Related papers: Stochastics of DNA Quantification
A central challenge in computational modeling of dynamic biological systems is parameter inference from experimental time course measurements. However, one would not only like to infer kinetic parameters but also study their variability…
Nanochannels provide means for detailed experiments on the effect of confinement on biomacromolecules, such as DNA. We here introduce a model for the complete unfolding of DNA from the circular to linear configuration. Two main ingredients…
Mathematical models of gene regulatory networks are widely used to study cell fate changes and transcriptional regulation. When designing such models, it is important to accurately account for sources of stochasticity. However, doing so can…
DNA-based biodiversity surveys involve collecting physical samples from survey sites and assaying the contents in the laboratory to detect species via their diagnostic DNA sequences. DNA-based surveys are increasingly being adopted for…
Synthetic DNA approaches 227.5 exabytes per gram of storage density with stability over millennial timescales. Realising this capacity requires error-correction codes that recover data from substantial synthesis and sequencing errors.…
Uncertainty quantification is an important and challenging problem in deep learning. Previous methods rely on dropout layers which are not present in modern deep architectures or batch normalization which is sensitive to batch sizes. In…
Real-time PCR, or Real-time Quantitative PCR (qPCR) is an effective approach to quantify nucleic acid samples. Given the complicated reaction system along with thermal cycles, there has been long-term confusion on accurately calculating the…
Phase insensitive optical amplification of an unknown quantum state is known to be a fundamentally noisy operation that inevitably adds noise to the amplified state [1 - 5]. However, this fundamental noise penalty in amplification can be…
DNA synthesis is considered as one of the most expensive components in current DNA storage systems. In this paper, focusing on a common synthesis machine, which generates multiple DNA strands in parallel following a fixed supersequence,we…
DNA has immense potential as an emerging data storage medium. The principle of DNA storage is the conversion and flow of digital information between binary code stream, quaternary base, and actual DNA fragments. This process will inevitably…
DNA methylation is a well-studied genetic modification that regulates gene transcription of Eukaryotes. Its alternations have been recognized as a significant component of cancer development. In this study, we use the DNA methylation 450k…
We analyze the structure of DNA molecules of different organisms by using the additive Markov chain approach. Transforming nucleotide sequences into binary strings, we perform statistical analysis of the corresponding "texts". We develop…
DNA has emerged as a promising alternative for long-term data storage due to its high capacity, durability, and low-energy potential. However, storing data in DNA presents several challenges. First, it requires complex and costly…
In Cowell et al. (2007), a Bayesian network for analysis of mixed traces of DNA was presented using gamma distributions for modelling peak sizes in the electropherogram. It was demonstrated that the analysis was sensitive to the choice of a…
Previous theoretical studies have shown that measuring the transverse current across DNA strands while they translocate through a nanopore or channel may provide a statistically distinguishable signature of the DNA bases, and may thus allow…
The mechanical properties of molecules are today captured by single molecule manipulation experiments, so that polymer features are tested at a nanometric scale. Yet devising mathematical models to get further insight beyond the commonly…
In this study, we explore how quantum pathfinding algorithm called Gaussian Amplitude Amplification (GAA) can be used to solve the DNA sequencing problem. To do this, sequencing by hybridization was assumed wherein short fragments of the…
Regulation of intrinsic noise in gene expression is essential for many cellular functions. Correspondingly, there is considerable interest in understanding how different molecular mechanisms of gene expression impact variations in protein…
A solid-state nanopore can electrophoretically capture a DNA molecule and pull it through in a folded configuration. The resulting ionic current signal indicates where along its length the DNA was captured. A statistical study using an 8 nm…
The assembly of RecA on single-stranded DNA is measured and interpreted as a stochastic finite-state machine that is able to discriminate fine differences between sequences, a basic computational operation. RecA filaments efficiently scan…