Nicola Mueller, PhD

Assistant Professor

We seek to quantify the transmission dynamics of bacterial and viral infectious diseases using pathogen genome sequence data, with the ultimate goal of informing public health interventions to reduce the disease burden. Methodologically, we use phylodynamic methods to infer transmission dynamics from pathogen genome sequence data. We are particularly interested in developing methods to infer transmission dynamics from multiple data sources, such as pathogen genome sequences, epidemiological data, and spatial data. We apply these methods to study the transmission dynamics of influenza viruses, SARS-CoV-2, and bacterial pathogens.
Education
PhD, 09/2019 - Epidemiology, Phylodynamics, ETH Zürich
MSc, 07/2016 - Biotechnology, Major in Systems Biology, ETH Zürich
BSc, 07/2015 - Biotechnology, ETH Zürich
Websites
Publications

  1. Müller NF, Bouckaert RR, Wu CH, Bedford T. MASCOT-Skyline integrates population and migration dynamics to enhance phylogeographic reconstructions. PLoS computational biology 2025. PMID: 41004543


  2. Paredes MI, Liang C, Suen SC, Holloway IW, Garrigues JM, Green NM, Bedford T, Müller NF, Osmundson J. Viral introductions and return to baseline sexual behaviors maintain low-level mpox incidence in Los Angeles County, USA, 2023-2024. medRxiv : the preprint server for health sciences 2025. PMID: 40162240


  3. Lloyd T, Khan SM, Heaton D, Shemsu M, Varghese V, Graham J, Gregory M, Dorfman P, Talton M, DeVol J, Müller NF, Trivedi KK. Genomic Modeling of an Outbreak of Multidrug-Resistant Shigella sonnei, California, USA, 2023-2024. Emerging infectious diseases 2025. PMID: 40359092


  4. Paredes MI, Perofsky AC, Frisbie L, Moncla LH, Roychoudhury P, Xie H, Bakhash SAM, Kong K, Arnould I, Nguyen TV, Wendm ST, Hajian P, Ellis S, Mathias PC, Greninger AL, Starita LM, Frazar CD, Ryke E, Zhong W, Gamboa L, Threlkeld M, Lee J, Stone J, McDermot E, Truong M, Shendure J, Oltean HN, Viboud C, Chu H, Müller NF, Bedford T. Local-scale phylodynamics reveal differential community impact of SARS-CoV-2 in a metropolitan US county. PLoS pathogens 2024. PMID: 38530853


  5. Müller NF, Bouckaert RR, Wu CH, Bedford T. MASCOT-Skyline integrates population and migration dynamics to enhance phylogeographic reconstructions. bioRxiv : the preprint server for biology 2024. PMID: 38496513


  6. Paredes MI, Ahmed N, Figgins M, Colizza V, Lemey P, McCrone JT, Müller N, Tran-Kiem C, Bedford T. Underdetected dispersal and extensive local transmission drove the 2022 mpox epidemic. Cell 2024. PMID: 38428425


  7. Walas N, Müller NF, Parker E, Henderson A, Capone D, Brown J, Barker T, Graham JP. Application of phylodynamics to identify spread of antimicrobial-resistant Escherichia coli between humans and canines in an urban environment. The Science of the total environment 2024. PMID: 38242459


  8. Paredes MI, Ahmed N, Figgins M, Colizza V, Lemey P, McCrone JT, Müller N, Tran-Kiem C, Bedford T. Early underdetected dissemination across countries followed by extensive local transmission propelled the 2022 mpox epidemic. medRxiv : the preprint server for health sciences 2023. PMID: 37577709


  9. Walas N, Müller NF, Parker E, Henderson A, Capone D, Brown J, Barker T, Graham JP. Phylodynamics Uncovers the Transmission of Antibiotic-Resistant Escherichia coli between Canines and Humans in an Urban Environment. bioRxiv : the preprint server for biology 2023. PMID: 37398411


  10. Lewinsohn MA, Bedford T, Müller NF, Feder AF. State-dependent evolutionary models reveal modes of solid tumour growth. Nature ecology & evolution 2023. PMID: 36894662


