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List of works by Björn A Grüning

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

scientific article

A proteomics sample metadata representation for multiomics integration and big data analysis

scientific article published in 2021

A single-cell RNA-sequencing training and analysis suite using the Galaxy framework

scientific article published on 01 October 2020

Accessible and reproducible mass spectrometry imaging data analysis in Galaxy

scientific article published on 01 December 2019

Alteration of the Route to Menaquinone towards Isochorismate-Derived Metabolites

scientific article published on 24 May 2019

An Accessible Proteogenomics Informatics Resource for Cancer Researchers

scientific article published on November 2017

An NGS Workflow Blueprint for DNA Sequencing Data and Its Application in Individualized Molecular Oncology.

scientific article

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

scientific article

Autosomal dominant immune dysregulation syndrome in humans with CTLA4 mutations

scientific article

BioContainers Registry: Searching Bioinformatics and Proteomics Tools, Packages, and Containers

scientific article published on 24 February 2021

BioContainers: An open-source and community-driven framework for software standardization

scientific article

BioHackEU22 Report: Enhancing Research Data Management in Galaxy and Data Stewardship Wizard by utilising RO-Crates

Bioconda

scientific article published on 01 July 2018

Bioconda: sustainable and comprehensive software distribution for the life sciences

scientific article published on 01 July 2018

Biomolecular Reaction and Interaction Dynamics Global Environment (BRIDGE)

scientific article published on 01 September 2019

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

scientific article

ChemicalToolBoX and its application on the study of the drug like and purchasable space.

scientific article published on 11 March 2014

Community-Driven Data Analysis Training for Biology

scientific article published on 01 June 2018

Community-driven ELIXIR activities in single-cell omics

scientific article published on 29 July 2022

Compounds In Literature (CIL): screening for compounds and relatives in PubMed.

scientific article published on 16 March 2011

DNA methylation signatures follow preformed chromatin compartments in cardiac myocytes

scientific article published on 21 November 2017

DOT1L Activity Promotes Proliferation and Protects Cortical Neural Stem Cells from Activation of ATF4-DDIT3-Mediated ER Stress In Vitro

scientific article published on 24 August 2015

Deciphering the Epigenetic Code of Cardiac Myocyte Transcription.

scientific article

Decitabine induces gene derepression on monosomic chromosomes: in vitro and in vivo effects in adverse-risk cytogenetics AML

scientific article published on 17 November 2020

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

scientific article

Draft Genome Sequence of Streptomyces viridochromogenes Strain Tu57, Producer of Avilamycin.

scientific article published on 20 June 2013

Dynamic DNA methylation orchestrates cardiomyocyte development, maturation and disease.

scientific article

Dynamic information system for small molecules.

scientific article published on 11 March 2014

EBF1 binds to EBNA2 and promotes the assembly of EBNA2 chromatin complexes in B cells.

scientific article published on 2 October 2017

ENASearch: A Python library for interacting with ENA's API

scientific article published on 25 October 2017

Echinocandin B biosynthesis: a biosynthetic cluster from Aspergillus nidulans NRRL 8112 and reassembly of the subclusters Ecd and Hty from Aspergillus pachycristatus NRRL 11440 reveals a single coherent gene cluster ⬇️

scientific article

Enhancing pre-defined workflows with ad hoc analytics using Galaxy, Docker and Jupyter

Enhancing the image analysis community in Galaxy

Ewastools: Infinium Human Methylation BeadChip pipeline for population epigenetics integrated into Galaxy

scientific article published on 01 May 2020

Expanding the Galaxy's reference data

publication published on 29 April 2022

Four simple recommendations to encourage best practices in research software

scientific article

Freely accessible ready to use global infrastructure for SARS-CoV-2 monitoring

scientific article

GLASSGo in Galaxy: high-throughput, reproducible and easy-to-integrate prediction of sRNA homologs

scientific article published on 03 June 2020

GRIN3B missense mutation as an inherited risk factor for schizophrenia: whole-exome sequencing in a family with a familiar history of psychotic disorders.

scientific article published on 30 January 2017

Galaxy HiCExplorer 3: a web server for reproducible Hi-C, capture Hi-C and single-cell Hi-C data analysis, quality control and visualization

scientific article published on 17 April 2020

Galaxy HiCExplorer: a web server for reproducible Hi-C data analysis, quality control and visualization

scientific article published in July 2018

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

scientific article published on 17 September 2013

Galaxy-ML: An accessible, reproducible, and scalable machine learning toolkit for biomedicine

scientific article published on 01 June 2021

Genome Sequence of the Fungus Glarea lozoyensis: the First Genome Sequence of a Species from the Helotiaceae Family

scientific article

Genome Sequence of the Fungus Glarea lozoyensis: the First Genome Sequence of a Species from the Helotiaceae Family.

scientific article

Genome sequence of Streptomyces sp. strain Tü6071.

