Related papers: Correlation Between GC-content and Palindromes in …
Inspired by a concept in comparative genomics, we investigate properties of randomly chosen members of G_1(m,n,t), the set of bipartite graphs with $m$ left vertices, n right vertices, t edges, and each vertex of degree at least one. We…
We use a semi-analytic model for globular cluster (GC) formation built on dark matter merger trees to explore the relative role of formation physics and hierarchical assembly in determining the properties of GC populations. Many previous…
RNA viruses form genetically diverse populations structured as mutant spectra, or quasispecies, whose internal organization influences their evolutionary and adaptive dynamics. While genetic diversity has been extensively characterized, the…
Generating diverse, high-quality outputs from language models is crucial for applications in education and content creation. Achieving true randomness and avoiding repetition remains a significant challenge. This study uses the Linear…
Graph structural information such as topologies or connectivities provides valuable guidance for graph convolutional networks (GCNs) to learn nodes' representations. Existing GCN models that capture nodes' structural information weight in-…
Genotype networks are a method used in systems biology to study the "innovability" of a set of genotypes having the same phenotype. In the past they have been applied to determine the genetic heterogeneity, and stability to mutations, of…
DNA codes have garnered significant interest due to their utilization in digital media storage, cryptography, and DNA computing. In this paper, we first extend the results of constructing reversible group codes \cite{Cengellenmis} and…
Much information is stored in amino acid composition of protein and base composition of DNA. We simulated the evolution of amino acid frequencies and genomic GC content by a linguistic model. It is showed that the evolution of genetic code…
Genetic variants (GVs) are defined as differences in the DNA sequences among individuals and play a crucial role in diagnosing and treating genetic diseases. The rapid decrease in next generation sequencing cost has led to an exponential…
Genetic mutations can cause disease by disrupting normal gene function. Identifying the disease-causing mutations from millions of genetic variants within an individual patient is a challenging problem. Computational methods which can…
The evolutionary dynamics of molecular populations are strongly dependent on the structure of genotype spaces. The map between genotype and phenotype determines how easily genotype spaces can be navigated and the accessibility of…
An oscillation with a period of around 500 kb in guanine and cytosine content (GC%) is observed in the DNA sequence of human chromosome 21. This oscillation is localized in the rightmost one-eighth region of the chromosome, from 43.5 Mb to…
Genome-wide association studies, in which as many as a million single nucleotide polymorphisms (SNP) are measured on several thousand samples, are quickly becoming a common type of study for identifying genetic factors associated with many…
For a genomically unstable cancer, a single tumour biopsy will often contain a mixture of competing tumour clones. These tumour clones frequently differ with respect to their genomic content (copy number of each gene) and structure (order…
Identifying drivers of complex traits from the noisy signals of genetic variation obtained from high throughput genome sequencing technologies is a central challenge faced by human geneticists today. We hypothesize that the variants…
Heterogeneous molecular entities and their interactions, commonly depicted as a network, are crucial for advancing our systems-level understanding of biology. With recent advancements in high-throughput data generation and a significant…
Genome data are crucial in modern medicine, offering significant potential for diagnosis and treatment. Thanks to technological advancements, many millions of healthy and diseased genomes have already been sequenced; however, obtaining the…
We provide, on an extensive dataset and using several different distances, confirmation of the hypothesis that CGR patterns are preserved along a genomic DNA sequence, and are different for DNA sequences originating from genomes of…
Spatial transcriptomics technologies enable the measurement of gene expression with spatial context, providing opportunities to understand how gene regulatory networks vary across tissue regions. However, existing graphical models focus…
The GC content of prokaryotic genomes is species-specific and takes values from 16 to 77 percent. There are currently no accepted explanations for this diversity of selection for GC content. We analyzed the known correlations between GC…