  11. Layan M, Müller NF, Dellicour S, De Maio N, Bourhy H, Cauchemez S, Baele G. Impact and mitigation of sampling bias to determine viral spread: Evaluating discrete phylogeography through CTMC modeling and structured coalescent model approximations. Virus evolution 2023. PMID: 36860641


  12. Müller NF, Kistler KE, Bedford T. A Bayesian approach to infer recombination patterns in coronaviruses. Nature communications 2022. PMID: 35859071


  13. Chakraborty D, Guinat C, Müller NF, Briand FX, Andraud M, Scoizec A, Lebouquin S, Niqueux E, Schmitz A, Grasland B, Guerin JL, Paul MC, Vergne T. Phylodynamic analysis of the highly pathogenic avian influenza H5N8 epidemic in France, 2016-2017. Transboundary and emerging diseases 2022. PMID: 35195353


  14. Stolz U, Stadler T, Müller NF, Vaughan TG. Joint Inference of Migration and Reassortment Patterns for Viruses with Segmented Genomes. Molecular biology and evolution 2022. PMID: 34893876


  15. Owuor DC, de Laurent ZR, Kikwai GK, Mayieka LM, Ochieng M, Müller NF, Otieno NA, Emukule GO, Hunsperger EA, Garten R, Barnes JR, Chaves SS, Nokes DJ, Agoti CN. Characterizing the Countrywide Epidemic Spread of Influenza A(H1N1)pdm09 Virus in Kenya between 2009 and 2018. Viruses 2021. PMID: 34696386


  16. Müller NF, Wagner C, Frazar CD, Roychoudhury P, Lee J, Moncla LH, Pelle B, Richardson M, Ryke E, Xie H, Shrestha L, Addetia A, Rachleff VM, Lieberman NAP, Huang ML, Gautom R, Melly G, Hiatt B, Dykema P, Adler A, Brandstetter E, Han PD, Fay K, Ilcisin M, Lacombe K, Sibley TR, Truong M, Wolf CR, Boeckh M, Englund JA, Famulare M, Lutz BR, Rieder MJ, Thompson M, Duchin JS, Starita LM, Chu HY, Shendure J, Jerome KR, Lindquist S, Greninger AL, Nickerson DA, Bedford T. Viral genomes reveal patterns of the SARS-CoV-2 outbreak in Washington State. Science translational medicine 2021. PMID: 33941621


  17. Moncla LH, Black A, DeBolt C, Lang M, Graff NR, Pérez-Osorio AC, Müller NF, Haselow D, Lindquist S, Bedford T. Repeated introductions and intensive community transmission fueled a mumps virus outbreak in Washington State. eLife 2021. PMID: 33871357


  18. Müller NF, Wüthrich D, Goldman N, Sailer N, Saalfrank C, Brunner M, Augustin N, Seth-Smith HM, Hollenstein Y, Syedbasha M, Lang D, Neher RA, Dubuis O, Naegele M, Buser A, Nickel CH, Ritz N, Zeller A, Lang BM, Hadfield J, Bedford T, Battegay M, Schneider-Sliwa R, Egli A, Stadler T. Characterising the epidemic spread of influenza A/H3N2 within a city through phylogenetics. PLoS pathogens 2020. PMID: 33211775


  19. Müller NF, Wagner C, Frazar CD, Roychoudhury P, Lee J, Moncla LH, Pelle B, Richardson M, Ryke E, Xie H, Shrestha L, Addetia A, Rachleff VM, Lieberman NAP, Huang ML, Gautom R, Melly G, Hiatt B, Dykema P, Adler A, Brandstetter E, Han PD, Fay K, Llcisin M, Lacombe K, Sibley TR, Truong M, Wolf CR, Boeckh M, Englund JA, Famulare M, Lutz BR, Rieder MJ, Thompson M, Duchin JS, Starita LM, Chu HY, Shendure J, Jerome KR, Lindquist S, Greninger AL, Nickerson DA, Bedford T. Viral genomes reveal patterns of the SARS-CoV-2 outbreak in Washington State. medRxiv : the preprint server for health sciences 2020. PMID: 33024981


