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---
layout: default
---
# Publications
@article{Schiml2023,
doi = {10.1186/s40793-023-00514-9},
url = {https://doi.org/10.1186/s40793-023-00514-9},
year = {2023},
month = jul,
publisher = {Springer Science and Business Media {LLC}},
volume = {18},
number = {1},
author = {Valerie C. Schiml and Francesco Delogu and Praveen Kumar and Benoit Kunath and B{\'{e}}r{\'{e}}nice Batut and Subina Mehta and James E. Johnson and Bj\"{o}rn Gr\"{u}ning and Phillip B. Pope and Pratik D. Jagtap and Timothy J. Griffin and Magnus {\O}. Arntzen},
title = {Integrative meta-omics in Galaxy and beyond},
journal = {Environmental Microbiome}
}
@article{Kumar2022,
doi = {10.1093/gigascience/giad028},
url = {https://doi.org/10.1093/gigascience/giad028},
year = {2022},
month = dec,
publisher = {Oxford University Press ({OUP})},
volume = {12},
author = {Anup Kumar and Gianmauro Cuccuru and Bj\"{o}rn Gr\"{u}ning and Rolf Backofen},
title = {An accessible infrastructure for artificial intelligence using a Docker-based {JupyterLab} in Galaxy},
journal = {{GigaScience}}
}
@article{2022,
doi = {10.1093/nar/gkac247},
url = {https://doi.org/10.1093/nar/gkac247},
year = {2022},
month = apr,
publisher = {Oxford University Press ({OUP})},
volume = {50},
number = {W1},
pages = {W345--W351},
author = {and Enis Afgan and Anton Nekrutenko and Bj{\'{o}}rn A Gr\"{u}ning and Daniel Blankenberg and Jeremy Goecks and Michael C Schatz and Alexander E Ostrovsky and Alexandru Mahmoud and Andrew J Lonie and Anna Syme and Anne Fouilloux and Anthony Bretaudeau and Anton Nekrutenko and Anup Kumar and Arthur C Eschenlauer and Assunta D DeSanto and Aysam Guerler and Beatriz Serrano-Solano and B{\'{e}}r{\'{e}}nice Batut and Bj\"{o}rn A Gr\"{u}ning and Bradley W Langhorst and Bridget Carr and Bryan A Raubenolt and Cameron J Hyde and Catherine J Bromhead and Christopher B Barnett and Coline Royaux and Crist{\'{o}}bal Gallardo and Daniel Blankenberg and Daniel J Fornika and Dannon Baker and Dave Bouvier and Dave Clements and David A de Lima Morais and David Lopez Tabernero and Delphine Lariviere and Engy Nasr and Enis Afgan and Federico Zambelli and Florian Heyl and Fotis Psomopoulos and Frederik Coppens and Gareth R Price and Gianmauro Cuccuru and Gildas Le Corguill{\'{e}} and Greg Von Kuster and Gulsum Gudukbay Akbulut and Helena Rasche and Hans-Rudolf Hotz and Ignacio Eguinoa and Igor Makunin and Isuru J Ranawaka and James P Taylor and Jayadev Joshi and Jennifer Hillman-Jackson and Jeremy Goecks and John M Chilton and Kaivan Kamali and Keith Suderman and Krzysztof Poterlowicz and Le Bras Yvan and Lucille Lopez-Delisle and Luke Sargent and Madeline E Bassetti and Marco Antonio Tangaro and Marius van den Beek and Martin {\v{C}}ech and Matthias Bernt and Matthias Fahrner and Mehmet Tekman and Melanie C F\"{o}ll and Michael C Schatz and Michael R Crusoe and Miguel Roncoroni and Natalie Kucher and Nate Coraor and Nicholas Stoler and Nick Rhodes and Nicola Soranzo and Niko Pinter and Nuwan A Goonasekera and Pablo A Moreno and Pavankumar Videm and Petera Melanie and Pietro Mandreoli and Pratik D Jagtap and Qiang Gu and Ralf J M Weber and Ross Lazarus and Ruben H P Vorderman and Saskia Hiltemann and Sergey Golitsynskiy and Shilpa Garg and Simon A Bray and Simon L Gladman and Simone Leo and Subina P Mehta and Timothy J Griffin and Vahid Jalili and Vandenbrouck Yves and Victor Wen and Vijay K Nagampalli and Wendi A Bacon and Willem de Koning and Wolfgang Maier and Peter J Briggs},
title = {The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2022 update},
journal = {Nucleic Acids Research}
}
@article{Hiltemann2023,
doi = {10.1371/journal.pcbi.1010752},
url = {https://doi.org/10.1371/journal.pcbi.1010752},
year = {2023},
month = jan,
publisher = {Public Library of Science ({PLoS})},
volume = {19},
number = {1},
pages = {e1010752},
author = {Saskia Hiltemann and Helena Rasche and Simon Gladman and Hans-Rudolf Hotz and Delphine Larivi{\`{e}}re and Daniel Blankenberg and Pratik D. Jagtap and Thomas Wollmann and Anthony Bretaudeau and Nadia Gou{\'{e}} and Timothy J. Griffin and Coline Royaux and Yvan Le Bras and Subina Mehta and Anna Syme and Frederik Coppens and Bert Droesbeke and Nicola Soranzo and Wendi Bacon and Fotis Psomopoulos and Crist{\'{o}}bal Gallardo-Alba and John Davis and Melanie Christine F\"{o}ll and Matthias Fahrner and Maria A. Doyle and Beatriz Serrano-Solano and Anne Claire Fouilloux and Peter van Heusden and Wolfgang Maier and Dave Clements and Florian Heyl and Bj\"{o}rn Gr\"{u}ning and B{\'{e}}r{\'{e}}nice Batut and},
editor = {Francis Ouellette},
title = {Galaxy Training: A powerful framework for teaching!},
journal = {{PLOS} Computational Biology}
}
@article{Bray2023,
doi = {10.1101/gr.276963.122},
url = {https://doi.org/10.1101/gr.276963.122},
year = {2023},
month = feb,
publisher = {Cold Spring Harbor Laboratory},
author = {Simon Bray and John Chilton and Matthias Bernt and Nicola Soranzo and Marius van den Beek and B{\'{e}}r{\'{e}}nice Batut and Helena Rasche and Martin {\v{C}}ech and Peter J.A. Cock and Bj\"{o}rn Gr\"{u}ning and Anton Nekrutenko},
title = {The Planemo toolkit for developing, deploying, and executing scientific data analyses in Galaxy and beyond},
journal = {Genome Research}
}
@article{Mehta2022,
doi = {10.3390/v14102205},
url = {https://doi.org/10.3390/v14102205},
year = {2022},
month = oct,
publisher = {{MDPI} {AG}},
volume = {14},
number = {10},
pages = {2205},
author = {Subina Mehta and Valdemir M. Carvalho and Andrew T. Rajczewski and Olivier Pible and Bj\"{o}rn A. Gr\"{u}ning and James E. Johnson and Reid Wagner and Jean Armengaud and Timothy J. Griffin and Pratik D. Jagtap},
title = {Catching the Wave: Detecting Strain-Specific {SARS}-{CoV}-2 Peptides in Clinical Samples Collected during Infection Waves from Diverse Geographical Locations},
journal = {Viruses}
}
@article{Meier_2022,
doi = {10.1038/s41408-022-00715-4},
url = {https://doi.org/10.1038%2Fs41408-022-00715-4},
year = 2022,
month = {aug},
publisher = {Springer Science and Business Media {LLC}},
volume = {12},
number = {8},
author = {Ruth Meier and Gabriele Greve and Dennis Zimmer and Helena Bresser and Bettina Berberich and Ralitsa Langova and Julia Stomper and Anne Rubarth and Lars Feuerbach and Daniel B. Lipka and Joschka Hey and Björn Grüning and Benedikt Brors and Justus Duyster and Christoph Plass and Heiko Becker and Michael Lübbert},
title = {The antileukemic activity of decitabine upon {PML}/{RARA}-negative {AML} blasts is supported by all-trans retinoic acid: in vitro and in vivo evidence for cooperation},
