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RNA Secondary Structures with Given Motif Specification: Combinatorics and Algorithms
The study of native motifs of RNA secondary structures helps us better understand the formation and eventually the functions of these molecules....
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Secondary Structure Ensemble Analysis via Community Detection
We explored the extent to which graph algorithms for community detection can improve the mining of structural information from the predicted...
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Qfold: a new modeling paradigm for the RNA folding problem
Ribonucleic acid (RNA) molecules play informational, structural, and metabolic roles in all living cells. RNAs are chains of nucleotides containing...
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On the Problem of Reconstructing a Mixture of rna Structures
A growing number of rna sequences are now known to exist in some distribution with two or more different stable structures. Recent algorithms attempt...
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Are RNA networks scale-free?
A network is scale-free if its connectivity density function is proportional to a power-law distribution. It has been suggested that scale-free...
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Cellular Dreams
A cell exists to produce a copy of itself. First, this means it must grow. Growth requires synthesising the RNA and proteins that make up most of the...
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Life Is a Spiral and It Is Cyclic: The Spiral Structures of the Biosphere
It is believed by most biologists that life began on this planet with the formation of ribonucleic acid (RNA) illustrated in Fig. 8.1 that have the...
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Folding Words Around Trees: Models Inspired by RNA
At the intersection of mathematics and biology, we find mathematical models built to address biological questions as well as new mathematical...
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Biomolecular Topology: Modelling and Analysis
With the great advancement of experimental tools, a tremendous amount of biomolecular data has been generated and accumulated in various databases....
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Modeling Airborne Disease Dynamics: Progress and Questions
It is crucial to understand the spread of infectious airborne diseases that has led to devastating pandemics like COVID-19 and Spanish flu based on...
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Long Non-coding RNA for Plants Using Big Data Analytics—A Review
This study delves into long non-coding RNAs (lncRNAs). The Long non-coding RNAs (lncRNAs) framework is a noteworthy section in non-coding RNAs and...
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Mathematical modelling of HIV-1 transcription inhibition: a comparative study between optimal control and impulsive approach
Through the utilization of a proactive approach, interaction with human immunodeficiency virus type I (HIV-1) is facilitated, enabling the sequential...
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Narayana Number, Chebyshev Polynomial and Motzkin Path on RNA Abstract Shapes
We consider a certain abstract of RNA secondary structures, which is closely related to so-called RNA shapes. The generating function counting the...
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An epidemic model integrating direct and fomite transmission as well as household structure applied to COVID-19
This paper stresses its base contribution on a new SIR-type model including direct and fomite transmission as well as the effect of distinct...
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The Rainbow Spectrum of RNA Secondary Structures
In this paper, we analyze the length spectrum of rainbows in RNA secondary structures. A rainbow in a secondary structure is a maximal arc with...
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Modeling RNA:DNA Hybrids with Formal Grammars
R-loops are nucleic acid structures consisting of a DNA:RNA hybrid and a DNA single strand. They form naturally during transcription when the nascent...
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Evidence of Increased Adaptation of Omicron SARS-CoV-2 Codons to Humans
Viruses are highly dependent on their hosts to carry out cellular mechanisms and cause productive infection. Thus, they undergo extensive adaptations...