Philipp C. Münch

SeqDesk is a sequencing-facility management system that ensures FAIR-compliant metadata submission by integrating standards-compliant metadata capture into routine operations.

The paper shows that E. faecalis evolves to metabolize fructoselysine, reducing S. Typhimurium colonization by limiting a key nutrient.

BAQLaVa improves viral profiling from metagenomes and metatranscriptomes, revealing reduced virome diversity in inflammatory bowel diseases and novel phage-host relationships.

This study evaluates LLMs for microbial phenotype annotation, finding varied performance across models and traits, with confidence scores correlating with accuracy.

This study benchmarks ML and rule-based methods for predicting antimicrobial resistance from microbial genomes, finding significant variation in performance across species and antibiotics.

This study benchmarks assemblers and variant callers for strain-resolved analysis of large DNA viruses, identifying best practices and challenges in handling low-divergent viral populations.

This paper introduces DiTaxa, a method for analyzing 16S rRNA sequences using nucleotide-pair encoding to improve microbiome phenotype classification and biomarker detection.