journal = {Blood Cancer Journal}
}
@article{Wolff2022,
doi = {10.1093/gigascience/giac061},
url = {https://doi.org/10.1093/gigascience/giac061},
year = {2022},
publisher = {Oxford University Press ({OUP})},
volume = {11},
author = {Joachim Wolff and Rolf Backofen and Bj\"{o}rn Gr\"{u}ning},
title = {Loop detection using Hi-C data with {HiCExplorer}},
journal = {{GigaScience}}
}
@article{VijayKrishna2022,
doi = {10.1093/bioadv/vbac030},
url = {https://doi.org/10.1093/bioadv/vbac030},
year = {2022},
month = jan,
publisher = {Oxford University Press ({OUP})},
volume = {2},
number = {1},
author = {Nagampalli VijayKrishna and Jayadev Joshi and Nate Coraor and Jennifer Hillman-Jackson and Dave Bouvier and Marius van den Beek and Ignacio Eguinoa and Frederik Coppens and John Davis and Micha{\l} Stolarczyk and Nathan C Sheffield and Simon Gladman and Gianmauro Cuccuru and Bj\"{o}rn Gr\"{u}ning and Nicola Soranzo and Helena Rasche and Bradley W Langhorst and Matthias Bernt and Dan Fornika and David Anderson de Lima Morais and Michel Barrette and Peter van Heusden and Mauro Petrillo and Antonio Puertas-Gallardo and Alex Patak and Hans-Rudolf Hotz and Daniel Blankenberg},
editor = {Sofia Forslund},
title = {Expanding the Galaxy's reference data},
journal = {Bioinformatics Advances}
}
@article{https://doi.org/10.11588/heibooks.979.c13724,
doi = {10.11588/HEIBOOKS.979.C13724},
url = {https://books.ub.uni-heidelberg.de/index.php/heibooks/catalog/book/979/c13724},
author = {M\"{u}hlhaus, Timo and Brillhaus, Dominik and Tsch\"{o}pe, Marcel and Maus, Oliver and Gr\"{u}ning, Bj\"{o}rn and Garth, Christoph and Martins Rodrigues, Cristina and Von Suchodoletz, Dirk},
title = {DataPLANT – Tools and Services to structure the Data Jungle for fundamental plant researchers},
publisher = {heiBOOKS},
year = {2022}
}
@article{Pinter2022,
doi = {10.1021/acs.jproteome.2c00051},
url = {https://doi.org/10.1021/acs.jproteome.2c00051},
year = {2022},
month = may,
publisher = {American Chemical Society ({ACS})},
author = {Niko Pinter and Damian Gl\"{a}tzer and Matthias Fahrner and Klemens Fr\"{o}hlich and James Johnson and Bj\"{o}rn Andreas Gr\"{u}ning and Bettina Warscheid and Friedel Drepper and Oliver Schilling and Melanie Christine F\"{o}ll},
title = {{MaxQuant} and {MSstats} in Galaxy Enable Reproducible Cloud-Based Analysis of Quantitative Proteomics Experiments for Everyone},
journal = {Journal of Proteome Research}
}
@article{Bray2022,
doi = {10.1186/s13321-022-00588-6},
url = {https://doi.org/10.1186/s13321-022-00588-6},
year = {2022},
month = apr,
publisher = {Springer Science and Business Media {LLC}},
volume = {14},
number = {1},
author = {Simon Bray and Tim Dudgeon and Rachael Skyner and Rolf Backofen and Bj\"{o}rn Gr\"{u}ning and Frank von Delft},
title = {Galaxy workflows for fragment-based virtual screening: a case study on the {SARS}-{CoV}-2 main protease},
journal = {Journal of Cheminformatics}
}
@article{Martin2022,
doi = {10.1093/molbev/msac061},
url = {https://doi.org/10.1093/molbev/msac061},
year = {2022},
month = mar,
publisher = {Oxford University Press ({OUP})},
author = {Darren P Martin and Spyros Lytras and Alexander G Lucaci and Wolfgang Maier and Bj\"{o}rn Gr\"{u}ning and Stephen D Shank and Steven Weaver and Oscar A MacLean and Richard J Orton and Philippe Lemey and Maciej F Boni and Houriiyah Tegally and Gordon W Harkins and Cathrine Scheepers and Jinal N Bhiman and Josie Everatt and Daniel G Amoako and James Emmanuel San and Jennifer Giandhari and Alex Sigal and Carolyn Williamson and Nei-yuan Hsiao and Anne von Gottberg and Arne De Klerk and Robert W Shafer and David L Robertson and Robert J Wilkinson and B Trevor Sewell and Richard Lessells and Anton Nekrutenko and Allison J Greaney and Tyler N Starr and Jesse D Bloom and Ben Murrell and Eduan Wilkinson and Ravindra K Gupta and Tulio de Oliveira and Sergei L Kosakovsky Pond and},
editor = {Keith Crandall},
title = {Selection analysis identifies clusters of unusual mutational changes in Omicron lineage {BA}.1 that likely impact Spike function},
journal = {Molecular Biology and Evolution}
}
@article{Brack2022,
doi = {10.1371/journal.pcbi.1009823},
url = {https://doi.org/10.1371/journal.pcbi.1009823},
year = {2022},
month = mar,
publisher = {Public Library of Science ({PLoS})},
volume = {18},
number = {3},
pages = {e1009823},
author = {Paul Brack and Peter Crowther and Stian Soiland-Reyes and Stuart Owen and Douglas Lowe and Alan R. Williams and Quentin Groom and Mathias Dillen and Frederik Coppens and Bj\"{o}rn Gr\"{u}ning and Ignacio Eguinoa and Philip Ewels and Carole Goble},
editor = {Scott Markel},
title = {Ten simple rules for making a software tool workflow-ready},
journal = {{PLOS} Computational Biology}
}
@article{Mossad2022,
doi = {10.1038/s41593-022-01027-3},
url = {https://doi.org/10.1038/s41593-022-01027-3},
year = {2022},
month = mar,
publisher = {Springer Science and Business Media {LLC}},
author = {Omar Mossad and B{\'{e}}r{\'{e}}nice Batut and Bahtiyar Yilmaz and Nikolaos Dokalis and Charlotte Mez\"{o} and Elisa Nent and Lara Susann Nabavi and Melanie Mayer and Feres Jos{\'{e}} Mocayar Maron and Joerg M. Buescher and Mercedes Gomez de Ag\"{u}ero and Antal Szalay and Tim L\"{a}mmermann and Andrew J. Macpherson and Stephanie C. Ganal-Vonarburg and Rolf Backofen and Daniel Erny and Marco Prinz and Thomas Blank},
title = {Gut microbiota drives age-related oxidative stress and mitochondrial damage in microglia via the metabolite N6-carboxymethyllysine},
journal = {Nature Neuroscience}
}
@article{Gao2022,
doi = {10.1038/s41467-022-28434-1},
url = {https://doi.org/10.1038/s41467-022-28434-1},
year = {2022},
month = feb,
publisher = {Springer Science and Business Media {LLC}},
volume = {13},
number = {1},
author = {Meijiang Gao and Marina Veil and Marcus Rosenblatt and Aileen Julia Riesle and Anna Gebhard and Helge Hass and Lenka Buryanova and Lev Y. Yampolsky and Bj\"{o}rn Gr\"{u}ning and Sergey V. Ulianov and Jens Timmer and Daria Onichtchouk},
title = {Pluripotency factors determine gene expression repertoire at zygotic genome activation},
journal = {Nature Communications}
}
@article{Fahrner2022,
doi = {10.1093/gigascience/giac005},
url = {https://doi.org/10.1093/gigascience/giac005},
year = {2022},
publisher = {Oxford University Press ({OUP})},
volume = {11},
author = {Matthias Fahrner and Melanie Christine F\"{o}ll and Bj\"{o}rn Andreas Gr\"{u}ning and Matthias Bernt and Hannes R\"{o}st and Oliver Schilling},
title = {Democratizing data-independent acquisition proteomics analysis on public cloud infrastructures via the Galaxy framework},
journal = {{GigaScience}}
