Daniel J Blankenberg

Microbiology Galaxy Lab: The first community-driven gateway for reproducible and FAIR analysis of microbial data

The paper introduces the Microbiology Galaxy Lab, a community-driven platform for reproducible and FAIR microbial data analysis, offering tools for various omics data types and use cases.

Mechanistic prediction of fecal microbiota transplant engraftment and Clostridioides difficile colonization resistance with μODE

This paper introduces muODE, a framework that simulates microbial community dynamics using metagenomics data to predict FMT outcomes and C. difficile resistance.

GalaxyMemMD: an end-to-end Galaxy toolset for reproducible membrane embedding, molecular dynamics simulation, and analysis of membrane proteins

GalaxyMemMD provides a reproducible, high-throughput pipeline for membrane protein simulation and analysis, integrating embedding, MD simulation, and downstream analysis.

HyperSketch: de Bruijn graph sketching for genomic similarity estimation with Hyperdimensional Computing

HyperSketch provides a structure-aware genomic similarity method using de Bruijn graphs and Hyperdimensional Computing, achieving high-resolution strain clustering and deep evolutionary scaling.

Predicting the toxicity of chemical compounds via Hyperdimensional Computing

This paper uses Hyperdimensional Computing to predict chemical compound toxicity efficiently, showing it can classify compounds as toxic or non-toxic with computational advantages over traditional methods.

Characterization of microbial dark matter at scale with MetaSBT and taxonomy-aware Sequence Bloom Trees

The paper introduces MetaSBT, a tool for classifying microbial genomes and MAGs, and presents databases of over 190,000 viral genomes, including many previously unknown species clusters.

Meta16S: large-scale discovery and taxonomic assignment of unknown microbes from 16S amplicon sequencing samples

The paper introduces Meta16S, a scalable pipeline for incremental clustering of 16S rRNA data to discover and classify unknown microbes.

A novel Vector-Symbolic Architecture for graph encoding and its application to viral pangenome-based species classification

The paper introduces a Vector-Symbolic Architecture for encoding viral pangenomes and evaluates its effectiveness in species classification, finding that a flat species-level model outperforms genus-level and hierarchical approaches.

Integrated forward and reverse degradomics uncovers the proteolytic landscape of aortic aneurysms and the roles of MMP9 and mast cell chymase

The paper uses forward and reverse degradomics to analyze proteolytic landscapes in aortic aneurysms, identifying key proteases like MMP9 and CMA1 and their roles in extracellular matrix remodeling.

Structural Basis of M1 Muscarinic and H3 Histamine Receptor Inhibition in OPC Differentiation

The paper identifies M1 muscarinic and H3 histamine receptors as targets for OPC differentiation and analyzes their ligand interactions using computational methods.

R2G2: A Python-R Framework for Seamless Integration of R/Bioconductor Tools into Galaxy

R2G2 automates the creation of Galaxy wrappers for R/Bioconductor packages, simplifying integration and reducing complexity for non-programmers.

Large-scale classification of metagenomic samples: a comparative analysis of classical machine learning techniques vs a novel brain-inspired hyperdimensional computing approach

This paper compares classical machine learning and a brain-inspired hyperdimensional computing approach for classifying metagenomic samples, showing HDC achieves comparable or better accuracy and efficiency.

Feature selection with vector-symbolic architectures: a case study on microbial profiles of shotgun metagenomic samples of colorectal cancer

The paper introduces a novel backward variable selection method for metagenomic data to identify microbial biomarkers in colorectal cancer, showing promising results compared to existing methods.

Genomics to Notebook (g2nb): extending the electronic notebook to address the challenges of bioinformatics analysis

The paper introduces g2nb, a notebook environment integrating bioinformatics platforms into a unified interface for genomics analysis.

Galaxy Training: A Powerful Framework for Teaching!

The paper introduces Galaxy Training Network (GTN) as a framework for creating and sharing FAIR training materials for data analysis, with recent improvements to support educators and expand its use in various learning environments.

PDAUG - a Galaxy based toolset for peptide library analysis, visualization, and machine learning modeling

PDAUG provides a Galaxy-based toolset for peptide library analysis, visualization, and machine learning modeling, demonstrating its utility in predicting anticancer peptide properties.

CNV-ClinViewer: Enhancing the clinical interpretation of large copy-number variants online

CNV-ClinViewer provides a web tool for clinical interpretation of large copy-number variants by integrating patient and population data with biomedical annotations.

Expanding the Galaxy's reference data

The paper describes integrating refgenie into Galaxy to manage and share reference datasets, with tools for retrieval and a global repository for easy access.

GenomicSuperSignature: interpretation of RNA-seq experiments through robust, efficient comparison to public databases

GenomicSuperSignature compares new RNA-seq datasets to public archives for rapid interpretation using precomputed axes of variation.

SimText: A text mining framework for interactive analysis and visualization of similarities among biomedical entities

Adding software to package management systems can increase their citation by 280%

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

A Single-cell RNA-seq Training and Analysis Suite using the Galaxy Framework

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.

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

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.

SVCurator: A Crowdsourcing app to visualize evidence of structural variants for the human genome

The paper introduces SVCurator, a crowdsourcing app for evaluating structural variants in the human genome, finding high concordance among curators and with existing benchmarks.

Galaxy External Display Applications: Closing a dataflow interoperability loop

The paper introduces GEDA, a framework enabling interoperability between Galaxy user data and external resources by accepting URLs pointing to user data.

Bioconda: A sustainable and comprehensive software distribution for the life sciences

Bioconda provides a sustainable, comprehensive distribution of bioinformatics software using Conda for reproducible analysis across platforms.

Infant Weight Gain Trajectories Linked To Oral Microbiome Composition

The paper links infant weight gain trajectories to oral microbiome composition and shows associations with gut microbiome and diet.