Björn Grüning
A5006559585- Scientific Computing and Data Management
- Research Data Management Practices
- Genetics, Bioinformatics, and Biomedical Research
- Genomics and Phylogenetic Studies
- Cancer Genomics and Diagnostics
- Genomics and Chromatin Dynamics
- Advanced Proteomics Techniques and Applications
- RNA modifications and cancer
- Distributed and Parallel Computing Systems
- Cell Image Analysis Techniques
- Epigenetics and DNA Methylation
- RNA and protein synthesis mechanisms
- Gene expression and cancer classification
- Single-cell and spatial transcriptomics
- Biomedical Text Mining and Ontologies
- Computational Drug Discovery Methods
- Bioinformatics and Genomic Networks
- RNA Research and Splicing
- CRISPR and Genetic Engineering
- Microbial Natural Products and Biosynthesis
- Chromosomal and Genetic Variations
- SARS-CoV-2 and COVID-19 Research
- Cancer-related molecular mechanisms research
- Astronomy and Astrophysical Research
- Molecular Biology Techniques and Applications
University of Freiburg
2016-2025
Kohler (New Zealand)
2019-2022
Life & Brain (Germany)
2015
University of Bonn
2015
We present an update to our Galaxy-based web server for processing and visualizing deeply sequenced data. Its core tool set, deepTools, allows users perform complete bioinformatic workflows ranging from quality controls normalizations of aligned reads integrative analyses, including clustering visualization approaches. Since we first described deepTools Galaxy in 2014, have implemented new solutions many requests the community users. Here, introduce significant enhancements tools further...
Galaxy (homepage: https://galaxyproject.org, main public server: https://usegalaxy.org) is a web-based scientific analysis platform used by tens of thousands scientists across the world to analyze large biomedical datasets such as those found in genomics, proteomics, metabolomics and imaging. Started 2005, continues focus on three key challenges data-driven science: making analyses accessible all researchers, ensuring are completely reproducible, it simple communicate so that they can be...
We present a Galaxy based web server for processing and visualizing deeply sequenced data. The server's core functionality consists of suite newly developed tools, called deepTools, that enable users with little bioinformatic background to explore the results their sequencing experiments in standardized setting. Users can upload pre-processed files continuous data standard formats generate heatmaps summary plots straight-forward, yet highly customizable manner. In addition, we offer several...
High-throughput data production technologies, particularly 'next-generation' DNA sequencing, have ushered in widespread and disruptive changes to biomedical research. Making sense of the large datasets produced by these technologies requires sophisticated statistical computational methods, as well substantial power. This has led an acute crisis life sciences, researchers without informatics training attempt perform computation-dependent analyses. Since 2005, Galaxy project worked address...
Galaxy is a mature, browser accessible workbench for scientific computing. It enables scientists to share, analyze and visualize their own data, with minimal technical impediments. A thriving global community continues use, maintain contribute the project, support from multiple national infrastructure providers that enable freely analysis training services. The Training Network supports free, self-directed, virtual >230 integrated tutorials. Project engagement metrics have continued grow...
Despite an abundance of new studies about topologically associating domains (TADs), the role genetic information in TAD formation is still not fully understood. Here we use our software, HiCExplorer (hicexplorer.readthedocs.io) to annotate >2800 high-resolution (570 bp) boundaries Drosophila melanogaster. We identify eight DNA motifs enriched at boundaries, including a motif bound by M1BP protein, and two boundary motifs. In contrast mammals, CTCF only on small fraction flanking inactive...
BioContainers (biocontainers.pro) is an open-source and community-driven framework which provides platform independent executable environments for bioinformatics software. allows labs of all sizes to easily install software, maintain multiple versions the same software combine tools into powerful analysis pipelines. based on popular projects Docker rkt frameworks, that allow be installed executed under isolated controlled environment. Also, it infrastructure basic guidelines create, manage...
Abstract Motivation Generating publication ready plots to display multiple genomic tracks can pose a serious challenge. Making desirable and accurate figures requires considerable effort. This is usually done by hand or using vector graphic software. Results pyGenomeTracks (PGT) modular plotting tool that easily combines tracks. It enables reproducible standardized generation of highly customizable images. Availability implementation PGT available through graphical interface on...