}
@article{Dai2021,
doi = {10.1038/s41467-021-26111-3},
url = {https://doi.org/10.1038/s41467-021-26111-3},
year = {2021},
month = oct,
publisher = {Springer Science and Business Media {LLC}},
volume = {12},
number = {1},
author = {Chengxin Dai and Anja F\"{u}llgrabe and Julianus Pfeuffer and Elizaveta M. Solovyeva and Jingwen Deng and Pablo Moreno and Selvakumar Kamatchinathan and Deepti Jaiswal Kundu and Nancy George and Silvie Fexova and Bj\"{o}rn Gr\"{u}ning and Melanie Christine F\"{o}ll and Johannes Griss and Marc Vaudel and Enrique Audain and Marie Locard-Paulet and Michael Turewicz and Martin Eisenacher and Julian Uszkoreit and Tim Van Den Bossche and Veit Schw\"{a}mmle and Henry Webel and Stefan Schulze and David Bouyssi{\'{e}} and Savita Jayaram and Vinay Kumar Duggineni and Patroklos Samaras and Mathias Wilhelm and Meena Choi and Mingxun Wang and Oliver Kohlbacher and Alvis Brazma and Irene Papatheodorou and Nuno Bandeira and Eric W. Deutsch and Juan Antonio Vizca{\'{\i}}no and Mingze Bai and Timo Sachsenberg and Lev I. Levitsky and Yasset Perez-Riverol},
title = {A proteomics sample metadata representation for multiomics integration and big data analysis},
journal = {Nature Communications}
}
@article{bray2020intuitive,
title={Intuitive, reproducible high-throughput molecular dynamics in Galaxy: a tutorial},
author={Bray, Simon A and Senapathi, Tharindu and Barnett, Christopher B and Gr{\"u}ning, Bj{\"o}rn A},
journal={Journal of Cheminformatics},
volume={12},
number={1},
pages={1--13},
year={2020},
publisher={BioMed Central}
}
@article{mehta2021asaim,
title={ASaiM-MT: a validated and optimized ASaiM workflow for metatranscriptomics analysis within Galaxy framework},
author={Mehta, Subina and Crane, Marie and Leith, Emma and Batut, B{\'e}r{\'e}nice and Hiltemann, Saskia and Arntzen, Magnus {\O} and Kunath, Benoit J and Pope, Phillip B and Delogu, Francesco and Sajulga, Ray and others},
journal={F1000Research},
volume={10},
year={2021},
publisher={Faculty of 1000 Ltd}
}
@incollection{batut2021rna,
title={RNA-Seq Data Analysis in Galaxy},
author={Batut, B{\'e}r{\'e}nice and Beek, Marius van den and Doyle, Maria A and Soranzo, Nicola},
booktitle={RNA Bioinformatics},
pages={367--392},
year={2021},
publisher={Springer}
}
@article{maier_ready--use_2021,
author = {Maier, Wolfgang and Bray, Simon and van den Beek, Marius and Bouvier, Dave and Coraor, Nathan and Miladi, Milad and Singh, Babita and De Argila, Jordi Rambla and Baker, Dannon and Roach, Nathan and Gladman, Simon and Coppens, Frederik and Martin, Darren P. and Lonie, Andrew and Grüning, Björn and Kosakovsky Pond, Sergei L. and Nekrutenko, Anton},
copyright = {2021 The Author(s), under exclusive licence to Springer Nature America, Inc.},
doi = {10.1038/s41587-021-01069-1},
issn = {1546-1696},
journal = {Nature Biotechnology},
keywords = {+Galactic, +IsGalaxy, +Project, +UsePublic, {\textgreater}UseGalaxy.eu, {\textgreater}UseGalaxy.org, {\textgreater}UseGalaxy.org.au},
language = {en},
month = {September},
note = {Bandiera\_abtest: a
Cg\_type: Nature Research Journals
Primary\_atype: Correspondence
Publisher: Nature Publishing Group
Subject\_term: Genomic analysis;SARS-CoV-2
Subject\_term\_id: genomic-analysis;sars-cov-2},
pages = {1--2},
title = {Ready-to-use public infrastructure for global {SARS}-{CoV}-2 monitoring},
url = {https://www.nature.com/articles/s41587-021-01069-1},
urldate = {2021-10-01},
year = {2021}
}
@article{Roncoroni2021,
doi = {10.1093/bioinformatics/btab421},
url = {https://doi.org/10.1093/bioinformatics/btab421},
year = {2021},
month = jun,
publisher = {Oxford University Press ({OUP})},
author = {Miguel Roncoroni and Bert Droesbeke and Ignacio Eguinoa and Kim De Ruyck and Flora D'Anna and Dilmurat Yusuf and Bj\"{o}rn Gr\"{u}ning and Rolf Backofen and Frederik Coppens},
editor = {Zhiyong Lu},
title = {A {SARS}-{CoV}-2 sequence submission tool for the European Nucleotide Archive},
journal = {Bioinformatics}
}
@article{Gu2021,
doi = {10.1371/journal.pcbi.1009014},
url = {https://doi.org/10.1371/journal.pcbi.1009014},
year = {2021},
month = jun,
publisher = {Public Library of Science ({PLoS})},
volume = {17},
number = {6},
pages = {e1009014},
author = {Qiang Gu and Anup Kumar and Simon Bray and Allison Creason and Alireza Khanteymoori and Vahid Jalili and Bj\"{o}rn Gr\"{u}ning and Jeremy Goecks},
editor = {Mihaela Pertea},
title = {Galaxy-{ML}: An accessible, reproducible, and scalable machine learning toolkit for biomedicine},
journal = {{PLOS} Computational Biology}
}
@article{rajczewski_rigorous_2021,
abstract = {The Coronavirus Disease 2019 (COVID-19) global pandemic has had a profound, lasting impact on the world's population. A key aspect to providing care for those with COVID-19 and checking its further spread is early and accurate diagnosis of infection, which has been generally done via methods for amplifying and detecting viral RNA molecules. Detection and quantitation of peptides using targeted mass spectrometry-based strategies has been proposed as an alternative diagnostic tool due to direct detection of molecular indicators from non-invasively collected samples as well as the potential for high-throughput analysis in a clinical setting; many studies have revealed the presence of viral peptides within easily accessed patient samples. However, evidence suggests that some viral peptides could serve as better indicators of COVID-19 infection status than others, due to potential misidentification of peptides derived from human host proteins, poor spectral quality, high limits of detection etc.},
author = {Rajczewski, Andrew T. and Mehta, Subina and Nguyen, Dinh Duy An and Grüning, Björn and Johnson, James E. and McGowan, Thomas and Griffin, Timothy J. and Jagtap, Pratik D.},
doi = {10.1186/s12014-021-09321-1},
issn = {1559-0275},
journal = {Clinical Proteomics},
keywords = {+Galactic, +Methods, +Shared, +UsePublic, {\textgreater}UseGalaxy.eu, Bioinformatics, Mass spectrometry, Pandemic, Peptide-detection, Viral proteome, Workflows},
month = {May},
number = {1},
pages = {15},
title = {A rigorous evaluation of optimal peptide targets for {MS}-based clinical diagnostics of {Coronavirus} {Disease} 2019 ({COVID}-19)},
url = {https://doi.org/10.1186/s12014-021-09321-1},
urldate = {2021-05-11},
volume = {18},
year = {2021}
}
@article{Guerler2021,
doi = {10.1101/2021.03.17.435706},
url = {https://doi.org/10.1101/2021.03.17.435706},
year = {2021},
month = mar,
publisher = {Cold Spring Harbor Laboratory},
author = {Aysam Guerler and Dannon Baker and Marius van den Beek and Bjoern Gruening and Dave Bouvier and Nate Coraor and Stephen D. Shank and Jordan D. Zehr and Michael C. Schatz and Anton Nekrutenko},
