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Items: 1 to 50 of 173


Identification of influenza urban transmission patterns by geographical, epidemiological and whole genome sequencing data: protocol for an observational study.

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.

BMJ Open. 2019 Aug 20;9(8):e030913. doi: 10.1136/bmjopen-2019-030913.


Inferring time-dependent migration and coalescence patterns from genetic sequence and predictor data in structured populations.

Müller NF, Dudas G, Stadler T.

Virus Evol. 2019 Aug 14;5(2):vez030. doi: 10.1093/ve/vez030. eCollection 2019 Jul.


Coupling adaptive molecular evolution to phylodynamics using fitness-dependent birth-death models.

Rasmussen DA, Stadler T.

Elife. 2019 Aug 15;8. pii: e45562. doi: 10.7554/eLife.45562.


Automatic generation of evolutionary hypotheses using mixed Gaussian phylogenetic models.

Mitov V, Bartoszek K, Stadler T.

Proc Natl Acad Sci U S A. 2019 Aug 20;116(34):16921-16926. doi: 10.1073/pnas.1813823116. Epub 2019 Aug 2.


[Benefits of Molecular Analyses in Thyroid Carcinoma].

Stadler TM, Morand GB, Rupp NJ, Freiberger SN, Broglie MA.

Praxis (Bern 1994). 2019 Jun;108(8):535-540. doi: 10.1024/1661-8157/a003240. German.


Species-specific diversification.

Stadler T.

Nat Ecol Evol. 2019 Jul;3(7):1003-1004. doi: 10.1038/s41559-019-0923-1. No abstract available.


Swapping Birth and Death: Symmetries and Transformations in Phylodynamic Models.

Stadler T, Steel M.

Syst Biol. 2019 Sep 1;68(5):852-858. doi: 10.1093/sysbio/syz039.


Ignoring stratigraphic age uncertainty leads to erroneous estimates of species divergence times under the fossilized birth-death process.

Barido-Sottani J, Aguirre-Fernández G, Hopkins MJ, Stadler T, Warnock R.

Proc Biol Sci. 2019 May 15;286(1902):20190685. doi: 10.1098/rspb.2019.0685.


Estimating Epidemic Incidence and Prevalence from Genomic Data.

Vaughan TG, Leventhal GE, Rasmussen DA, Drummond AJ, Welch D, Stadler T.

Mol Biol Evol. 2019 Aug 1;36(8):1804-1816. doi: 10.1093/molbev/msz106.


Exploring the power of Bayesian birth-death skyline models to detect mass extinction events from phylogenies with only extant taxa.

Culshaw V, Stadler T, Sanmartín I.

Evolution. 2019 Jun;73(6):1133-1150. doi: 10.1111/evo.13753. Epub 2019 May 9.


Asymmetric division events promote variability in cell cycle duration in animal cells and Escherichia coli.

Berge U, Bochenek D, Schnabel R, Wehling A, Schroeder T, Stadler T, Kroschewski R.

Nat Commun. 2019 Apr 23;10(1):1901. doi: 10.1038/s41467-019-09413-5.


Earlier Initiation of Antiretroviral Treatment Coincides With an Initial Control of the HIV-1 Sub-Subtype F1 Outbreak Among Men-Having-Sex-With-Men in Flanders, Belgium.

Vinken L, Fransen K, Cuypers L, Alexiev I, Balotta C, Debaisieux L, Seguin-Devaux C, García Ribas S, Gomes P, Incardona F, Kaiser R, Ruelle J, Sayan M, Paraschiv S, Paredes R, Peeters M, Sönnerborg A, Vancutsem E, Vandamme AM, Van den Wijngaert S, Van Ranst M, Verhofstede C, Stadler T, Lemey P, Van Laethem K.

Front Microbiol. 2019 Mar 26;10:613. doi: 10.3389/fmicb.2019.00613. eCollection 2019.


BEAST 2.5: An advanced software platform for Bayesian evolutionary analysis.

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.

PLoS Comput Biol. 2019 Apr 8;15(4):e1006650. doi: 10.1371/journal.pcbi.1006650. eCollection 2019 Apr.


