相关论文: Dynamic modeling of gene expression data

This paper describes characteristic features of networks reconstructed from gene expression time series data. Several null models are considered in order to discriminate between informations embedded in the network that are related to real…

Gene regulation is an important fundamental biological process. The regulation of gene expression is managed through a variety of methods including epigenetic processes (e.g., DNA methylation). Understanding the role of epigenetic changes…

Multi-sample microarray experiments have become a standard experimental method for studying biological systems. A frequent goal in such studies is to unravel the regulatory relationships between genes. During the last few years, regression…

Biological foundation models have shown strong performance in single-cell representation learning by applying transformer architectures directly to gene-expression matrices. However, these approaches predominantly operate in static settings…

We propose a probabilistic model for interpreting gene expression levels that are observed through single-cell RNA sequencing. In the model, each cell has a low-dimensional latent representation. Additional latent variables account for…

In many longitudinal microarray studies, the gene expression levels in a random sample are observed repeatedly over time under two or more conditions. The resulting time courses are generally very short, high-dimensional, and may have…

Evolution of gene regulation is crucial for our understanding of the phenotypic differences between species, populations and individuals. Sequence-specific binding of transcription factors to the regulatory regions on the DNA is a key…

Developing models with high interpretability and even deriving formulas to quantify relationships between biological data is an emerging need. We propose here a framework for ab initio derivation of sequence motifs and linear formula using…

The evolutionary processes of complex systems contain critical information regarding their functional characteristics. The generation time of edges provides insights into the historical evolution of various networked complex systems, such…

One of the outstanding challenges in comparative genomics is to interpret the evolutionary importance of regulatory variation between species. Rigorous molecular evolution-based methods to infer evidence for natural selection from…

We examine the evolution of expression patterns and the organization of genetic information in populations of self-replicating digital organisms. Seeding the experiments with a linearly expressed ancestor, we witness the development of…

We define truncated Mellin moments of parton distributions by restricting the integration range over the Bjorken variable to the experimentally accessible subset x_0 < x < 1 of the allowed kinematic range 0 < x < 1. We derive the evolution…

Gene expression programming is an evolutionary optimization algorithm with the potential to generate interpretable and easily implementable equations for regression problems. Despite knowledge gained from previous optimizations being…

The expression of genes usually follows a two-step procedure. First, a gene (encoded in the genome) is transcribed resulting in a strand of (messenger) RNA. Afterwards, the RNA is translated into protein. Classically, this gene expression…

A key problem in computational biology is discovering the gene expression changes that regulate cell fate transitions, in which one cell type turns into another. However, each individual cell cannot be tracked longitudinally, and cells at…

Gene expression is a stochastic process governed by the presence of specific transcription factors. Here we study the dynamics of gene expression in the presence of feedback, where a gene regulates its own expression. The nonlinear coupling…

Modelling gene regulatory networks not only requires a thorough understanding of the biological system depicted but also the ability to accurately represent this system from a mathematical perspective. Throughout this chapter, we aim to…

The regulation of a gene depends on the binding of transcription factors to specific sites located in the regulatory region of the gene. The generation of these binding sites and of cooperativity between them are essential building blocks…

In this work, the dynamics of fluctuations in gene expression time series is investigated. By using collected data of gene expression from yeast and human organisms, we found that the fluctuations of gene expression level and its average…

Recently, evolving networks are becoming a suitable form to model many real-world complex systems, due to their peculiarities to represent the systems and their constituting entities, the interactions between the entities and the…