Nicola Mueller, PhD

Title(s)Assistant Professor, Medicine
SchoolSchool of Medicine
Address1001 Potrero Avenue
San Francisco CA 94110
ORCID ORCID Icon0000-0002-2927-1002 Additional info
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    ETH Zürich, Zürich, SwitzerlandBSc07/2015Biotechnology
    ETH Zürich, Zürich, SwitzerlandMSc07/2016Biotechnology, Major in Systems Biology
    ETH Zürich, Zürich, SwitzerlandPhD09/2019Epidemiology, Phylodynamics

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    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.

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    Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Researchers can login to make corrections and additions, or contact us for help. to make corrections and additions.
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    Altmetrics Details PMC Citations indicate the number of times the publication was cited by articles in PubMed Central, and the Altmetric score represents citations in news articles and social media. (Note that publications are often cited in additional ways that are not shown here.) Fields are based on how the National Library of Medicine (NLM) classifies the publication's journal and might not represent the specific topic of the publication. Translation tags are based on the publication type and the MeSH terms NLM assigns to the publication. Some publications (especially newer ones and publications not in PubMed) might not yet be assigned Field or Translation tags.) Click a Field or Translation tag to filter the publications.
    1. Local-scale phylodynamics reveal differential community impact of SARS-CoV-2 in a metropolitan US county. PLoS Pathog. 2024 Mar; 20(3):e1012117. 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. PMID: 38530853; PMCID: PMC10997136.
      View in: PubMed   Mentions: 1     Fields:    Translation:HumansCellsPHPublic Health
    2. MASCOT-Skyline integrates population and migration dynamics to enhance phylogeographic reconstructions. bioRxiv. 2024 Mar 13. Müller NF, Bouckaert RR, Wu CH, Bedford T. PMID: 38496513; PMCID: PMC10942421.
      View in: PubMed   Mentions:
    3. Underdetected dispersal and extensive local transmission drove the 2022 mpox epidemic. Cell. 2024 Mar 14; 187(6):1374-1386.e13. Paredes MI, Ahmed N, Figgins M, Colizza V, Lemey P, McCrone JT, Müller N, Tran-Kiem C, Bedford T. PMID: 38428425; PMCID: PMC10962340.
      View in: PubMed   Mentions:    Fields:    Translation:HumansCellsPHPublic Health
    4. Application of phylodynamics to identify spread of antimicrobial-resistant Escherichia coli between humans and canines in an urban environment. Sci Total Environ. 2024 Mar 15; 916:170139. Walas N, Müller NF, Parker E, Henderson A, Capone D, Brown J, Barker T, Graham JP. PMID: 38242459.
      View in: PubMed   Mentions:    Fields:    Translation:HumansAnimalsCells
    5. Early underdetected dissemination across countries followed by extensive local transmission propelled the 2022 mpox epidemic. medRxiv. 2023 Dec 07. Paredes MI, Ahmed N, Figgins M, Colizza V, Lemey P, McCrone JT, Müller N, Tran-Kiem C, Bedford T. PMID: 37577709; PMCID: PMC10418578.
      View in: PubMed   Mentions:
    6. Phylodynamics Uncovers the Transmission of Antibiotic-Resistant Escherichia coli between Canines and Humans in an Urban Environment. bioRxiv. 2023 Jun 01. Walas N, Müller NF, Parker E, Henderson A, Capone D, Brown J, Barker T, Graham JP. PMID: 37398411; PMCID: PMC10312604.
      View in: PubMed   Mentions:
    7. State-dependent evolutionary models reveal modes of solid tumour growth. Nat Ecol Evol. 2023 04; 7(4):581-596. Lewinsohn MA, Bedford T, Müller NF, Feder AF. PMID: 36894662; PMCID: PMC10089931.
      View in: PubMed   Mentions: 12     Fields:    Translation:Humans
    8. Impact and mitigation of sampling bias to determine viral spread: Evaluating discrete phylogeography through CTMC modeling and structured coalescent model approximations. Virus Evol. 2023; 9(1):vead010. Layan M, Müller NF, Dellicour S, De Maio N, Bourhy H, Cauchemez S, Baele G. PMID: 36860641; PMCID: PMC9969415.
      View in: PubMed   Mentions: 11  
    9. A Bayesian approach to infer recombination patterns in coronaviruses. Nat Commun. 2022 07 20; 13(1):4186. Müller NF, Kistler KE, Bedford T. PMID: 35859071; PMCID: PMC9297283.
      View in: PubMed   Mentions: 19     Fields:    Translation:HumansCells
    10. Phylodynamic analysis of the highly pathogenic avian influenza H5N8 epidemic in France, 2016-2017. Transbound Emerg Dis. 2022 Sep; 69(5):e1574-e1583. 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. PMID: 35195353.
      View in: PubMed   Mentions: 4     Fields:    Translation:AnimalsCellsPHPublic Health
    11. Joint Inference of Migration and Reassortment Patterns for Viruses with Segmented Genomes. Mol Biol Evol. 2022 01 07; 39(1). Stolz U, Stadler T, Müller NF, Vaughan TG. PMID: 34893876; PMCID: PMC8789051.
      View in: PubMed   Mentions: 4     Fields:    Translation:HumansAnimalsCells
    12. Characterizing the Countrywide Epidemic Spread of Influenza A(H1N1)pdm09 Virus in Kenya between 2009 and 2018. Viruses. 2021 09 29; 13(10). 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. PMID: 34696386; PMCID: PMC8539974.
