Related papers: Stochastics of DNA Quantification
In the last years, tens of thousands gene expression profiles for cells of several organisms have been monitored. Gene expression is a complex transcriptional process where mRNA molecules are translated into proteins, which control most of…
A probabilistic clustering algorithm is proposed for the analysis of forensic DNA mixtures in which individual cells are isolated and short tandem repeats are amplified using the polymerase chain reaction to generate single cell…
Rigorous assessment of uncertainty is crucial to the utility of DNS results. Uncertainties in the computed statistics arise from two sources: finite statistical sampling and the discretization of the Navier-Stokes equations. Due to the…
DNA replication stands as one of the fundamental biological processes crucial for cellular functioning. Recent experimental developments enable the study of replication dynamics at the single-molecule level for complete genomes,…
The intrinsic stochasticity of gene expression can lead to large variability of protein levels across a population of cells. Variability (or noise) in protein distributions can be modulated by cellular mechanisms of gene regulation; in…
We introduce a model of DNA sequence evolution which can account for biases in mutation rates that depend on the identity of the neighboring bases. An analytic solution for this class of non-equilibrium models is developed by adopting…
The synthesis of DNA strands remains the most costly part of the DNA storage system. Thus, to make DNA storage system more practical, the time and materials used in the synthesis process have to be optimized. We consider the most common…
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…
DNA data storage systems encode digital data into DNA strands, enabling dense and durable storage. Efficient data retrieval depends on coverage depth, a key performance metric. We study the random access coverage depth problem and focus on…
Over the past years, the ever-growing trend on data storage demand, more specifically for "cold" data (rarely accessed data), has motivated research for alternative systems of data storage. Because of its biochemical characteristics,…
A purely electrical sensing scheme is presented that determines the concentration of macromolecules in solution by measuring the capacitance between planar microelectrodes. Concentrations of DNA in the ng/mL range have been used in samples…
Sequencing by synthesis is the underlying technology for many next-generation DNA sequencing platforms. We developed a new model, the fixed flow cycle model, to derive the distributions of sequence length for a given number of flow cycles…
DNA hybridization is a fundamental reaction with wide-ranging applications in biotechnology. The nearest-neighbor (NN) model provides the most reliable description of the energetics of duplex formation. Most DNA thermodynamics studies have…
Single-cell RNA-seq data are challenging because of the sparseness of the read counts, the tiny expression of many relevant genes, and the variability in the efficiency of RNA extraction for different cells. We consider a simple…
Gel electrophoresis, a widely used technique to separate DNA according to their size and weight, generates images that can be analyzed automatically. Manual or semiautomatic image processing presents a bottleneck for further development and…
The density estimation is one of the core problems in statistics. Despite this, existing techniques like maximum likelihood estimation are computationally inefficient due to the intractability of the normalizing constant. For this reason an…
In this brief paper, we go through the theoretical steps of the spectral clustering on quantum computers by employing the phase estimation and the amplitude amplification algorithms. We discuss circuit designs for each step and show how to…
Recently, some authors have shown that a DNA molecule produces electromagnetic signals and communicates with other DNA molecules or other molecules. In fact, a DNA acts like a receiver or transmitter of radio waves. In this paper, we…
Diffusion models have recently dominated image synthesis tasks. However, the iterative denoising process is expensive in computations at inference time, making diffusion models less practical for low-latency and scalable real-world…
The main obstacles for the practical deployment of DNA-based data storage platforms are the prohibitively high cost of synthetic DNA and the large number of errors introduced during synthesis. In particular, synthetic DNA products contain…