Bjoern Andreas Gruening (Bjorn Grüning, Björn A Grüning, Björn Andreas Grüning, Bjorn Gruening, Björn Grüning, Bjoern Gruening)

Publication Activity (10 Years)

Years Active: 2015-2024
Publications (10 Years): 40

Top Topics

Respiratory Syndrome Coronavirus

Gene Expression

Top Venues

Nature biotechnology

Journal of proteome research

This page only lists publications with an associated author ORCID identifier.

Publications

Delphine Larivière, Linelle Abueg, Nadolina Brajuka, Cristóbal Gallardo-Alba, Bjoern Andreas Gruening, Byung June Ko, Alex Ostrovsky, Marc Palmada-Flores, Brandon D Pickett, Keon Rabbani, Agostinho Antunes, Jennifer R Balacco, Mark J P Chaisson, Haoyu Cheng, Joanna Collins, Melanie Couture, Alexandra A Denisova, Olivier Fedrigo, Guido Roberto Gallo, Alice Maria Giani, Grenville MacDonald Gooder, Kathleen Horan, Nivesh Jain, Cassidy Johnson, Heebal Kim, Chul Lee, Tomas Marques-Bonet, Brian O'Toole, Arang Rhie, Simona Secomandi, Marcella Sozzoni, Tatiana Tilley, Marcela Uliano-Silva, Marius van den Beek, Robert W Williams, Robert M Waterhouse, Adam M Phillippy, Erich D Jarvis, Michael C Schatz, Anton Nekrutenko, Giulio Formenti
Scalable, accessible and reproducible reference genome assembly and evaluation in Galaxy. Nature biotechnology (2024)
Delphine Larivière, Linelle Abueg, Nadolina Brajuka, Cristóbal Gallardo-Alba, Bjoern Andreas Gruening, Byung June Ko, Alex Ostrovsky, Marc Palmada-Flores, Brandon D Pickett, Keon Rabbani, Agostinho Antunes, Jennifer R Balacco, Mark J P Chaisson, Haoyu Cheng, Joanna Collins, Melanie Couture, Alexandra A Denisova, Olivier Fedrigo, Guido Roberto Gallo, Alice Maria Giani, Grenville MacDonald Gooder, Kathleen Horan, Nivesh Jain, Cassidy Johnson, Heebal Kim, Chul Lee, Tomas Marques-Bonet, Brian O'Toole, Arang Rhie, Simona Secomandi, Marcella Sozzoni, Tatiana Tilley, Marcela Uliano-Silva, Marius van den Beek, Robert W Williams, Robert M Waterhouse, Adam M Phillippy, Erich D Jarvis, Michael C Schatz, Anton Nekrutenko, Giulio Formenti
Scalable, accessible and reproducible reference genome assembly and evaluation in Galaxy. Nature biotechnology 42 (3) (2024)
Delphine Larivière, Linelle Abueg, Nadolina Brajuka, Cristóbal Gallardo-Alba, Bjoern Andreas Gruening, Byung June Ko, Alex Ostrovsky, Marc Palmada-Flores, Brandon D Pickett, Keon Rabbani, Agostinho Antunes, Jennifer R Balacco, Mark J P Chaisson, Haoyu Cheng, Joanna Collins, Melanie Couture, Alexandra A Denisova, Olivier Fedrigo, Guido Roberto Gallo, Alice Maria Giani, Grenville MacDonald Gooder, Kathleen Horan, Nivesh Jain, Cassidy Johnson, Heebal Kim, Chul Lee, Tomas Marques-Bonet, Brian O'Toole, Arang Rhie, Simona Secomandi, Marcella Sozzoni, Tatiana Tilley, Marcela Uliano-Silva, Marius van den Beek, Robert W Williams, Robert M Waterhouse, Adam M Phillippy, Erich D Jarvis, Michael C Schatz, Anton Nekrutenko, Giulio Formenti
Scalable, accessible and reproducible reference genome assembly and evaluation in Galaxy. Nature biotechnology (2024)
Delphine Larivière, Linelle Abueg, Nadolina Brajuka, Cristóbal Gallardo-Alba, Bjoern Andreas Gruening, Byung June Ko, Alex Ostrovsky, Marc Palmada-Flores, Brandon D Pickett, Keon Rabbani, Agostinho Antunes, Jennifer R Balacco, Mark J P Chaisson, Haoyu Cheng, Joanna Collins, Melanie Couture, Alexandra A Denisova, Olivier Fedrigo, Guido Roberto Gallo, Alice Maria Giani, Grenville MacDonald Gooder, Kathleen Horan, Nivesh Jain, Cassidy Johnson, Heebal Kim, Chul Lee, Tomas Marques-Bonet, Brian O'Toole, Arang Rhie, Simona Secomandi, Marcella Sozzoni, Tatiana Tilley, Marcela Uliano-Silva, Marius van den Beek, Robert W Williams, Robert M Waterhouse, Adam M Phillippy, Erich D Jarvis, Michael C Schatz, Anton Nekrutenko, Giulio Formenti
