Related papers: An introduction to reconstructing ancestral genome…
Protein is linked to almost every life process. Therefore, analyzing the biological structure and property of protein sequences is critical to the exploration of life, as well as disease detection and drug discovery. Traditional protein…
Species tree estimation is a complex problem, due to the fact that different parts of the genome can have different evolutionary histories than the genome itself. One of the causes for this discord is incomplete lineage sorting (also called…
Since the advent of modern bioinformatics, the challenging, multifaceted problem of reconstructing phylogenetic history from biological sequences has hatched perennial statistical and algorithmic innovation. Studies of the phylogenetic…
What is a population? This review considers how a population may be defined in terms of understanding the structure of the underlying genetics of the individuals involved. The main approach is to consider statistically identifiable groups…
In recent years, several machine learning approaches have been proposed to predict gene expression and epigenetic signals from the DNA sequence alone. These models are often used to deduce, and, to some extent, assess putative new…
Phylogenetic trees are simple models of evolutionary processes. They describe conditionally independent divergent evolution of taxa from common ancestors. Phylogenetic trees commonly do not have enough flexibility to adequately model all…
Genetic regulation is a key component in development, but a clear understanding of the structure and dynamics of genetic networks is not yet at hand. In this work we investigate these properties within an artificial genome model originally…
The statistical methods derived and described in this thesis provide new ways to elucidate the structural properties of text and other symbolic sequences. Generically, these methods allow detection of a difference in the frequency of a…
Although the role of lateral gene transfer is well recognized in the evolution of bacteria, it is generally assumed that it has had less influence among eukaryotes. To explore this hypothesis we compare the dynamics of genome evolution in…
Because genomes are products of natural processes rather than intelligent design, all genomes contain functional and nonfunctional parts. The fraction of the genome that has no biological function is called rubbish DNA. Rubbish DNA consists…
Phylogenetic networks are increasingly used in evolutionary biology to represent the history of species that have undergone reticulate events such as horizontal gene transfer, hybrid speciation and recombination. One of the most fundamental…
The formation of DNA loops by proteins and protein complexes is ubiquitous to many fundamental cellular processes, including transcription, recombination, and replication. Here we review recent advances in understanding the properties of…
The study of correlation structure in the primary sequences of DNA is reviewed. The issues reviewed include: symmetries among 16 base-base correlation functions, accurate estimation of correlation measures, the relationship between $1/f$…
Identifying similar documents within extensive volumes of data poses a significant challenge. To tackle this issue, researchers have developed a variety of effective distributed computing techniques. With the advancement of computing power…
Inversions, also sometimes called reversals, are a major contributor to variation among bacterial genomes, with studies suggesting that those involving small numbers of regions are more likely than larger inversions. Deletions may arise in…
Proteins, essential to biological systems, perform functions intricately linked to their three-dimensional structures. Understanding the relationship between protein structures and their amino acid sequences remains a core challenge in…
For most deep learning practitioners, sequence modeling is synonymous with recurrent networks. Yet recent results indicate that convolutional architectures can outperform recurrent networks on tasks such as audio synthesis and machine…
Advanced observational facilities allow to trace back the chemical evolution of the Universe, on the one hand, from local objects of different ages and, secondly, by direct observations of redshifted objects. The chemical enrichment serves…
A hypercomplex representation of DNA is proposed to facilitate comparison of DNA sequences with fuzzy composition. Using hypercomplex number representation, conventional sequence analysis method, such as, dot matrix analysis, dynamic…
We are facing a real challenge when coping with the continuous acceleration of scientific production and the increasingly changing nature of science. In this article, we extend the classical framework of co-word analysis to the study of…