Publications
And up to date List of publications can be found here: Google Scholar
2023Permalink
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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).
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 -
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.
https://doi.org/10.1101%2F2023.06.01.543064 -
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.”
medRxiv
https://doi.org/10.1101/2023.07.27.23293266 -
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.”
medRxiv
https://doi.org/10.1101/2022.12.15.22283536 -
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.”
BioRxiv
https://doi.org/10.1101/2022.10.27.514108
2022Permalink
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N. F. Müller, K. Kistler, T. Bedford
“A Bayesian approach to infer recombination patterns in coronaviruses.”
Nature Communications 13, 4186.
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
2021Permalink
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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 2021 May 26;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, A. Drummond, T. Stadler
“Inference of species histories in the presence of gene flow.”
BioRxiv
https://doi.org/10.1101/348391
2020Permalink
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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.
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, …, 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.
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
2019Permalink
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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.
https://doi.org/10.1093/ve/vez030 -
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.
https://doi.org/10.1371/journal.pcbi.10071 -
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.
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), p.e030913.
https://doi.org/10.1136/bmjopen-2019-030913
2018Permalink
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N. F. Müller, D. A. Rasmussen, T. Stadler
“MASCOT: parameter and state inference under the marginal structured coalescent approximation.”
Bioinformatics, bty406.
https://doi.org/10.1093/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.
https://doi.org/10.1093/sysbio/syx060
2017Permalink
- 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.
https://doi.org/10.1093/molbev/msx186