      View in: PubMed   Mentions: 2     Fields:    Translation:HumansCellsPHPublic Health
    13. Viral genomes reveal patterns of the SARS-CoV-2 outbreak in Washington State. Sci Transl Med. 2021 05 26; 13(595). 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. PMID: 33941621; PMCID: PMC8158963.
      View in: PubMed   Mentions: 34     Fields:    Translation:HumansCellsPHPublic Health
    14. Repeated introductions and intensive community transmission fueled a mumps virus outbreak in Washington State. Elife. 2021 04 19; 10. Moncla LH, Black A, DeBolt C, Lang M, Graff NR, Pérez-Osorio AC, Müller NF, Haselow D, Lindquist S, Bedford T. PMID: 33871357; PMCID: PMC8079146.
      View in: PubMed   Mentions: 5     Fields:    Translation:HumansCellsPHPublic Health
    15. Characterising the epidemic spread of influenza A/H3N2 within a city through phylogenetics. PLoS Pathog. 2020 11; 16(11):e1008984. 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. PMID: 33211775; PMCID: PMC7676729.
      View in: PubMed   Mentions: 9     Fields:    Translation:HumansCellsPHPublic Health
    16. Viral genomes reveal patterns of the SARS-CoV-2 outbreak in Washington State. medRxiv. 2020 Sep 30. 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. PMID: 33024981; PMCID: PMC7536883.
      View in: PubMed   Mentions:
    17. Adaptive Metropolis-coupled MCMC for BEAST 2. PeerJ. 2020; 8:e9473. Müller NF, Bouckaert RR. PMID: 32995072; PMCID: PMC7501786.
      View in: PubMed   Mentions: 13     Fields:    
    18. Cryptic transmission of SARS-CoV-2 in Washington state. Science. 2020 10 30; 370(6516):571-575. 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. PMID: 32913002; PMCID: PMC7810035.
      View in: PubMed   Mentions: 170     Fields:    Translation:HumansCellsPHPublic Health
    19. Bayesian inference of reassortment networks reveals fitness benefits of reassortment in human influenza viruses. Proc Natl Acad Sci U S A. 2020 07 21; 117(29):17104-17111. Müller NF, Stolz U, Dudas G, Stadler T, Vaughan TG. PMID: 32631984; PMCID: PMC7382287.
      View in: PubMed   Mentions: 18     Fields:    Translation:HumansCells
    20. Identification of influenza urban transmission patterns by geographical, epidemiological and whole genome sequencing data: protocol for an observational study. BMJ Open. 2019 08 20; 9(8):e030913. 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. PMID: 31434783; PMCID: PMC6707652.
      View in: PubMed   Mentions: 1     Fields:    Translation:HumansCellsPHPublic Health
    21. Inferring time-dependent migration and coalescence patterns from genetic sequence and predictor data in structured populations. Virus Evol. 2019 Jul; 5(2):vez030. Müller NF, Dudas G, Stadler T. PMID: 31428459; PMCID: PMC6693038.
      View in: PubMed   Mentions: 16  
    22. Bayesian phylodynamics of avian influenza A virus H9N2 in Asia with time-dependent predictors of migration. PLoS Comput Biol. 2019 08; 15(8):e1007189. Yang J, Müller NF, Bouckaert R, Xu B, Drummond AJ. PMID: 31386651; PMCID: PMC6684064.
      View in: PubMed   Mentions: 15     Fields:    Translation:AnimalsCellsPHPublic Health
    23. Regulatory mechanisms underlying coordination of amino acid and glucose catabolism in Escherichia coli. Nat Commun. 2019 07 26; 10(1):3354. Zampieri M, Hörl M, Hotz F, Müller NF, Sauer U. PMID: 31350417; PMCID: PMC6659692.
      View in: PubMed   Mentions: 44     Fields:    Translation:Cells
    24. BEAST 2.5: An advanced software platform for Bayesian evolutionary analysis. PLoS Comput Biol. 2019 04; 15(4):e1006650. 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. PMID: 30958812; PMCID: PMC6472827.
      View in: PubMed   Mentions: 998     Fields:    Translation:HumansAnimals
    25. Evaluation of two workflows for whole genome sequencing-based typing of influenza A viruses. J Virol Methods. 2019 04; 266:30-33. Wüthrich D, Lang D, Müller NF, Neher RA, Stadler T, Egli A. PMID: 30677464.
      View in: PubMed   Mentions: 4     Fields:    Translation:HumansCells
    26. MASCOT: parameter and state inference under the marginal structured coalescent approximation. Bioinformatics. 2018 11 15; 34(22):3843-3848. Müller NF, Rasmussen D, Stadler T. PMID: 29790921; PMCID: PMC6223361.
      View in: PubMed   Mentions: 43     Fields:    Translation:Cells
    27. Planar cell polarity signalling coordinates heart tube remodelling through tissue-scale polarisation of actomyosin activity. Nat Commun. 2018 06 04; 9(1):2161. Merks AM, Swinarski M, Meyer AM, Müller NV, Özcan I, Donat S, Burger A, Gilbert S, Mosimann C, Abdelilah-Seyfried S, Panáková D. PMID: 29867082; PMCID: PMC5986786.
      View in: PubMed   Mentions: 18     Fields:    Translation:AnimalsCells
    28. Taming the BEAST-A Community Teaching Material Resource for BEAST 2. Syst Biol. 2018 01 01; 67(1):170-174. 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. PMID: 28673048; PMCID: PMC5925777.
      View in: PubMed   Mentions: 37     Fields:    
    29. The Structured Coalescent and Its Approximations. Mol Biol Evol. 2017 Nov 01; 34(11):2970-2981. Müller NF, Rasmussen DA, Stadler T. PMID: 28666382; PMCID: PMC5850743.
      View in: PubMed   Mentions: 41     Fields:    Translation:Humans
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