Portrait of Prof. Dr. Christian Müller, Group Leader, Institute of Computational Biology

Group Leader, Institute of Computational Biology

Prof. Dr. Christian L. Müller

"I am an interdisciplinary scientist with expertise in Statistics, Computational Science, and Biology. My research focuses on developing rigorous statistical algorithms and workflows for analyzing high-throughput multimodal biological data."

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Academic Career and Research Areas

Christian L. Müller’s academic trajectory is defined by a sustained effort to bridge computational methods and biological data analysis. He began his training in bioinformatics at the University of Tübingen, complemented by studies in computational mathematics at Uppsala University, establishing an early interdisciplinary foundation. This dual perspective matured during his Ph.D. at ETH Zürich, where he worked on black-box optimization methods and their application to biological systems. 

His postdoctoral years at ETH Zürich and New York University marked a transition toward systems biology and applied mathematics, where he began focusing on statistical learning in biological contexts. This direction crystallized during his tenure at the Flatiron Institute (2014–2019), where he led projects within large collaborative efforts such as CBIOMES. There, he contributed to advancing microbiome data analysis through compositional data modeling, network estimation, and optimal transport methods—tools essential for understanding complex ecological and biological systems. 

Since 2019, Müller has served as Group Leader at Helmholtz Munich and Professor of Statistics at LMU Munich, where he leads research at the intersection of statistics, machine learning, and computational biology. His work centers on extracting structure from high-dimensional biological data, particularly microbial, epigenetic, and single-cell datasets. Key contributions include the development of (microbial) network estimation, Bayesian and variational methods for compositional data, and optimal transport schemes. His recent research extends into biomedical applications, including antimicrobial discovery using learned molecular representations. 

Beyond research, Müller has played an active role in shaping the field through teaching, mentorship, and community building, organizing workshops and training programs in computational biology, statistics,  and optimization. His career reflects a consistent emphasis on methodological innovation driven by real-world biological questions, positioning him as an active contributor within modern data-driven life sciences.

Fields of Work and Expertise

Statistics

Optimization

Data Science

Open-Source Software

High-Throughput Sequencing

Single-Cell Sequencing

Flow Cytometry

Microbiome in Health and Disease 

Professional Background

Since 2019

Group Leader, Computational Health Center, Helmholtz Munich, Germany Professor, Department of Statistics, LMU München, Germany, Visiting Scholar, Center for Computational Mathematics, Flatiron Institute, New York, USA

2020

Interim Head, Helmholtz AI Consultants, Helmholtz Munich

2014 - 2019

Research Scientist / Project Leader, Flatiron Institute, Simons Foundation, New York, USA

2011 - 2014

Postdoctoral Researcher, ETH Zürich, Switzerland & NYU (Systems Biology & Courant Institute), New York, USA

1999 - 2011

Diploma, Bioinformatics, University of Tübingen, Germany; M.Sc., Computer Science, Uppsala University, Sweden; Ph.D., Computer Science, ETH Zürich, Switzerland

Honors and Awards

  • 2022 - 2025 Member of the StressRegNet consortium (https://bayresq.net/en/projekte-stressregnet-en/) as part of the Bavarian Research Network - New Strategies Against Multi-Resistant Pathogens by Means of Digital Networking (bayresq.net)
  • 2017 - Member of the Simons Collaboration on Computational Biogeochemical Modeling of Marine Ecosystems (CBIOMES, cbiomes.org)

Recent Publications

2026 Machine Learning

Chris Kolb, Christian L. Müller, Bernd Bischl, David Rügamer

Smoothing the Edges: Smooth Optimization for Sparse Regularization using Hadamard Overparametrization
2026 bioRxiv

Oleg Vlasovets, Marie Standl, Lisa Maier, Stefanie Gilles, Harald Grallert, Claudia Traidl-Hoffmann, Annette Peters, Christian L. Müller

The role of IgE patterns and their link to the gut microbiome in allergic sensitization
2023 Nature Reviews Genetics

Lukas Heumos, Anna C. Schaar, Christopher Lance, Anastasia Litinetskaya, Felix Drost, Luke Zappia, Malte D. Lücken, Daniel C. Strobl, Juan Henao, Fabiola Curion, Single-cell Best Practices Consortium, Herbert B. Schiller & Fabian J. Theis

Best practices for single-cell analysis across modalities
2021 Nature Communications

Maren Buettner, Johannes Ostner, Christian L Mueller, Fabian J Theis, Benjamin Schubert

scCODA is a Bayesian model for compositional single-cell data analysis
2015 PLoS Computational Biology

Zachary D Kurtz, Christian L Müller, Emily R Miraldi, Dan R Littman, Martin J Blaser, Richard A Bonneau

Sparse and Compositionally Robust Inference of Microbial Ecological Networks

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