Related papers: Genome organization: experiments and modelling
The 3D organisation of the genome in interphase cells is not a randomly folded polymer. Rather, experiments show that chromosomes arrange into a network of 3D compartments that correlate with biological processes, such as transcription,…
In this paper, we conduct theoretical analyses on inferring the structure of gene regulatory networks. Depending on the experimental method and data type, the inference problem is classified into 20 different scenarios. For each scenario,…
It has been widely recognized that the performance of a multi-agent system is highly affected by its organization. A large scale system may have billions of possible ways of organization, which makes it impractical to find an optimal choice…
We present a model for evolving agents using both genetic and cultural inheritance mechanisms. Within each agent our model maintains two distinct information stores we call the genome and the memome. Processes of adaptation are modeled as…
This article is preface to the SIGMA special issue "Tensor Models, Formalism and Applications", http://www.emis.de/journals/SIGMA/Tensor_Models.html. The issue is a collection of eight excellent, up to date reviews on random tensor models.…
Genetic Regulatory Networks (GRNs) plays a vital role in the understanding of complex biological processes. Modeling GRNs is significantly important in order to reveal fundamental cellular processes, examine gene functions and understanding…
Since genetic algorithm was proposed by John Holland (Holland J. H., 1975) in the early 1970s, the study of evolutionary algorithm has emerged as a popular research field (Civicioglu & Besdok, 2013). Researchers from various scientific and…
This brief `New & Notable' (perspectives-type) article contains a mini-review on stochastic modelling of cell migration before elaborating on the article by Klimek et al., arXiv:2311.16753 [Biophys. J. 123, 1173-1183 (2024)].
The scientific world is becoming more open to the public and fellow researchers. Open access publishing is becoming accepted, even if some publishers are resisting. The next step is the open code and data paradigm, which was briefly…
Chromosome analysis is vital for diagnosing genetic disorders and guiding cancer therapy decisions through the identification of somatic clonal aberrations. However, developing an AI model are hindered by the overwhelming complexity and…
Ascertaining the feasibility of independent falsification or repetition of published results is vital to the scientific process, and replication or reproduction experiments are routinely performed in many disciplines. Unfortunately, such…
The purpose of this paper is to give an introduction to the field of Schema Theory written by a mathematician and for mathematicians. In particular, we endeavor to to highlight areas of the field which might be of interest to a…
This paper is a follow-up work about the artificial ecosystem model: number soup (Liu and Sumpter, J. Royal Soc. Interface, 2017). It elaborates more details about this model and points out future directions.
We investigate the problem of signal transduction via a descriptive analysis of the spatial organization of the complement of proteins exerting a certain function within a cellular compartment. We propose a scheme to assign a numerical…
These lecture notes introduce key concepts of mathematical population genetics within the most elementary setting and describe a few recent applications to microbial evolution experiments. Pointers to the literature for further reading are…
In biomedical applications of machine learning, relevant information often has a rich structure that is not easily encoded as real-valued predictors. Examples of such data include DNA or RNA sequences, gene sets or pathways, gene…
Cells with the same genome can exist in different phenotypes. and can change between distinct phenotypes when subject to specific stimuli and microenvironments. Some examples include cell differentiation during development, reprogramming…
We summarize recent progress on the theory and applications of structural identifiability of compartmental models. On the applications side, we review identifiability analyses undertaken recently for models arising in epidemiology,…
Simulation models are an absolute necessity in the human and social sciences, which can only very exceptionally use experimental science methods to construct their knowledge. Models enable the simulation of social processes by replacing the…
Organogenesis is a tightly regulated process that has been studied experimentally for decades. We are developing mechanistic models for the morphogenesis of limbs, lungs, and kidneys with a view to integrate available knowledge and to…