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A key goal of systems biology is the predictive mathematical description of gene regulatory circuits. Different approaches are used such as deterministic and stochastic models, models that describe cell growth and division explicitly or…
An important task in microbiome studies is to test the existence of and give characterization to differences in the microbiome composition across groups of samples. Important challenges of this problem include the large within-group…
Many machine learning (ML) approaches are widely used to generate bioclimatic models for prediction of geographic range of organism as a function of climate. Applications such as prediction of range shift in organism, range of invasive…
We propose a method for finding metabolic parameters of cells, organs and whole organisms, which is based on the earlier discovered general growth law. Based on the obtained results and analysis of available biological models, we propose a…
Ecological modelling of increasingly more complex microbial populations is necessary to reflect the highly functional and diverse behaviour inherent to many systems found in reality. Anaerobic digestion is one such process that has…
Systems biology models are useful models of complex biological systems that may require a large amount of experimental data to fit each model's parameters or to approximate a likelihood function. These models range from a few to thousands…
The growth rate of matter perturbations is computed in a magnetized environment for the LambdaCDM and wCDM paradigms. It is argued that the baryons do not necessarily follow into the dark matter potential wells after they are released from…
We extend the varying coefficient functional linear model to the nonlinear model and propose a varying coefficient functional additive model. The proposed method can represent the relationship between functional predictors and a scalar…
Microbial ecosystems are commonly modeled by fixed interactions between species in steady exponential growth states. However, microbes often modify their environments so strongly that they are forced out of the exponential state into…
Main goal: The aim of this note is to propose a modeling approach for assessing the effectiveness of pest biocontrol by natural enemies in diversified agricultural landscapes including several pesticide-based management strategies. Our…
High dimensional and heterogeneous count data are collected in various applied fields. In this paper, we look closely at high-resolution sequencing data on the microbiome, which have enabled researchers to study the genomes of entire…
We study the interplay of population growth and evolutionary dynamics using a stochastic model based on birth and death events. In contrast to the common assumption of an independent population size, evolution can be strongly affected by…
A challenge in developing machine learning regression models is that it is difficult to know whether maximal performance has been reached on a particular dataset, or whether further model improvement is possible. In biology this problem is…
Cell decision-making refers to the process by which cells gather information from their local microenvironment and regulate their internal states to create appropriate responses. Microenvironmental cell sensing plays a key role in this…
Protein distributions measured under a broad set of conditions in bacteria and yeast were shown to exhibit a common skewed shape, with variances depending quadratically on means. For bacteria these properties were reproduced by temporal…
Mathematical modelling of the evolution of the size-spectrum dynamics in aquatic ecosystems was discovered to be a powerful tool to have a deeper insight into impacts of human- and environmental driven changes on the marine ecosystem. In…
Emulation of complex computer simulations have become an effective tool in the exploration of the behaviour of the simulated processes. Agriculture is one such area where the simulation of crop growth, nutrition, soil condition and…
The current global food system produces substantial waste and carbon emissions while exacerbating the effects of global hunger and protein deficiency. This study aims to address these challenges by exploring the use of lignocellulosic…
The mechanism by which cells measure the dimension of the organ in which they are embedded, and slow down their growth when the final size is reached, is a long-standing problem of developmental biology. The role of mechanics in this…
Microbial ecosystems are remarkably diverse, stable, and often consist of a balanced mixture of core and peripheral species. Here we propose a conceptual model exhibiting all these emergent properties in quantitative agreement with real…