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 investigates how bacterial and host factors contribute to Salmonella 'blooming' in a gnotobiotic mouse model of enterocolitis, showing that inflammation and specific Salmonella traits influence microbial community shifts and pathogen abundance.

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.