Differences in Effective Ploidy Drive Genome-Wide Endosperm Expression Polarization and Seed Failure in Wild Tomato Hybrids.

Roth M, Florez-Rueda AM, Städler T.

Genetics. 2019 May;212(1):141-152. doi: 10.1534/genetics.119.302056. Epub 2019 Mar 22.


Congenital fistula of the fourth branchial arch: Report of case with long-lasting misdiagnosis.

Stadler TM, Morand GB, Schmid S, Broglie MA.

Clin Case Rep. 2019 Jan 1;7(2):295-298. doi: 10.1002/ccr3.1965. eCollection 2019 Feb.


Evaluation of two workflows for whole genome sequencing-based typing of influenza A viruses.

Wüthrich D, Lang D, Müller NF, Neher RA, Stadler T, Egli A.

J Virol Methods. 2019 Apr;266:30-33. doi: 10.1016/j.jviromet.2019.01.009. Epub 2019 Jan 21.


Tracking external introductions of HIV using phylodynamics reveals a major source of infections in rural KwaZulu-Natal, South Africa.

Rasmussen DA, Wilkinson E, Vandormael A, Tanser F, Pillay D, Stadler T, de Oliveira T.

Virus Evol. 2018 Dec 11;4(2):vey037. doi: 10.1093/ve/vey037. eCollection 2018 Jul.


Closing the gap between palaeontological and neontological speciation and extinction rate estimates.

Silvestro D, Warnock RCM, Gavryushkina A, Stadler T.

Nat Commun. 2018 Dec 7;9(1):5237. doi: 10.1038/s41467-018-07622-y.


The relationship between transmission time and clustering methods in Mycobacterium tuberculosis epidemiology.

Meehan CJ, Moris P, Kohl TA, Pečerska J, Akter S, Merker M, Utpatel C, Beckert P, Gehre F, Lempens P, Stadler T, Kaswa MK, Kühnert D, Niemann S, de Jong BC.

EBioMedicine. 2018 Nov;37:410-416. doi: 10.1016/j.ebiom.2018.10.013. Epub 2018 Oct 16.


Tracing Antibody Repertoire Evolution by Systems Phylogeny.

Yermanos AD, Dounas AK, Stadler T, Oxenius A, Reddy ST.

Front Immunol. 2018 Oct 2;9:2149. doi: 10.3389/fimmu.2018.02149. eCollection 2018. Review.


Detection of HIV transmission clusters from phylogenetic trees using a multi-state birth-death model.

Barido-Sottani J, Vaughan TG, Stadler T.

J R Soc Interface. 2018 Sep;15(146). pii: 20180512. doi: 10.1098/rsif.2018.0512.


Wild tomato endosperm transcriptomes reveal common roles of genomic imprinting in both nuclear and cellular endosperm.

Roth M, Florez-Rueda AM, Paris M, Städler T.

Plant J. 2018 Sep;95(6):1084-1101. doi: 10.1111/tpj.14012. Epub 2018 Jul 29.


Phylodynamic Model Adequacy Using Posterior Predictive Simulations.

Duchene S, Bouckaert R, Duchene DA, Stadler T, Drummond AJ.

Syst Biol. 2019 Mar 1;68(2):358-364. doi: 10.1093/sysbio/syy048.


TreeSimGM: Simulating phylogenetic trees under general Bellman-Harris models with lineage-specific shifts of speciation and extinction in R.

Hagen O, Stadler T.

Methods Ecol Evol. 2018 Mar;9(3):754-760. doi: 10.1111/2041-210X.12917. Epub 2017 Nov 13.


Tuberculosis outbreak investigation using phylodynamic analysis.

Kühnert D, Coscolla M, Brites D, Stucki D, Metcalfe J, Fenner L, Gagneux S, Stadler T.

Epidemics. 2018 Dec;25:47-53. doi: 10.1016/j.epidem.2018.05.004. Epub 2018 May 22.


MASCOT: parameter and state inference under the marginal structured coalescent approximation.

Müller NF, Rasmussen D, Stadler T.

Bioinformatics. 2018 Nov 15;34(22):3843-3848. doi: 10.1093/bioinformatics/bty406.