Abstract The heart is a highly specialized organ with essential function for the organism throughout life. significance of DNA methylation in shaping phenotype remains only partially known. Here we generate and analyse methylomes from purified cardiomyocytes neonatal, adult healthy failing hearts. We identify large genomic regions that are differentially methylated during cardiomyocyte development maturation. Demethylation gene bodies correlates strongly increased expression. Silencing...
The Galaxy HiCExplorer provides a web service at https://hicexplorer.usegalaxy.eu. It enables the integrative analysis of chromosome conformation by providing tools and computational resources to pre-process, analyse visualize Hi-C, Capture Hi-C (cHi-C) single-cell (scHi-C) data. Since last publication, has been expanded considerably with new facilitate cHi-C provide an in-depth Moreover, it supports scHi-C data offering broad range tools. With help standard graphical user interface Galaxy,...
The NCBI BLAST suite has become ubiquitous in modern molecular biology and is used for small tasks such as checking capillary sequencing results of single PCR products, genome annotation or even larger scale pan-genome analyses. For early adopters the Galaxy web-based biomedical data analysis platform, integrating into was a natural step sequence comparison workflows.The command line BLAST+ tool wrapped use within Galaxy. Appropriate datatypes were defined needed. integration goal making...
Galaxy HiCExplorer is a web server that facilitates the study of 3D conformation chromatin by allowing Hi-C data processing, analysis and visualization. With server, users with little bioinformatic background can perform every step in one workflow: mapping raw sequence data, creation contact matrices, quality assessment, correction matrices identification topological associated domains (TADs) A/B compartments. Users create publication ready plots matrix, compartments, TADs on selected...
Epigenetic mechanisms and transcription factor networks essential for differentiation of cardiac myocytes have been uncovered. However, reshaping the epigenome these terminally differentiated cells during fetal development, postnatal maturation, in disease remains unknown. Here, we investigate dynamics myocyte development chronic heart failure. We find that prenatal maturation are characterized by a cooperation active CpG methylation histone marks at cis-regulatory genic regions to shape...
The primary problem with the explosion of biomedical datasets is not data, computational resources, and required storage space, but general lack trained skilled researchers to manipulate analyze these data. Eliminating this requires development comprehensive educational resources. Here we present a community-driven framework that enables modern, interactive teaching data analytics in life sciences facilitates training materials. key feature our system it static continuously improved...
Abstract Galaxy (https://galaxyproject.org) is deployed globally, predominantly through free-to-use services, supporting user-driven research that broadens in scope each year. Users are attracted to public services by platform stability, tool and reference dataset diversity, training, support integration, which enables complex, reproducible, shareable data analysis. Applying the principles of user experience design (UXD), has driven improvements accessibility, discoverability...
An increasing number of researchers support reproducibility by including pointers to and descriptions datasets, software methods in their publications. However, scientific articles may be ambiguous, incomplete difficult process automated systems. In this paper we introduce RO-Crate, an open, community-driven, lightweight approach packaging research artefacts along with metadata a machine readable manner. RO-Crate is based on Schema$.$org annotations JSON-LD, aiming establish best practices...
Among the 30 nonsynonymous nucleotide substitutions in Omicron S-gene are 13 that have only rarely been seen other SARS-CoV-2 sequences. These mutations cluster within three functionally important regions of at sites will likely impact (1) interactions between subunits Spike trimer and predisposition to shift from down up configurations, (2) with ACE2 receptors, (3) priming for membrane fusion. We show here that, based on both rarity these intrapatient sequencing reads patterns selection...
There is an ongoing explosion of scientific datasets being generated, brought on by recent technological advances in many areas the natural sciences. As a result, life sciences have become increasingly computational nature, and bioinformatics has taken central role research studies. However, basic skills, data analysis, stewardship are still rarely taught science educational programs, resulting skills gap researchers tasked with analysing these big datasets. In order to address this empower...
The Galaxy Project offers the popular web browser-based platform for running bioinformatics tools and constructing simple workflows. Here, we present a broad collection of additional large scale analysis gene protein sequences. motivating research theme is identification specific genes interest in range non-model organisms, our central example prediction "effector" proteins produced by plant pathogens order to manipulate their host plant. This functional annotation pathogen's predicted...
Life sciences are yielding huge data sets that underpin scientific discoveries fundamental to improvement in human health, agriculture and the environment. In support of these discoveries, a plethora databases tools deployed, technically complex diverse implementations, across spectrum disciplines. The corpus documentation resources is fragmented Web, with much redundancy, has lacked common standard information. outcome scientists must often struggle find, understand, compare use best for...