Robust classification of protein variation using structural modelling and large-scale data integration von Baugh, Evan H, Simmons-Edler, Riley, Müller, Christian L, Alford, Rebecca F, Volfovsky, Natalia, Lash, Alex E, Bonneau, Richard

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Fused Regression for Multi-source Gene Regulatory Network Inference von Lam, Kari Y, Westrick, Zachary M, Müller, Christian L, Christiaen, Lionel, Bonneau, Richard

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One third of dynamic protein expression profiles can be predicted by a simple rate equation von Tchourine, Konstantine, Poultney, Christopher S, Wang, Li, Silva, Gustavo M, Manohar, Sandhya, Mueller, Christian L, Bonneau, Richard, Vogel, Christine

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NetCoMi: network construction and comparison for microbiome data in R von Peschel, Stefanie, Müller, Christian L, von Mutius, Erika, Boulesteix, Anne-Laure, Depner, Martin

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Sparse and compositionally robust inference of microbial ecological networks von Kurtz, Zachary D, Müller, Christian L, Miraldi, Emily R, Littman, Dan R, Blaser, Martin J, Bonneau, Richard A

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asteRIa enables robust interaction modeling between chromatin modifications and epigenetic readers von Stadler, Mara, Lukauskas, Saulius, Bartke, Till, Müller, Christian L

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Microbial Networks in SPRING - Semi-parametric Rank-Based Correlation and Partial Correlation Estimation for Quantitative Microbiome Data von Yoon, Grace, Gaynanova, Irina, Müller, Christian L

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Negative binomial factor regression with application to microbiome data analysis von Mishra, Aditya K., Müller, Christian L.

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Tree-aggregated predictive modeling of microbiome data von Bien, Jacob, Yan, Xiaohan, Simpson, Léo, Müller, Christian L.

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Stability selection enables robust learning of differential equations from limited noisy data von Maddu, Suryanarayana, Cheeseman, Bevan L, Sbalzarini, Ivo F, Müller, Christian L

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Scaffold Matcher: A CMA-ES based algorithm for identifying hotspot aligned peptidomimetic scaffolds von Claussen, Erin R, Renfrew, P Douglas, Müller, Christian L, Drew, Kevin

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Perspective maximum likelihood-type estimation via proximal decomposition von Combettes, Patrick L., Müller, Christian L.

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Over-optimism in unsupervised microbiome analysis: Insights from network learning and clustering von Ullmann, Theresa, Peschel, Stefanie, Finger, Philipp, Müller, Christian L, Boulesteix, Anne-Laure

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A single early-in-life macrolide course has lasting effects on murine microbial network topology and immunity von Ruiz, Victoria E., Battaglia, Thomas, Kurtz, Zachary D., Bijnens, Luc, Ou, Amy, Engstrand, Isak, Zheng, Xuhui, Iizumi, Tadasu, Mullins, Briana J., Müller, Christian L., Cadwell, Ken, Bonneau, Richard, Perez-Perez, Guillermo I., Blaser, Martin J.

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Fungi stabilize connectivity in the lung and skin microbial ecosystems von Tipton, Laura, Müller, Christian L, Kurtz, Zachary D, Huang, Laurence, Kleerup, Eric, Morris, Alison, Bonneau, Richard, Ghedin, Elodie

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Antibiotic perturbation of the murine gut microbiome enhances the adiposity, insulin resistance, and liver disease associated with high-fat diet von Mahana, Douglas, Trent, Chad M, Kurtz, Zachary D, Bokulich, Nicholas A, Battaglia, Thomas, Chung, Jennifer, Müller, Christian L, Li, Huilin, Bonneau, Richard A, Blaser, Martin J

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STENCIL-NET for equation-free forecasting from data von Maddu, Suryanarayana, Sturm, Dominik, Cheeseman, Bevan L., Müller, Christian L., Sbalzarini, Ivo F.

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Inverse Dirichlet weighting enables reliable training of physics informed neural networks von Maddu, Suryanarayana, Sturm, Dominik, Müller, Christian L, Sbalzarini, Ivo F

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Decoding chromatin states by proteomic profiling of nucleosome readers von Lukauskas, Saulius, Tvardovskiy, Andrey, Nguyen, Nhuong V., Stadler, Mara, Faull, Peter, Ravnsborg, Tina, Özdemir Aygenli, Bihter, Dornauer, Scarlett, Flynn, Helen, Lindeboom, Rik G. H., Barth, Teresa K., Brockers, Kevin, Hauck, Stefanie M., Vermeulen, Michiel, Snijders, Ambrosius P., Müller, Christian L., DiMaggio, Peter A., Jensen, Ole N., Schneider, Robert, Bartke, Till

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Regression Models for Compositional Data: General Log-Contrast Formulations, Proximal Optimization, and Microbiome Data Applications von Combettes, Patrick L., Müller, Christian L.

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