title = {Fast and accurate genome-wide predictions and structural modeling of protein-protein interactions using Galaxy}
}
@article{Wolff2021,
doi = {10.1093/bioinformatics/btab394},
url = {https://doi.org/10.1093/bioinformatics/btab394},
year = {2021},
month = may,
publisher = {Oxford University Press ({OUP})},
author = {Joachim Wolff and Rolf Backofen and Bj\"{o}rn Gr\"{u}ning},
editor = {Pier Luigi Martelli},
title = {Robust and efficient single-cell Hi-C clustering with approximate k-nearest neighbor graphs},
journal = {Bioinformatics}
}
@article{10.1371/journal.pcbi.1008922,
doi = {10.1371/journal.pcbi.1008922},
author = {Gallardo-Alba, Cristóbal AND Grüning, Björn AND Serrano-Solano, Beatriz},
journal = {PLOS Computational Biology},
publisher = {Public Library of Science},
title = {A constructivist-based proposal for bioinformatics teaching practices during lockdown},
year = {2021},
month = {05},
volume = {17},
url = {https://doi.org/10.1371/journal.pcbi.1008922},
pages = {1-11},
abstract = {The Coronavirus Disease 2019 (COVID-19) outbreaks have caused universities all across the globe to close their campuses and forced them to initiate online teaching. This article reviews the pedagogical foundations for developing effective distance education practices, starting from the assumption that promoting autonomous thinking is an essential element to guarantee full citizenship in a democracy and for moral decision-making in situations of rapid change, which has become a pressing need in the context of a pandemic. In addition, the main obstacles related to this new context are identified, and solutions are proposed according to the existing bibliography in learning sciences.},
number = {5},
}
@article{10.1371/journal.pcbi.1008923,
doi = {10.1371/journal.pcbi.1008923},
author = {Serrano-Solano, Beatriz AND Föll, Melanie C. AND Gallardo-Alba, Cristóbal AND Erxleben, Anika AND Rasche, Helena AND Hiltemann, Saskia AND Fahrner, Matthias AND Dunning, Mark J. AND Schulz, Marcel H. AND Scholtz, Beáta AND Clements, Dave AND Nekrutenko, Anton AND Batut, Bérénice AND Grüning, Björn A.},
journal = {PLOS Computational Biology},
publisher = {Public Library of Science},
title = {Fostering accessible online education using Galaxy as an e-learning platform},
year = {2021},
month = {05},
volume = {17},
url = {https://doi.org/10.1371/journal.pcbi.1008923},
pages = {1-10},
abstract = {The COVID-19 pandemic is shifting teaching to an online setting all over the world. The Galaxy framework facilitates the online learning process and makes it accessible by providing a library of high-quality community-curated training materials, enabling easy access to data and tools, and facilitates sharing achievements and progress between students and instructors. By combining Galaxy with robust communication channels, effective instruction can be designed inclusively, regardless of the students’ environments.},
number = {5},
}
@article{Moreno2021,
doi = {10.1038/s41592-021-01102-w},
url = {https://doi.org/10.1038/s41592-021-01102-w},
year = {2021},
month = mar,
publisher = {Springer Science and Business Media {LLC}},
author = {Pablo Moreno and Ni Huang and Jonathan R. Manning and Suhaib Mohammed and Andrey Solovyev and Krzysztof Polanski and Wendi Bacon and Ruben Chazarra and Carlos Talavera-L{\'{o}}pez and Maria A. Doyle and Guilhem Marnier and Bj\"{o}rn Gr\"{u}ning and Helena Rasche and Nancy George and Silvie Korena Fexova and Mohamed Alibi and Zhichao Miao and Yasset Perez-Riverol and Maximilian Haeussler and Alvis Brazma and Sarah Teichmann and Kerstin B. Meyer and Irene Papatheodorou},
title = {User-friendly, scalable tools and workflows for single-cell {RNA}-seq analysis},
journal = {Nature Methods}
}
@article{Bai2021,
doi = {10.1021/acs.jproteome.0c00904},
url = {https://doi.org/10.1021/acs.jproteome.0c00904},
year = {2021},
month = feb,
publisher = {American Chemical Society ({ACS})},
author = {Jingwen Bai and Chakradhar Bandla and Jiaxin Guo and Roberto Vera Alvarez and Mingze Bai and Juan Antonio Vizca{\'{\i}}no and Pablo Moreno and Bj\"{o}rn Gr\"{u}ning and Olivier Sallou and Yasset Perez-Riverol},
title = {{BioContainers} Registry: Searching Bioinformatics and Proteomics Tools, Packages, and Containers},
journal = {Journal of Proteome Research}
}
@article{Videm2021,
doi = {10.1093/gigascience/giaa158},
url = {https://doi.org/10.1093/gigascience/giaa158},
year = {2021},
month = jan,
publisher = {Oxford University Press ({OUP})},
volume = {10},
number = {2},
author = {Pavankumar Videm and Anup Kumar and Oleg Zharkov and Bj\"{o}rn Andreas Gr\"{u}ning and Rolf Backofen},
title = {{ChiRA}: an integrated framework for chimeric read analysis from {RNA}-{RNA} interactome and {RNA} structurome data},
journal = {{GigaScience}}
}
@article{Greve2020,
doi = {10.1158/0008-5472.can-20-1430},
url = {https://doi.org/10.1158/0008-5472.can-20-1430},
year = {2020},
month = nov,
publisher = {American Association for Cancer Research ({AACR})},
pages = {canres.1430.2020},
author = {Gabriele Greve and Julia Sch\"{u}ler and Bj\"{o}rn A. Gr\"{u}ning and Bettina Berberich and Julia Stomper and Dennis Zimmer and Lea Gutenkunst and Ulrike B\"{o}nisch and Ruth Meier and Nadja Blagitko-Dorfs and Olga Grishina and Dietmar Pfeifer and Dieter Weichenhan and Christoph Plass and Michael L\"{u}bbert},
title = {Decitabine induces gene derepression on monosomic chromosomes: in vitro and in vivo effects in adverse-risk cytogenetics {AML}},
journal = {Cancer Research}
}
@article{10.1093/gigascience/giaa152,
author = {Kumar, Anup and Rasche, Helena and Grüning, Björn and Backofen, Rolf},
title = "{Tool recommender system in Galaxy using deep learning}",
journal = {GigaScience},
volume = {10},
number = {1},
year = {2021},
month = {01},
abstract = "{Galaxy is a web-based and open-source scientific data-processing platform. Researchers compose pipelines in Galaxy to analyse scientific data. These pipelines, also known as workflows, can be complex and difficult to create from thousands of tools, especially for researchers new to Galaxy. To help researchers with creating workflows, a system is developed to recommend tools that can facilitate further data analysis.A model is developed to recommend tools using a deep learning approach by analysing workflows composed by researchers on the European Galaxy server. The higher-order dependencies in workflows, represented as directed acyclic graphs, are learned by training a gated recurrent units neural network, a variant of a recurrent neural network. In the neural network training, the weights of tools used are derived from their usage frequencies over time and the sequences of tools are uniformly sampled from training data. Hyperparameters of the neural network are optimized using Bayesian optimization. Mean accuracy of 98\\% in recommending tools is achieved for the top-1 metric.The model is accessed by a Galaxy API to provide researchers with recommended tools in an interactive manner using multiple user interface integrations on the European Galaxy server. High-quality and highly used tools are shown at the top of the recommendations. The scripts and data to create the recommendation system are available under MIT license at https://github.com/anuprulez/galaxy\_tool\_recommendation.}",
