Related papers: Master regulators as order parameters of gene expr…
Gene regulatory networks (GRNs) play a central role in cellular decision-making. Understanding their structure and how it impacts their dynamics constitutes thus a fundamental biological question. GRNs are frequently modeled as Boolean…
Learning or memory formation are associated with the strengthening of the synaptic connections between neurons according to a pattern reflected by the input. According to this theory a retained memory sequence is associated to a dynamic…
Gene regulatory networks (GRNs) perform a wide range of biological functions. It is, however, often challenging to reveal their functioning mechanism with the conventional approach focusing on the network topological structure from a…
We investigate the computational limits of the memory retrieval dynamics of modern Hopfield models from the fine-grained complexity analysis. Our key contribution is the characterization of a phase transition behavior in the efficiency of…
We consider two models of Hopfield-like associative memory with $q$-valued neurons: Potts-glass neural network (PGNN) and parametrical neural network (PNN). In these models neurons can be in more than two different states. The models have…
Gene expression-based heterogeneity analysis has been extensively conducted. In recent studies, it has been shown that network-based analysis, which takes a system perspective and accommodates the interconnections among genes, can be more…
Multicellular organisms contain a wide variety of highly specialized cell types. The consistency and robustness of developmental trajectories suggest that complex gene regulatory networks effectively act as low-dimensional cell fate…
The study of gene regulation and expression is often discussed in quantitative terms. In particular, the expression of genes is regularly characterized with respect to how much, how fast, when and where. Whether discussing the level of gene…
Central to the functioning of a living cell is its ability to control the readout or expression of information encoded in the genome. In many cases, a single transcription factor protein activates or represses the expression of many genes.…
We analyze the storage capacity of the Hopfield models on classes of random graphs. While such a setup has been analyzed for the case that the underlying random graph model is an Erd\"{o}s-Renyi graph, other architectures, including those…
Embryonic development leads to the reproducible and ordered appearance of complexity from egg to adult. The successive differentiation of different cell types, that elaborates this complexity, result from the activity of gene networks and…
A blood cell lineage consists of several consecutive developmental stages from the pluri- or multipotent stem cell to a state of terminal differentiation. Despite their importance for human biology, the regulatory pathways and gene networks…
We present results for two different kinds of high order connections between neurons acting as corrections to the Hopfield model. Equilibrium properties are analyzed using the replica mean-field theory and compared with numerical…
Sequence memory is an essential attribute of natural and artificial intelligence that enables agents to encode, store, and retrieve complex sequences of stimuli and actions. Computational models of sequence memory have been proposed where…
Structural and dynamical fingerprints of evolutionary optimization in biological networks are still unclear. We here analyze the dynamics of genetic regulatory networks responsible for the regulation of cell cycle and cell differentiation…
Gene regulatory networks (GRNs) control cellular function and decision making during tissue development and homeostasis. Mathematical tools based on dynamical systems theory are often used to model these networks, but the size and…
Understanding the memory capacity of neural networks remains a challenging problem in implementing artificial intelligence systems. In this paper, we address the notion of capacity with respect to Hopfield networks and propose a dynamic…
Characterization of pluripotent states, in which cells can both self-renew and differentiate, and the irreversible loss of pluripotency are important research areas in developmental biology. In particular, an understanding of these…
Cells can often choose among several stably heritable phenotypes. Examples are the expression of genes in eukaryotic cells where long chromosomal regions can adopt persistent and heritable silenced or active states, that may be associated…
Gene expression is a central process to any form of life. It involves multiple temporal and functional scales that extend from specific protein-DNA interactions to the coordinated regulation of multiple genes in response to intracellular…