Scalable, accessible and reproducible reference genome assembly and evaluation in Galaxy. Nature biotechnology 42 (3) (2024)
Heinrich Lukas Weil, Kevin Schneider, Marcel Tschöpe, Jonathan Bauer, Oliver Maus, Kevin Frey, Dominik Brilhaus, Cristina Martins Rodrigues, Gajendra Doniparthi, Florian Wetzels, Jonas Lukasczyk, Angela Kranz, Bjoern Andreas Gruening, David Zimmer, Stefan Deßloch, Dirk von Suchodoletz, Björn Usadel, Christoph Garth, Timo Mühlhaus
PLANTdataHUB: a collaborative platform for continuous FAIR data sharing in plant research. The Plant journal : for cell and molecular biology (2023)
Anup Kumar, Gianmauro Cuccuru, Bjoern Andreas Gruening, Rolf Backofen
An accessible infrastructure for artificial intelligence using a Docker-based JupyterLab in Galaxy. GigaScience 12 (2023)
Helena Rasche, Cameron J Hyde, John Davis, Simon Gladman, Nate Coraor, Anthony Bretaudeau, Gianmauro Cuccuru, Wendi Bacon, Beatriz Serrano-Solano, Jennifer Hillman-Jackson, Saskia Hiltemann, Miaomiao Zhou, Bjoern Andreas Gruening, Andrew Peter Stubbs
Training Infrastructure as a Service. GigaScience 12 (2023)
Romain David, Arina Rybina, Jean-Marie Burel, Jean-Karim Hériché, Pauline Audergon, Jan-Willem Boiten, Frederik Coppens, Sara Crockett, Katrina Exter, Sven Fahrner, Maddalena Fratelli, Carole Goble, Philipp Gormanns, Tobias Grantner, Bjoern Andreas Gruening, Kim Tamara Gurwitz, John M Hancock, Henriette Harmse, Petr Holub, Nick Juty, Geoffrey Karnbach, Emma Karoune, Antje Keppler, Jessica Klemeier, Carla Lancelotti, Jean-Luc Legras, Allyson L Lister, Dario Livio Longo, Rebecca Ludwig, Bénédicte Madon, Marzia Massimi, Vera Matser, Rafaele Matteoni, Michaela Th Mayrhofer, Christian Ohmann, Maria Panagiotopoulou, Helen Parkinson, Isabelle Perseil, Claudia Pfander, Roland Pieruschka, Michael Raess, Andreas Rauber, Audrey S Richard, Paolo Romano, Antonio Rosato, Álex Sánchez-Pla, Susanna-Assunta Sansone, Siddhant Tripathi, Beatriz Serrano-Solano, Jing Tang, Ziaurrehman Tanoli, Jonathan Tedds, Harald Wagener, Martin Weise, Hans Victor Westerhoff, Rudolf Wittner, Jonathan J Ewbank, Niklas Blomberg, Philip Gribbon
"Be sustainable": EOSC-Life recommendations for implementation of FAIR principles in life science data handling. The EMBO journal (2023)
Anup Kumar, Gianmauro Cuccuru, Bjoern Andreas Gruening, Rolf Backofen
An accessible infrastructure for artificial intelligence using a Docker-based JupyterLab in Galaxy. GigaScience 12 (2023)
Delphine Larivière, Linelle Abueg, Nadolina Brajuka, Cristóbal Gallardo-Alba, Bjoern Andreas Gruening, Byung June Ko, Alexander Ostrovsky, Marc Palmada-Flores, Brandon D Pickett, Keon Rabbani, Jennifer R Balacco, Mark J P Chaisson, Haoyu Cheng, Joanna Collins, Alexandra Denisova, Olivier Fedrigo, Guido Roberto Gallo, Alice Maria Giani, Grenville MacDonald Gooder, Nivesh Jain, Cassidy Johnson, Heebal Kim, Chul Lee, Tomas Marques-Bonet, Brian O'Toole, Arang Rhie, Simona Secomandi, Marcella Sozzoni, Tatiana Tilley, Marcela Uliano-Silva, Marius van den Beek, Robert M Waterhouse, Adam M Phillippy, Erich D Jarvis, Michael C Schatz, Anton Nekrutenko, Giulio Formenti
