biol., 2021

A constructivist-based proposal for bioinformatics teaching practices during lockdown.

Cristóbal Gallardo-Alba, Björn A. Grüning, Beatriz Serrano-Solano

PLoS Comput. Biol., 2021

Workflows Community Summit: Bringing the Scientific Workflows Community Together.

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 A. 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

CoRR, 2021

Scool: a new data storage format for single-cell Hi-C data.

Joachim Wolff, Nezar Abdennur, Rolf Backofen, Björn A. Grüning

Bioinform., 2021

A SARS-CoV-2 sequence submission tool for the European Nucleotide Archive.

Miguel Roncoroni, Bert Droesbeke, Ignacio Eguinoa, Kim De Ruyck, Flora D'anna, Dilmurat Yusuf, Björn A. Grüning, Rolf Backofen, Frederik Coppens

Bioinform., 2021

pyGenomeTracks: reproducible plots for multivariate genomic datasets.

Lucille Lopez-Delisle, Leily Rabbani, Joachim Wolff, Vivek Bhardwaj, Rolf Backofen, Björn A. Grüning, Fidel Ramírez, Thomas Manke

Bioinform., 2021

GYAN: Accelerating Bioinformatics Tools in Galaxy with GPU-Aware Computation Mapping.

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

Proceedings of the IEEE International Parallel and Distributed Processing Symposium Workshops, 2021

2020

Galaxy HiCExplorer 3: a web server for reproducible Hi-C, capture Hi-C and single-cell Hi-C data analysis, quality control and visualization.

Joachim Wolff, Leily Rabbani, Ralf Gilsbach, Gautier Richard, Thomas Manke, Rolf Backofen, Björn A. Grüning

Nucleic Acids Res., 2020

The omics discovery REST interface.

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

Nucleic Acids Res., 2020

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

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

J. Cheminformatics, 2020

The ChemicalToolbox: reproducible, user-friendly cheminformatics analysis on the Galaxy platform.

Simon Bray, Xavier Lucas, Anup Kumar, Björn A. Grüning

J. Cheminformatics, 2020

GLASSgo in Galaxy: high-throughput, reproducible and easy-to-integrate prediction of sRNA homologs.

Richard A. Schäfer, Steffen Lott, Jens Georg, Björn A. Grüning, Wolfgang R. Hess, Björn Voß

Bioinform., 2020

2019

The RNA workbench 2.0: next generation RNA data analysis.

Jörg Fallmann, Pavankumar Videm, Andrea Bagnacani, Bérénice Batut, Maria A. Doyle, Tomas Klingström, Florian Eggenhofer, Peter F. Stadler, Rolf Backofen, Björn A. Grüning

Nucleic Acids Res., 2019

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

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

F1000Research, 2019

Biomolecular Reaction and Interaction Dynamics Global Environment (BRIDGE).

Tharindu Senapathi, Simon Bray, Christopher B. Barnett, Björn A. Grüning, Kevin J. Naidoo

Bioinform., 2019

Parkour LIMS: high-quality sample preparation in next generation sequencing.

Evgeny Anatskiy, Devon Patrick Ryan, Björn A. Grüning, Laura Arrigoni, Thomas Manke, Ulrike Bönisch

Bioinform., 2019

2018

Galaxy HiCExplorer: a web server for reproducible Hi-C data analysis, quality control and visualization.

Joachim Wolff, Vivek Bhardwaj, Stephan Nothjunge, Gautier Richard, Gina Renschler, Ralf Gilsbach, Thomas Manke, Rolf Backofen, Fidel Ramírez, Björn A. Grüning

Nucleic Acids Res., 2018

The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2018 update.

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

Nucleic Acids Res., 2018

Recommendations for the packaging and containerizing of bioinformatics software.

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

F1000Research, 2018

2017

Jupyter and Galaxy: Easing entry barriers into complex data analyses for biomedical researchers.

Björn A. Grüning, Eric Rasche, Boris Rebolledo-Jaramillo, Carl Eberhard, Torsten Houwaart, John Chilton, Nate Coraor, Rolf Backofen, James Taylor, Anton Nekrutenko

PLoS Comput. Biol., 2017

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

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

Nucleic Acids Res., 2017

ENASearch: A Python library for interacting with ENA's API.

Bérénice A. Batut, Björn A. Grüning

J. Open Source Softw., 2017

Four simple recommendations to encourage best practices in research software.

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 L. 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

F1000Research, 2017

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

Felipe da Veiga Leprevost, Björn A. Grüning, Saulo Aflitos, Hannes L. Röst, Julian Uszkoreit, Harald Barsnes, Marc Vaudel, Pablo A. Moreno, Laurent Gatto, Jonas Weber, Mingze Bai, Rafael C. Jiménez, Timo Sachsenberg, Julianus Pfeuffer, Roberto Vera Alvarez, Johannes Griss, Alexey I. Nesvizhskii, Yasset Pérez-Riverol

Bioinform., 2017

Virtualisierte wissenschaftliche Forschungsumgebungen und die zukünftige Rolle der Rechenzentren.

Konrad Meier, Björn A. Grüning, Clemens Blank, Michael Janczyk, Dirk von Suchodoletz

Proceedings of the 10. DFN-Forum, 2017

2016

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

Fidel Ramírez, Devon Patrick Ryan, Björn A. Grüning, Vivek Bhardwaj, Fabian Kilpert, Andreas S. Richter, Steffen Heyne, Friederike Dündar, Thomas Manke

Nucleic Acids Res., 2016

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

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. Jiménez, 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

Nucleic Acids Res., 2016

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

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

Nucleic Acids Res., 2016

2015

The Purchasable Chemical Space: A Detailed Picture.

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

J. Chem. Inf. Model., 2015

2014

deepTools: a flexible platform for exploring deep-sequencing data.

Fidel Ramírez, Friederike Dündar, Sarah Diehl, Björn A. Grüning, Thomas Manke

Nucleic Acids Res., 2014

Dynamic information system for small molecules.

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

J. Cheminformatics, 2014

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

Xavier Lucas, Björn A. Grüning, Stefan Günther

J. Cheminformatics, 2014

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

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

Bioinform., 2014

2013

StreptomeDB: a resource for natural compounds isolated from <i>Streptomyces</i> species.

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

Nucleic Acids Res., 2013

2012

Mining and evaluation of molecular relationships in literature.

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

Bioinform., 2012

2011

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

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

Bioinform., 2011

2009

SuperToxic: a comprehensive database of toxic compounds.

Ulrike Schmidt, Swantje Struck, Björn A. Grüning, Julia Hossbach, Ines S. Jaeger, Roza Parol, Ulrike Lindequist, Eberhard Teuscher, Robert Preissner

Nucleic Acids Res., 2009

Voronoia: analyzing packing in protein structures.

Kristian Rother, Peter Werner Hildebrand, Andrean Goede, Björn A. Grüning, Robert Preissner

Nucleic Acids Res., 2009

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

Alexander S. Rose, Stephan Lorenzen, Andrean Goede, Björn A. Grüning, Peter Werner Hildebrand

Nucleic Acids Res., 2009

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

Peter Werner Hildebrand, Andrean Goede, Raphael A. Bauer, Björn A. Grüning, Jochen Ismer, Elke Michalsky, Robert Preissner

Nucleic Acids Res., 2009

SuperScent - a database of flavors and scents.

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

Nucleic Acids Res., 2009