Related papers: Universal and idiosyncratic characteristic lengths…
In this research, we consider a mixture of genome fragments of a certain bacteria set. The problem of mixture separation is studied under the assumption that all the genomes present in the mixture are completely sequenced or are close to…
We introduce a notion of genus range as a set of values of genera over all surfaces into which a graph is embedded cellularly, and we study the genus ranges of a special family of four-regular graphs with rigid vertices that has been used…
DNA storage is now being considered as a new archival storage method for its durability and high information density, but still facing some challenges like high costs and low throughput. By reducing sequencing sample size for decoding…
Genome-wide gene expression profiles, as measured with microarrays or RNA-Seq experiments, have revolutionized biological and biomedical research by providing a quantitative measure of the entire mRNA transcriptome. Typically, researchers…
Protein variability in single cells has been studied extensively in populations, but little is known about temporal protein fluctuations in a single cell over extended times. We present here traces of protein copy number measured in…
Maximum distance profile codes are characterized by the property that two trajectories which start at the same state and proceed to a different state will have the maximum possible distance from each other relative to any other…
The principal permanent rank characteristic sequence is a binary sequence $r_0 r_1 \ldots r_n$ where $r_k = 1$ if there exists a principal square submatrix of size $k$ with nonzero permanent and $r_k = 0$ otherwise, and $r_0 = 1$ if there…
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…
Applying machine learning to biological sequences - DNA, RNA and protein - has enormous potential to advance human health, environmental sustainability, and fundamental biological understanding. However, many existing machine learning…
We report a theoretical study of DNA flexibility and quantitatively predict the ring closure probability as a function of DNA contour length. Recent experimental studies show that the flexibility of short DNA fragments (as compared to the…
DNA is a leading candidate as the next archival storage media due to its density, durability and sustainability. To read (and write) data DNA storage exploits technology that has been developed over decades to sequence naturally occurring…
Cellular phenotype is characterized by different components such as cell size, protein content and cell cycle time. These are global variables that are the outcome of multiple internal microscopic processes. Accordingly, they display some…
We consider force-induced unzipping transition for a heterogeneous DNA model with a correlated base-sequence. Both finite-range and long-range correlated situations are considered. It is shown that finite-range correlations increase…
We study the electronic properties of DNA by way of a tight-binding model applied to four particular DNA sequences. The charge transfer properties are presented in terms of localisation lengths, crudely speaking the length over which…
DNA labeling is a powerful tool in molecular biology and biotechnology that allows for the visualization, detection, and study of DNA at the molecular level. Under this paradigm, a DNA molecule is being labeled by specific k patterns and is…
We propose a novel combination of methods that (i) portrays quantitative characteristics of a DNA sequence as an image, (ii) computes distances between these images, and (iii) uses these distances to output a map wherein each sequence is a…
Complexity metrics and machine learning (ML) models have been utilized to analyze the lengths of segmental genomic entities like: exons, introns, intergenic and repeat/unique DNA sequences, in each of the 22 human chromosomes. The purpose…
The evolution of the full repertoire of proteins encoded in a given genome is mostly driven by gene duplications, deletions, and sequence modifications of existing proteins. Indirect information about relative rates and other intrinsic…
The helical coil is ubiquitous in biological and natural systems and often it is the basic form that leads to complex structures. This paper considers the question of its dimensionality in biological information as the helical coil goes…
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…