Scalable, accessible, and reproducible reference genome assembly and evaluation in Galaxy. bioRxiv : the preprint server for biology (2023)
Meijiang Gao, Marina Veil, Marcus Rosenblatt, Aileen Julia Riesle, Anna Gebhard, Helge Hass, Lenka Buryanova, Lev Y Yampolsky, Bjoern Andreas Gruening, Sergey V Ulianov, Jens Timmer, Daria Onichtchouk
Pluripotency factors determine gene expression repertoire at zygotic genome activation. Nature communications 13 (1) (2022)
Paul Brack, Peter Crowther, Stian Soiland-Reyes, Stuart Owen, Douglas Lowe, Alan R Williams, Quentin J Groom, Mathias Dillen, Frederik Coppens, Bjoern Andreas Gruening, Ignacio Eguinoa, Philip A Ewels, Carole Goble
Ten simple rules for making a software tool workflow-ready. PLoS computational biology 18 (3) (2022)
Joachim Wolff, Rolf Backofen, Bjoern Andreas Gruening
Loop detection using Hi-C data with HiCExplorer. GigaScience 11 (2022)
Nagampalli VijayKrishna, Jayadev Joshi, Nate Coraor, Jennifer Hillman-Jackson, Dave Bouvier, Marius van den Beek, Ignacio Eguinoa, Frederik Coppens, John Davis, Michał Stolarczyk, Nathan C Sheffield, Simon Gladman, Gianmauro Cuccuru, Bjoern Andreas Gruening, Nicola Soranzo, Helena Rasche, Bradley W Langhorst, Matthias Bernt, Dan Fornika, David Anderson de Lima Morais, Michel Barrette, Peter van Heusden, Mauro Petrillo, Antonio Puertas Gallardo, Alex Patak, Hans-Rudolf Hotz, Daniel Blankenberg
Expanding the Galaxy's reference data. Bioinformatics advances 2 (1) (2022)
Niko Pinter, Damian Glätzer, Matthias Fahrner, Klemens Fröhlich, James Johnson, Bjoern Andreas Gruening, Bettina Warscheid, Friedel Drepper, Oliver Schilling, Melanie Christine Föll
MaxQuant and MSstats in Galaxy Enable Reproducible Cloud-Based Analysis of Quantitative Proteomics Experiments for Everyone. Journal of proteome research 21 (6) (2022)
Matthias Fahrner, Melanie Christine Föll, Bjoern Andreas Gruening, Matthias Bernt, Hannes L Röst, Oliver Schilling
Democratizing data-independent acquisition proteomics analysis on public cloud infrastructures via the Galaxy framework. GigaScience 11 (2022)
Simon A Bray, Tim Dudgeon, Rachael E Skyner, Rolf Backofen, Bjoern Andreas Gruening, Frank von Delft
Galaxy workflows for fragment-based virtual screening: a case study on the SARS-CoV-2 main protease. Journal of cheminformatics 14 (1) (2022)
Qiang Gu, Anup Kumar, Simon A Bray, Allison L Creason, Ali Reza Khanteymoori, Vahid Jalili, Bjoern Andreas Gruening, Jeremy Goecks
Galaxy-ML: An accessible, reproducible, and scalable machine learning toolkit for biomedicine. PLoS computational biology 17 (6) (2021)
Pablo Moreno, Ni Huang, Jonathan R Manning, Suhaib Mohammed, Andrey Solovyev, Krzysztof Polański, Wendi Bacon, Ruben Chazarra, Carlos Talavera-López, Maria A Doyle, Guilhem Marnier, Bjoern Andreas Gruening, Helena Rasche, Nancy George, Silvie Korena Fexova, Mohamed Alibi, Zhichiao Miao, Yasset Perez Riverol, Maximilian Haeussler, Alvis Brazma, Sarah A Teichmann, Kerstin B Meyer, Irene Papatheodorou
User-friendly, scalable tools and workflows for single-cell RNA-seq analysis. Nature methods 18 (4) (2021)
Jingwen Bai, Chakradhar Bandla, Jiaxin Guo, Roberto Vera Alvarez, Mingze Bai, Juan Antonio Vizcaino, Pablo Moreno, Bjoern Andreas Gruening, Olivier Sallou, Yasset Perez Riverol
BioContainers Registry: Searching Bioinformatics and Proteomics Tools, Packages, and Containers. Journal of proteome research 20 (4) (2021)
