Related papers: Characteristics of transposable element exonizatio…
The continuity of life and its evolution, we proposed, emerge from an interactive group process manifested in networks of interaction. We term this process \textit{survival-of-the-fitted}. Here, we reason that survival of the fitted results…
Understanding how protein mutations affect protein-nucleic acid binding is critical for unraveling disease mechanisms and advancing therapies. Current experimental approaches are laborious, and computational methods remain limited in…
The mechanical properties of biological materials are spatially heterogeneous. Typical tissues are made up of a spanning fibrous extracellular matrix in which various inclusions, such as living cells, are embedded. While the influence of…
The next step in the understanding of the genome organization, after the determination of complete sequences, involves proteomics. The proteome includes the whole set of protein-protein interactions, and two recent independent studies have…
The evolution of complex molecular traits such as disulphide bridges often requires multiple mutations. The intermediate steps in such evolutionary trajectories are likely to be selectively neutral or deleterious. Therefore, large…
We study transfers of ions and debris from bioceramics implanted in bone sites. A contamination of surrounding tissues may play a major role in aseptic loosening of the implant. For these reasons, bioceramics require studies of…
Phenotypes of individuals in a population of organisms are not fixed. Phenotypic fluctuations, which describe temporal variation of the phenotype of an individual or individual-to-individual variation across a population, are present in…
BACKGROUND: An important question is whether evolution favors properties such as mutational robustness or evolvability that do not directly benefit any individual, but can influence the course of future evolution. Functionally similar…
Conventional population genetics considers the evolution of a limited number of genotypes corresponding to phenotypes with different fitness. As model phenotypes, in particular RNA secondary structure, have become computationally tractable,…
Today's densely instrumented world offers tremendous opportunities for continuous acquisition and analysis of multimodal sensor data providing temporal characterization of an individual's behaviors. Is it possible to efficiently couple such…
Motivation: Genome rearrangement plays an important role in evolutionary biology and has profound impacts on phenotype in organisms ranging from microbes to humans. The mechanisms for genome rearrangement events remain unclear. Lots of…
A new model for evolving Evolutionary Algorithms (EAs) is proposed in this paper. The model is based on the Multi Expression Programming (MEP) technique. Each MEP chromosome encodes an evolutionary pattern that is repeatedly used for…
In the human genomes, recombination frequency between homologous chromosomes during meiosis is highly correlated with their physical length while it differs significantly when their coding density is considered. Furthermore, it has been…
Evolutionary analyses of large populations commonly incorporate stochasticity through temporal variation in selection while treating genetic transmission as fixed. Much less attention has been given to stochasticity in transmission itself.…
Kinetic theory and thermodynamics are applied to DNA polymerases with exonuclease activity, taking into account the dependence of the rates on the previously incorportated nucleotide. The replication fidelity is shown to increase…
We illuminate the influence of transition mutations and disorder on charge localization and transfer along B-DNA sequences. Homopolymers are the best for charge transfer (cf. Refs.~ \cite{LVBMS:2018, MLTS:2019}). Hence, we consider as…
This paper presents an approach to parsing humans when there is significant occlusion. We model humans using a graphical model which has a tree structure building on recent work [32, 6] and exploit the connectivity prior that, even in…
Entrainment of randomly coupled oscillator networks by periodic external forcing applied to a subset of elements is numerically and analytically investigated. For a large class of interaction functions, we find that the entrainment window…
Complexity metrics and machine learning (ML) models have been utilized to analyze the lengths of segmental genomic entities like: exons, introns, intergenic and repeat/unique DNA sequences, in each of the 22 human chromosomes. The purpose…
Transcription is the first step of gene expression, in which a particular segment of DNA is copied to RNA by the enzyme RNA polymerase (RNAP). Despite many details of the complex interactions between DNA and RNA synthesis disclosed…