Impact of the tree prior on estimating clock rates during epidemic outbreaks.

Möller S, du Plessis L, Stadler T.

Proc Natl Acad Sci U S A. 2018 Apr 17;115(16):4200-4205. doi: 10.1073/pnas.1713314115. Epub 2018 Apr 2.


The fossilized birth-death model for the analysis of stratigraphic range data under different speciation modes.

Stadler T, Gavryushkina A, Warnock RCM, Drummond AJ, Heath TA.

J Theor Biol. 2018 Jun 14;447:41-55. doi: 10.1016/j.jtbi.2018.03.005. Epub 2018 Mar 14.


Advanced Rotator Cuff Tear Score (ARoCuS): a multi-scaled tool for the classification and description of rotator cuff tears.

Walter SG, Stadler T, Thomas TS, Thomas W.

Musculoskelet Surg. 2019 Apr;103(1):37-45. doi: 10.1007/s12306-018-0535-y. Epub 2018 Mar 2.


Quantifying the fitness cost of HIV-1 drug resistance mutations through phylodynamics.

Kühnert D, Kouyos R, Shirreff G, Pečerska J, Scherrer AU, Böni J, Yerly S, Klimkait T, Aubert V, Günthard HF, Stadler T, Bonhoeffer S; Swiss HIV Cohort Study.

PLoS Pathog. 2018 Feb 20;14(2):e1006895. doi: 10.1371/journal.ppat.1006895. eCollection 2018 Feb.


Transmission of ESBL-producing Enterobacteriaceae and their mobile genetic elements-identification of sources by whole genome sequencing: study protocol for an observational study in Switzerland.

Stadler T, Meinel D, Aguilar-Bultet L, Huisman JS, Schindler R, Egli A, Seth-Smith HMB, Eichenberger L, Brodmann P, Hübner P, Bagutti C, Tschudin-Sutter S.

BMJ Open. 2018 Feb 17;8(2):e021823. doi: 10.1136/bmjopen-2018-021823.


The influence of phylodynamic model specifications on parameter estimates of the Zika virus epidemic.

Boskova V, Stadler T, Magnus C.

Virus Evol. 2018 Jan 29;4(1):vex044. doi: 10.1093/ve/vex044. eCollection 2018 Jan.


A Practical Guide to Estimating the Heritability of Pathogen Traits.

Mitov V, Stadler T.

Mol Biol Evol. 2018 Jan 9. doi: 10.1093/molbev/msx328. [Epub ahead of print]


Incidence and developmental timing of endosperm failure in post-zygotic isolation between wild tomato lineages.

Roth M, Florez-Rueda AM, Griesser S, Paris M, Städler T.

Ann Bot. 2018 Jan 25;121(1):107-118. doi: 10.1093/aob/mcx133.


Vaccination of dogs in an African city interrupts rabies transmission and reduces human exposure.

Zinsstag J, Lechenne M, Laager M, Mindekem R, Naïssengar S, Oussiguéré A, Bidjeh K, Rives G, Tessier J, Madjaninan S, Ouagal M, Moto DD, Alfaroukh IO, Muthiani Y, Traoré A, Hattendorf J, Lepelletier A, Kergoat L, Bourhy H, Dacheux L, Stadler T, Chitnis N.

Sci Transl Med. 2017 Dec 20;9(421). pii: eaaf6984. doi: 10.1126/scitranslmed.aaf6984.


Bayesian Inference of Species Networks from Multilocus Sequence Data.

Zhang C, Ogilvie HA, Drummond AJ, Stadler T.

Mol Biol Evol. 2018 Feb 1;35(2):504-517. doi: 10.1093/molbev/msx307.


On the statistical analysis of single cell lineage trees.

Stadler T, Skylaki S, D Kokkaliaris K, Schroeder T.

J Theor Biol. 2018 Feb 14;439:160-165. doi: 10.1016/j.jtbi.2017.11.023. Epub 2017 Dec 5.


Long-term continuous renal replacement therapy and anticoagulation with citrate in critically ill patients with severe liver dysfunction.

Klingele M, Stadler T, Fliser D, Speer T, Groesdonk HV, Raddatz A.

