Stefanie Muff

Stefanie Muff
Norwegian University of Science and Technology | NTNU · Department of Mathematical Sciences

PhD

About

56
Publications
23,218
Reads
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1,989
Citations
Citations since 2017
37 Research Items
1261 Citations
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Introduction
I'm a researcher in ecological statistics and biostatistics. My research interests cover quantitave genetics, statistical genomics, biologging, measurement error modeling and good statistical practice. I like to take a Bayesian approach using MCMC or INLA. Thanks to my collaborations with evolutionary biologists and ecologists, my research ideas are often inspired by limitations of statistical methodology required to tackle applied problems.
Additional affiliations
September 2019 - present
Norwegian University of Science and Technology
Position
  • Professor (Associate)
August 2017 - January 2018
Norwegian University of Science and Technology
Position
  • Researcher
February 2012 - June 2015
University of Zurich
Position
  • PostDoc Position

Publications

Publications (56)
Preprint
Full-text available
1. Step selection analysis (SSA) is a common framework for understanding animal movement and resource selection using telemetry data. Such data are, however, inherently autocorrelated in space, a complication that could impact SSA-based inference if left unaddressed. Accounting for spatial correlation is standard statistical practice when analyzing...
Article
Third molar extraction is a painful treatment for patients, and thus, it can be used to investigate the effects of analgesics on pain. Hypnosis can help to reduce pain and to decrease the intake of postoperative systemic analgesics. In this study, the effectiveness of a brief hypnotic induction for patients undergoing third molar extractions was in...
Article
Full-text available
Heritable genetic variation among free‐living animals or plants is essential for populations to respond to selection and adapt. It is therefore important to be able to estimate additive genetic variance VA, which can be obtained using a generalized linear mixed model known as the animal model. An underlying assumption of the standard animal model i...
Article
Despite much criticism, black-or-white null-hypothesis significance testing with an arbitrary P-value cutoff still is the standard way to report scientific findings. One obstacle to progress is likely a lack of knowledge about suitable alternatives. Here, we suggest language of evidence that allows for a more nuanced approach to communicate scienti...
Preprint
Full-text available
Heritable genetic variation among free-living animals or plants is essential for populations to respond to selection and adapt. It is therefore important to be able to estimate additive genetic variance V A , which can be obtained using a generalized linear mixed model known as the animal model . An underlying assumption of the standard animal mode...
Article
Full-text available
IMPORTANCE In observational studies, patients' treatment outcome expectations have been associated with better outcomes (ie, a placebo response), whereas concerns about adverse side effects have been associated with an increase in the negative effects of treatments (ie, a nocebo response). Some randomized trials have suggested that communication fr...
Article
Full-text available
Ongoing adaptive evolution, and resulting “evolutionary rescue” of declining populations, requires additive genetic variation in fitness. Such variation can be increased by gene flow resulting from immigration, potentially facilitating evolution. But, gene flow could in fact constrain rather than facilitate local adaptive evolution if immigrants ha...
Article
Inbreeding may increase the extinction risk of small populations. Yet, studies using modern genomic tools to investigate inbreeding depression in nature have been limited to single populations, and little is known about the dynamics of inbreeding depression in subdivided populations over time. Natural populations often experience different environm...
Article
Full-text available
Host parasite relationships are likely to change over the coming decades in response to climate change and increased anthropogenic stressors. Understanding the genetic architecture of parasite resistance will aid prediction of species’ responses to intensified parasite challenge. The gapeworm “Syngamus trachea” is prevalent in natural bird populati...
Data
The Supplementary Information file contains: Supplementary Figs. 1-4, Supplementary Tables 1-9, Supplementary Methods.
Article
Full-text available
Many studies document negative inbreeding effects on individuals, and conservation efforts to preserve rare species routinely employ strategies to reduce inbreeding. Despite this, there are few clear examples in nature of inbreeding decreasing the growth rates of populations, and the extent of population-level effects of inbreeding in the wild rema...
Article
Full-text available
The riparian vegetation belt is one of the few remaining structures that provide coverage for wildlife in many anthropogenic landscapes. It provides shelter for many species and functions as corridors for dispersal. However, this landscape is increasingly utilised by humans for leisure activities. The loss of riparian vegetation with a concurrent i...
Article