Wolfgang Maier, Simon Bray, Marius van den Beek, Dave Bouvier, Nathaniel Coraor, Milad Miladi, Babita Singh, Jordi Rambla De Argila, Dannon Baker, Nathan Roach, Simon Gladman, Frederik Coppens, Darren P Martin, Andrew Lonie, Bjoern Andreas Gruening, Sergei L Kosakovsky Pond, Anton Nekrutenko
Freely accessible ready to use global infrastructure for SARS-CoV-2 monitoring. bioRxiv : the preprint server for biology (2021)
Peter S Thuy-Boun, Subina Mehta, Bjoern Andreas Gruening, Thomas McGowan, An Nguyen, Andrew T Rajczewski, James E Johnson, Timothy J Griffin, Dennis W Wolan, Pratik D Jagtap
Metaproteomics Analysis of SARS-CoV-2-Infected Patient Samples Reveals Presence of Potential Coinfecting Microorganisms. Journal of proteome research 20 (2) (2021)
Cristóbal Gallardo-Alba, Bjoern Andreas Gruening, Beatriz Serrano-Solano
A constructivist-based proposal for bioinformatics teaching practices during lockdown. PLoS computational biology 17 (5) (2021)
Chengxin Dai, Anja Füllgrabe, Julianus Pfeuffer, Elizaveta M Solovyeva, Jingwen Deng, Pablo Moreno, Selvakumar Kamatchinathan, Deepti Jaiswal Kundu, Nancy George, Silvie Fexova, Bjoern Andreas Gruening, Melanie Christine Föll, Johannes Griss, Marc Vaudel, Enrique Audain, Marie Locard-Paulet, Michael Turewicz, Martin Eisenacher, Julian Uszkoreit, Tim Van Den Bossche, Veit Schwämmle, Henry Webel, Stefan Schulze, David Bouyssié, Savita Jayaram, Vinay Kumar Duggineni, Patroklos Samaras, Mathias Wilhelm, Meena Choi, Mingxun Wang, Oliver Kohlbacher, Alvis Brazma, Irene Papatheodorou, Nuno Bandeira, Eric W Deutsch, Juan Antonio Vizcaino, Mingze Bai, Timo Sachsenberg, Lev I Levitsky, Yasset Perez Riverol
A proteomics sample metadata representation for multiomics integration and big data analysis. Nature communications 12 (1) (2021)
Simon A Bray, Xavier Lucas, Anup Kumar, Bjoern Andreas Gruening
The ChemicalToolbox: reproducible, user-friendly cheminformatics analysis on the Galaxy platform. Journal of cheminformatics 12 (1) (2020)
Ray Sajulga, Caleb W Easterly, Michael Riffle, Bart Mesuere, Thilo Muth, Subina Mehta, Praveen Kumar, James Johnson, Bjoern Andreas Gruening, Henning Schiebenhoefer, Carolin A Kolmeder, Stephan Fuchs, Brook L Nunn, Joel Rudney, Timothy J Griffin, Pratik D Jagtap
Survey of metaproteomics software tools for functional microbiome analysis. PloS one 15 (11) (2020)
Simon A Bray, Tharindu Senapathi, Christopher B Barnett, Bjoern Andreas Gruening
Intuitive, reproducible high-throughput molecular dynamics in Galaxy: a tutorial. Journal of cheminformatics 12 (1) (2020)
Dannon Baker, Marius van den Beek, Daniel Blankenberg, Dave Bouvier, John M Chilton, Nate Coraor, Frederik Coppens, Ignacio Eguinoa, Simon Gladman, Bjoern Andreas Gruening, Nicholas Keener, Delphine Larivière, Andrew J Lonie, Sergei L Kosakovsky Pond, Wolfgang Maier, Anton Nekrutenko, James Taylor, Steven Weaver
No more business as usual: Agile and effective responses to emerging pathogen threats require open data and open analytics. PLoS pathogens 16 (8) (2020)
Daniel Wibberg, Bérénice Batut, Peter Belmann, Jochen Blom, Frank Oliver Glöckner, Bjoern Andreas Gruening, 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 (2019)
Marina Veil, Lev Y Yampolsky, Bjoern Andreas Gruening, Daria Onichtchouk
Pou5f3, SoxB1, and Nanog remodel chromatin on high nucleosome affinity regions at zygotic genome activation. Genome research 29 (3) (2019)
