Related papers: Long-Tail Feature of DNA Words Over- and Under-Rep…
DNA sequences encode critical genetic information, yet their variable length and discrete nature impede direct utilization in deep learning models. Existing DNA representation schemes convert sequences into numerical vectors but fail to…
Transcription factor proteins bind specific DNA sequences to control the expression of genes. They contain DNA binding domains which belong to several super-families, each with a specific mechanism of DNA binding. The total number of…
Convolutional codes are error-correcting linear codes that utilize shift registers to encode. These codes have an arbitrary block size and they can incorporate both past and current information bits. DNA codes represent DNA sequences and…
Given several number sequences, determining the longest common subsequence is a classical problem in computer science. This problem has applications in bioinformatics, especially determining transposable genes. Nevertheless, related works…
Genetic interactions have been widely used to define functional relationships between proteins and pathways. In this study, we demonstrated that yeast synthetic lethal genetic interactions can be explained by the genetic interactions…
The problem of differentiating the informational content of coding (exons) and non-coding (introns) regions of a DNA sequence is one of the central problems of genomics. The introns are estimated to be nearly 95% of the DNA and since they…
Effects of sequence disorder on looping and cyclization of the double-stranded DNA are studied theoretically. Both random intrinsic curvature and inhomogeneous bending rigidity are found to result in a remarkably wide distribution of…
We perform a statistical study of the distances between successive occurrencies of a given dinucleotide in the DNA sequence for a number of organisms of different complexity. Our analysis highlights peculiar features of the dinucleotide CG…
We observe regular patterns emerging across multiple length scales with high-concentration DNA solutions in microfluidic pillar arrays at low Reynolds numbers and high Deborah. Interacting vortices between pillars lead to long-range order…
The codons, sixtyfour in number, are distributed over the coding parts of DNA sequences. The distribution function is the plot of frequency-versus-rank of the codons. These distributions are characterised by parameters that are almost…
Background: The length of a protein sequence is largely determined by its function, i.e. each functional group is associated with an optimal size. However, comparative genomics revealed that proteins length may be affected by additional…
We present a new approach for the analysis of genome-wide expression data. Our method is designed to overcome the limitations of traditional techniques, when applied to large-scale data. Rather than alloting each gene to a single cluster,…
The most common gene regulation mechanism is when a transcription factor protein binds to a regulatory sequence to increase or decrease RNA transcription. However, transcription factors face two main challenges when searching for these…
One of the basic questions of phylogenomics is how gene function evolves, whether among species or inside gene families. In this chapter, we provide a brief overview of the problems associated with defining gene function in a manner which…
We study a minimal model for genome evolution whose elementary processes are single site mutation, duplication and deletion of sequence regions and insertion of random segments. These processes are found to generate long-range correlations…
Regulatory networks have evolved to allow gene expression to rapidly track changes in the environment as well as to buffer perturbations and maintain cellular homeostasis in the absence of change. Theoretical work and empirical…
We study electronic transport in long DNA chains using the tight-binding approach for a ladder-like model of DNA. We find insulating behavior with localizaton lengths xi ~ 25 in units of average base-pair seperation. Furthermore, we observe…
Most DNA sequencing technologies are based on the shotgun paradigm: many short reads are obtained from random unknown locations in the DNA sequence. A fundamental question, studied in arXiv:1203.6233, is what read length and coverage depth…
We introduce a coarse-grained model of DNA with bases modeled as rigid-body ellipsoids to capture their anisotropic stereochemistry. Interaction potentials are all physicochemical and generated from all-atom simulation/parameterization with…
Genomes may be analyzed from an information viewpoint as very long strings, containing functional elements of variable length, which have been assembled by evolution. In this work an innovative information theory based algorithm is…