I am a project leader in systems biology at the Simons Center for Data Analysis.
I am interested in developing novel computational statistics tools and their applications in systems biology.
On the computational side I am interested in:
- High-dimensional variable selection schemes such as the LASSO and the TREX
- Black-box (a.k.a. gradient-free, derivative-free, direct search) optimization and sampling algorithms such as CMA-ES, Gaussian Adaptation, and adaptive MCMC
- Proximal algorithms and their application in statistics
- Statistical and spectral methods to analyze complex networks
- Statistical tools to describe energy and fitness landscapes
On the biological side my research interests revolve around:
- Inference of microbial interaction networks from 16S rRNA data
- Inference of transcriptional regulatory networks from high-throughput measurements
- Robustness of parameter spaces in biological networks
- Protein conformation spaces and prediction of deleterious mutations in proteins
A recent CV can be found here (pdf).
My ResearchGate profile can be found here.
My personal github repository is here.
We are currently organizing the second workshop on statistical and computational challenges in microbiome research which will take place on the 16th-17th of February 2017 at the Broad Institute, Cambridge. Stay tuned for more information.
We have organized a workshop on statistical and computational challenges in microbiome research on the 25th-26th of February 2016 at the Simons Foundation, New York. Further information can be found here.
Please find below a list of representative publications. If you’re interested in working with me at SCDA, I am currently having two research scientist positions available. Please contact me via cmueller[at]simonsfoundation.org for further information.
Recent manuscripts under review/in preparation
Asmus J, Müller CL, Sbalzarini IF. Approximate Design Centering and Robustness Quantification of Biological and Electronic Networks. submitted
Äijö, T, Müller CL, Bonneau R, Temporal probabilistic modeling of bacterial compositions derived from 16S rRNA sequencing. http://biorxiv.org/content/early/2016/09/22/076836 [code]
Bien J, Gaynanova I, Lederer J, Müller CL. Auto-tuned high-dimensional regression: theoretical guarantees and non-convex global optimization. In preparation 2015 [overview]
Cázáls F, Robert C, Roth A, Müller CL, Towards Morse Theory for Point Cloud Data. HAL preprint, 2013.
Mahana, D, Trent CM, Kurtz, ZD, Bokulich, NA, Battaglia T,Chung, J, Müller CL, Li, H, Bonneau RA, Blaser MJ. Antibiotic perturbation of the murine gut microbiome enhances the adiposity, insulin resistance, and liver disease associated with high-fat diet Genome Medicine, 8:48, 2016.
Raviram R, Rocha PP, Müller CL, Miraldi ER, Fu Y, Swanzey E, Badri S, Proudhon C, Snetkova V, Bonneau R, Skok JA. 4C-ker: A method to reproducibly identify genome-wide interactions captured by 4C-Seq experiments. PLoS Comput Biol 2016; 12(3): e1004780.[code]
Baugh EH, Simmons-Edler R, Müller CL, Alford RF, Volfovsky N, Lash AE, Bonneau R. Robust Classification of Protein Variation Using Structural Modeling and Large-Scale Data Integration Nucl. Acids Res. 2016; 44 (6): 2501-2513. [code]
Hill SM et al., HPN-DREAM Consortium, Inferring causal molecular networks: empirical assessment through a community-based effort. Nature Methods, 2016.
Kurtz ZD*, Müller CL*, Miraldi ER*, Littman DR, Blaser MJ, Bonneau RA. Sparse and compositionally robust inference of microbial ecological networks. PLoS Comput Biol. 2015;11(5):e1004226 (* joint first authors) [code]
Lederer J*, Müller CL*. Don’t fall for tuning parameters: Tuning-free variable selection in high dimensions with the TREX. Proceedings of the Twenty-Ninth AAAI Conference on Artificial Intelligence, 2015. (* joint first authors). [code]
Optimization and Monte Carlo sampling
Stich SU, Müller CL, Gärtner B. Variable Metric Random Pursuit. Math Program A, May 24, 2015.
Müller CL. Stochastic methods for single objective global optimization. In: AAIA Computational Intelligence in Aerospace Sciences, 2014. 63-112.
Stich SU, Müller CL, Gärtner B. Optimization of convex functions with Random Pursuit. SIAM J Optim 2013;23(2):1284-1309.
