Nicola Mueller, PhD
Assistant Professor
Medicine
School of Medicine

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.

• Phylodynamics Uncovers the Transmission of Antibiotic-Resistant Escherichia coli between Canines and Humans in an Urban Environment.
  bioRxiv : the preprint server for biology 2023 Walas N, Müller NF, Parker E, Henderson A, Capone D, Brown J, Barker T, Graham JP
• State-dependent evolutionary models reveal modes of solid tumour growth.
  Nature ecology & evolution 2023 Lewinsohn MA, Bedford T, Müller NF, Feder AF
• Impact and mitigation of sampling bias to determine viral spread: Evaluating discrete phylogeography through CTMC modeling and structured coalescent model approximations.
  Virus evolution 2023 Layan M, Müller NF, Dellicour S, De Maio N, Bourhy H, Cauchemez S, Baele G
• A Bayesian approach to infer recombination patterns in coronaviruses.
  Nature communications 2022 Müller NF, Kistler KE, Bedford T
• Phylodynamic analysis of the highly pathogenic avian influenza H5N8 epidemic in France, 2016-2017.
  Transboundary and emerging diseases 2022 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
• Joint Inference of Migration and Reassortment Patterns for Viruses with Segmented Genomes.
  Molecular biology and evolution 2022 Stolz U, Stadler T, Müller NF, Vaughan TG
• Characterizing the Countrywide Epidemic Spread of Influenza A(H1N1)pdm09 Virus in Kenya between 2009 and 2018.
  Viruses 2021 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
• Viral genomes reveal patterns of the SARS-CoV-2 outbreak in Washington State.
  Science translational medicine 2021 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 …
• Repeated introductions and intensive community transmission fueled a mumps virus outbreak in Washington State.
  eLife 2021 Moncla LH, Black A, DeBolt C, Lang M, Graff NR, Pérez-Osorio AC, Müller NF, Haselow D, Lindquist S, Bedford T
• Characterising the epidemic spread of influenza A/H3N2 within a city through phylogenetics.
  PLoS pathogens 2020 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, …
• Viral genomes reveal patterns of the SARS-CoV-2 outbreak in Washington State.
  medRxiv : the preprint server for health sciences 2020 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 …
• Adaptive Metropolis-coupled MCMC for BEAST 2.
  PeerJ 2020 Müller NF, Bouckaert RR
• Cryptic transmission of SARS-CoV-2 in Washington state.
  Science (New York, N.Y.) 2020 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…
• 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 Müller NF, Stolz U, Dudas G, Stadler T, Vaughan TG
• Identification of influenza urban transmission patterns by geographical, epidemiological and whole genome sequencing data: protocol for an observational study.
  BMJ open 2019 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 …
• Inferring time-dependent migration and coalescence patterns from genetic sequence and predictor data in structured populations.
  Virus evolution 2019 Müller NF, Dudas G, Stadler T
• Bayesian phylodynamics of avian influenza A virus H9N2 in Asia with time-dependent predictors of migration.
  PLoS computational biology 2019 Yang J, Müller NF, Bouckaert R, Xu B, Drummond AJ
• Regulatory mechanisms underlying coordination of amino acid and glucose catabolism in Escherichia coli.
  Nature communications 2019 Zampieri M, Hörl M, Hotz F, Müller NF, Sauer U
• BEAST 2.5: An advanced software platform for Bayesian evolutionary analysis.
  PLoS computational biology 2019 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, …
• Evaluation of two workflows for whole genome sequencing-based typing of influenza A viruses.
  Journal of virological methods 2019 Wüthrich D, Lang D, Müller NF, Neher RA, Stadler T, Egli A
• MASCOT: parameter and state inference under the marginal structured coalescent approximation.
  Bioinformatics (Oxford, England) 2018 Müller NF, Rasmussen D, Stadler T
• Planar cell polarity signalling coordinates heart tube remodelling through tissue-scale polarisation of actomyosin activity.
  Nature communications 2018 Merks AM, Swinarski M, Meyer AM, Müller NV, Özcan I, Donat S, Burger A, Gilbert S, Mosimann C, Abdelilah-Seyfried S, Panáková D
• Taming the BEAST-A Community Teaching Material Resource for BEAST 2.
  Systematic biology 2018 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
• The Structured Coalescent and Its Approximations.
  Molecular biology and evolution 2017 Müller NF, Rasmussen DA, Stadler T