Related papers: Time series model based on global structure of com…
We investigate disease spreading on eight empirical data sets of human contacts (mostly proximity networks recording who is close to whom, at what time). We compare three levels of representations of these data sets: temporal networks,…
We present a proof-of-concept of a model comparison approach for analyzing spatio-temporal observations of interacting populations. Our model variants are a collection of structurally similar Bayesian networks. Their distinct Noisy-Or…
We have computed a grid of multiphase chemical evolution models whose results are valid for any spiral galaxy, using as input the maximum rotation velocity and the morphological type or index T.
In this article, we review existing probabilistic models for modeling abundance of fixed-length strings (k-mers) in DNA sequencing data. These models capture dependence of the abundance on various phenomena, such as the size and repeat…
Bacterial growth models are commonly used for the prediction of microbial safety and the shelf life of perishable foods. Growth is affected by several environmental factors such as temperature, acidity level and salt concentration. In this…
We analyse a simple discrete-time stochastic process for the theoretical modeling of the evolution of protein lengths. At every step of the process a new protein is produced as a modification of one of the proteins already existing and its…
We consider the problem of quantifying temporal coordination between multiple high-dimensional responses. We introduce a family of multi-way stochastic blockmodels suited for this problem, which avoids preprocessing steps such as binning…
Recently described stochastic models of protein evolution have demonstrated that the inclusion of structural information in addition to amino acid sequences leads to a more reliable estimation of evolutionary parameters. We present a…
Various genome evolutionary models have been proposed these last decades to predict the evolution of a DNA sequence over time, essentially described using a mutation matrix. By essence, all of these models relate the evolution of DNA…
I consider how cell shape and environmental geometry affect the rate of nutrient capture and the consequent maximum growth rate of a cell, focusing on rod-like species like \textit{E.\ coli}. Simple modeling immediately implies that it is…
We study non-equilibrium bacterial colony growth using a geometry-first, time-resolved analysis of morphology. From time-lapse microscopy data, we track the coupled evolution of area, perimeter, and boundary-sensitive shape descriptors…
Temporal evolution of a clonal bacterial population is modelled taking into account reversible mutation and selection mechanisms. For the mutation model, an efficient algorithm is proposed to verify whether experimental data can be…
We introduce the concept of time series motifs for time series analysis. Time series motifs consider not only the spatial information of mutual visibility but also the temporal information of relative magnitude between the data points. We…
Boolean networks have been used in a variety of settings, as models for general complex systems as well as models of specific systems in diverse fields, such as biology, engineering, and computer science. Traditionally, their properties as…
Correlation of gene histories in the human genome determines the patterns of genetic variation (haplotype structure) and is crucial to understanding genetic factors in common diseases. We derive closed analytical expressions for the…
In the context of bacteria and models of their evolution under genome rearrangement, we explore a novel application of group representation theory to the inference of evolutionary history. Our contribution is to show, in a very general…
We study the effects of interspecific correlations in a biological coevolution model in which organisms are represented by genomes of bitstrings. We present preliminary results for this model, indicating that these correlations do not…
Longevity of a taxonomic group is an important issue in understanding the dynamics of evolution. In this respect a key observation is that genera, families or orders can each be assigned a characteristic average lifetime [Van Valen, L.,…
First we shortly review the different kinds of network modelling methods for systems biology with an emphasis on the different subtypes of logical models, which we review in more detail. Then we show the advantages of Boolean networks…
Time series prediction is a widespread and well studied problem with applications in many domains (medical, geoscience, network analysis, finance, econometry etc.). In the case of multivariate time series, the key to good performances is to…