Related papers: An introduction to reconstructing ancestral genome…
Clusters of genes that have evolved by repeated segmental duplication present difficult challenges throughout genomic analysis, from sequence assembly to functional analysis. Improved understanding of these clusters is of utmost importance,…
The reconstruction of a central tendency `species tree' from a large number of conflicting gene trees is a central problem in systematic biology. Moreover, it becomes particularly problematic when taxon coverage is patchy, so that not all…
Changing base composition during the evolution of biological sequences can mislead some of the phylogenetic inference techniques in current use. However, detecting whether such a process has occurred may be difficult, since convergent…
In this article, we review the different models and methods to understand and estimate correlated evolution within the same genome, individual or species. We describe correlated evolution among traits, among genetic components and finally…
DNA sequencing is the basic workhorse of modern day biology and medicine. Shotgun sequencing is the dominant technique used: many randomly located short fragments called reads are extracted from the DNA sequence, and these reads are…
With the number of fully-sequenced genomes now well over a hundred it has become possible to start investigating if there are any quantitative regularities in the genetic make-up of genomes. In (physics/0307001), I originally showed that…
In this article we show that the reconstructions of semiconductor surfaces can be determined using a genetic procedure. Coupled with highly optimized interatomic potentials, the present approach represents an efficient tool for finding and…
Background. Models of ancestral gene order reconstruction have progressively integrated different evolutionary patterns and processes such as unequal gene content, gene duplications, and implicitly sequence evolution via reconciled gene…
We have presented the basic knowledge on the structure of molecules coding the genetic information, mechanisms of transfer of this information from DNA to proteins and phenomena connected with replication of DNA. In particular, we have…
Phylogenetic trees and networks are graphs used to model evolutionary relationships, with trees representing strictly branching histories and networks allowing for events in which lineages merge, called reticulation events. While the…
As researchers collect increasingly large molecular data sets to reconstruct the Tree of Life, the heterogeneity of signals in the genomes of diverse organisms poses challenges for traditional phylogenetic analysis. A class of phylogenetic…
In a complex network, different groups of nodes may have existed for different amounts of time. To detect the evolutionary history of a network is of great importance. We present a general method based on spectral analysis to address this…
Molecular phenotypes are important links between genomic information and organismic functions, fitness, and evolution. Complex phenotypes, which are also called quantitative traits, often depend on multiple genomic loci. Their evolution…
In this paper we treat some fractal and statistical features of the DNA sequences. First, a fractal record model of DNA sequence is proposed by mapping DNA sequences to integer sequences, followed by R/S analysis of the model and…
We investigate the symmetry of circular genome rearrangement models, discuss the implementation of a new representation-theoretic method of calculating evolutionary distances between circular genomes, and give the results of some initial…
Large scale databases are available that contain homologous gene families constructed from hundreds of complete genome sequences from across the three domains of Life. Here we discuss approches of increasing complexity aimed at extracting…
Sequence comparison across multiple organisms aids in the detection of regions under selection. However, resource limitations require a prioritization of genomes to be sequenced. This prioritization should be grounded in two considerations:…
High-throughput sequencing (HTS) technologies have revolutionized the field of genomics, enabling rapid and cost-effective genome analysis for various applications. However, the increasing volume of genomic data generated by HTS…
Genomic data I used in many fields but, it has become known that most of the platforms used in the sequencing process produce significant errors. This means that the analysis and inferences generated from these data may have some errors…
DNA sequence encoding is fundamental to gene function prediction, protein synthesis, and diverse downstream biological tasks. Despite the substantial progress achieved by large-scale DNA sequence pretraining, existing studies have…