Tanja Stadler
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View article: Single-cell phylodynamics reveal rapid late-stage colorectal cancer expansions
Single-cell phylodynamics reveal rapid late-stage colorectal cancer expansions Open
Single-cell whole-genome sequencing of 335 cells from seven colorectal cancers, coupled with Bayesian phylodynamic modeling, revealed tumors often originate decades before diagnosis, remain indolent, and expand rapidly within two years. St…
View article: Determinants and spatio-temporal structure of variability in wastewater SARS-CoV-2 viral load measurements in Switzerland: Key insights for future surveillance efforts
Determinants and spatio-temporal structure of variability in wastewater SARS-CoV-2 viral load measurements in Switzerland: Key insights for future surveillance efforts Open
Background: Wastewater-based surveillance (WBS) has emerged as a valuable tool for monitoring the circulation of infectious pathogens in the population, offering a complement to classical surveillance methods. However, the interpretation o…
View article: Robust real-time estimation of pathogen transmission dynamics from wastewater
Robust real-time estimation of pathogen transmission dynamics from wastewater Open
Wastewater monitoring has proven effective for tracking SARS-CoV-2 transmission during the COVID-19 pandemic. However, estimating transmission parameters for other pathogens remains difficult due to lower concentrations in sewage, uncertai…
View article: Real-time outlier detection in digital PCR data for wastewater-based pathogen surveillance
Real-time outlier detection in digital PCR data for wastewater-based pathogen surveillance Open
Wastewater-based epidemiology provides insights into the spread of infectious diseases by sampling and analyzing wastewater from wastewater treatment plant catchments. Longitudinal measurements of pathogen concentrations in wastewater have…
View article: Genetic Cluster of Extended-Spectrum β-lactamase–Producing <i>Klebsiella pneumoniae</i> in Humans and Food, Switzerland, 2018–2019
Genetic Cluster of Extended-Spectrum β-lactamase–Producing <i>Klebsiella pneumoniae</i> in Humans and Food, Switzerland, 2018–2019 Open
We describe a cluster of genetically related extended-spectrum β-lactamase-producing Klebsiella pneumoniae sequence type 14 recovered from human clinical samples and an alfalfa-cress sample collected by systematic food sampling in Basel, S…
View article: From clinics to sewers: leveraging environmental surveillance and whole genome sequencing to inform transmission of ESBL-Escherichia coli in Switzerland
From clinics to sewers: leveraging environmental surveillance and whole genome sequencing to inform transmission of ESBL-Escherichia coli in Switzerland Open
Extended-spectrum beta-lactamase (ESBL)-producing Escherichia coli is a major antimicrobial resistance concern spreading across human, animal, and environmental domains. To assess between-source transitions, we analysed 762 ESBL-E. coli ge…
View article: Phylodynamic estimation of the within-host evolutionary rate of extended-spectrum beta-lactamase-producing Enterobacterales
Phylodynamic estimation of the within-host evolutionary rate of extended-spectrum beta-lactamase-producing Enterobacterales Open
Despite their clinical relevance, the within-host evolution of extended-spectrum beta-lactamase (ESBL)-producing Enterobacterales is still poorly understood. To estimate the within-host evolutionary rates of ESBL-producing Escherichia coli…
View article: Bayesian phylodynamics for developmental biology: incorporating age-dependence
Bayesian phylodynamics for developmental biology: incorporating age-dependence Open
As novel technologies for single-cell lineage tracing emerge, phylogenetic and phylodynamic tools are increasingly being used to study developmental processes. However, traditional phylodynamic methods, which were originally developed to s…
View article: Poultry farm density and proximity drive highly pathogenic avian influenza spread
Poultry farm density and proximity drive highly pathogenic avian influenza spread Open
The continuous spread of highly pathogenic avian influenza H5 viruses poses significant challenges, particularly in regions with high poultry farm densities where conventional control measures are less effective. Using phylogeographic and …
View article: Characterizing influenza A virus lineages and clinically relevant mutations through high-coverage wastewater sequencing
Characterizing influenza A virus lineages and clinically relevant mutations through high-coverage wastewater sequencing Open
Influenza A virus poses significant public health challenges, causing seasonal outbreaks and pandemics. Its rapid evolution motivates continuous monitoring of circulating influenza genomes to inform vaccine and antiviral development. Waste…
View article: The relative contribution of close-proximity contacts, shared classroom exposure and indoor air quality to respiratory virus transmission in schools.