1.Popular frameworks for studying habitat selection include resource‐selection functions (RSFs) and step‐selection functions (SSFs), estimated using logistic and conditional logistic regression, respectively. Both frameworks compare environmental covariates associated with locations animals visit with environmental covariates at a set of locations...
Article
1.Measurement error and other forms of uncertainty are commonplace in ecology and evolution and may bias estimates of parameters of interest. Although a variety of approaches to obtain unbiased estimators are available, these usually require the formulation of an explicit (parametric) model for the error‐prone variable, and a latent model for the u...
Article
Full-text available
Two histopathological subtypes of Meniere's disease (MD) were recently described in a human post-mortem pathology study. The first subtype demonstrated a degenerating distal endolymphatic sac (ES) in the affected inner ear (subtype MD-dg); the second subtype (MD-hp) demonstrated an ES that was developmentally hypoplastic. The two subtypes were asso...
Article
Full-text available
Background The animal model is a key tool in quantitative genetics and has been used extensively to estimate fundamental parameters, such as additive genetic variance or heritability. An implicit assumption of animal models is that all founder individuals derive from a single population. This assumption is commonly violated, for instance in crossbr...
Preprint
Measurement error and other forms of uncertainty are commonplace in ecology and evolution and may bias estimates of parameters of interest. Although a variety of approaches to obtain unbiased estimators are available, these often require that errors are explicitly modeled and that a latent model for the unobserved error-free variable can be specifi...
Preprint
Full-text available
1. Popular frameworks for studying habitat selection include resource-selection functions (RSFs) and step-selection functions (SSFs) estimated using logistic and conditional logistic regression, respectively. Both frameworks compare environmental covariates associated with locations animals visit with environmental covariates at a set of locations...
Article
Full-text available
Inbreeding depression, the deterioration in mean trait value in progeny of related parents, is a fundamental quantity in genetics, evolutionary biology, animal and plant breeding, and conservation biology. The magnitude of inbreeding depression can be quantified by the inbreeding load, typically measured in numbers of lethal equivalents, a populati...
Article
Quantitative genetic analyses require extensive measurements of phenotypic traits, a task that is often not trivial, especially in wild populations. On top of instrumental measurement error, some traits may undergo transient (i.e. non‐persistent) fluctuations that are biologically irrelevant for selection processes. These two sources of variability...
Article
In this study, we assessed intracorporal mercury concentrations in subjects living on partially mercury-contaminated soils in a defined area in Switzerland. We assessed 64 mothers and 107 children who resided in a defined area for at least 3 months. Mercury in biological samples (urine and hair) was measured, a detailed questionnaire was administer...
Article
Full-text available
Health-risks from contaminated soils are assessed all over the world. An aspect that many risk assessments share is the heterogeneity in the distribution of contaminants. In a preceding study, we assessed potential health-risks for mothers and children living on mercury-contaminated soils in Switzerland using human biomonitoring-values (HBM) and so...
Preprint
Full-text available
1. The animal model is a key tool in quantitative genetics and has been used extensively to estimate fundamental parameters, such as additive genetic variance, heritability, or inbreeding effects. An implicit assumption of animal models is that all founder individuals derive from a single population. This assumption is commonly violated, for instan...
Preprint
Quantitative genetic analyses require extensive measurements of phe-notypic traits, which may be especially challenging to obtain in wild populations. On top of operational measurement challenges, some traits undergo transient fluctuations that might be irrelevant for selection processes. The presence of transient variability, denoted here as measu...
Article
Human related mortality is a major threat for large carnivores all over the world and there is increasing evidence that large predators respond to human related risks in a similar way as prey respond to predation risk. This insight recently led to the conceptual development of a landscape of coexistence that can be used to identify areas which can...
Article
Measurement error (ME) in explanatory variables is a common problem in regression and survival analysis, as it may cause bias in the estimated parameters. It is shown how the integrated nested Laplace approximations (INLA) method can handle classical and Berkson ME in a single explanatory variable, illustrated for the case of a Weibull regression m...
Article
Count outcomes occur in virtually all disciplines, such as medicine, epidemiology or biology, but they often contain error. Recently, it has been shown that self-reported numbers of exacerbations of Chronic Obstructive Pulmonary Disease patients can be considerably miscounted. Motivated by this result, we reanalysed data from the Towards a Revoluti...
Article
Full-text available
