BG
Björn Grüning
SoftwarebioinformaticsGalaxyComputational BiologygenomicsreproducibilityCOVID-19Databases, FactualGenomicsproteomics
On Valency
published · living versionsW_xbcpb9k9·v1 · currentpublished
3Dtrees.earth: community research infrastructure for tree and forest analysis using close-range LiDAR data
with Janusch Vajna-Jehle, Kilian Gerberding, Daniel Lusk, Teja Kattenborn +273
1 version
Preprints & journals
151 papers in the corpus · 1969–2026SIMORGH: Ensemble-Aware Geometric Deep Learning for Apo-State and Cryptic Ligand Binding Site Prediction10.64898/2026.10.02.756215v1 · Mokhtari, O., Naghsh Nilchi, A., Grüning, B. et al.2026 · 0 citationsbioRxiv
Bioimage management and analysis in Galaxy: Tools, workflows, training, and community practices.42709042 · Kostrykin, Leonid, Massei, Riccardo, Chiang, Diana et al.2026 · 0 citationsJournal of microscopy. 2026
LiraSearch-ultrafast ligand shape and electrostatic matching server.42222671 · Montalvão, Rinaldo W, Bray, Simon, Veríssimo-Alves, Marcos et al.2026 · 0 citationsBioinformatics advances. 2026;6(1):vbag139
Machine learning-based prediction of memory requirements for metagenomic assembly in high-performance computing environments10.64898/2026.05.12.724571v1 · Zierep, P. F., Faack, S., Beracochea, M. et al.2026 · 0 citationsbioRxiv
Sub-pixel mapping of disturbance and tree mortality dynamics from Sentinel-2 time series around the globex5b18w · Clemens Mosig, Teja Kattenborn, David Montero Loaiza et al.2026 · 4 citationsEarthArXiv
Ten common misconceptions about Galaxy (and why they are wrong!).41701727 · Bacon, Wendi Anne, Batut, Bérénice, Srikakulam, Sanjay Kumar et al.2026 · 4 citationsPLoS computational biology. 2026;22(2):e1013869
Prioritizing DNA methylation biomarkers using graph neural networks and explainable AI10.64898/2026.01.26.701692v1 · Kumar, A., Do, T. A., Gruening, B. et al.2026 · 0 citationsbioRxiv
Chamber-specific chromatin architecture guides functional interpretation of disease-associated Cis-regulatory elements in human cardiomyocytes.41526351 · Haydar, S, Bednarz, R, Laurette, P et al.2026 · 2 citationsNature communications. 2026;17(1):117
Standardizing RNA-seq Analysis of Fungal Pathogens Using BRC-Analytics and Agentic AI: A Candidozyma auris Case Study.41509213 · Nekrutenko, Anton, Callan, Danielle, Van Den Beek, Marius et al.2026 · 0 citationsbioRxiv : the preprint server for biology. 2025
Fibroblast growth factor signaling induces a chondrocyte-like state of peripheral nerve fibroblast during aging.41238529 · Stefanovska, Dragana, Sassu, Eliza, Tekman, Mehmet et al.2025 · 0 citationsNature communications. 2025;16(1):10020
From data to publication in a browser with BRC-Analytics: Evolutionary dynamics of coding overlaps in measles virus.41279440 · Nekrutenko, Anton, Callan, Danielle, Van Den Beek, Marius et al.2025 · 2 citationsbioRxiv : the preprint server for biology. 2025
Galaxy single-cell & spatial omics community update: Navigating new frontiers in 2025.40997812 · Loach, Marisa, Naghsh Nilchi, Amirhossein, Chiang, Diana et al.2025 · 7 citationsCell genomics. 2025;5(10):101005
Microbiology Galaxy Lab: The first community-driven gateway for reproducible and FAIR analysis of microbial data.39764050 · Nasr, Engy, Pechlivanis, Nikos, Strepis, Nikolaos et al.2025 · 5 citationsbioRxiv : the preprint server for biology. 2025
Flexynesis: A deep learning toolkit for bulk multi-omics data integration for precision oncology and beyond.40940333 · Uyar, Bora, Savchyn, Taras, Naghsh Nilchi, Amirhossein et al.2025 · 15 citationsNature communications. 2025;16(1):8261
varVAMP: degenerate primer design for tiled full genome sequencing and qPCR.40449995 · Fuchs, Jonas, Kleine, Johanna, Schemmerer, Mathias et al.2025 · 8 citationsNature communications. 2025;16(1):5067