The relative contribution of close-proximity contacts, shared classroom exposure and indoor air quality to respiratory virus transmission in schools. Open
Close-proximity interactions are considered a key risk factor for respiratory virus transmission, but their importance relative to shared space and air quality remains unclear. We conducted a six-week longitudinal study in a Swiss secondar…
View article: Estimated transmission dynamics of SARS-CoV-2 variants from wastewater are unbiased and robust to differential shedding
Estimated transmission dynamics of SARS-CoV-2 variants from wastewater are unbiased and robust to differential shedding Open
The COVID-19 pandemic has accelerated the development and adoption of wastewater-based epidemiology. Wastewater samples can provide genomic information for detecting and assessing the spread of SARS-CoV-2 variants in communities and for es…
View article: Characterizing Co-Circulating Respiratory Virus Genomic Diversity in Switzerland with Hybrid-Capture Sequencing and Phylogenetic Reconstructions: Insights into the 2023/24 Season
Characterizing Co-Circulating Respiratory Virus Genomic Diversity in Switzerland with Hybrid-Capture Sequencing and Phylogenetic Reconstructions: Insights into the 2023/24 Season Open
Respiratory viruses circulate yearly with strain-specific patterns. Although SARS-CoV-2 and Influenza A/B genomic surveillance is well-developed, most respiratory viruses are unevenly monitored, lacking geographical diversity to capture wi…
View article: Response to "No evidence that transmissible cancer has shifted from emergence to endemism in Tasmanian devils"
Response to "No evidence that transmissible cancer has shifted from emergence to endemism in Tasmanian devils" Open
Herein, we rebut the critique of Patton et al. 2020, entitled, No evidence that a transmissible cancer has shifted from emergence to endemism, by Stammnitz et al. 2024. First and foremost, the authors do not conduct any phylogenetic or epi…
View article: Post-sampling degradation of viral RNA in wastewater impacts the quality of PCR-based concentration estimates
Post-sampling degradation of viral RNA in wastewater impacts the quality of PCR-based concentration estimates Open
Successful wastewater-based infectious disease surveillance programs depend on regular, reliable molecular detection of nucleic acids in municipal wastewater systems. This process is challenged by the gradual degradation of the viral conte…
View article: Bayesian Phylodynamic Inference of Multitype Population Trajectories Using Genomic Data
Bayesian Phylodynamic Inference of Multitype Population Trajectories Using Genomic Data Open
Phylodynamic methods provide a coherent framework for the inference of population parameters directly from genetic data. They are an important tool for understanding both the spread of epidemics as well as long-term macroevolutionary trend…
View article: Determinants and spatio-temporal structure of variability in wastewater SARS-CoV-2 viral load measurements in Switzerland: key insights for future surveillance efforts
Determinants and spatio-temporal structure of variability in wastewater SARS-CoV-2 viral load measurements in Switzerland: key insights for future surveillance efforts Open
Background: Wastewater-based surveillance (WBS) has emerged as a valuable tool for monitoring the circulation of infectious pathogens in the population, offering a complement to classical surveillance methods. However, the interpretation o…
View article: Enhancing Evolutionary Timelines: The Impact of Stratigraphic Range Information on Phylogenetic Inference
Enhancing Evolutionary Timelines: The Impact of Stratigraphic Range Information on Phylogenetic Inference Open
Coherent phylogenetic analyses of molecular and fossil datasets have deepened our understanding of evolutionary biology. A core model facilitating such coherent analyses is the fossilised birth-death (FBD) model which directly incorporates…
View article: Wastewater sequencing reveals the genomic landscape of Influenza A virus in Switzerland
Wastewater sequencing reveals the genomic landscape of Influenza A virus in Switzerland Open
Influenza A virus poses significant public health challenges, causing seasonal outbreaks and pandemics. Its rapid evolution motivates continuous monitoring of circulating influenza genomes to inform vaccine and antiviral development. Waste…
View article: Highly pathogenic avian influenza management in high-density poultry farming areas
