Related papers: Reconstructing probabilistic trees of cellular dif…
Computational modeling of single-cell gene expression is crucial for understanding cellular processes, but generating realistic expression profiles remains a major challenge. This difficulty arises from the count nature of gene expression…
Stochastic models for collections of interacting populations have crucial roles in scientific fields such as epidemiology and ecology, yet the standard approach to extending an ordinary differential equation model to a Markov chain does not…
We consider the Wright-Fisher model for a population of $N$ individuals, each identified with a sequence of a finite number of sites, and single-crossover recombination between them. We trace back the ancestry of single individuals from the…
Can evolving networks be inferred and modeled without directly observing their nodes and edges? In many applications, the edges of a dynamic network might not be observed, but one can observe the dynamics of stochastic cascading processes…
We address phylogenetic reconstruction when the data is generated from a mixture distribution. Such topics have gained considerable attention in the biological community with the clear evidence of heterogeneity of mutation rates. In our…
Background: Single-cell RNA sequencing (scRNA-seq) enables gene expression profiling at cellular resolution but is inherently affected by sparsity caused by dropout events, where expressed genes are recorded as zeros due to technical…
It is known that the stationary distribution of the random walk process is dependent on the structure of the network. This could provide us a solution of the network reconstruction. However, the stationary distribution of the random walk…
We analyse the statistical properties of genealogical trees in a neutral model of a closed population with sexual reproduction and non-overlapping generations. By reconstructing the genealogy of an individual from the population evolution,…
Understanding functional organization of genetic information is a major challenge in modern biology. Following the initial publication of the human genome sequence in 2001, advances in high-throughput measurement technologies and efficient…
In this study, we develop consistent estimators for key parameters that govern the dynamics of tumor cell populations when subjected to pharmacological treatments. While these treatments often lead to an initial reduction in the abundance…
When analysing gene expression time series data an often overlooked but crucial aspect of the model is that the regulatory network structure may change over time. Whilst some approaches have addressed this problem previously in the…
Despite their growing capabilities, language models still frequently reproduce content from their training data, generate repetitive text, and favor common grammatical patterns and vocabulary. A possible cause is the decoding strategy: the…
Motivated by DNA-based storage applications, we study the problem of reconstructing a coded sequence from multiple traces. We consider the model where the traces are outputs of independent deletion channels, where each channel deletes each…
The homogeneous reconstructed evolutionary process is a birth-death process without observed extinct lineages. Each species evolves independently with the same diversification rates (speciation rate $\lambda(t)$ and extinction rate…
Dynamics and function of neuronal networks are determined by their synaptic connectivity. Current experimental methods to analyze synaptic network structure on the cellular level, however, cover only small fractions of functional neuronal…
Single-cell RNA sequencing (scRNA-seq) data are important for studying the laws of life at single-cell level. However, it is still challenging to obtain enough high-quality scRNA-seq data. To mitigate the limited availability of data,…
Phylogenetic networks represent evolutionary history of species and can record natural reticulate evolutionary processes such as horizontal gene transfer and gene recombination. This makes phylogenetic networks a more comprehensive…
We develop a new Markov chain on graph partitions that makes relatively global moves yet is computationally feasible to be used as the proposal in the Metropolis-Hastings method. Our resulting algorithm can be made reversible and able to…
The different cell types in a living organism acquire their identity through the process of cell differentiation in which the multipotent progenitor cells differentiate into distinct cell types. Experimental evidence and analysis of…
Populations of heterogeneous cells play an important role in many biological systems. In this paper we consider systems where each cell can be modelled by an ordinary differential equation. To account for heterogeneity, parameter values are…