Martin Hölzer

This paper introduces a hybrid training model to enhance bioinformatics capacity globally, demonstrating its effectiveness through an Eastern European workshop series.

This paper provides an overview and analysis of nanopore sequencing, offering guidelines to address challenges and maximize information gain from the technology.

CoVerage predicts and characterizes SARS-CoV-2 Variants of Interest by analyzing lineage frequency dynamics and antigenic changes from GISAID data.

The paper introduces CLEAN, a pipeline to remove contaminants from sequencing data, improving reproducibility and analysis quality.

This study uses Nanopore sequencing to analyze DNA methylation in four bacterial species, identifying species-specific and novel methylation motifs and improving basecalling accuracy for reliable methylation detection.

This study evaluates sequencing accuracy and systematic errors in direct RNA sequencing across species and synthetic RNA, identifying error patterns and their implications for downstream applications.

varVAMP designs pan-specific primers for tiled sequencing and qPCR of diverse viruses, ensuring specificity through minimal variability regions and degenerate nucleotides.

The paper evaluates how reference design affects SARS-CoV-2 lineage abundance estimation from wastewater sequencing data using synthetic and real-world datasets.

VIRify identifies and classifies viral contigs and prophages from metagenomic data with high accuracy across prokaryotic and eukaryotic viruses.

RIBAP improves pangenome analysis by using ILP to refine gene clusters, outperforming existing tools in identifying core genes across diverse bacterial genomes.

The paper assembles 35 European Mycoplasma bovis genomes using a hybrid approach, identifies clade-specific genes, and reveals geographic clustering in a phylogenetic tree.

The paper assembles repetitive TALomes in Xanthomonas using Oxford Nanopore sequencing and presents a correction pipeline to improve accuracy.

The paper analyzes 61 Chlamydia psittaci genomes to identify genomic features correlated with host tropism and phylogeny.

What the Phage provides a scalable, parallel workflow for phage sequence identification and analysis using multiple prediction tools and downstream annotation.

DarkQ enables instant sharing and discovery of newly sequenced genomes through a message queue system to improve timely access for stakeholders.

MUFFIN is a metagenomics workflow that integrates short and long reads to produce high-quality bins and annotations for microbial community analysis.

EpiDope uses a deep neural network to predict linear B-cell epitopes with higher accuracy than existing tools, reducing laboratory costs and time.

PoSeiDon detects recombination events and positive selection in protein-coding sequences using a Nextflow pipeline with Docker support.

PCAGO is a web tool that uses PCA to analyze RNA-Seq data, offering normalization, filtering, visualization, and parameter selection to improve clustering and interpretation.

The paper annotates and analyzes non-coding RNAs in 16 bat genomes, revealing new expression patterns and providing a resource for studying bat biology and host-virus interactions.

This study uses direct RNA nanopore sequencing to analyze full-length coronavirus genomes, identifying structural variants and methylation sites in viral RNAs.

SilentMutations (SIM) analyzes the effect of mutations on long-range RNA-RNA interactions in viral genomes, predicting disruptive and compensatory mutants.