Highly pathogenic avian influenza management in high-density poultry farming areas Open
The continuous spread of highly pathogenic avian influenza H5 viruses poses significant challenges, particularly in regions with high poultry farm densities where conventional control measures are less effective. Using phylogeographic and …
View article: Onset of infectiousness explains differences in transmissibility across Mycobacterium tuberculosis lineages
Onset of infectiousness explains differences in transmissibility across Mycobacterium tuberculosis lineages Open
Mycobacterium tuberculosis complex (MTBC) lineages show substantial variability in virulence, but the epidemiological consequences of this variability have not been studied in detail. Here, we aimed for a lineage-specific epidemiological c…
View article: Wastewater-based sequencing of Respiratory Syncytial Virus enables tracking of lineages and identifying mutations at antigenic sites
Wastewater-based sequencing of Respiratory Syncytial Virus enables tracking of lineages and identifying mutations at antigenic sites Open
Respiratory Syncytial Virus (RSV) infections pose a substantial health burden, especially for vulnerable populations such as infants and the elderly. While novel immunoprophylaxis offer promising protection, many countries lack robust surv…
View article: Artificial intelligence for modelling infectious disease epidemics
Artificial intelligence for modelling infectious disease epidemics Open
View article: A Bayesian phylodynamic inference framework for single-cell CRISPR/Cas9 lineage tracing barcode data with dependent target sites
A Bayesian phylodynamic inference framework for single-cell CRISPR/Cas9 lineage tracing barcode data with dependent target sites Open
Analysing single-cell lineage relationships of an organism is crucial towards understanding the fundamental cellular dynamics that drive development. Clustered regularly interspaced short palindromic repeats (CRISPR)-based dynamic lineage …
View article: "A mathematical theory of evolution": phylogenetic models dating back 100 years
"A mathematical theory of evolution": phylogenetic models dating back 100 years Open
View article: Strategies for resolving cellular phylogenies from sequential lineage tracing data
Strategies for resolving cellular phylogenies from sequential lineage tracing data Open
A combination of recent advancements in molecular recording devices and sequencing technologies has made it possible to generate lineage tracing data on the order of thousands of cells. Dynamic lineage recorders are able to generate random…
View article: Assessing the inference of single-cell phylogenies and population dynamics from genetic lineage tracing data
Assessing the inference of single-cell phylogenies and population dynamics from genetic lineage tracing data Open
Background Multicellular organisms develop from a single cell by repeated rounds of cell division, differentiation and apoptosis, which can be displayed in a single-cell phylogenetic tree. Genetic lineage tracing allows us to investigate t…
View article: Viral Simulation Reveals Overestimation Bias in Within-Host Phylodynamic Migration Rate Estimates Under Selection
Viral Simulation Reveals Overestimation Bias in Within-Host Phylodynamic Migration Rate Estimates Under Selection Open
Phylodynamic methods are widely used to infer the population dynamics of viruses between and within hosts. For HIV-1, these methods have been used to estimate migration rates between different anatomical compartments within a host. These m…
View article: Patterns and drivers of excess mortality during the COVID-19 pandemic in 13 Western European countries
Patterns and drivers of excess mortality during the COVID-19 pandemic in 13 Western European countries Open
These results suggest the benefit of early implementation of NPIs and swift rollout of vaccines to the most vulnerable. Further analyses are required at a more granular level to better understand how these factors impacted excess mortality…
View article: Bayesian phylodynamic inference of multi-type population trajectories using genomic data
Bayesian phylodynamic inference of multi-type population trajectories using genomic data Open
Phylodynamic methods provide a coherent framework for the inference of population parameters directly from genetic data. They are an important tool for understanding both the spread of epidemics as well as long-term macroevolutionary trend…