issn = {2047-217X},
doi = {10.1093/gigascience/giaa152},
url = {https://doi.org/10.1093/gigascience/giaa152},
note = {giaa152},
eprint = {https://academic.oup.com/gigascience/article-pdf/10/1/giaa152/35531816/giaa152.pdf},
}
@article{Wolff2021,
doi = {10.1093/bioinformatics/btab243},
url = {https://doi.org/10.1093/bioinformatics/btab243},
year = {2021},
month = may,
publisher = {Oxford University Press ({OUP})},
author = {Joachim Wolff and Nezar Abdennur and Rolf Backofen and Bj\"{o}rn Gr\"{u}ning},
title = {Scool: a new data storage format for single-cell Hi-C data},
journal = {Bioinformatics}
}
@article{marais2020genome,
title={Genome Evolution: Mutation Is the Main Driver of Genome Size in Prokaryotes},
author={Marais, Gabriel AB and Batut, B{\'e}r{\'e}nice and Daubin, Vincent},
journal={Current Biology},
volume={30},
number={19},
pages={R1083--R1085},
year={2020},
publisher={Elsevier}
}
@article{garcia2020ten,
author = {Garcia, Leyla AND Batut, Bérénice AND Burke, Melissa L. AND Kuzak, Mateusz AND Psomopoulos, Fotis AND Arcila, Ricardo AND Attwood, Teresa K. AND Beard, Niall AND Carvalho-Silva, Denise AND Dimopoulos, Alexandros C. AND del Angel, Victoria Dominguez AND Dumontier, Michel AND Gurwitz, Kim T. AND Krause, Roland AND McQuilton, Peter AND Le Pera, Loredana AND Morgan, Sarah L. AND Rauste, Päivi AND Via, Allegra AND Kahlem, Pascal AND Rustici, Gabriella AND van Gelder, Celia W. G. AND Palagi, Patricia M.},
journal = {PLOS Computational Biology},
publisher = {Public Library of Science},
title = {Ten simple rules for making training materials FAIR},
year = {2020},
month = {05},
volume = {16},
url = {https://doi.org/10.1371/journal.pcbi.1007854},
pages = {1-9},
abstract = {Author summary Everything we do today is becoming more and more reliant on the use of computers. The field of biology is no exception; but most biologists receive little or no formal preparation for the increasingly computational aspects of their discipline. In consequence, informal training courses are often needed to plug the gaps; and the demand for such training is growing worldwide. To meet this demand, some training programs are being expanded, and new ones are being developed. Key to both scenarios is the creation of new course materials. Rather than starting from scratch, however, it’s sometimes possible to repurpose materials that already exist. Yet finding suitable materials online can be difficult: They’re often widely scattered across the internet or hidden in their home institutions, with no systematic way to find them. This is a common problem for all digital objects. The scientific community has attempted to address this issue by developing a set of rules (which have been called the Findable, Accessible, Interoperable and Reusable [FAIR] principles) to make such objects more findable and reusable. Here, we show how to apply these rules to help make training materials easier to find, (re)use, and adapt, for the benefit of all.},
number = {5},
doi = {10.1371/journal.pcbi.1007854}
}
@article{batut2018asaim,
title={ASaiM: a Galaxy-based framework to analyze microbiota data},
author={Batut, B{\'e}r{\'e}nice and Gravouil, Kevin and Defois, Clemence and Hiltemann, Saskia and Brug{\`e}re, Jean-Fran{\c{c}}ois and Peyretaillade, Eric and Peyret, Pierre},
journal={GigaScience},
volume={7},
number={6},
pages={giy057},
year={2018},
publisher={Oxford University Press}
}
@article{Tekman2020,
doi = {10.1093/gigascience/giaa102},
url = {https://doi.org/10.1093/gigascience/giaa102},
year = {2020},
month = oct,
publisher = {Oxford University Press ({OUP})},
volume = {9},
number = {10},
author = {Mehmet Tekman and B{\'{e}}r{\'{e}}nice Batut and Alexander Ostrovsky and Christophe Antoniewski and Dave Clements and Fidel Ramirez and Graham J Etherington and Hans-Rudolf Hotz and Jelle Scholtalbers and Jonathan R Manning and Lea Bellenger and Maria A Doyle and Mohammad Heydarian and Ni Huang and Nicola Soranzo and Pablo Moreno and Stefan Mautner and Irene Papatheodorou and Anton Nekrutenko and James Taylor and Daniel Blankenberg and Rolf Backofen and Bj\"{o}rn Gr\"{u}ning},
title = {A single-cell {RNA}-sequencing training and analysis suite using the Galaxy framework},
journal = {{GigaScience}}
}
@article{deKoning2020,
doi = {10.1093/gigascience/giaa105},
url = {https://doi.org/10.1093/gigascience/giaa105},
year = {2020},
month = oct,
publisher = {Oxford University Press ({OUP})},
volume = {9},
number = {10},
author = {Willem de~Koning and Milad Miladi and Saskia Hiltemann and Astrid Heikema and John P Hays and Stephan Flemming and Marius van~den~Beek and Dana A Mustafa and Rolf Backofen and Bj\"{o}rn Gr\"{u}ning and Andrew P Stubbs},
title = {{NanoGalaxy}: Nanopore long-read sequencing data analysis in Galaxy},
journal = {{GigaScience}}
}
@article{Rasche2020,
doi = {10.1101/2020.08.23.263509},
url = {https://doi.org/10.1101/2020.08.23.263509},
year = {2020},
month = aug,
publisher = {Cold Spring Harbor Laboratory},
author = {Helena Rasche and Bjoern Andreas Gruening},
title = {Training Infrastructure as a Service}
}
@article{Baker2020,
doi = {10.1371/journal.ppat.1008643},
url = {https://doi.org/10.1371/journal.ppat.1008643},
year = {2020},
month = aug,
publisher = {Public Library of Science ({PLoS})},
volume = {16},
number = {8},
pages = {e1008643},
author = {Dannon Baker and Marius van den Beek and Daniel Blankenberg and Dave Bouvier and John Chilton and Nate Coraor and Frederik Coppens and Ignacio Eguinoa and Simon Gladman and Bj\"{o}rn Gr\"{u}ning and Nicholas Keener and Delphine Larivi{\`{e}}re and Andrew Lonie and Sergei Kosakovsky Pond and Wolfgang Maier and Anton Nekrutenko and James Taylor and Steven Weaver},
editor = {Carolyn B. Coyne},
title = {No more business as usual: Agile and effective responses to emerging pathogen threats require open data and open analytics},
journal = {{PLOS} Pathogens}
}
@article{LopezDelisle2020,
