Björn Andreas Grüning

This study shows that publishing software in package management systems increases its cited scholarly papers by 280%.

The paper introduces a Galaxy-based suite for scRNA-seq analysis, offering workflows, training resources, and tools for preprocessing, normalization, and clustering across 10x and alternative platforms.

The paper highlights the importance of open data and analytics in responding to public health emergencies, using COVID-19 genomic data to demonstrate the effectiveness of community-driven software tools and infrastructure.

This study uses direct RNA sequencing to identify RNA modifications in SARS-CoV-2 isolated from human lung cells, revealing conserved modification patterns across isolates.

The paper introduces the OmicsDI REST interface for programmatic access to omics datasets and provides R and Python libraries for interacting with the API.

The paper introduces an approximate k-nearest neighbors method using MinHash to reduce the dimensionality of single-cell Hi-C data, enabling efficient clustering of large datasets.

The paper integrates mass spectrometry imaging tools into Galaxy to enable accessible, reproducible, and transparent analysis of MSI data.

GraphClust2 improves RNA clustering and annotation by integrating sequence and structural data, revealing conserved structures in long non-coding RNAs and targets of Roquin-1.

The paper introduces a workflow for identifying functional upstream open reading frames (uORFs) using ribosome profiling data and provides a human uORF annotation file.

EWAS-Galaxy provides a user-friendly tool suite for DNA methylation analysis using the Infinium Methylation Assay, integrated into the Galaxy platform.

The paper investigates how Pou5f3, SoxB1, and Nanog influence chromatin remodeling at High Nucleosome Affinity Regions during Zygotic Genome Activation in zebrafish.

Parkour is a web-based software package for managing next generation sequencing sample preparation workflows, improving efficiency and quality through automated tracking and staff assignment.

The paper presents technologies that make computational reproducibility practical by integrating package management, containerization, and workflow systems.

The paper presents a community-driven framework for interactive data analytics training in life sciences, enabling researchers to learn through web-based computation without software installation.

This study examines the dynamics of the cardiac myocyte epigenome during development and in chronic heart failure, revealing distinct epigenetic programs in health and disease.

The paper identifies DNA motifs at TAD boundaries in flies and shows they encode 3D genome architecture, with an online database for exploration.

This paper reviews techniques and software for analyzing bisulfite sequencing data, focusing on quality checks, differential methylation, segmentation, and annotation methods.

The paper describes a hybrid platform integrating predefined workflows with ad hoc analytics to simplify and reproduce the raw data-to-publication process in biomedical research.