• M. A. Lewinsohn, T. Bedford, N. F. Müller*, A. F. Feder*
    “State-dependent evolutionary models reveal modes of solid tumor growth”
    Accepted for publication in Nat Ecol Evol 7, 581–596 (2023).

  • 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

  • N. Walas, N. F. Müller, E. Parker, A. Henderson, D. Capone, J. Brown, T. Barker, J. P. Graham
    “Phylodynamics Uncovers the Transmission of Antibiotic-Resistant Escherichia coli between Canines and Humans in an Urban Environment.”
    BioRxiv, 2023.

  • M. I. Paredes, N. Ahmed, M. Figgins, V. Colizza, P. Lemey, J. T. McCrone, N. F. Müller, C. Tran-Kiem, T. Bedford
    “Early underdetected dissemination across countries followed by extensive local transmission propelled the 2022 mpox epidemic.”

  • M. I. Paredes, A. C. Perofsky, C. Viboud, H. Chu, N. F. Müller*, T. Bedford*
    “Local-Scale phylodynamics reveal differential community impact of SARS-CoV-2 in metropolitan US county.”

  • N. F. Müller, S. Duchêne, D. A. Williamson, B. Howden, D. J. Ingle
    “Tracking the horizontal transfer of plasmids in Shigella sonnei and Shigella flexneri using phylogenetics.”


  • N. F. Müller, K. Kistler, T. Bedford
    “A Bayesian approach to infer recombination patterns in coronaviruses.”
    Nature Communications 13, 4186.

  • 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.

  • 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.


  • 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.

  • 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 2021 May 26;13(595).

  • 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.

  • N. F. Müller, H. Ogilvie, C. Zhang, A. Drummond, T. Stadler
    “Inference of species histories in the presence of gene flow.”


  • N. F. Müller, D. Wüthrich, 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.

  • N. F. Müller, R. Bouckaert
    “Adaptive Metropolis-coupled MCMC for BEAST 2”
    PeerJ 8:e9473.

  • 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;

  • T. Bedford, A. L. Greninger, P. Roychoudhury, …, N. F. Müller, …, H. Y. Chu, J. Shendure, K. R. Jerome,
    “Cryptic transmission of SARS-CoV-2 in Washington state”,
    Science 370, no. 6516 (2020): 571-575.

  • 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.”


  • 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.

  • J. Yang, N. F. Müller, R. Bouckaert, B. Xu & A. J. Drummond
    “Bayesian phylodynamics of avian influenza virus H9N2 in Asia with time-dependent predictors of migration”
    PLoS Computational Biology.

  • 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.

  • 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), p.e030913.


  • N. F. Müller, D. A. Rasmussen, T. Stadler
    “MASCOT: parameter and state inference under the marginal structured coalescent approximation.”
    Bioinformatics, bty406.

  • J. Barido-Sottani, V. Boskova, L. du Plessis, D. Kühnert, C. Magnus, V. Mitov, N. F. Müller, J. Pecerska, D. 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, Volume 67, Issue 1, Pages 170–174.


  • N. F. Müller, D. A. Rasmussen, T. Stadler
    “The Structured Coalescent and its Approximations.”
    Molecular Biology and Evolution, Volume 34, Issue 11, Pages 2970–2981.