doi = {10.1093/bioinformatics/btaa692},
url = {https://doi.org/10.1093/bioinformatics/btaa692},
year = {2020},
month = aug,
publisher = {Oxford University Press ({OUP})},
author = {Lucille Lopez-Delisle and Leily Rabbani and Joachim Wolff and Vivek Bhardwaj and Rolf Backofen and Bj\"{o}rn Gr\"{u}ning and Fidel Ram{\'{\i}}rez and Thomas Manke},
editor = {Peter Robinson},
title = {{pyGenomeTracks}: reproducible plots for multivariate genomic data sets},
journal = {Bioinformatics}
}
@article{Dass2020,
doi = {10.1093/nar/gkaa326},
url = {https://doi.org/10.1093/nar/gkaa326},
year = {2020},
month = may,
publisher = {Oxford University Press ({OUP})},
volume = {48},
number = {W1},
pages = {W380--W384},
author = {Gaurhari Dass and Manh-Tu Vu and Pan Xu and Enrique Audain and Marc-Phillip Hitz and Bj\"{o}rn~A Gr\"{u}ning and Henning Hermjakob and Yasset Perez-Riverol},
title = {The omics discovery {REST} interface},
journal = {Nucleic Acids Research}
}
@article{Wolff2020,
doi = {10.1093/nar/gkaa220},
url = {https://doi.org/10.1093/nar/gkaa220},
year = {2020},
month = apr,
publisher = {Oxford University Press ({OUP})},
volume = {48},
number = {W1},
pages = {W177--W184},
author = {Joachim Wolff and Leily Rabbani and Ralf Gilsbach and Gautier Richard and Thomas Manke and Rolf Backofen and Bj\"{o}rn A Gr\"{u}ning},
title = {Galaxy {HiCExplorer} 3: a web server for reproducible Hi-C, capture Hi-C and single-cell Hi-C data analysis, quality control and visualization},
journal = {Nucleic Acids Research}
}
@article{Schfer2020,
doi = {10.1093/bioinformatics/btaa556},
url = {https://doi.org/10.1093/bioinformatics/btaa556},
year = {2020},
month = jun,
publisher = {Oxford University Press ({OUP})},
author = {Richard A Sch\"{a}fer and Steffen C Lott and Jens Georg and Bj\"{o}rn A Gr\"{u}ning and Wolfgang R Hess and Bj\"{o}rn Vo{\ss}},
editor = {Jan Gorodkin},
title = {{GLASSGo} in Galaxy: high-throughput, reproducible and easy-to-integrate prediction of {sRNA} homologs},
journal = {Bioinformatics}
}
@article{Bray2020,
doi = {10.1186/s13321-020-00442-7},
url = {https://doi.org/10.1186/s13321-020-00442-7},
year = {2020},
month = jun,
publisher = {Springer Science and Business Media {LLC}},
volume = {12},
number = {1},
author = {Simon A. Bray and Xavier Lucas and Anup Kumar and Bj\"{o}rn A. Gr\"{u}ning},
title = {The {ChemicalToolbox}: reproducible, user-friendly cheminformatics analysis on the Galaxy platform},
journal = {Journal of Cheminformatics}
}
@article{Hille2020,
doi = {10.1111/jth.14895},
url = {https://doi.org/10.1111/jth.14895},
year = {2020},
month = may,
publisher = {Wiley},
author = {Laura Hille and Maximilian Lenz and Andreas Vlachos and Bj\"{o}rn Gr\"{u}ning and Lutz Hein and Franz-Josef Neumann and Thomas G. N\"{u}hrenberg and Dietmar Trenk},
title = {Ultrastructural, transcriptional and functional differences between human reticulated and non-reticulated platelets},
journal = {Journal of Thrombosis and Haemostasis}
}
@article{Murat2020,
doi = {10.1093/gigascience/giaa049},
url = {https://doi.org/10.1093/gigascience/giaa049},
year = {2020},
month = may,
publisher = {Oxford University Press ({OUP})},
volume = {9},
number = {5},
author = {Katarzyna Murat and Bj\"{o}rn Gr\"{u}ning and Paulina Wiktoria Poterlowicz and Gillian Westgate and Desmond J Tobin and Krzysztof Poterlowicz},
title = {Ewastools: Infinium Human Methylation {BeadChip} pipeline for population epigenetics integrated into Galaxy},
journal = {{GigaScience}}
}
@incollection{PerezRiverol2020,
doi = {10.1039/9781788019880-00415},
url = {https://doi.org/10.1039/9781788019880-00415},
year = {2020},
publisher = {Royal Society of Chemistry},
pages = {415--426},
author = {Yasset Perez-Riverol and Olivier Sallou and Bj\"{o}rn A. Gr\"{u}ning},
title = {{CHAPTER} 19. Cross-platform Software Development and Distribution with Bioconda and {BioContainers}},
booktitle = {Processing Metabolomics and Proteomics Data with Open Software}
}
@article{Wolff2020,
doi = {10.1101/2020.03.05.979096},
url = {https://doi.org/10.1101/2020.03.05.979096},
year = {2020},
month = mar,
publisher = {Cold Spring Harbor Laboratory},
author = {Joachim Wolff and Rolf Backofen and Bj\"{o}rn Gr\"{u}ning},
title = {Loop detection using Hi-C data with {HiCExplorer}}
}
@article{Wolff2020,
doi = {10.1101/2020.03.05.978569},
url = {https://doi.org/10.1101/2020.03.05.978569},
year = {2020},
month = mar,
publisher = {Cold Spring Harbor Laboratory},
author = {Joachim Wolff and Rolf Backofen and Bj\"{o}rn Gr\"{u}ning},
title = {Approximate k-nearest neighbors graph for single-cell Hi-C dimensional reduction with {MinHash}}
}
@article{https://doi.org/10.11588/heibooks.598.c8418,
doi = {10.11588/HEIBOOKS.598.C8418},
url = {https://books.ub.uni-heidelberg.de/index.php/heibooks/catalog/book/598/c8418},
author = {Dirk von Suchodoletz and Jonathan Bauer and Oleg Zharkov and Susanne Mocken and Bj\"{o}rn A. Gr\"{u}ning},
language = {eng},
title = {Lessons learned from Virtualized Research Environments in today’s scientific compute infrastructures},
journal = {E-Science-Tage 2019},
publisher = {University Library Heidelberg},
year = {2020}
}
@article{Anatskiy2018,
doi = {10.1093/bioinformatics/bty820},
url = {https://doi.org/10.1093/bioinformatics/bty820},
year = {2018},
month = sep,
publisher = {Oxford University Press ({OUP})},
volume = {35},
number = {8},
pages = {1422--1424},
author = {E Anatskiy and D P Ryan and B A Gr\"{u}ning and L Arrigoni and T Manke and U B\"{o}nisch},
editor = {Alfonso Valencia},
title = {Parkour {LIMS}: high-quality sample preparation in next generation sequencing},
journal = {Bioinformatics}
}
@article{Senapathi2019,
doi = {10.1093/bioinformatics/btz107},
url = {https://doi.org/10.1093/bioinformatics/btz107},
year = {2019},
month = feb,
publisher = {Oxford University Press ({OUP})},
volume = {35},
number = {18},
pages = {3508--3509},
author = {Tharindu Senapathi and Simon Bray and Christopher B Barnett and Bj\"{o}rn Gr\"{u}ning and Kevin J Naidoo},
editor = {Alfonso Valencia},
title = {Biomolecular Reaction and Interaction Dynamics Global Environment ({BRIDGE})},
journal = {Bioinformatics}
}
@article{Gruening2019,
doi = {10.12688/f1000research.15140.2},
url = {https://doi.org/10.12688/f1000research.15140.2},
year = {2019},
month = mar,
publisher = {F1000 Research Ltd},
volume = {7},
pages = {742},
author = {Bjorn Gruening and Olivier Sallou and Pablo Moreno and Felipe da Veiga Leprevost and Herv{\'{e}} M{\'{e}}nager and Dan S{\o}ndergaard and Hannes R\"{o}st and Timo Sachsenberg and Brian O{\textquotesingle}Connor and F{\'{a}}bio Madeira and Victoria Dominguez Del Angel and Michael R. Crusoe and Susheel Varma and Daniel Blankenberg and Rafael C. Jimenez and Yasset Perez-Riverol and},
