Research Associate, Harvard T.H. Chan School of Public Health
Staff Scientist, Helmholtz Centre for Infection Research
My work and research interests focus on machine learning for genomics and metaresearch, including deep learning method development, automated architecture search, and practical tools that use DL and LLMs to make research workflows more reproducible, scalable, and efficient.
Outside research and software, I am interested in Baroque and classical music, Expressionist art, and twentieth-century European literature. I also enjoy hiking in the Alps, fly fishing, and spending time with dogs.
I am the main developer of these tools, spanning secure research infrastructure, sequencing operations, and scientific writing support.
Presents BAQLaVa for high-resolution viral profiling from metagenomic and metatranscriptomic data. The framework supports scalable virome epidemiology and virus-host interaction analysis.
Evaluates how well large language models support structured microbial phenotype annotation. The study compares model behavior across traits and uses confidence to prioritize reliable outputs.
Presents GenomeNet-Architect, a framework for automated neural architecture optimization on genomic sequence tasks. The approach searches model layouts and training hyperparameters for compact, efficient genomic classifiers.
Studies strain-level microbiome responses to repeated antibiotic perturbations in gnotobiotic mice. The paper highlights how treatment pulses can reshape community dynamics and resistance.
Introduces Self-GenomeNet, a self-supervised approach tailored to genomic sequences. The method uses reverse-complement structure to improve learning in data-scarce genomic prediction tasks.
Maps natural CRISPR-Cas systems across human microbiome metagenomes. The work links CRISPR spacers, cas genes, body sites, taxa, and putative viral or mobile-element targets.
For a complete list, see my Google Scholar profile.
Harvard T.H. Chan School of Public Health
Research Associate
Helmholtz Centre for Infection Research
Staff Scientist
Helmholtz Centre for Infection Research
Graduate Research Associate
Harvard T.H. Chan School of Public Health
Guest Researcher
Heinrich Heine University Düsseldorf
Research Associate
Max Planck Institute for Informatics
Research Assistant
German Research Center for Environmental Health
Research Unit of Molecular Epidemiology, Research Assistant
Max Planck Institute for Informatics
Computational Genomics and Epidemiology Group, Research Assistant
Max von Pettenkofer-Institute, University of Munich
Dr. rer. nat., Medical Faculty. Supervisor: Prof. Dr. Bärbel Stecher.
University of Munich
M.Sc. in Epidemiology
University of Applied Sciences Weihenstephan
B.Sc. in Bioinformatics
Immunity, Inflammation and Disease - Wiley
Editor
Current Protocols in Bioinformatics - Wiley
Editor
Current Protocols in Bioinformatics - Wiley
Associate Editor
For collaborations, research questions, or speaking requests, email muench@hsph.harvard.edu or philipp.muench@helmholtz-hzi.de.
Angaben gemäß § 5 DDG
Dr. Philipp Münch - AI Software & SaaSE-Mail: mail@pmuench.com
USt-IdNr. gemäß § 27a UStG: DE460209447