Related papers: Simplifying the mosaic description of DNA sequence…
Modeling genomic sequences faces two unsolved challenges: the information density varies widely across different regions, while there is no clearly defined minimum vocabulary unit. Relying on either four primitive bases or independently…
The complementary strands of DNA molecules can be separated when stretched apart by a force; the unzipping signal is correlated to the base content of the sequence but is affected by thermal and instrumental noise. We consider here the…
Branched junction molecule assembly of DNA nanostructures, pioneered by Seeman's laboratory in the 1980s, has become increasingly sophisticated, as have the assembly targets. A critical design step is finding minimal sets of branched…
Nearly thirty years after its inception, the field of DNA-programmed colloidal self-assembly has begun to realize its initial promise. In this review, we summarize recent developments in designing effective interactions and understanding…
We developed NameMyGene, a web tool and a stand alone program to easily generate putative family-based names for small RNA sequences so that laboratories can easily organize, analyze, and observe patterns from, the massive amount of data…
Although the free energy of a genome packing into a virus is dominated by DNA-DNA interactions, ordering of the DNA inside the capsid is elasticity-driven, suggesting general solutions with DNA organized into spool-like domains. Using…
We study DNA self-assembly and DNA computation using a coarse-grained DNA model within the directional dynamic bonding framework {[}C. Svaneborg, Comp. Phys. Comm. 183, 1793 (2012){]}. In our model, a single nucleotide or domain is…
DNA sequencing is the process of determining the exact order of the nucleotide bases of an individual's genome in order to catalogue sequence variation and understand its biological implications. Whole-genome sequencing techniques produce…
DNA as a data storage medium has several advantages, including far greater data density compared to electronic media. We propose that schemes for data storage in the DNA of living organisms may benefit from studying the reconstruction…
Modern biological science produces vast amounts of genomic sequence data. This is fuelling the need for efficient algorithms for sequence compression and analysis. Data compression and the associated techniques coming from information…
The main statistical distributions applicable to the analysis of genome architecture and genome tracks are briefly discussed and critically assessed. Although the observed features in distributions of element lengths can be equally well…
DNA is not only the genetic material of life, but also a favorable material for a new computing model. Various research works based on DNA computing have been carried out in recent years. DNA sequence design is the foundation of such…
Transcriptional activity has been shown to relate to the organization of chromosomes in the eukaryotic nucleus and in the bacterial nucleoid. In particular, highly transcribed genes, RNA polymerases and transcription factors gather into…
It is shown that metric representation of DNA sequences is one-to-one. By using the metric representation method, suppression of nucleotide strings in the DNA sequences is determined. For a DNA sequence, an optimal string length to display…
The variation in DNA copy number carries information on the modalities of genome evolution and misregulation of DNA replication in cancer cells; its study can be helpful to localize tumor suppressor genes, distinguish different populations…
All known terrestrial proteins are coded as continuous strings of ~20 amino acids. The patterns formed by the repetitions of elements in groups of finite sequences describes the natural architectures of protein families. We present a method…
In this review paper, we delve into the nascent field of molecular data storage, focusing on system implementations and code constructions. We start by providing an overview of basic concepts in synthetic and computational biology.…
Training medical image segmentation models usually requires a large amount of labeled data. By contrast, humans can quickly learn to accurately recognise anatomy of interest from medical (e.g. MRI and CT) images with some limited guidance.…
Living cells provide a fluctuating, out-of-equilibrium environment in which genes must coordinate cellular function. DNA looping, which is a common means of regulating transcription, is very much a stochastic process; the loops arise from…
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,…