A more up to date List of publications can be found here: Google Scholar

2025

  • N. F. Müller, R. R. Wick, L. M. Judd, D. A. Williamson, T. Bedford, B. P. Howden, S. Duchêne*, D. J. Ingle* “Quantifying plasmid movement in drug-resistant Shigella species using phylodynamic inference” BioRxiv https://doi.org/10.1101/2022.10.27.514108

  • M. I. Paredes, C. Liang, S. Suen, I. W. Holloway, J. M. Garrigues, N. M. Green, T. Bedford, N. F. Müller*, J. Osmundson* “Viral introductions and return to baseline sexual behaviors maintain low-level mpox incidence in Los Angeles County, USA, 2023-2024” medRxiv https://doi.org/10.1101/2025.03.14.25323999

  • N. F. Müller, R. R. Bouckaert, C. H. Wu, T. Bedford “MASCOT-Skyline integrates population and migration dynamics to enhance phylogeographic reconstructions” PLOS Computational Biology 21(9): e1013421 https://doi.org/10.1371/journal.pcbi.1013421

  • T. Lloyd, S. M. Khan, D. Heaton, M. Shemsu, V. Varghese, J. Graham, M. Gregory, P. Dorfman, M. Talton, J. DeVol, N. F. Müller, T. Bedford “Genomic Modeling of an Outbreak of Multidrug-Resistant Shigella sonnei, California, USA, 2023-2024” Emerging Infectious Diseases 31(Suppl 1): S98 https://doi.org/10.3201/eid3101.AD3101

  • N. T. Parker, V. Hong, G. S. Davis, M. Pomichowski, I. A. Reyes, F. Xie, N. F. Müller, I. Rodriguez-Barraquer, S. Y. Tartof, J. A. Lewnard “Clinical progression parameters associated with SARS-CoV-2, influenza, and respiratory syncytial virus infections” medRxiv https://doi.org/10.1101/2025.05.15.24307345

  • R. R. Bouckaert, P. H. Weidemüller, L. R. E. Gomez, N. F. Müller “Improving the Scalability of Bayesian Phylodynamic Inference through Efficient MCMC Proposals” bioRxiv https://doi.org/10.1101/2025.06.15.601234

  • J. Lewnard, M. I. Paredes, M. Yechezkel, G. S. Davis, V. Hong, J. Skela, U. Pandey, N. T. Parker, L. C. Granskog, M. E. Pomichowski, N. F. Müller, T. Bedford “Extensive cryptic circulation sustains mpox among men who have sex with men” medRxiv https://doi.org/10.1101/2025.08.15.25257321

2024

  • M. I. Paredes, N. Ahmed, M. Figgins, V. Colizza, P. Lemey, J. T. McCrone, N. F. Müller, C. Tran-Kiem, T. Bedford “Underdetected dispersal and extensive local transmission drove the 2022 mpox epidemic” Cell 187(6): 1374-1386 https://doi.org/10.1016/j.cell.2024.02.003

  • M. I. Paredes, A. C. Perofsky, L. Frisbie, L. H. Moncla, P. Roychoudhury, H. Xie, S. A. M. Bakhash, K. Kong, I. Arnould, T. V. Nguyen, N. F. Müller, T. Bedford “Local-scale phylodynamics reveal differential community impact of SARS-CoV-2 in a metropolitan US county” PLoS Pathogens 20(3): e1012117 https://doi.org/10.1371/journal.ppat.1012117

  • N. Walas, N. F. Müller, E. Parker, A. Henderson, D. Capone, J. Brown, T. Barker, J. P. Graham “Application of phylodynamics to identify spread of antimicrobial-resistant Escherichia coli between humans and canines in an urban environment” Science of The Total Environment 916: 170139 https://doi.org/10.1016/j.scitotenv.2024.170139

2023

  • M. A. Lewinsohn, T. Bedford, N. F. Müller*, A. F. Feder*
    “State-dependent evolutionary models reveal modes of solid tumor growth”
    Nature Ecology & Evolution 7(4): 581–596
    https://doi.org/10.1038/s41559-023-02000-4

  • M. Layan, N. F. Müller, S. Dellicour, N. De Maio, H. Bourhy, S. Cauchemez, G. Baele
    “Impact and mitigation of sampling bias to determine viral spread: evaluating discrete phylogeography through CTMC modeling and structured coalescent model approximations”
    Virus Evolution, vead010
    https://doi.org/10.1093/ve/vead010

