Impact of high platelet turnover on the platelet transcriptome: Results from platelet RNA-sequencing in patients with sepsis.

Authors: Thomas G Nührenberg, Jasmin Stöckle, Federico Marini, Mark Zurek, Björn A Grüning, Vladimir Benes, Lutz Hein, Franz-Josef Neumann, Christian Stratz, Marco Cederqvist, Willibald Hochholzer

Source: PLoS ONE, Vol 17, Iss 1, p e0260222 (2022)

Subject Terms: Medicine, Science

File Description: electronic resource

Relation: https://doaj.org/toc/1932-6203

Access URL: https://doaj.org/article/412c81b9eb1f449180b7f6b5c9cd35d6

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

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

Source: PLoS Computational Biology, Vol 17, Iss 5, p e1008923 (2021)

Subject Terms: Biology (General), QH301-705.5

File Description: electronic resource

Relation: https://doaj.org/toc/1553-734X; https://doaj.org/toc/1553-7358

Access URL: https://doaj.org/article/2203f8fac2ff4349a06b32591ebcd459

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

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

Source: PLoS Computational Biology, Vol 13, Iss 5, p e1005425 (2017)

Subject Terms: Biology (General), QH301-705.5

File Description: electronic resource

Relation: http://europepmc.org/articles/PMC5444614?pdf=render; https://doaj.org/toc/1553-734X; https://doaj.org/toc/1553-7358

Access URL: https://doaj.org/article/b9ffb2544292468abd071231c8278d0e

PubMedPortable: A Framework for Supporting the Development of Text Mining Applications.

Authors: Kersten Döring, Björn A Grüning, Kiran K Telukunta, Philippe Thomas, Stefan Günther

Source: PLoS ONE, Vol 11, Iss 10, p e0163794 (2016)

Subject Terms: Medicine, Science

File Description: electronic resource

Relation: http://europepmc.org/articles/PMC5051953?pdf=render; https://doaj.org/toc/1932-6203

Access URL: https://doaj.org/article/2de02fd3fb974d1db4048e6d61629f80

5'-Hydroxymethylcytosine Precedes Loss of CpG Methylation in Enhancers and Genes Undergoing Activation in Cardiomyocyte Maturation.

Authors: David K Kranzhöfer, Ralf Gilsbach, Björn A Grüning, Rolf Backofen, Thomas G Nührenberg, Lutz Hein

Source: PLoS ONE, Vol 11, Iss 11, p e0166575 (2016)

Subject Terms: Medicine, Science

File Description: electronic resource

Relation: http://europepmc.org/articles/PMC5112848?pdf=render; https://doaj.org/toc/1932-6203

Access URL: https://doaj.org/article/40b536f07ff944f1a313b193bb66d2fa

Anatomy of BioJS, an open source community for the life sciences

Authors: Guy Yachdav, Tatyana Goldberg, Sebastian Wilzbach, David Dao, Iris Shih, Saket Choudhary, Steve Crouch, Max Franz, Alexander García, Leyla J García, Björn A Grüning, Devasena Inupakutika, Ian Sillitoe, Anil S Thanki, Bruno Vieira, José M Villaveces, Maria V Schneider, Suzanna Lewis, Steve Pettifer, Burkhard Rost, Manuel Corpas

Source: eLife, Vol 4 (2015)

Subject Terms: cutting edge, open source, JavaScript, community, bioinformatic, visualization, Medicine, Science, Biology (General), QH301-705.5

File Description: electronic resource

Relation: https://elifesciences.org/articles/07009; https://doaj.org/toc/2050-084X

Access URL: https://doaj.org/article/7fb5ebfc85a04bf98d4c2252c71b3442

Catching the Wave: Detecting Strain-Specific SARS-CoV-2 Peptides in Clinical Samples Collected during Infection Waves from Diverse Geographical Locations

Authors: Subina Mehta, Valdemir M. Carvalho, Andrew T. Rajczewski, Olivier Pible, Björn A. Grüning, James E. Johnson, Reid Wagner, Jean Armengaud, Timothy J. Griffin, Pratik D. Jagtap

Source: Viruses, Vol 14, Iss 10, p 2205 (2022)

Subject Terms: SARS-CoV-2, variant detection, strain-specific, mass-spectrometry, Microbiology, QR1-502

File Description: electronic resource

Relation: https://www.mdpi.com/1999-4915/14/10/2205; https://doaj.org/toc/1999-4915

Access URL: https://doaj.org/article/54b988d980714905b8379386a16a7840

Galaxy tools and workflows for sequence analysis with applications in molecular plant pathology

Authors: Peter J.A. Cock, Björn A. Grüning, Konrad Paszkiewicz, Leighton Pritchard

Source: PeerJ, Vol 1, p e167 (2013)

Subject Terms: Galaxy, Pipeline, Accessibility, Effector proteins, Workflow, Reproducibility, Medicine, Biology (General), QH301-705.5

File Description: electronic resource

Relation: https://peerj.com/articles/167.pdf; https://peerj.com/articles/167/; https://doaj.org/toc/2167-8359

