| Sparse and compositionally robust inference of microbial ecological networks ZD Kurtz, CL Müller, ER Miraldi, DR Littman, MJ Blaser, RA Bonneau PLoS computational biology 11 (5), e1004226, 2015 | 1725 | 2015 |
| Best practices for single-cell analysis across modalities L Heumos, AC Schaar, C Lance, A Litinetskaya, F Drost, L Zappia, ... Nature Reviews Genetics, 1-23, 2023 | 998 | 2023 |
| NetCoMi: network construction and comparison for microbiome data in R S Peschel, CL Müller, E von Mutius, AL Boulesteix, M Depner Briefings in Bioinformatics, 2020 | 489 | 2020 |
| scCODA is a Bayesian model for compositional single-cell data analysis M Buettner, J Ostner, CL Mueller, FJ Theis, B Schubert Nature communications 12 (1), 6876, 2021 | 337 | 2021 |
| Inferring causal molecular networks: empirical assessment through a community-based effort SM Hill, LM Heiser, T Cokelaer, M Unger, NK Nesser, DE Carlin, Y Zhang, ... Nature methods 13 (4), 310-318, 2016 | 284 | 2016 |
| Fungi stabilize connectivity in the lung and skin microbial ecosystems L Tipton, CL Müller, ZD Kurtz, L Huang, E Kleerup, A Morris, R Bonneau, ... Microbiome 6, 1-14, 2018 | 214 | 2018 |
| Antibiotic perturbation of the murine gut microbiome enhances the adiposity, insulin resistance, and liver disease associated with high-fat diet D Mahana, CM Trent, ZD Kurtz, NA Bokulich, T Battaglia, J Chung, ... Genome medicine 8 (1), 48, 2016 | 207 | 2016 |
| A single early-in-life macrolide course has lasting effects on murine microbial network topology and immunity VE Ruiz, T Battaglia, ZD Kurtz, L Bijnens, A Ou, I Engstrand, X Zheng, ... Nature communications 8 (1), 518, 2017 | 155* | 2017 |
| Microbial networks in SPRING-Semi-parametric rank-based correlation and partial correlation estimation for quantitative microbiome data G Yoon, I Gaynanova, CL Müller Frontiers in genetics 10, 516, 2019 | 145 | 2019 |
| Inverse Dirichlet weighting enables reliable training of physics informed neural networks S Maddu, D Sturm, CL Müller, IF Sbalzarini Machine Learning: Science and Technology 3 (1), 015026, 2022 | 131 | 2022 |
| 4C-ker: a method to reproducibly identify genome-wide interactions captured by 4C-Seq experiments R Raviram, PP Rocha, CL Müller, ER Miraldi, S Badri, Y Fu, E Swanzey, ... PLoS computational biology 12 (3), e1004780, 2016 | 106 | 2016 |
| Temporal probabilistic modeling of bacterial compositions derived from 16S rRNA sequencing T Äijö, CL Müller, R Bonneau Bioinformatics 34 (3), 372-380, 2018 | 90 | 2018 |
| Don't fall for tuning parameters: tuning-free variable selection in high dimensions with the TREX J Lederer, C Müller Proceedings of the AAAI conference on artificial intelligence 29 (1), 2015 | 84 | 2015 |
| Robust classification of protein variation using structural modelling and large-scale data integration EH Baugh, R Simmons-Edler, CL Müller, RF Alford, N Volfovsky, AE Lash, ... Nucleic acids research 44 (6), 2501-2513, 2016 | 81 | 2016 |
| Optimization of convex functions with random pursuit SU Stich, CL Muller, B Gartner SIAM Journal on Optimization 23 (2), 1284-1309, 2013 | 72 | 2013 |
| The RNA ligase RtcB reverses MazF-induced ribosome heterogeneity in Escherichia coli H Temmel, C Müller, M Sauert, O Vesper, A Reiss, J Popow, J Martinez, ... Nucleic acids research 45 (8), 4708-4721, 2017 | 68 | 2017 |
| Stability selection enables robust learning of differential equations from limited noisy data S Maddu, BL Cheeseman, IF Sbalzarini, CL Müller Proceedings of the Royal Society A 478 (2262), 20210916, 2022 | 66 | 2022 |
| Particle swarm CMA evolution strategy for the optimization of multi-funnel landscapes CL Muller, B Baumgartner, IF Sbalzarini Evolutionary Computation, 2009. CEC'09. IEEE Congress on, 2685-2692, 2009 | 66 | 2009 |
| Global characterization of the CEC 2005 fitness landscapes using fitness-distance analysis CL Müller, IF Sbalzarini European conference on the applications of evolutionary computation, 294-303, 2011 | 65 | 2011 |
| Shrinkage improves estimation of microbial associations under different normalization methods M Badri, ZD Kurtz, R Bonneau, CL Müller NAR genomics and bioinformatics 2 (4), lqaa100, 2020 | 64* | 2020 |
Richard BonneauGenentech & RocheVerified email at gene.com
