Results 1 to 10 of about 5,237 (25)

Quantifying the noise in bursty gene expression under regulation by small RNAs [PDF]

International Journal of Modern Physics C (IJMPC), Vol. 30, No. 07, 1940002 (2019), 2021
Gene expression is a fundamental process in a living system. The small RNAs (sRNAs) is widely observed as a global regulator in gene expression. The inherent nonlinearity in this regulatory process together with the bursty production of messenger RNA (mRNA), sRNA and protein make the exact solution for this stochastic process intractable.
arxiv   +1 more source

Messenger RNA Fluctuations and Regulatory RNAs Shape the Dynamics of Negative Feedback Loop [PDF]

Phys. Rev. E 81, 031924 (2010), 2010
Single cell experiments of simple regulatory networks can markedly differ from cell population experiments. Such differences arise from stochastic events in individual cells that are averaged out in cell populations. For instance, while individual cells may show sustained oscillations in the concentrations of some proteins, such oscillations may appear
arxiv   +1 more source

Network Representation of Large-Scale Heterogeneous RNA Sequences with Integration of Diverse Multi-omics, Interactions, and Annotations Data [PDF]

Pacific Symposium on Biocomputing, Vol 25, 2020, 2019
Long non-coding RNA, microRNA, and messenger RNA enable key regulations of various biological processes through a variety of diverse interaction mechanisms. Identifying the interactions and cross-talk between these heterogeneous RNA classes is essential in order to uncover the functional role of individual RNA transcripts, especially for unannotated ...
arxiv   +1 more source

Fluctuating diffusivity of RNA-protein particles: Analogy with thermodynamics [PDF]

Entropy 2021, 23, 333, 2020
A formal analogy of fluctuating diffusivity to thermodynamics is discussed for messenger RNA molecules fluorescently fused to a protein in living cells. Regarding the average value of the fluctuating diffusivity of such RNA-protein particles as the analog of the internal energy, the analogs of the quantity of heat and work are identified.
arxiv   +1 more source

Interacting RNA polymerase motors on DNA track: effects of traffic congestion and intrinsic noise on RNA synthesis [PDF]

Physical Review E 77, 011921 (2008), 2007
RNA polymerase (RNAP) is an enzyme that synthesizes a messenger RNA (mRNA) strand which is complementary to a single-stranded DNA template. From the perspective of physicists, an RNAP is a molecular motor that utilizes chemical energy input to move along the track formed by a DNA. In many circumstances, which are described in this paper, a large number
arxiv   +1 more source

Systematic transcriptome wide analysis of lncRNA-miRNA interactions [PDF]

, 2012
Long noncoding RNAs (lncRNAs) are a recently discovered class of non-protein coding RNAs which have now increasingly been shown to be involved in a wide variety of biological processes as regulatory molecules. Little is known regarding the regulatory interactions between noncoding RNA classes.
arxiv   +1 more source

Deep learning models for predicting RNA degradation via dual crowdsourcing [PDF]

arXiv, 2021
Messenger RNA-based medicines hold immense potential, as evidenced by their rapid deployment as COVID-19 vaccines. However, worldwide distribution of mRNA molecules has been limited by their thermostability, which is fundamentally limited by the intrinsic instability of RNA molecules to a chemical degradation reaction called in-line hydrolysis ...
arxiv  

The Spanning Tree Model and the Assembly Kinetics of RNA Viruses [PDF]

arXiv, 2021
Single-stranded (ss) RNA viruses self-assemble spontaneously in solutions that contain the viral RNA genome molecules and the viral capsid proteins. The self-assembly of empty capsids can be understood on the basis of free energy minimization of rather simple models.
arxiv  

The Spanning Tree Model and the Assembly Kinetics of RNA Viruses [PDF]

arXiv, 2022
Single-stranded (ss) RNA viruses self-assemble spontaneously in solutions that contain the viral RNA genome molecules and viral capsid proteins. The self-assembly of empty capsids can be understood on the basis of free energy minimization. However, during the self-assembly of complete viral particles in the cytoplasm of an infected cell, the viral ...
arxiv  

Deciphering transcriptional dynamics in vivo by counting nascent RNA molecules [PDF]

, 2013
Transcription of genes is the focus of most forms of regulation of gene expression. Even though careful biochemical experimentation has revealed the molecular mechanisms of transcription initiation for a number of different promoters in vitro, the dynamics of this process in cells is still poorly understood.
arxiv   +1 more source