Access URL: https://doaj.org/article/60ce2e01f069463d97796af9fa7ab979

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

Authors: Björn A. Grüning (Bioinformatics Group, Department of Computer Science, University of Freiburg), Jörg Fallmann (Bioinformatics Group, Department of Computer Science, and Interdisciplinary Center for Bioinformatics, University of Leipzig), Dilmurat Yusuf (Berlin Institute for Medical Systems Biology), Sebastian Will (Department of Theoretical Chemistry, Faculty of Chemistry, University of Vienna), Anika Erxleben (Bioinformatics Group, Department of Computer Science, University of Freiburg), Florian Eggenhofer (Bioinformatics Group, Department of Computer Science, University of Freiburg), Torsten Houwaart (Bioinformatics Group, Department of Computer Science, University of Freiburg), Bérénice Batut (Bioinformatics Group, Department of Computer Science, University of Freiburg), Pavankumar Videm (Bioinformatics Group, Department of Computer Science, University of Freiburg), Andrea Bagnacani (Department of Systems Biology and Bioinformatics, University of Rostock), Markus Wolfien (Department of Systems Biology and Bioinformatics, University of Rostock), Steffen C. Lott (Genetics and Experimental Bioinformatics, Faculty of Biology, University of Freiburg), Youri Hoogstrate (Department of Urology, Erasmus University Medical Center), Wolfgang R. Hess (Genetics and Experimental Bioinformatics, Faculty of Biology, University of Freiburg), Olaf Wolkenhauer (Department of Systems Biology and Bioinformatics, University of Rostock), Steve Hoffmann (Bioinformatics Group, Department of Computer Science, and Interdisciplinary Center for Bioinformatics, University of Leipzig), Altuna Akalin (Berlin Institute for Medical Systems Biology), Uwe Ohler (Berlin Institute for Medical Systems Biology), Peter F. Stadler (Department of Theoretical Chemistry, Faculty of Chemistry, University of Vienna), Rolf Backofen (Bioinformatics Group, Department of Computer Science, University of Freiburg)

Availability: http://data.europeana.eu/aggregation/europeana/1300/https___phaidra_univie_ac_at_o_907611

The Purchasable Chemical Space: A Detailed Picture.

Authors: Xavier Lucas¹, Björn A. Grüning¹, Stefan Bleher¹, Stefan Günther¹

Source: Journal of Chemical Information & Modeling; May2015, Vol. 55 Issue 5, p915-924, 10p

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

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

Source: Journal of Cheminformatics, Vol 12, Iss 1, Pp 1-13 (2020)

Subject Terms: Galaxy, Molecular Dynamics, Reproducible, Information technology, T58.5-58.64, Chemistry, QD1-999

File Description: electronic resource

Relation: http://link.springer.com/article/10.1186/s13321-020-00451-6; https://doaj.org/toc/1758-2946

Access URL: https://doaj.org/article/97899385994e41b0a076064064b6661b

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

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

Source: Journal of Cheminformatics, Vol 12, Iss 1, Pp 1-7 (2020)

Subject Terms: Cheminformatics, Protein-ligand docking, QSAR, Galaxy, Molecular dynamics, Information technology, T58.5-58.64, Chemistry, QD1-999

File Description: electronic resource

Relation: http://link.springer.com/article/10.1186/s13321-020-00442-7; https://doaj.org/toc/1758-2946

Access URL: https://doaj.org/article/44c41ccbe7794d758f00bf43872ae33e

High-resolution TADs reveal DNA sequences underlying genome organization in flies

Authors: Fidel Ramírez, Vivek Bhardwaj, Laura Arrigoni, Kin Chung Lam, Björn A. Grüning, José Villaveces, Bianca Habermann, Asifa Akhtar, Thomas Manke

Source: Nature Communications, Vol 9, Iss 1, Pp 1-15 (2018)

Subject Terms: Science

File Description: electronic resource

Relation: https://doaj.org/toc/2041-1723

Access URL: https://doaj.org/article/f48cef696c874fc680f5d90d7c13d700

Distinct epigenetic programs regulate cardiac myocyte development and disease in the human heart in vivo

Authors: Ralf Gilsbach, Martin Schwaderer, Sebastian Preissl, Björn A. Grüning, David Kranzhöfer, Pedro Schneider, Thomas G. Nührenberg, Sonia Mulero-Navarro, Dieter Weichenhan, Christian Braun, Martina Dreßen, Adam R. Jacobs, Harald Lahm, Torsten Doenst, Rolf Backofen, Markus Krane, Bruce D. Gelb, Lutz Hein

Source: Nature Communications, Vol 9, Iss 1, Pp 1-14 (2018)

Subject Terms: Science

File Description: electronic resource

Relation: https://doaj.org/toc/2041-1723

Access URL: https://doaj.org/article/e46b79bc29434dea9a7d59690c85ee94

DNA methylation signatures follow preformed chromatin compartments in cardiac myocytes

Authors: Stephan Nothjunge, Thomas G. Nührenberg, Björn A. Grüning, Stefanie A. Doppler, Sebastian Preissl, Martin Schwaderer, Carolin Rommel, Markus Krane, Lutz Hein, Ralf Gilsbach

Source: Nature Communications, Vol 8, Iss 1, Pp 1-9 (2017)

Subject Terms: Science

File Description: electronic resource

Relation: https://doaj.org/toc/2041-1723

Access URL: https://doaj.org/article/8b3e486861b4468d9a0816e1f96f830b

Characterization and phylogenetic analysis of the mitochondrial genome of Glarea lozoyensis indicates high diversity within the order Helotiales.

Authors: Loubna Youssar, Björn Andreas Grüning, Stefan Günther, Wolfgang Hüttel

Source: PLoS ONE, Vol 8, Iss 9, p e74792 (2013)

Subject Terms: Medicine, Science

File Description: electronic resource

Relation: http://europepmc.org/articles/PMC3783487?pdf=render; https://doaj.org/toc/1932-6203

Access URL: https://doaj.org/article/becc09b8607b48a5b0e1c737ea528e7e