相关论文: On Gene Duplication Models for Evolving Regulatory…
Background: The evolution of microRNA regulation in metazoans is a mysterious process: MicroRNA sequences are highly conserved among distal organisms, but on the other hand, there is no evident conservation of their targets. Results: We…
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…
The effects of link rewiring are considered for the class of directed networks where each node has the same fixed out-degree. We model a network generated by three mechanisms that are present in various networked systems; growth, global…
Regulatory interactions between genes show a large amount of cross-species variability, even when the underlying functions are conserved: There are many ways to achieve the same function. Here we investigate the ability of regulatory…
The two most fundamental processes describing change in biology, development and evolu-tion, occur over drastically different timescales, difficult to reconcile within a unified framework. Development involves temporal sequences of cell…
In eukaryotes, DNA replication is initiated along each chromosome at multiple sites called replication origins. Locally, each replication origin is "licensed", or specified, at the end of the M and the beginning of G1 phases of the cell…
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…
Background: Recent models of genome-proteome evolution have shown that some of the key traits displayed by the global structure of cellular networks might be a natural result of a duplication-diversification (DD) process. One of the…
Generative convolutional deep neural networks, e.g. popular GAN architectures, are relying on convolution based up-sampling methods to produce non-scalar outputs like images or video sequences. In this paper, we show that common up-sampling…
In a recent paper, Krapivsky and Redner (Phys. Rev. E, 71 (2005) 036118) proposed a new growing network model with new nodes being attached to a randomly selected node, as well to all ancestors of the target node. The model leads to a…
Designing algorithms that generate networks with a given degree sequence while varying both subgraph composition and distribution of subgraphs around nodes is an important but challenging research problem. Current algorithms lack control of…
With complex networks emerging as an effective tool to tackle multidisciplinary problems, models of network generation have gained an importance of their own. These models allow us to extensively analyze the data obtained from real-world…
Genomic duplication-divergence events, which are the primary source of new protein functions, occur stochastically at a wide range of genomic scales, from single gene to whole genome duplications. Clearly, this fundamental evolutionary…
The biological processes of cellular decision making and differentiation involve a plethora of signalling pathways and gene regulatory circuits. These networks, in their turn, exhibit a multitude of motifs playing crucial parts in…
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…
We study theoretically the replication of Kinetoplast DNA consisting of several thousands separate mini-circles found in organisms of the class Kinetoplastida. When the cell is not actively dividing these are topologically connected in a…
In this letter, we proposed an ungrowing scale-free network model, wherein the total number of nodes is fixed and the evolution of network structure is driven by a rewiring process only. In spite of the idiographic form of $G$, by using a…
The E.coli transcription network has an essentially feedforward structure, with, however, abundant feedback at the level of self-regulations. Here, we investigate how these properties emerged during evolution. An assessment of the role of…
Biological networks such as gene regulatory networks possess desirable properties. They are more robust and controllable than random networks. This motivates the search for structural and dynamical features that evolution has incorporated…
Systemic properties of living cells are the result of molecular dynamics governed by so-called genetic regulatory networks (GRN). These networks capture all possible features of cells and are responsible for the immense levels of adaptation…