Related papers: Genome Sizes and the Benford Distribution
Engineering the entire genome of an organism enables large-scale changes in organization, function, and external interactions, with significant implications for industry, medicine, and the environment. Improvements to DNA synthesis and…
The complex pattern of presence and absence of many genes across different species provides tantalising clues as to how genes evolved through the processes of gene genesis, gene loss and lateral gene transfer (LGT). The extent of LGT,…
We study the length distribution of a particular class of DNA sequences known as 5'UTR exons. These exons belong to the messanger RNA of protein coding genes, but they are not coding (they are located upstream of the coding portion of the…
The yearly global production of data is growing exponentially, outpacing the capacity of existing storage media, such as tape and disk, and surpassing our ability to store it. DNA storage - the representation of arbitrary information as…
The prevalence of neutral mutations implies that biological systems typically have many more genotypes than phenotypes. But can the way that genotypes are distributed over phenotypes determine evolutionary outcomes? Answering such questions…
Although both RNA and proteins have densely packed native structures, chain organizations of these two biopolymers are fundamentally different. Motivated by the recent discoveries in chromatin folding that interphase chromosomes have…
Background: Recent studies in a growing number of organisms have yielded accumulating evidence that a significant portion of the non-coding region in the genome is transcribed. We address this issue in the yeast Saccharomyces cerevisiae.…
The RNA world hypothesis, that RNA genomes and catalysts preceded DNA genomes and genetically-encoded protein catalysts, has been central to models for the early evolution of life on Earth. A key part of such models is continuity between…
Gene expression is a central process to any form of life. It involves multiple temporal and functional scales that extend from specific protein-DNA interactions to the coordinated regulation of multiple genes in response to intracellular…
The amount of non-unique sequence (non-singletons) in a genome directly affects the difficulty of read alignment to a reference assembly for high throughput-sequencing data. Although a greater length increases the chance for reads being…
Background: In addition to known protein-coding genes, large amount of apparently non-coding sequence are conserved between the human and mouse genomes. It seems reasonable to assume that these conserved regions are more likely to contain…
Understanding functional organization of genetic information is a major challenge in modern biology. Following the initial publication of the human genome sequence in 2001, advances in high-throughput measurement technologies and efficient…
We study the growth of random networks under a constraint that the diameter, defined as the average shortest path length between all nodes, remains approximately constant. We show that if the graph maintains the form of its degree…
Searching for similar genomic sequences is an essential and fundamental step in biomedical research and an overwhelming majority of genomic analyses. State-of-the-art computational methods performing such comparisons fail to cope with the…
The solution space of genome-scale models of cellular metabolism provides a map between physically viable flux configurations and cellular metabolic phenotypes described, at the most basic level, by the corresponding growth rates. By…
Several processes in the cell, such as gene regulation, start when key proteins recognise and bind to short DNA sequences. However, as these sequences can be hundreds of million times shorter than the genome, they are hard to find by simple…
Shaped by natural selection and other evolutionary forces, an organism's evolutionary history is reflected through its genome sequence, content of functional elements and organization. Consequently, organisms connected through phylogeny,…
Background: Duplication of genes is important for evolution of molecular networks. Many authors have therefore considered gene duplication as a driving force in shaping the topology of molecular networks. In particular it has been noted…
The evolutionary pressures that underlie the large-scale functional organization of the genome are not well understood in eukaryotes. Recent evidence suggests that functionally similar genes may colocalize (cluster) in the eukaryotic…
The frequency distributions of DNA k-mers are shaped by fundamental biological processes and offer a window into genome structure and evolution. Inspired by analogies to natural language, prior studies have attempted to model genomic k-mer…