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Reading Frame Retrieval of Genes: A New Parameter of Codon Usage Based on the Circular Code Theory
Based on the circular code theory, we define a new function f that quantifies the property of reading frame retrieval (RFR) of genes from their codon...
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Four Billion Years: The Story of an Ancient Protein Family
Comparison of protein sequences has long been a very effective tool for producing biological knowledge. It was initially based on the alignment of...
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Assessing the Potential of Gene Tree Parsimony for Microbial Phylogenomics
A key challenge in microbial phylogenomics is that microbial gene families are often affected by extensive horizontal gene transfer (HGT). As a...
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Transcription Factors Across the Escherichia coli Pangenome: A 3D Perspective
Identification of complete sets of transcription factors (TFs) is a foundational step in the inference of genetic regulatory networks. The...
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Pseudo-Rate Matrices, Beyond Dayhoff’s Model
One of the fundamental techniques of biology is sequence alignment, namely transforming one sequence into another with minimal change. Sequence...
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Reconciliation with Segmental Duplication, Transfer, Loss and Gain
We generalize the reconciliation approach, used for inferring the evolution of a single gene family given a species tree, to groups of co-localized...
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Network-Based Computational Modeling to Unravel Gene Essentiality
Essential genes are reductively defined as those fundamental for an organism’s reproductive success and growth. Still, the so-called essentiality of...
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Epilogue
This chapter turns to some philosophical questions. Can life be defined? What can thermodynamics tell us about life elsewhere in the universe? Can...
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Splendid Molecular Machines
This chapter is about ATP, the key carrier molecule in cells. ATP’s most important role is as a ratchet, a chemical demon which allows nanoengines to...
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On the Distribution of Synteny Blocks Under a Neutral Model of Genome Dynamics
Prokaryotes are a rich source of versatile molecular functional systems that typically consist of multiple, interacting proteins. The study of such...
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A Solution of Fractional Bio-Chemical Reaction Model by Adomian Decomposition Method
This paper focuses on the modeling of the bio-chemical reaction viz anaerobic digestion which is biochemical process of producing biogas which is the...
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Biological Background—Information, Energy, and Matter
In this chapter, we provide a brief introduction of the biological background. We summarize the essential features of life from the view of...
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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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Development of a Model for the Process of Anaerobic Digestion and Its Solution by the Modified Adomian Decomposition Method
Modeling the transformation of biomass into biogas is complex, because it involves a nonlinear and coupled set of ordinary differential equations....
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Microbial Degradation of Fenitrothion (an Insecticide) Found in Agriculture Soils—A Review
Increase in the expenditure of insecticides is more and more, year by year, there has a substantial qualitative, quantitative change in insecticide...
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Sensitivity Analysis for Verification of an Anaerobic Digestion Model
In this article, the first-order sensitivity coefficients for a system of stiff nonlinear differential equations from the anaerobic digestion model...
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The structure of the genetic code as an optimal graph clustering problem
The standard genetic code (SGC) is the set of rules by which genetic information is translated into proteins, from codons, i.e. triplets of...
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On the Comparison of Incompatibility of Split Systems Across Different Numbers of Taxa
We consider the problem of the minimum number of phylogenetic trees it would take to display all splits in a given set, a problem related to k -compati...
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A Strang Splitting Approach Combined with Chebyshev Wavelets to Solve the Regularized Long-Wave Equation Numerically
In this manuscript, a Strang splitting approach combined with Chebyshev wavelets has been used to obtain the numerical solutions of regularized...
