Related papers: Genome replication in asynchronously growing micro…
We study theoretically the in vitro evolution of a DNA sequence by binding to a transcription factor. Using a simple model of protein-DNA binding and available binding constants for the Mnt protein, we perform large-scale, realistic…
Background: Significance analysis plays a major role in identifying and ranking genes, transcription factor binding sites, DNA methylation regions, and other high-throughput features for association with disease. We propose a new approach,…
We study the stochastic dynamics of sequences evolving by single site mutations, segmental duplications, deletions, and random insertions. These processes are relevant for the evolution of genomic DNA. They define a universality class of…
The rate of recombination affects the mode of molecular evolution. In high-recombining sequence, the targets of selection are individual genetic loci; under low recombination, selection collectively acts on large, genetically linked genomic…
Due to recent breakthroughs in state-of-the-art DNA sequencing technology, genomics data sets have become ubiquitous. The emergence of large-scale data sets provides great opportunities for better understanding of genomics, especially gene…
How DNA repair enzymes find the relatively rare sites of damage is not known in great detail. Recent experiments and molecular data suggest that the individual repair enzymes do not work independently of each other, but rather interact with…
The chromatin folding and the spatial arrangement of chromosomes in the cell play a crucial role in DNA replication and genes expression. An improper chromatin folding could lead to malfunctions and, over time, diseases. For eukaryotes,…
This study proposes a data condensation method for multivariate kernel density estimation by genetic algorithm. First, our proposed algorithm generates multiple subsamples of a given size with replacement from the original sample. The…
We study a stochastic model proposed recently in the genetic literature to explain the heterogeneity of cell populations or of gene products. Cells are located in two colonies, whose sizes fluctuate as birth and migration processes in…
In biological cells, DNA replication is carried out by the replisome, a protein complex encompassing multiple DNA polymerases. DNA replication is semi-discontinuous: a DNA polymerase synthesizes one (leading) strand of the DNA continuously,…
Replication time is among the most important components of a bacterial cell's reproductive fitness. Paradoxically, larger cells replicate in less time than smaller cells despite the fact that building a larger cell requires increased…
We develop a stochastic framework for viral population dynamics at the cellular level that explicitly incorporates the replication cycle with random stage durations. The model is formulated as a structured birth-death process coupled with a…
Evolving biomolecular networks have to combine the stability against perturbations with flexibility allowing their constituents to assume new roles in the cell. Gene duplication followed by functional divergence of associated proteins is a…
Many questions that we have about the history and dynamics of organisms have a geographical component: How many are there, and where do they live? How do they move and interbreed across the landscape? How were they moving a thousand years…
DNA amplification is the process of replication of a specified DNA sequence \emph{in vitro} through time-dependent manipulation of its external environment. A theoretical framework for determination of the optimal dynamic operating…
This paper details an observation that for more primitive organisms, such as some yeasts, the statistical distribution of the origins of replication sometimes looks remarkably like the distribution of eigenvalues from the Circular…
Foundation models in genomics have shown mixed success compared to their counterparts in natural language processing. Yet, the reasons for their limited effectiveness remain poorly understood. In this work, we investigate the role of…
It is known that the majority of the human genome consists of repeated sequences. Furthermore, it is believed that a significant part of the rest of the genome also originated from repeated sequences and has mutated to its current form. In…
A distributed computing system is a collection of processors that communicate either by reading and writing from a shared memory or by sending messages over some communication network. Most prior biologically inspired distributed computing…
Reference-guided DNA sequencing and alignment is an important process in computational molecular biology. The amount of DNA data grows very fast, and many new genomes are waiting to be sequenced while millions of private genomes need to be…