Crit Care. 2017 Nov 29;21(1):294. doi: 10.1186/s13054-017-1870-3.


Mathematical Models for the Epidemiology and Evolution of Mycobacterium tuberculosis.

Pečerska J, Wood J, Tanaka MM, Stadler T.

Adv Exp Med Biol. 2017;1019:281-307. doi: 10.1007/978-3-319-64371-7_15. Review.


Comparison of methods for phylogenetic B-cell lineage inference using time-resolved antibody repertoire simulations (AbSim).

Yermanos A, Greiff V, Krautler NJ, Menzel U, Dounas A, Miho E, Oxenius A, Stadler T, Reddy ST.

Bioinformatics. 2017 Dec 15;33(24):3938-3946. doi: 10.1093/bioinformatics/btx533.


Impact of stroke volume assessment by integrating multi-detector computed tomography and Doppler data on the classification of aortic stenosis.

Stähli BE, Stadler T, Holy EW, Nguyen-Kim TDL, Hoffelner L, Erhart L, Obeid S, Niemann M, Jenni R, Hamada S, Manka R, Lüscher TF, Maisano F, Nietlispach F, Frauenfelder T, Tanner FC.

Int J Cardiol. 2017 Nov 1;246:80-86. doi: 10.1016/j.ijcard.2017.03.112.


New innovative ecosystems in France to develop the Bioeconomy.

Stadler T, Chauvet JM.

N Biotechnol. 2018 Jan 25;40(Pt A):113-118. doi: 10.1016/j.nbt.2017.07.009. Epub 2017 Aug 9. Review.


Taming the BEAST-A Community Teaching Material Resource for BEAST 2.

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.

Syst Biol. 2018 Jan 1;67(1):170-174. doi: 10.1093/sysbio/syx060.


The Structured Coalescent and Its Approximations.

Müller NF, Rasmussen DA, Stadler T.

Mol Biol Evol. 2017 Nov 1;34(11):2970-2981. doi: 10.1093/molbev/msx186.


Phylodynamics on local sexual contact networks.

Rasmussen DA, Kouyos R, Günthard HF, Stadler T.

PLoS Comput Biol. 2017 Mar 28;13(3):e1005448. doi: 10.1371/journal.pcbi.1005448. eCollection 2017 Mar.


Bayesian Total-Evidence Dating Reveals the Recent Crown Radiation of Penguins.

Gavryushkina A, Heath TA, Ksepka DT, Stadler T, Welch D, Drummond AJ.

Syst Biol. 2017 Jan 1;66(1):57-73. doi: 10.1093/sysbio/syw060.


Phylogenetic Tools for Generalized HIV-1 Epidemics: Findings from the PANGEA-HIV Methods Comparison.

Ratmann O, Hodcroft EB, Pickles M, Cori A, Hall M, Lycett S, Colijn C, Dearlove B, Didelot X, Frost S, Hossain AS, Joy JB, Kendall M, Kühnert D, Leventhal GE, Liang R, Plazzotta G, Poon AF, Rasmussen DA, Stadler T, Volz E, Weis C, Leigh Brown AJ, Fraser C; PANGEA-HIV Consortium.

Mol Biol Evol. 2017 Jan;34(1):185-203. doi: 10.1093/molbev/msw217. Epub 2016 Oct 7.


Outbreak investigation for toxigenic Corynebacterium diphtheriae wound infections in refugees from Northeast Africa and Syria in Switzerland and Germany by whole genome sequencing.

Meinel DM, Kuehl R, Zbinden R, Boskova V, Garzoni C, Fadini D, Dolina M, Blümel B, Weibel T, Tschudin-Sutter S, Widmer AF, Bielicki JA, Dierig A, Heininger U, Konrad R, Berger A, Hinic V, Goldenberger D, Blaich A, Stadler T, Battegay M, Sing A, Egli A.

Clin Microbiol Infect. 2016 Dec;22(12):1003.e1-1003.e8. doi: 10.1016/j.cmi.2016.08.010. Epub 2016 Aug 30.


Estimating shifts in diversification rates based on higher-level phylogenies.

Stadler T, Smrckova J.

Biol Lett. 2016 Oct;12(10). pii: 20160273.

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