Daniel Wibberg, Bérénice Batut, Peter Belmann, Jochen Blom, Frank Oliver Glöckner, Bjoern Andreas Gruening, 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)
Andrea Argentini, An Staes, Bjoern Andreas Gruening, Subina Mehta, Caleb W Easterly, Timothy J Griffin, Pratik D Jagtap, Francis Impens, Lennart Martens
Update on the moFF Algorithm for Label-Free Quantitative Proteomics. Journal of proteome research 18 (2) (2018)
Bjoern Andreas Gruening, Olivier Sallou, Pablo Moreno, Felipe da Veiga Leprevost, Hervé Ménager, Dan Søndergaard, Hannes Röst, Timo Sachsenberg, Brian O'Connor, Fábio Madeira, Victoria Dominguez Del Angel, Michael R Crusoe, Susheel Varma, Daniel Blankenberg, Rafael C Jimenez, null null, Yasset Perez Riverol
Recommendations for the packaging and containerizing of bioinformatics software. F1000Research 7 (2018)
Fidel Ramírez, Vivek Bhardwaj, Laura Arrigoni, Kin Chung Lam, Bjoern Andreas Gruening, José Villaveces, Bianca Habermann, Asifa Akhtar, Thomas Manke
High-resolution TADs reveal DNA sequences underlying genome organization in flies. Nature communications 9 (1) (2018)
Bjoern Andreas Gruening, Olivier Sallou, Pablo Moreno, Felipe da Veiga Leprevost, Hervé Ménager, Dan Søndergaard, Hannes Röst, Timo Sachsenberg, Brian O'Connor, Fábio Madeira, Victoria Dominguez Del Angel, Michael R Crusoe, Susheel Varma, Daniel Blankenberg, Rafael C Jimenez, null null, Yasset Perez Riverol
Recommendations for the packaging and containerizing of bioinformatics software. F1000Research (2018)
Rafael C Jimenez, Mateusz Kuzak, Monther Alhamdoosh, Michelle Barker, Bérénice Batut, Mikael Borg, Salvador Capella, Neil Chue Hong, Martin Cook, Manuel Corpas, Madison Flannery, Leyla Garcia, Josep Ll Gelpí, Simon Gladman, Carole Goble, Montserrat González Ferreiro, Alejandra Gonzalez-Beltran, Philippa C Griffin, Bjoern Andreas Gruening, Jonas Hagberg, Petr Holub, Rob W W Hooft, Jon Ison, Daniel S Katz, Brane Leskošek, Federico López Gómez, Luis J Oliveira, David Mellor, Rowland Mosbergen, Nicola M Mulder, Yasset Perez Riverol, Robert Pergl, Horst Pichler, Bernard Pope, Ferran Sanz, Maria V Schneider, Victoria Stodden, Radosław Suchecki, Radka Svobodová Vařeková, Harry-Anton Talvik, Ilian Todorov, Andrew 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)
Laura V Glaser, Simone Rieger, Sybille Thumann, Sophie Beer, Cornelia Kuklik-Roos, Dietmar E Martin, Kerstin C Maier, Marie L Harth-Hertle, Bjoern Andreas Gruening, Rolf Backofen, Stefan Krebs, Helmut Blum, Ralf Zimmer, Florian Erhard, Bettina Kempkes
EBF1 binds to EBNA2 and promotes the assembly of EBNA2 chromatin complexes in B cells. PLoS pathogens 13 (10) (2017)
Bjoern Andreas Gruening, Helena Rasche, Boris Rebolledo-Jaramillo, Carl Eberhard, Torsten Houwaart, John M Chilton, Nate Coraor, Rolf Backofen, James Taylor, Anton Nekrutenko
Jupyter and Galaxy: Easing entry barriers into complex data analyses for biomedical researchers. PLoS computational biology 13 (5) (2017)
Fidel Ramírez, Devon P Ryan, Bjoern Andreas Gruening, 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 research 44 (W1) (2016)
Guy Yachdav, Tatyana Goldberg, Sebastian Wilzbach, David Dao, Iris Shih, Saket Choudhary, Steve Crouch, Max Franz, Alexander García, Leyla J García, Bjoern Andreas Gruening, Devasena Inupakutika, Ian Sillitoe, Anil S Thanki, Bruno Vieira, José M Villaveces, Maria V Schneider, Suzanna Lewis, Steve Pettifer, Burkhard Rost, Manuel Corpas
Anatomy of BioJS, an open source community for the life sciences. eLife 4 (2015)