An Ecosystem of Services for FAIR Computational Workflows2505.15988v2 · Sean R. Wilkinson, Johan Gustafsson, Finn Bacall et al.2025 · 0 citationsarXiv
WorkflowHub: a registry for computational workflows.40399296 · Gustafsson, Ove Johan Ragnar, Wilkinson, Sean R, Bacall, Finn et al.2025 · 50 citationsScientific data. 2025;12(1):837
Open-Source and FAIR Research Software for Proteomics.40267229 · Perez-Riverol, Yasset, Bittremieux, Wout, Noble, William S et al.2025 · 21 citationsJournal of proteome research. 2025;24(5):2222-2234
Guidance framework to apply best practices in ecological data analysis: lessons learned from building Galaxy-Ecology.39937595 · Royaux, Coline, Mihoub, Jean-Baptiste, Jossé, Marie et al.2025 · 9 citationsGigaScience. 2025;14
PathoGFAIR: a collection of FAIR and adaptable (meta)genomics workflows for (foodborne) pathogens detection and tracking.41004266 · Nasr, Engy, Henger, Anna, Grüning, Björn et al.2025 · 5 citationsGigaScience. 2025;14
blast2galaxy: a CLI and Python API for BLAST+ and DIAMOND searches on Galaxy servers.39659591 · König, Patrick, Fiebig, Anne, Münch, Thomas et al.2024 · 2 citationsBioinformatics advances. 2024;4(1):vbae185
Author Correction: The European Reference Genome Atlas: piloting a decentralised approach to equitable biodiversity genomics.39407030 · Mc Cartney, Ann M, Formenti, Giulio, Mouton, Alice et al.2024 · 2 citationsnpj biodiversity. 2024;3(1):31
The European Reference Genome Atlas: piloting a decentralised approach to equitable biodiversity genomics.39289538 · Mc Cartney, Ann M, Formenti, Giulio, Mouton, Alice et al.2025 · 64 citationsnpj biodiversity. 2024;3(1):28
varVAMP: automated pan-specific primer design for tiled full genome sequencing and qPCR of highly diverse viral pathogens.10.1101/2024.05.08.593102v1 · Fuchs, J., Kleine, J., Schemmerer, M. et al.2024 · 4 citationsbioRxiv
DIMet: an open-source tool for differential analysis of targeted isotope-labeled metabolomics data.38656970 · Galvis, Johanna, Guyon, Joris, Dartigues, Benjamin et al.2024 · 3 citationsBioinformatics (Oxford, England). 2024;40(5)
Mobilisation and analyses of publicly available SARS-CoV-2 data for pandemic responses.38358325 · Rahman, Nadim, O'Cathail, Colman, Zyoud, Ahmad et al.2024 · 11 citationsMicrobial genomics. 2024;10(2)
Right-sizing compute resource allocations for bioinformatics tools with Total Perspective Vortex2312.02060v1 · Nuwan Goonasekera, Catherine Bromhead, Simon Gladman et al.2023 · 0 citationsarXiv
Transformer-based tool recommendation system in Galaxy.38012574 · Kumar, Anup, Grüning, Björn, Backofen, Rolf2023 · 5 citationsBMC bioinformatics. 2023;24(1):446
"Be sustainable": EOSC-Life recommendations for implementation of FAIR principles in life science data handling.37964598 · David, Romain, Rybina, Arina, Burel, Jean-Marie et al.2023 · 31 citationsThe EMBO journal. 2023;42(23):e115008
PLANTdataHUB: a collaborative platform for continuous FAIR data sharing in plant research.37818860 · Weil, Heinrich Lukas, Schneider, Kevin, Tschöpe, Marcel et al.2023 · 50 citationsThe Plant journal : for cell and molecular biology. 2023;116(4):974-988
Activator-blocker model of transcriptional regulation by pioneer-like factors.37709752 · Riesle, Aileen Julia, Gao, Meijiang, Rosenblatt, Marcus et al.2023 · 17 citationsNature communications. 2023;14(1):5677
Integrative meta-omics in Galaxy and beyond.37420292 · Schiml, Valerie C, Delogu, Francesco, Kumar, Praveen et al.2024 · 20 citationsEnvironmental microbiome. 2023;18(1):56
Scalable, accessible, and reproducible reference genome assembly and evaluation in Galaxy.37425881 · Larivière, Delphine, Abueg, Linelle, Brajuka, Nadolina et al.2024 · 74 citationsbioRxiv : the preprint server for biology. 2023