Background Identifying ways to promote physical activity and decrease sedentary time during childhood is a key public health issue. Research on the putative influences on preschool children’s physical activity (PA) and sedentary behavior (SB) is limited and has yielded inconsistent results. Our aim was to identify correlates of PA and SB in prescho...
Article
1.Correlated data are ubiquitous in ecological and evolutionary research, and appropriate statistical analysis requires that these correlations are taken into account. For regressions with correlated, non-normal outcomes, two main approaches are used: conditional and marginal modelling. The former leads to generalized linear mixed models (GLMMs), w...
Research
Measurement error (ME) in explanatory variables is a common problem in survival analysis, causing bias in standard regression procedures. In this paper we show how classical and Berkson ME in explanatory variables of a Weibull regression model can be handled using the integrated nested Laplace approximations (INLA) method, and illustrate that error...
Article
Covariate measurement error may cause biases in parameters of regression coefficients in generalized linear models. The influence of measurement error on interaction parameters has, however, only rarely been investigated in depth, and if so, attenuation effects were reported. In this paper, we show that also reverse attenuation of interaction effec...
Article
To account for measurement error (ME) in explanatory variables, Bayesian approaches provide a flexible framework, as expert knowledge can be incorporated in the prior distributions. Recently, integrated nested Laplace approximations have been proven to be a computationally convenient alternative to sampling approaches for Bayesian inference in late...
Article
Full-text available
To account for measurement error (ME) in explanatory variables, Bayesian approaches provide a flexible framework, as expert knowledge about unobserved covariates can be incorporated in the prior distributions. However, given the analytic intractability of the posterior distribution, model inference so far has to be performed via time-consuming and...
Article
Full-text available
Wordom is a versatile, user-friendly, and efficient program for manipulation and analysis of molecular structures and dynamics. The following new analysis modules have been added since the publication of the original Wordom paper in 2007: assignment of secondary structure, calculation of solvent accessible surfaces, elastic network model, motion cr...
Article
Simulations are important for understanding complex reactions, but their interpretation is challenging owing to the large number of degrees of freedom typically involved. To address this issue, various means for relating the dynamics of a stochastic system to its structural and energetic features have been introduced. Here, we show how two leading...
Article
Full-text available
Ecology Letters (2010) 13: 442–452 Species extinctions pose serious threats to the functioning of ecological communities worldwide. We used two qualitative and quantitative pollination networks to simulate extinction patterns following three removal scenarios: random removal and systematic removal of the strongest and weakest interactors. We accoun...
Article
The rate of protein folding is governed by the transition state so that a detailed characterization of its structure is essential for understanding the folding process. In vitro experiments have provided a coarse-grained description of the folding transition state ensemble (TSE) of small proteins. Atomistic details could be obtained by molecular dy...
Article
It is difficult to investigate folding kinetics by conventional atomistic simulations of proteins. The replica exchange molecular dynamics (REMD) simulation technique enhances conformational sampling at the expenses of reduced kinetic information, which in REMD is directly available only for very short time scales. Here, we propose a procedure for...
Article
We have investigated the site-specific folding kinetics of a photoswitchable cross-linked α-helical peptide by using single ¹³C = ¹⁸O isotope labeling together with time-resolved IR spectroscopy. We observe that the folding times differ from site to site by a factor of eight at low temperatures (6°C), whereas at high temperatures (45°C), the spread...
Article
The conformational space of a 20-residue three-stranded antiparallel beta-sheet peptide (double hairpin) was sampled by equilibrium folding/unfolding molecular dynamics simulations for a total of 20 micros. The resulting one-dimensional free-energy profiles (FEPs) provide a detailed description of the free-energy basins and barriers for the folding...
Article
The effects of a single-point mutation on folding thermodynamics and kinetics are usually interpreted by focusing on the native structure and the transition state. Here, the entire conformational spaces of a 20-residue three-stranded antiparallel beta-sheet peptide (double hairpin) and of its single-point mutant W10V are sampled close to the meltin...
Article
Full-text available
Many complex networks have an underlying modular structure, i.e., structural subunits (communities or clusters) characterized by highly interconnected nodes. The modularity has been introduced as a measure to assess the quality of clusterizations. has a global view, while in many real-world networks clusters are linked mainly locally among each oth...

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