相关论文: Inferring processes underlying B-cell repertoire d…

Biological cells replicate their genomes in a well-planned manner. The DNA replication program of an organism determines the timing at which different genomic regions are replicated, with fundamental consequences for cell homeostasis and…

We present a novel mathematical model of heterogeneous cell proliferation where the total population consists of a subpopulation of slow-proliferating cells and a subpopulation of fast-proliferating cells. The model incorporates two…

DNA supercoiling, the under or overwinding of DNA, is a key physical mechanism both participating to compaction of bacterial genomes and making genomic sequences adopt various structural forms. DNA supercoiling may lead to the formation 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…

In an attempt to explain the uniqueness of the coding mechanism of living cells as contrasted with multi-species structure of ecosystems we examine two models of individuals with some replicative properties. In the first model the system…

Diffusion models are a class of generative models that learn to synthesize samples by inverting a diffusion process that gradually maps data into noise. While these models have enjoyed great success recently, a full theoretical…

In the human genomes, recombination frequency between homologous chromosomes during meiosis is highly correlated with their physical length while it differs significantly when their coding density is considered. Furthermore, it has been…

T-cell receptors (TCR) are key proteins of the adaptive immune system, generated randomly in each individual, whose diversity underlies our ability to recognize infections and malignancies. Modeling the distribution of TCR sequences is of…

Cell type (e.g. pluripotent cell, fibroblast) is the end result of many complex processes that unfold due to evolutionary, developmental, and transformational stimuli. A cell's phenotype and the discrete, a priori states that define various…

All stem cell fate transitions, including the metabolic reprogramming of stem cells and the somatic reprogramming of fibroblasts into pluripotent stem cells, can be understood from a unified theoretical model of cell fates. Each cell fate…

Black box deep learning models trained on genomic sequences excel at predicting the outcomes of different gene regulatory mechanisms. Therefore, interpreting these models may provide novel insights into the underlying biology, supporting…

Genomic sequence analysis plays a crucial role in various scientific and medical domains. Traditional machine-learning approaches often struggle to capture the complex relationships and hierarchical structures of sequence data when working…

Replication of genetic material is an important process for all living organisms. Origins of replication initiate the copying of DNA at many points on a chromosome, and it is the distribution of these points that is relevant here, as it…

Understanding cell fate selection remains a central challenge in developmental biology. We present a class of simple yet biologically-motivated mathematical models for cell differentiation that generically generate oscillations and hence…

Consider a branching process with a homogeneous reproduction law. Sampling a single cell uniformly from the population at a time $T > 0$ and looking along the sampled cell's ancestral lineage, we find that the reproduction law is…

The amplification cycle of many replicators (natural or artificial) involves the usage of a host compartment, inside of which the replicator express phenotypic compounds necessary to carry out its genetic replication. For example, viruses…

Development combines three basic processes asymmetric --- cell division, signaling and gene regulation --- in a multitude of ways to create an overwhelming diversity of multicellular life-forms. Here, we attempt to chart this diversity…

Motivation: The reconstruction of gene networks from gene expression microarrays is gaining popularity as methods improve and as more data become available. The reliability of such networks could be judged by the probability that a…

Our world is ambiguous and this is reflected in the data we use to train our algorithms. This is particularly true when we try to model natural processes where collected data is affected by noisy measurements and differences in measurement…

We study random string-duplication systems, which we call P\'olya string models. These are motivated by DNA storage in living organisms, and certain random mutation processes that affect their genome. Unlike previous works that study the…