A comparative gene expression matrix in Apoe-deficient mice identifies unique and atherosclerotic disease stage-specific gene regulation patterns in monocytes and macrophages.36940535 · Härdtner, Carmen, Kumar, Anup, Ehlert, Carolin A et al.2023 · 11 citationsAtherosclerosis. 2023;371:1-13
The Planemo toolkit for developing, deploying, and executing scientific data analyses in Galaxy and beyond.36828587 · Bray, Simon, Chilton, John, Bernt, Matthias et al.2023 · 14 citationsGenome research. 2023;33(2):261-268
Galaxy Training: A powerful framework for teaching!36622853 · Hiltemann, Saskia, Rasche, Helena, Gladman, Simon et al.2023 · 114 citationsPLoS computational biology. 2023;19(1):e1010752
An accessible infrastructure for artificial intelligence using a Docker-based JupyterLab in Galaxy.37099385 · Kumar, Anup, Cuccuru, Gianmauro, Grüning, Björn et al.2023 · 6 citationsGigaScience. 2022;12
Training Infrastructure as a Service.37395629 · Rasche, Helena, Hyde, Cameron, Davis, John et al.2023 · 8 citationsGigaScience. 2022;12
Catching the Wave: Detecting Strain-Specific SARS-CoV-2 Peptides in Clinical Samples Collected during Infection Waves from Diverse Geographical Locations.36298760 · Mehta, Subina, Carvalho, Valdemir M, Rajczewski, Andrew T et al.2022 · 1 citationViruses. 2022;14(10)
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.35995769 · Meier, Ruth, Greve, Gabriele, Zimmer, Dennis et al.2022 · 22 citationsBlood cancer journal. 2022;12(8):122
A Web-based Software Resource for Interactive Analysis of Multiplex Tissue Imaging Datasets10.1101/2022.08.18.504436v3 · Creason, A. L., Watson, C., Gu, Q. et al.2022 · 8 citationsbioRxiv
Loop detection using Hi-C data with HiCExplorer.35809047 · Wolff, Joachim, Backofen, Rolf, Grüning, Björn2022 · 78 citationsGigaScience. 2022;11
MaxQuant and MSstats in Galaxy Enable Reproducible Cloud-Based Analysis of Quantitative Proteomics Experiments for Everyone.35503992 · Pinter, Niko, Glätzer, Damian, Fahrner, Matthias et al.2022 · 22 citationsJournal of proteome research. 2022;21(6):1558-1565
Expanding the Galaxy's reference data.35669346 · VijayKrishna, Nagampalli, Joshi, Jayadev, Coraor, Nate et al.2025 · 4 citationsBioinformatics advances. 2022;2(1):vbac030
Galaxy workflows for fragment-based virtual screening: a case study on the SARS-CoV-2 main protease.35414112 · Bray, Simon, Dudgeon, Tim, Skyner, Rachael et al.2022 · 8 citationsJournal of cheminformatics. 2022;14(1):22
Selection Analysis Identifies Clusters of Unusual Mutational Changes in Omicron Lineage BA.1 That Likely Impact Spike Function.35325204 · Martin, Darren P, Lytras, Spyros, Lucaci, Alexander G et al.2022 · 116 citationsMolecular biology and evolution. 2022;39(4)
Ten simple rules for making a software tool workflow-ready.35324885 · Brack, Paul, Crowther, Peter, Soiland-Reyes, Stian et al.2022 · 18 citationsPLoS computational biology. 2022;18(3):e1009823
Planemo: a command-line toolkit for developing, deploying, and executing scientific data analyses10.1101/2022.03.13.483965v1 · Bray, S., Bernt, M., Soranzo, N. et al.2022 · 2 citationsbioRxiv
Democratizing data-independent acquisition proteomics analysis on public cloud infrastructures via the Galaxy framework.35166338 · Fahrner, Matthias, Föll, Melanie Christine, Grüning, Björn Andreas et al.2022 · 13 citationsGigaScience. 2022;11
Pluripotency factors determine gene expression repertoire at zygotic genome activation.35145080 · Gao, Meijiang, Veil, Marina, Rosenblatt, Marcus et al.2022 · 31 citationsNature communications. 2022;13(1):788
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