title = {Recommendations for the packaging and containerizing of bioinformatics software},
journal = {F1000Research}
}
@article{Dass2020,
author = {Dass, Gaurhari and Vu, Manh-Tu and Xu, Pan and Audain, Enrique and Hitz, Marc-Phillip and Grüning, Björn A and Hermjakob, Henning and Perez-Riverol, Yasset},
title = "{The omics discovery REST interface}",
journal = {Nucleic Acids Research},
year = {2020},
month = {05},
abstract = "{The Omics Discovery Index is an open source platform that can be used to access, discover and disseminate omics datasets. OmicsDI integrates proteomics, genomics, metabolomics, models and transcriptomics datasets. Using an efficient indexing system, OmicsDI integrates different biological entities including genes, transcripts, proteins, metabolites and the corresponding publications from PubMed. In addition, it implements a group of pipelines to estimate the impact of each dataset by tracing the number of citations, reanalysis and biological entities reported by each dataset. Here, we present the OmicsDI REST interface (www.omicsdi.org/ws/) to enable programmatic access to any dataset in OmicsDI or all the datasets for a specific provider (database). Clients can perform queries on the API using different metadata information such as sample details (species, tissues, etc), instrumentation (mass spectrometer, sequencer), keywords and other provided annotations. In addition, we present two different libraries in R and Python to facilitate the development of tools that can programmatically interact with the OmicsDI REST interface.}",
issn = {0305-1048},
doi = {10.1093/nar/gkaa326},
url = {https://doi.org/10.1093/nar/gkaa326},
note = {gkaa326},
eprint = {https://academic.oup.com/nar/advance-article-pdf/doi/10.1093/nar/gkaa326/33177979/gkaa326.pdf},
}
@article{wibberg2019nbi,
title={The de. NBI/ELIXIR-DE training platform-Bioinformatics training in Germany and across Europe within ELIXIR},
author={Wibberg, Daniel and Batut, B{\'e}r{\'e}nice and Belmann, Peter and Blom, Jochen and Gl{\"o}ckner, Frank Oliver and Gr{\"u}ning, Bj{\"o}rn and Hoffmann, Nils and Kleinb{\"o}lting, Nils and Rahn, Ren{\'e} and Rey, Maja and others},
journal={F1000Research},
volume={8},
year={2019},
publisher={Faculty of 1000 Ltd}
}
@article{Nhrenberg2018,
doi = {10.1155/2018/8989252},
url = {https://doi.org/10.1155/2018/8989252},
year = {2018},
month = nov,
publisher = {Hindawi Limited},
volume = {2018},
pages = {1--9},
author = {Thomas G. N\"{u}hrenberg and Marco Cederqvist and Federico Marini and Christian Stratz and Bj\"{o}rn A. Gr\"{u}ning and Dietmar Trenk and Harald Binder and Ralf Gilsbach and Franz-Josef Neumann and Lutz Hein},
title = {Uncontrolled Diabetes Mellitus Has No Major Influence on the Platelet Transcriptome},
journal = {{BioMed} Research International}
}
@article{Afgan2018,
doi = {10.1093/nar/gky379},
url = {https://doi.org/10.1093/nar/gky379},
year = {2018},
month = may,
publisher = {Oxford University Press ({OUP})},
volume = {46},
number = {W1},
pages = {W537--W544},
author = {Enis Afgan and Dannon Baker and B{\'{e}}r{\'{e}}nice Batut and Marius van~den~Beek and Dave Bouvier and Martin {\v{C}}ech and John Chilton and Dave Clements and Nate Coraor and Bj\"{o}rn A Gr\"{u}ning and Aysam Guerler and Jennifer Hillman-Jackson and Saskia Hiltemann and Vahid Jalili and Helena Rasche and Nicola Soranzo and Jeremy Goecks and James Taylor and Anton Nekrutenko and Daniel Blankenberg},
title = {The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2018 update},
journal = {Nucleic Acids Research}
}
@Article{Gruning_Rasche_Rebolledo-Jaramillo-Jupyt_and_Galax-2017,
author = {Gruning, Bjorn A. and Rasche, Eric and Rebolledo-Jaramillo,
Boris and Eberhard, Carl and Houwaart, Torsten and Chilton,
John and Coraor, Nate and Backofen, Rolf and Taylor, James
and Nekrutenko, Anton},
title = {Jupyter and {Galaxy}: {Easing} entry barriers into complex
data analyses for biomedical researchers},
journal = {PLoS Comput Biol},
year = {2017},
volume = {13},
number = {5},
pages = {e1005425},
user = {backofen},
pmid = {28542180},
doi = {10.1371/journal.pcbi.1005425},
issn = {1553-734X},
issn = {1553-7358},
abstract = {What does it take to convert a heap of sequencing data into
a publishable result? First, common tools are employed to
reduce primary data (sequencing reads) to a form suitable
for further analyses (i.e., the list of variable sites). The
subsequent exploratory stage is much more ad hoc and
requires the development of custom scripts and pipelines,
making it problematic for biomedical researchers. Here, we
describe a hybrid platform combining common analysis
pathways with the ability to explore data interactively. It
aims to fully encompass and simplify the "raw
data-to-publication" pathway and make it reproducible.}
}
@Article{Scholz2019,
doi = {10.1371/journal.pone.0222459},
url = {https://doi.org/10.1371/journal.pone.0222459},
year = {2019},
month = sep,
publisher = {Public Library of Science ({PLoS})},
volume = {14},
number = {9},
pages = {e0222459},
author = {Anica Scholz and Florian Eggenhofer and Rick Gelhausen and Bj\"{o}rn Gr\"{u}ning and Kathi Zarnack and Bernhard Br\"{u}ne and Rolf Backofen and Tobias Schmid},
editor = {Eric Jan},
title = {{uORF}-Tools{\textemdash}Workflow for the determination of translation-regulatory upstream open reading frames},
journal = {{PLOS} {ONE}}
}
@Article{Backofen_Engelhardt_Erxleben-RNA_Tools_servi-2017,
author = {Backofen, Rolf and Engelhardt, Jan and Erxleben, Anika and
Fallmann, Jorg and Gruning, Bjorn and Ohler, Uwe and
Rajewsky, Nikolaus and Stadler, Peter F.},
title = {RNA-bioinformatics: {Tools}, services and databases for
the analysis of {RNA}-based regulation},
journal = {J Biotechnol},
year = {2017},
volume = {},
number = {},
pages = {},
user = {backofen},
pmid = {28554830},
doi = {10.1016/j.jbiotec.2017.05.019},
issn = {1873-4863},
issn = {0168-1656},
abstract = {The importance of RNA-based regulation is becoming more and
more evident. Genome-wide sequencing efforts have shown that
the majority of the DNA in eukaryotic genomes is
transcribed. Advanced high-throughput techniques like CLIP
for the genome-wide detection of RNA-protein interactions
have shown that post-transcriptional regulation by
RNA-binding proteins matches the complexity of
transcriptional regulation. The need for a specialized and
integrated analysis of RNA-based data has led to the
foundation of the RNA Bioinformatics Center (RBC) within the
German Network of Bioinformatics Infrastructure (de.NBI).
