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Social interaction between microbes can be described at many levels of details, ranging from the biochemistry of cell-cell interactions to the ecological dynamics of populations. Choosing the best level to model microbial communities…
Recent research has extended methods from the fields of thermodynamics and statistical mechanics into other disciplines. Most notably, one recent work creates a unified theoretical framework to understand evolutionary biology, machine…
Metabolomic based approaches have gained much attention in recent years due to their promising potential to deliver objective tools for assessment of food intake. In particular, multiple biomarkers have emerged for single foods. However,…
Identifying patterns of relations among the units of a complex system from measurements of their activities in time is a fundamental problem with many practical applications. Here, we introduce a method that detects dependencies of any…
Mathematical models are invaluable for understanding and predicting how biological systems behave, although their construction requires specifying mechanisms and relationships that are often not perfectly known. In the presence of multiple…
Numerical simulations are widely used to predict the behavior of physical systems, with Bayesian approaches being particularly well suited for this purpose. However, experimental observations are necessary to calibrate certain simulator…
Studying the neurological, genetic and evolutionary basis of human vocal communication mechanisms using animal vocalization models is an important field of neuroscience. The data sets typically comprise structured sequences of syllables or…
Biological processes involve a variety of spatial and temporal scales. A holistic understanding of many biological processes therefore requires multi-scale models which capture the relevant properties on all these scales. In this manuscript…
High-dimensional mediation analysis aims to identify mediating pathways and to estimate indirect effects linking an exposure to an outcome. In this paper, we propose a Bayesian framework to address key challenges in these analyses,…
Motivated by recent experimental developments in functional genomics, we construct and test a numerical technique for inferring it process pathways, in which one process calls another process, from time series data. We validate using a case…
We introduce time-ordered multibody interactions to describe complex systems manifesting temporal as well as multibody dependencies. First, we show how the dynamics of multivariate Markov chains can be decomposed in ensembles of…
Molecular simulations and biophysical experiments can be used to provide independent and complementary insights into the molecular origin of biological processes. A particularly useful strategy is to use molecular simulations as a modelling…
Time series analysis has proven to be a powerful method to characterize several phenomena in biology, neuroscience and economics, and to understand some of their underlying dynamical features. Despite a plethora of methods have been…
Cells must continuously sense and respond to time-varying environmental stimuli. These signals are transmitted and processed by biochemical signalling networks. However, the biochemical reactions making up these networks are intrinsically…
With the rise in engineered biomolecular devices, there is an increased need for tailor-made biological sequences. Often, many similar biological sequences need to be made for a specific application meaning numerous, sometimes prohibitively…
This paper introduces a new behavioral system model with distinct external and internal signals possibly evolving on different time scales. This allows to capture abstraction processes or signal aggregation in the context of control and…
Computer simulations have become an important tool across the biomedical sciences and beyond. For many important problems several different models or hypotheses exist and choosing which one best describes reality or observed data is not…
Considerable interest has recently been focused on studying multiple phenotypes simultaneously in both epidemiological and genomic studies, either to capture the multidimensionality of complex disorders or to understand shared etiology of…
A critical task in systems biology is the identification of genes that interact to control cellular processes by transcriptional activation of a set of target genes. Many methods have been developed to use statistical correlations in…
To be fully useful for public health practice, models for epidemic response must be able to do more than predict -- it is also important to incorporate the mechanisms underlying transmission dynamics to enable policymakers and practitioners…