2022

  • N. F. Müller, K. Kistler, T. Bedford
    “A Bayesian approach to infer recombination patterns in coronaviruses.”
    Nature Communications 13(1): 1-9
    https://doi.org/10.1038/s41467-022-31749-8

  • D. Chakraborty, C. Guinat, N. F. Müller, F. Briand, M. Andraud, A. Scoizec, S. Lebouquin, E. Niqueux, A. Schmitz, B. Grasland, J. Guerin, M. C. Paul, T. Vergne
    “Phylodynamic assessment of control measures for highly pathogenic avian influenza epidemics in France.”
    Transboundary and emerging diseases.
    https://doi.org/10.1111/tbed.14490

  • U. Stolz, T. Stadler, N. F. Müller*, T. G. Vaughan*
    “Joint inference of migration and reassortment patterns for viruses with segment genomes”
    Molecular Biology and Evolution, msab342.
    https://doi.org/10.1093/molbev/msab342

2021

  • D. C. Owuor, Z. R. de Laurent, G. K. Kikwai, L. M. Mayieka, M. Ochieng, N. F. Müller, N. A. Otieno, E. N. Hunsperger, R. Garten, J. R. Barnes, S. S. Chaves, J. D. Nokes, C. N. Agoti
    “Characterizing the countrywide epidemic spread of influenza A(H1N1)pdm09 virus in Kenya between 2009 and 2018.”
    Viruses 13, no. 10: 1956.
    https://doi.org/10.3390/v13101956

  • N. F. Müller*, C. Wagner*, C. D. Frazar*, P. Roychoudhury*, A. L. Greninger, D. A. Nickerson, T. Bedford
    “Viral genomes reveal patterns of the SARS-CoV-2 outbreak in Washington State.”
    Science Translational Medicine 13(595)
    https://doi.org/10.1126/scitranslmed.abf0202

  • L. H. Moncla, A. Black, C. DeBolt, M. Lang, N. R. Graff, A. C. Pérez-Osorio, N. F. Müller, D. Haselow, S. Lindquist, T. Bedford
    “Repeated introductions and intensive community transmission fueled a mumps virus outbreak in Washington State.”
    Elife 10 (2021): e66448.
    https://doi.org/10.7554/eLife.66448

  • N. F. Müller, H. Ogilvie, C. Zhang, M. C. Fontaine, J. E. Amaya-Romero, A. Drummond, T. Stadler
    “Joint inference of species histories and gene flow.”
    BioRxiv
    https://doi.org/10.1101/348391

2020

  • N. F. Müller, D. Wüthrich, N. Goldman, N. Sailer, C. Saalfrank, M. Brunner, N. Augustin, H. M. B. Seth-Smith, Y. Hollenstein, M. Syedbasha, D. Lang, R. A. Neher, O. Dubuis, M. Naegele, A. Buser, C. H. Nickel, N. Ritz, A. Zeller, B. M. Lang, J. Hadfield, T. Bedford, M. Battegay, R. Schneider-Sliwa, A. Egli, T. Stadler
    “Characterising the epidemic spread of Influenza A/H3N2 within a city through phylogenetics”
    PLOS Pathogens 16(11): e1008984
    https://doi.org/10.1371/journal.ppat.1008984

  • N. F. Müller, R. Bouckaert
    “Adaptive Metropolis-coupled MCMC for BEAST 2”
    PeerJ 8:e9473.
    https://doi.org/10.7717/peerj.9473

  • N. F. Müller, U. Stolz, G. Dudas, T. Stadler, T. G. Vaughan
    “Bayesian inference of reassortment networks reveals fitness benefits of reassortment in human influenza viruses”
    Proceedings of the National Academy of Sciences Jul 2020, 117 (29) 17104-17111;
    https://doi.org/10.1073/pnas.1918304117

  • T. Bedford, A. L. Greninger, P. Roychoudhury, L. M. Starita, M. Famulare, M. L. Huang, A. Nalla, G. Pepper, A. Reinhardt, H. Xie, N. F. Müller, H. Y. Chu, J. Shendure, K. R. Jerome
    “Cryptic transmission of SARS-CoV-2 in Washington state”
    Science 370(6516): 571-575
    https://doi.org/10.1126/science.abc0523

