SuperScent - a database of flavors and scents. - Mathias Dunkel; Ulrike Schmidt 001; 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)

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)

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)

Voronoia: analyzing packing in protein structures. - Kristian Rother; Peter Werner Hildebrand; Andrean Goede; Björn A. Grüning; Robert Preissner (Nucleic Acids Res., 2009)

SuperToxic: a comprehensive database of toxic compounds. - Ulrike Schmidt 001; Swantje Struck; Björn A. Grüning; Julia Hossbach; Ines S. Jaeger; Roza Parol; Ulrike Lindequist; Eberhard Teuscher; Robert Preissner (Nucleic Acids Res., 2009)

Compounds In Literature (CIL): screening for compounds and relatives in PubMed. - Björn A. Grüning; Christian Senger; Anika Erxleben; Stephan Flemming; Stefan Günther (Bioinform., 2011)

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)

StreptomeDB: a resource for natural compounds isolated from Streptomyces species. - Xavier Lucas; Christian Senger; Anika Erxleben; Björn A. Grüning; Kersten Döring; Johannes Mosch; Stephan Flemming; Stefan Günther (Nucleic Acids Res., 2013)

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)

ChemicalToolBoX and its application on the study of the drug like and purchasable space. - Xavier Lucas; Björn A. Grüning; Stefan Günther (J. Cheminformatics, 2014)

Dynamic information system for small molecules. - Kiran K. Telukunta; Xavier Lucas; Kersten Döring; Björn A. Grüning; Stefan Günther (J. Cheminformatics, 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)

The Purchasable Chemical Space: A Detailed Picture. - Xavier Lucas; Björn A. Grüning; Stefan Bleher; Stefan Günther (J. Chem. Inf. Model., 2015)

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; et al. (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; et al. (Nucleic Acids Res., 2016)

deepTools2: a next generation web server for deep-sequencing data analysis. - Fidel Ramírez; Devon Patrick Ryan; Björn A. Grüning; Vivek Bhardwaj 002; Fabian Kilpert; Andreas S. Richter; Steffen Heyne; Friederike Dündar; Thomas Manke (Nucleic Acids Res., 2016)

Virtualisierte wissenschaftliche Forschungsumgebungen und die zukünftige Rolle der Rechenzentren. - Konrad Meier; Björn A. Grüning; Clemens Blank; Michael Janczyk; Dirk von Suchodoletz (DFN-Forum Kommunikationstechnologien, 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; et al. (Bioinform., 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; et al. (F1000Research, 2017)

ENASearch: A Python library for interacting with ENA's API. - Bérénice A. Batut; Björn A. Grüning (J. Open Source Softw., 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; et al. (Nucleic Acids Res., 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 001; Anton Nekrutenko (PLoS Comput. Biol., 2017)

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; et al. (F1000Research, 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; et al. (Nucleic Acids Res., 2018)

Galaxy HiCExplorer: a web server for reproducible Hi-C data analysis, quality control and visualization. - Joachim Wolff; Vivek Bhardwaj 002; Stephan Nothjunge; Gautier Richard; Gina Renschler; Ralf Gilsbach; Thomas Manke; Rolf Backofen; Fidel Ramírez; Björn A. Grüning (Nucleic Acids Res., 2018)

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)

Biomolecular Reaction and Interaction Dynamics Global Environment (BRIDGE). - Tharindu Senapathi; Simon Bray; Christopher B. Barnett; Björn A. Grüning; Kevin J. Naidoo (Bioinform., 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; et al. (F1000Research, 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)

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)

The ChemicalToolbox: reproducible, user-friendly cheminformatics analysis on the Galaxy platform. - Simon Bray; Xavier Lucas; Anup Kumar; Björn A. Grüning (J. Cheminformatics, 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 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)

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)

GLASSgo Setup & Usage. - Richard A. Schäfer; Steffen Lott; Jens Georg; Björn A. Grüning; Wolfgang R. Hess; Björn Voß (DaRUS, 2020)

GLASSgo Setup & Usage. - Richard A. Schäfer; Steffen Lott; Jens Georg; Björn A. Grüning; Wolfgang R. Hess; Björn Voß (DaRUS, 2020)

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 (IPDPS Workshops, 2021)

pyGenomeTracks: reproducible plots for multivariate genomic datasets. - Lucille Lopez-Delisle; Leily Rabbani; Joachim Wolff; Vivek Bhardwaj 002; Rolf Backofen; Björn A. Grüning; Fidel Ramírez; Thomas Manke (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)

Scool: a new data storage format for single-cell Hi-C data. - Joachim Wolff; Nezar Abdennur; Rolf Backofen; Björn A. Grüning (Bioinform., 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; et al. (CoRR, 2021)

A constructivist-based proposal for bioinformatics teaching practices during lockdown. - Cristóbal Gallardo-Alba; Björn A. Grüning; Beatriz Serrano-Solano (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)

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; et al. (PLoS Comput. Biol., 2021)

Robust and efficient single-cell Hi-C clustering with approximate k-nearest neighbor graphs. - Joachim Wolff; Rolf Backofen; Björn A. Grüning (Bioinform., 2021)

Packaging research artefacts with RO-Crate. - Stian Soiland-Reyes; Peter Sefton; Mercè Crosas; Leyla Jael Castro; Frederik Coppens; José María Fernández 001; Daniel Garijo; Björn A. Grüning; Marco La Rosa; Simone Leo; Eoghan Ó Carragáin; Marc Portier; et al. (Data Sci., 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)

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)

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; et al. (Nucleic Acids Res., 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; et al. (PLoS Comput. Biol., 2022)

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 001; Björn A. Grüning; Simone Leo; Luca Pireddu; et al. (CoRDI, 2023)

Interactive Tools (IT) in Galaxy Combining Synchronous and Asynchronous Workflows. - Tunc Kayikcioglu; Sanjay Kumar Srikakulam; Wolfgang Maier 003; Björn A. Grüning (CoRDI, 2023)

Galaxy and RDM Being More Than a Workflow Manager: Living the Data Life Cycle. - Sebastian Schaaf; Anika Erxleben-Eggenhofer; Björn A. Grüning (CoRDI, 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 (CoRDI, 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)

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; et al. (PLoS Comput. Biol., 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., 2023)

Transformer-based tool recommendation system in Galaxy. - Anup Kumar; Björn A. Grüning; Rolf Backofen (BMC Bioinform., 2023)

FAIR Digital Objects for Seamless Research Data Management for Researchers and Higher Education Institutions. - Markus Stocker; Björn A. Grüning; Tomasz Miksa; Claudia Biniossek; Dirk Betz (FDO, 2024)

WorkflowHub: a registry for computational workflows. - Johan Gustafsson 001; Sean R. Wilkinson; Finn Bacall; Luca Pireddu; Stian Soiland-Reyes; Simone Leo; Stuart Owen; Nick S. Juty; José María Fernández 001; Björn A. Grüning; Tom Brown; Hervé Ménager; et al. (CoRR, 2024)

An Ecosystem of Services for FAIR Computational Workflows. - Sean R. Wilkinson; Johan Gustafsson 001; Finn Bacall; Khalid Belhajjame; Salvador Capella; José María Fernández González; Jacob Fosso Tande; Luiz Gadelha; Daniel Garijo; Patricia Grubel; Björn A. Grüning; Farah Zaib Khan; et al. (CoRR, 2025)