  20. Müller NF, Bouckaert RR. Adaptive Metropolis-coupled MCMC for BEAST 2. PeerJ 2020. PMID: 32995072


  21. Bedford T, Greninger AL, Roychoudhury P, Starita LM, Famulare M, Huang ML, Nalla A, Pepper G, Reinhardt A, Xie H, Shrestha L, Nguyen TN, Adler A, Brandstetter E, Cho S, Giroux D, Han PD, Fay K, Frazar CD, Ilcisin M, Lacombe K, Lee J, Kiavand A, Richardson M, Sibley TR, Truong M, Wolf CR, Nickerson DA, Rieder MJ, Englund JA, Seattle Flu Study Investigators, Hadfield J, Hodcroft EB, Huddleston J, Moncla LH, Müller NF, Neher RA, Deng X, Gu W, Federman S, Chiu C, Duchin JS, Gautom R, Melly G, Hiatt B, Dykema P, Lindquist S, Queen K, Tao Y, Uehara A, Tong S, MacCannell D, Armstrong GL, Baird GS, Chu HY, Shendure J, Jerome KR. Cryptic transmission of SARS-CoV-2 in Washington state. Science (New York, N.Y.) 2020. PMID: 32913002


  22. Müller NF, Stolz U, Dudas G, Stadler T, Vaughan TG. Bayesian inference of reassortment networks reveals fitness benefits of reassortment in human influenza viruses. Proceedings of the National Academy of Sciences of the United States of America 2020. PMID: 32631984


  23. Egli A, Saalfrank C, Goldman N, Brunner M, Hollenstein Y, Vogel T, Augustin N, Wüthrich D, Seth-Smith HMB, Roth E, Syedbasha M, Mueller NF, Vogt D, Bauer J, Amar-Sliwa N, Meinel DM, Dubuis O, Naegele M, Tschudin-Sutter S, Buser A, Nickel CH, Zeller A, Ritz N, Battegay M, Stadler T, Schneider-Sliwa R. Identification of influenza urban transmission patterns by geographical, epidemiological and whole genome sequencing data: protocol for an observational study. BMJ open 2019. PMID: 31434783


  25. Yang J, Müller NF, Bouckaert R, Xu B, Drummond AJ. Bayesian phylodynamics of avian influenza A virus H9N2 in Asia with time-dependent predictors of migration. PLoS computational biology 2019. PMID: 31386651


  26. Zampieri M, Hörl M, Hotz F, Müller NF, Sauer U. Regulatory mechanisms underlying coordination of amino acid and glucose catabolism in Escherichia coli. Nature communications 2019. PMID: 31350417


  27. Bouckaert R, Vaughan TG, Barido-Sottani J, Duchêne S, Fourment M, Gavryushkina A, Heled J, Jones G, Kühnert D, De Maio N, Matschiner M, Mendes FK, Müller NF, Ogilvie HA, du Plessis L, Popinga A, Rambaut A, Rasmussen D, Siveroni I, Suchard MA, Wu CH, Xie D, Zhang C, Stadler T, Drummond AJ. BEAST 2.5: An advanced software platform for Bayesian evolutionary analysis. PLoS computational biology 2019. PMID: 30958812


  28. Wüthrich D, Lang D, Müller NF, Neher RA, Stadler T, Egli A. Evaluation of two workflows for whole genome sequencing-based typing of influenza A viruses. Journal of virological methods 2019. PMID: 30677464


  29. Müller NF, Rasmussen D, Stadler T. MASCOT: parameter and state inference under the marginal structured coalescent approximation. Bioinformatics (Oxford, England) 2018. PMID: 29790921


  30. Merks AM, Swinarski M, Meyer AM, Müller NV, Özcan I, Donat S, Burger A, Gilbert S, Mosimann C, Abdelilah-Seyfried S, Panáková D. Planar cell polarity signalling coordinates heart tube remodelling through tissue-scale polarisation of actomyosin activity. Nature communications 2018. PMID: 29867082


  31. Barido-Sottani J, Bošková V, Plessis LD, Kühnert D, Magnus C, Mitov V, Müller NF, PecErska J, Rasmussen DA, Zhang C, Drummond AJ, Heath TA, Pybus OG, Vaughan TG, Stadler T. Taming the BEAST-A Community Teaching Material Resource for BEAST 2. Systematic biology 2018. PMID: 28673048


  32. Müller NF, Rasmussen DA, Stadler T. The Structured Coalescent and Its Approximations. Molecular biology and evolution 2017. PMID: 28666382