Comparative analysis of bacterial essential and nonessential genes with Hurst exponent based on chaos game representation

Zhou, Qian; Yu, Yong‐Ming

doi:10.1016/j.chaos.2014.10.003

Cited by 12 publications

(5 citation statements)

References 35 publications

(45 reference statements)

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“…It is thought that these stochastic fractal dynamics can lead to phenotypic diversity [ 50 , 51 ]. Another study in a variety of bacteria found ranges of H between 0.3–0.8 for different genes, showing a negative correlation with the gene length [ 52 ]. The use of fBm is particularly common in financial modelling [ 53 – 55 ], but it has also been used to describe diffusion within crowded fluids (such as the cytoplasm of cells) [ 56 ] and the kinetics of transcription factors [ 57 ].…”

Section: Discussionmentioning

confidence: 99%

A mathematical modelling framework for the regulation of intra-cellular OCT4 in human pluripotent stem cells

et al. 2021

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Human pluripotent stem cells (hPSCs) have the potential to differentiate into all cell types, a property known as pluripotency. A deeper understanding of how pluripotency is regulated is required to assist in controlling pluripotency and differentiation trajectories experimentally. Mathematical modelling provides a non-invasive tool through which to explore, characterise and replicate the regulation of pluripotency and the consequences on cell fate. Here we use experimental data of the expression of the pluripotency transcription factor OCT4 in a growing hPSC colony to develop and evaluate mathematical models for temporal pluripotency regulation. We consider fractional Brownian motion and the stochastic logistic equation and explore the effects of both additive and multiplicative noise. We illustrate the use of time-dependent carrying capacities and the introduction of Allee effects to the stochastic logistic equation to describe cell differentiation. We conclude both methods adequately capture the decline in OCT4 upon differentiation, but the Allee effect model has the advantage of allowing differentiation to occur stochastically in a sub-set of cells. This mathematical framework for describing intra-cellular OCT4 regulation can be extended to other transcription factors and developed into predictive models.

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Section: Discussionmentioning

confidence: 99%

A mathematical modelling framework for the regulation of intra-cellular OCT4 in human pluripotent stem cells

et al. 2021

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“…The Hurst exponent is a characteristic parameter which describes the degree of self-similarity of a data set. For genes of similar length, the average Hurst exponent of essential genes is smaller than that of non-essential genes ( Zhou and Yu, 2014 ).…”

Section: Computational Methods For the Prediction Of Essential Genesmentioning

confidence: 99%

A Comprehensive Overview of Online Resources to Identify and Predict Bacterial Essential Genes

et al. 2017

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Genes critical for the survival or reproduction of an organism in certain circumstances are classified as essential genes. Essential genes play a significant role in deciphering the survival mechanism of life. They may be greatly applied to pharmaceutics and synthetic biology. The continuous progress of experimental method for essential gene identification has accelerated the accumulation of gene essentiality data which facilitates the study of essential genes in silico. In this article, we present some available online resources related to gene essentiality, including bioinformatic software tools for transposon sequencing (Tn-seq) analysis, essential gene databases and online services to predict bacterial essential genes. We review several computational approaches that have been used to predict essential genes, and summarize the features used for gene essentiality prediction. In addition, we evaluate the available online bacterial essential gene prediction servers based on the experimentally validated essential gene sets of 30 bacteria from DEG. This article is intended to be a quick reference guide for the microbiologists interested in the essential genes.

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“…[ 100,102] Hurst exponent Essential genes have a lower average Hurst exponent. [103] Context-related features…”

Section: ]mentioning

confidence: 99%

Recent advances in the characterization of essential genes and development of a database of essential genes

Liang,

Luo,

Lin

et al. 2024

iMeta

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Over the past few decades, there has been a significant interest in the study of essential genes, which are crucial for the survival of an organism under specific environmental conditions and thus have practical applications in the fields of synthetic biology and medicine. An increasing amount of experimental data on essential genes has been obtained with the continuous development of technological methods. Meanwhile, various computational prediction methods, related databases and web servers have emerged accordingly. To facilitate the study of essential genes, we have established a database of essential genes (DEG), which has become popular with continuous updates to facilitate essential gene feature analysis and prediction, drug and vaccine development, as well as artificial genome design and construction. In this article, we summarized the studies of essential genes, overviewed the relevant databases, and discussed their practical applications. Furthermore, we provided an overview of the main applications of DEG and conducted comprehensive analyses based on its latest version. However, it should be noted that the essential gene is a dynamic concept instead of a binary one, which presents both opportunities and challenges for their future development.

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Comparative analysis of bacterial essential and nonessential genes with Hurst exponent based on chaos game representation

Cited by 12 publications

References 35 publications

A mathematical modelling framework for the regulation of intra-cellular OCT4 in human pluripotent stem cells

A mathematical modelling framework for the regulation of intra-cellular OCT4 in human pluripotent stem cells

A Comprehensive Overview of Online Resources to Identify and Predict Bacterial Essential Genes

Recent advances in the characterization of essential genes and development of a database of essential genes

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