This paper describes the tools, services and databases
provided by the RBC, and shows example applications.
Furthermore, we have setup an RNA workbench within the
Galaxy framework. For an easy dissemination, we offer a
virtualized version of Galaxy (via Galaxy Docker) enabling
other groups to use our RNA workbench in a very simple way.}
}
@Article{Gruning_Fallmann_Yusuf-The_RNA_workb-NAR2017,
author = {Gruning, Bjorn A. and Fallmann, Jorg and Yusuf, Dilmurat
and Will, Sebastian and Erxleben, Anika and Eggenhofer,
Florian and Houwaart, Torsten and Batut, Berenice and Videm,
Pavankumar and Bagnacani, Andrea and Wolfien, Markus and
Lott, Steffen C. and Hoogstrate, Youri and Hess, Wolfgang R.
and Wolkenhauer, Olaf and Hoffmann, Steve and Akalin, Altuna
and Ohler, Uwe and Stadler, Peter F. and Backofen, Rolf},
title = {The {RNA} workbench: best practices for {RNA} and
high-throughput sequencing bioinformatics in {Galaxy}},
journal = NAR,
year = {2017},
volume = {},
number = {},
pages = {},
user = {backofen},
pmid = {28582575},
doi = {10.1093/nar/gkx409},
issn = {1362-4962},
issn = {0305-1048},
abstract = {RNA-based regulation has become a major research topic in
molecular biology. The analysis of epigenetic and expression
data is therefore incomplete if RNA-based regulation is not
taken into account. Thus, it is increasingly important but
not yet standard to combine RNA-centric data and analysis
tools with other types of experimental data such as RNA-seq
or ChIP-seq. Here, we present the RNA workbench, a
comprehensive set of analysis tools and consolidated
workflows that enable the researcher to combine these two
worlds. Based on the Galaxy framework the workbench
guarantees simple access, easy extension, flexible adaption
to personal and security needs, and sophisticated analyses
that are independent of command-line knowledge. Currently,
it includes more than 50 bioinformatics tools that are
dedicated to different research areas of RNA biology
including RNA structure analysis, RNA alignment, RNA
annotation, RNA-protein interaction, ribosome profiling,
RNA-seq analysis and RNA target prediction. The workbench is
developed and maintained by experts in RNA bioinformatics
and the Galaxy framework. Together with the growing
community evolving around this workbench, we are committed
to keep the workbench up-to-date for future standards and
needs, providing researchers with a reliable and robust
framework for RNA data analysis. AVAILABILITY: The RNA
workbench is available at
https://github.com/bgruening/galaxy-rna-workbench.}
}
@article{erxleben2011genome,
title={Genome sequence of Streptomyces sp. T{\"u}6071},
author={Erxleben, Anika and Wunsch-Palasis, Julia and Gr{\"u}ning, Bj{\"o}rn A and Luzhetska, Marta and Bechthold, Andreas and G{\"u}nther, Stefan},
journal={Journal of bacteriology},
pages={JB--00377},
year={2011},
publisher={American Society for Microbiology}
}
@article{gruning2011compounds,
title={Compounds In Literature (CIL): screening for compounds and relatives in PubMed},
author={Gr{\"u}ning, Bj{\"o}rn A and Senger, Christian and Erxleben, Anika and Flemming, Stephan and G{\"u}nther, Stefan},
journal={Bioinformatics},
volume={27},
number={9},
pages={1341--1342},
year={2011},
publisher={Oxford University Press}
}
@article{youssar2012genome,
title={Genome sequence of the fungus Glarea lozoyensis: the first genome sequence of a species from the Helotiaceae family},
author={Youssar, Loubna and Gr{\"u}ning, Bj{\"o}rn Andreas and Erxleben, Anika and G{\"u}nther, Stefan and H{\"u}ttel, Wolfgang},
journal={Eukaryotic cell},
volume={11},
number={2},
pages={250--250},
year={2012},
publisher={American Society for Microbiology}
}
@article{senger2012mining,
title={Mining and evaluation of molecular relationships in literature},
author={Senger, Christian and Gr{\"u}ning, Bj{\"o}rn A and Erxleben, Anika and D{\"o}ring, Kersten and Patel, Hitesh and Flemming, Stephan and Merfort, Irmgard and G{\"u}nther, Stefan},
journal={Bioinformatics},
volume={28},
number={5},
pages={709--714},
year={2012},
publisher={Oxford University Press}
}
@article{bieschke2011small,
title={Small-molecule conversion of toxic oligomers to nontoxic $\beta$-sheet--rich amyloid fibrils},
author={Bieschke, Jan and Herbst, Martin and Wiglenda, Thomas and Friedrich, Ralf P and Boeddrich, Annett and Schiele, Franziska and Kleckers, Daniela and del Amo, Juan Miguel Lopez and Gr{\"u}ning, Bj{\"o}rn A and Wang, Qinwen and others},
journal={Nature Chemical Biology},
volume={8},
number={1},
pages={93--101},
year={2011},
publisher={Nature Publishing Group}
}
@article{rother2008voronoia,
title={Voronoia: analyzing packing in protein structures},
author={Rother, Kristian and Hildebrand, Peter Werner and Goede, Andrean and Gruening, Bjoern and Preissner, Robert},
journal={Nucleic acids research},
volume={37},
number={suppl\_1},
pages={D393--D395},
year={2008},
publisher={Oxford University Press}
}
@article{hildebrand2009superlooper,
title={SuperLooper—a prediction server for the modeling of loops in globular and membrane proteins},
author={Hildebrand, Peter W and Goede, Andrean and Bauer, Raphael A and Gruening, Bjoern and Ismer, Jochen and Michalsky, Elke and Preissner, Robert},
journal={Nucleic acids research},
volume={37},
number={suppl\_2},
pages={W571--W574},
year={2009},
publisher={Oxford University Press}
}
@article{dunkel2008superscent,
title={SuperScent—a database of flavors and scents},
author={Dunkel, Mathias and Schmidt, Ulrike and Struck, Swantje and Berger, Lena and Gruening, Bjoern and Hossbach, Julia and Jaeger, Ines S and Effmert, Uta and Piechulla, Birgit and Eriksson, Roger and others},
journal={Nucleic acids research},
volume={37},
number={suppl\_1},
pages={D291--D294},
year={2008},
publisher={Oxford University Press}
}
@article{schmidt2008supertoxic,
title={SuperToxic: a comprehensive database of toxic compounds},
author={Schmidt, Ulrike and Struck, Swantje and Gruening, Bjoern and Hossbach, Julia and Jaeger, Ines S and Parol, Roza and Lindequist, Ulrike and Teuscher, Eberhard and Preissner, Robert},
journal={Nucleic acids research},
volume={37},
number={suppl\_1},
pages={D295--D299},
year={2008},
publisher={Oxford University Press}
}
@article{rose2009rhythm,
title={RHYTHM—a server to predict the orientation of transmembrane helices in channels and membrane-coils},
author={Rose, Alexander and Lorenzen, Stephan and Goede, Andrean and Gruening, Bj{\"o}rn and Hildebrand, Peter W},