Marius van den Beek

Verifiable Agentic Science on Public Infrastructure

This paper demonstrates agentic science on public infrastructure to ensure reproducibility by making all agent actions and workflows publicly accessible.

Standardizing RNA-seq Analysis of Fungal Pathogens Using BRC-Analytics and Agentic AI: A Candidozyma auris Case Study

The paper demonstrates a framework using BRC-Analytics and agentic AI to standardize RNA-seq analysis of fungal pathogens, achieving reproducible results across studies with differing annotations.

From data to publication in a browser with BRC-Analytics: Evolutionary dynamics of coding overlaps in measles virus

The paper introduces BRC-Analytics, a browser-based platform for pathogen genomics, demonstrating its use in analyzing measles virus evolutionary dynamics and revealing asymmetric frame evolution under selective pressures.

Scalable, accessible, and reproducible reference genome assembly and evaluation in Galaxy

The paper presents a scalable pipeline for reference genome assembly and evaluation, demonstrating its effectiveness across 51 vertebrate species using Galaxy.

Fast and accurate genome-wide predictions and structural modeling of protein-protein interactions using Galaxy

The paper presents a pipeline for predicting genome-wide protein-protein interactions and generating structural models, validated on human and yeast genomes and applied to SARS-CoV2 proteins.

Planemo: a command-line toolkit for developing, deploying, and executing scientific data analyses

Planemo is a command-line toolkit for developing, deploying, and executing Galaxy tools and workflows, promoting best practices in scientific data analysis.

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.

Evolution and genomic signatures of spontaneous somatic mutation in Drosophila intestinal stem cells

This study analyzes spontaneous somatic mutations in Drosophila intestinal stem cells using whole-genome sequencing to understand early cancer mutation dynamics and genomic signatures.

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.

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

The paper presents a global, community-maintained platform for analyzing SARS-CoV-2 genomic data, demonstrating its utility in variant detection and reanalysis of existing datasets.

Somatic transposition in the Drosophila intestine occurs in active chromatin and is associated with tumor suppressor gene inactivation

The paper identifies somatic transposition in Drosophila intestine, showing it occurs in active chromatin and is linked to tumor suppressor gene inactivation.

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.

Galaxy-Kubernetes integration: scaling bioinformatics workflows in the cloud

This paper integrates Galaxy with Kubernetes to enable scalable, cloud-agnostic bioinformatics workflows.

Dual-layer transposon repression in heads of Drosophila melanogaster

The paper investigates piRNA pathway activity in Drosophila adult tissues and identifies a dual-layer mechanism for transposon repression involving Piwi and Dicer-2.

Practical computational reproducibility in the life sciences

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

Metavisitor, a suite of Galaxy tools for simple and rapid detection and discovery of viruses in deep sequence data

Metavisitor provides Galaxy tools for detecting and reconstructing viral genomes from deep sequence data, enabling rapid and accessible virus discovery.