scientific article published on 24 June 2011

GraphClust2: Annotation and discovery of structured RNAs with scalable and accessible integrative clustering

scientific article published on 01 December 2019

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

scientific article published on 15 January 2018

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

scientific article published on 10 September 2020

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

scientific article

Metaproteomics Analysis of SARS-CoV-2-Infected Patient Samples Reveals Presence of Potential Coinfecting Microorganisms

scientific article published on 04 January 2021

MicroRNA Profiling in Aqueous Humor of Individual Human Eyes by Next-Generation Sequencing.

scientific article

Mining and evaluation of molecular relationships in literature

scientific article published on 13 January 2012

NCBI BLAST+ integrated into Galaxy

scientific article published on 21 January 2015

NCBI BLAST+ integrated into Galaxy.

scientific article published on 25 August 2015

NanoGalaxy: Nanopore long-read sequencing data analysis in Galaxy

scientific article published on 01 October 2020

No more business as usual: Agile and effective responses to emerging pathogen threats require open data and open analytics

scientific article published on 13 August 2020

PLANTdataHUB: a collaborative platform for continuous FAIR data sharing in plant research

scientific article published on 11 October 2023

Packaging research artefacts with RO-Crate

scientific article published on 20 July 2022

Pluripotency factors determine gene expression repertoire at zygotic genome activation

scientific article published on 10 February 2022

Pou5f3, SoxB1, and Nanog remodel chromatin on high nucleosome affinity regions at zygotic genome activation

scientific article published on 23 January 2019

Practical Computational Reproducibility in the Life Sciences

scientific article published on 01 June 2018

Practical computational reproducibility in the life sciences

scientific article published on 10 October 2017

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

scientific article

PyWATER: a PyMOL plug-in to find conserved water molecules in proteins by clustering.

scientific article

RNA-bioinformatics: Tools, services and databases for the analysis of RNA-based regulation

scientific article

ReGaTE: Registration of Galaxy Tools in Elixir.

scientific article published on 10 April 2017

Recent advances in RNA folding

scientific article

Recommendations for the packaging and containerizing of bioinformatics software

scientific article published on 14 June 2018

Regio- and Stereoselective Intermolecular Oxidative Phenol Coupling in Streptomyces

scientific article published on 18 April 2014

Scool: a new data storage format for single-cell Hi-C data

scientific article published on 02 November 2020

Small-molecule conversion of toxic oligomers to nontoxic β-sheet-rich amyloid fibrils

scientific article

Software engineering for scientific big data analysis

scientific article published on 01 May 2019

Strategies for analyzing bisulfite sequencing data

scientific article

StreptomeDB: a resource for natural compounds isolated from Streptomyces species

scientific article

SuperLooper--a prediction server for the modeling of loops in globular and membrane proteins

scientific article published on 8 May 2009

SuperScent--a database of flavors and scents

scientific article published on 17 October 2008

SuperToxic: a comprehensive database of toxic compounds

scientific article

Survey of metaproteomics software tools for functional microbiome analysis

scientific article published on 10 November 2020

Ten simple rules for making a software tool workflow-ready

scientific article published on 24 March 2022

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

scientific article published in June 2020

The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2016 update

scientific article

The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2018 update.

scientific article published in July 2018

The Galaxy platform for accessible, reproducible, and collaborative data analyses: 2024 update

scientific article published on 20 May 2024

The RNA workbench 2.0: next generation RNA data analysis

scientific article published on 01 July 2019

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

scientific article published on 05 June 2017

The bio.tools registry of software tools and data resources for the life sciences

article

The de.NBI / ELIXIR-DE training platform - Bioinformatics training in Germany and across Europe within ELIXIR

scientific article published on 07 November 2019

The omics discovery REST interface

scientific article published on 06 May 2020

The purchasable chemical space: a detailed picture.

scientific article published on 30 April 2015

Tool recommender system in Galaxy using deep learning

scientific article published on 01 January 2021

Tools and data services registry: a community effort to document bioinformatics resources

scientific article

Toxicity versus potency: elucidation of toxicity properties discriminating between toxins, drugs, and natural compounds

scientific article published in January 2008

Training Infrastructure as a Service

scientific article published on 28 December 2022

Ultrastructural, transcriptional and functional differences between human reticulated and non-reticulated platelets

scientific article published on 19 May 2020

Uncontrolled Diabetes Mellitus Has No Major Influence on the Platelet Transcriptome

scientific article published on 01 November 2018

Update on the moFF Algorithm for Label-Free Quantitative Proteomics

scientific article published on 14 December 2018

User-friendly, scalable tools and workflows for single-cell RNA-seq analysis

scientific article

Voronoia: analyzing packing in protein structures

scientific article published on 23 October 2008

blast2galaxy: a CLI and Python API for BLAST+ and DIAMOND searches on Galaxy servers

scientific article published in 2024

deepTools2: a next generation web server for deep-sequencing data analysis

scientific article

deepTools: a flexible platform for exploring deep-sequencing data.

scientific article

pyGenomeTracks: reproducible plots for multivariate genomic data sets

scientific article published on 03 August 2020

uORF-Tools-Workflow for the determination of translation-regulatory upstream open reading frames

scientific article published on 12 September 2019

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