  • A. Egli, N. Goldman, N. F. Müller, M. Brunner, D. Wüthrich, S. Tschudin-Sutter, E. Hodcroft, R. Neher, C. Saalfrank, J. Hadfield, T. Bedford, M. Syedbasha, T. Vogel, N. Augustin, J. Bauer, N. Sailer, N. Amar-Sliwa, D. Lang, H. M.B. Seth-Smith, A. Blaich, Y. Hollenstein, O. Dubuis, M. Nägele, A. Buser, C. H. Nickel, N. Ritz, A. Zeller, T. Stadler, M. Battegay, R. Schneider-Sliwa
    “High-resolution influenza mapping of a city reveals socioeconomic determinants of transmission within and between urban quarters.”
    BioRxiv
    https://doi.org/10.1101/2020.04.03.023135

2019

  • N. F. Müller, G. Dudas, T. Stadler
    “Inferring time-dependent migration and coalescence patterns from genetic sequence and predictor data in structured populations”
    Virus Evolution 5(2): vez030
    https://doi.org/10.1093/ve/vez030

  • J. Yang, N. F. Müller, R. Bouckaert, B. Xu, A. J. Drummond
    “Bayesian phylodynamics of avian influenza A virus H9N2 in Asia with time-dependent predictors of migration”
    PLoS Computational Biology 15(8): e1007189
    https://doi.org/10.1371/journal.pcbi.1007189

  • M. Zampieri, M. Hörl, F. Hotz, N. F. Müller, U. Sauer
    “Regulatory mechanisms underlying coordination of amino acid and glucose catabolism in Escherichia coli”
    Nature Communications 10(1): 3354
    https://doi.org/10.1038/s41467-019-11331-5

  • A. Egli, C. Saalfrank, N. Goldman, M. Brunner, Y. Hollenstein, T. Vogel, N. Augustin, D. Wüthrich, H. M. B. Seth-Smith, E. Roth, M. Syedbasha, N. F. Müller, D. Vogt, J. Bauer, N. Amar-Sliwa, D. M. Meinel, O. Dubuis, M. Naegele, S. Tschudin-Sutter, A. Buser, C. H. Nickel, A. Zeller, N. Ritz, M. Battegay, T. Stadler, R. Schneider-Sliwa
    “Identification of influenza urban transmission patterns by geographical, epidemiological and whole genome sequencing data: protocol for an observational study”
    BMJ Open 9(8): e030913
    https://doi.org/10.1136/bmjopen-2019-030913

2018

  • N. F. Müller, D. A. Rasmussen, T. Stadler
    “MASCOT: Parameter and state inference under the marginal structured coalescent approximation”
    Bioinformatics 34(22): 3843-3848
    https://doi.org/10.1093/bioinformatics/bty406

  • J. Barido-Sottani, V. Bošková, L. du Plessis, D. Kühnert, C. Magnus, V. Mitov, N. F. Müller, J. Pečerska, D. A. Rasmussen, C. Zhang, A. J. Drummond, T. Heath, O. Pybus, T. Vaughan, T. Stadler
    “Taming the BEAST—A Community Teaching Material Resource for BEAST 2”
    Systematic Biology 67(1): 170-174
    https://doi.org/10.1093/sysbio/syx060

  • R. Bouckaert, T. G. Vaughan, J. Barido-Sottani, S. Duchêne, M. Fourment, A. Gavryushkina, J. Heled, G. Jones, D. Kühnert, N. De Maio, M. Matschiner, F. K. Mendes, N. F. Müller, H. A. Ogilvie, L. du Plessis, A. Popinga, A. Rambaut, D. Rasmussen, I. Siveroni, M. A. Suchard, C. Wu, D. Xie, C. Zhang, T. Stadler, A. J. Drummond
    “BEAST 2.5: An advanced software platform for Bayesian evolutionary analysis”
    PLoS Computational Biology 15(4): e1006650
    https://doi.org/10.1371/journal.pcbi.1006650

  • D. Wüthrich, D. Lang, N. F. Müller, R. A. Neher, T. Stadler, A. Egli
    “Evaluation of two workflows for whole genome sequencing-based typing of influenza A viruses”
    Journal of Virological Methods 266: 30-33
    https://doi.org/10.1016/j.jviromet.2019.01.005

2017

  • N. F. Müller, D. A. Rasmussen, T. Stadler
    “The Structured Coalescent and its Approximations”
    Molecular Biology and Evolution 34(11): 2970-2981
    https://doi.org/10.1093/molbev/msx186