Müller CL, Sbalzarini IF. Gaussian adaptation revisited: an entropic view on covariance matrix adaptation. In: Di Chio C, Cagnoni S, Cotta, C, et al., Applications of Evolutionary Computation: EvoApplications 2010. Berlin and Heidelberg, Germany: Springer; 2010:432-441. [code]
Müller CL, Baumgartner B, Sbalzarini IF. Particle swarm CMA evolution strategy for the optimization of multi-funnel landscapes. Proc. IEEE Congress on Evolutionary Computation (CEC), May 18-21, 2009; Trondheim, Norway. [code]
Fitness and energy landscapes
Müller CL, Sbalzarini IF. Global characterization of the CEC 2005 fitness landscapes using fitness-distance analysis. In: Di Chio C, Cagnoni S, Cotta C, et al., eds. Applications of Evolutionary Computation: EvoApplications 2011. Berlin and Heidelberg, Germany: Springer; 2011:294-303.
Biological data analysis and modeling
Plessis A, Hafemeister C, Wilkins O, Gonzaga ZJ, Meyer RS, Pires I, Müller CL, Septiningsih EM, Bonneau R, Purugganan M. Multiple abiotic stimuli are integrated in the regulation of rice gene expression under field conditions. eLIFE 2015.
Tchourine K*, Poultney CS*, Wang L*, Silva GM, Manohar S, Mueller CL, Bonneau R, and Vogel C. One third of dynamic protein expression profiles can be predicted by a simple rate equation. Mol Biosyst. 2014;10:2850-2862. (* joint first authors)
Billerbeck S, Calles B, Müller CL, de Lorenzo V, Panke S. Towards Functional Orthogonalisation of Protein Complexes: Individualisation of GroEL Monomers Leads to Distinct Quasihomogeneous Single Rings. Chembiochem. 2013;14(17):2310-2321.
Müller CL, Sbalzarini IF, van Gunsteren WF, Zagrovic B, Hünenberger PH. In the eye of the beholder: inhomogeneous distribution of high resolution shapes within the random walk ensemble. J Chem Phys. 2009;130(21):214904.
Müller CL. Black-box landscapes: characterization, optimization, sampling and application to geometric configuration problems [Dissertation]. Zürich, Switzerland: ETH Zürich; 2010.
Müller CL. Parameter sensitivity analysis in behavioral and analog circuit simulations of neuro-fuzzy models [Diploma thesis]. Tübingen, Germany: University of Tübingen; 2006.
Müller CL. die erde dreht sich zu laut: gedichte von der schwedischen oberfläche [Certificate thesis]. Tübingen, Germany: University of Tübingen; 2005.
Müller CL. High order accurate numerical solution of the linearized Euler equations for sound propagation in the atmosphere [Master’s thesis]. Uppsala, Sweden: Uppsala University, 2004.
Johannes. Lederer, Statistics Department, UW Seattle, USA, High-dimensional statistics.
Jacob Bien, Department BSCB, Cornell University, USA, High-dimensional statistics.
Jane Skok, New York School of Medicine, USA, Statistical Analysis of chromosomal interactions.
Martin Blaser, New York School of Medicine, USA, Microbiome data analysis.
Ivo F. Sbalzarini, Max-Planck-Institute for Cell Biology, Dresden, Germany, Markov Chain Monte Carlo, Optimization.
Thomas J. Fuchs, Memorial Sloan Kettering Cancer Center, New York, USA, Approximate Bayesian Computation .
Frederic Cazals, INRIA Sophia-Antipolis, Sophia-Antipolis, France, Computational topological analysis of high-dimensional sampled landscapes.
Bojan Zagrovic, Max F. Perutz Laboratories and University of Vienna, Vienna, Austria, Conformation space analysis of chain molecules.
Co-Principal Supervision of Students
PhD theses (since 2010):
Sebastian Stich (completed, with Dr. Bernd Gärtner, ETH Zürich) now at UC Louvain, Belgium
Josefine Asmus (ongoing, with Dr. Ivo F. Sbalzarini, MPI Dresden)
Master/diploma theses (2006-2010, ETH Zürich):
Ana Tusek, Benedikt Baumgartner, Christian Fiegl, Georg Ofenbeck, Markus König, Daniel Zünd, (with Ivo F. Sbalzarini), Thomas Lampart (with Peter Widmayer)
Bachelor/semester theses (2006-2010, ETH Zürich):
Johannes Lederer, Yannick Misteli, Patrick Plattner (with Ivo F. Sbalzarini)
Mentoring of Graduate Students
PhD theses (since 2013):
Zachary Kurtz, Ramya Raviram, Evan Baugh, Kostya Tchourine (all with Richard Bonneau, NYU)
Josh Fass (with John Chodera, Thomas Fuchs, MSKCC)