Related papers: A new Standard DNA damage (SDD) data format
We develop and study the evolution of a model of radiation induced apoptosis in cells using stochastic simulations, and identified key protein targets for effective mitigation of radiation damage. We identified several key proteins…
Unsupervised domain adaptation (UDA) is to learn classification models that make predictions for unlabeled data on a target domain, given labeled data on a source domain whose distribution diverges from the target one. Mainstream UDA…
Deep shotgun sequencing and analysis of genomes, transcriptomes, amplified single-cell genomes, and metagenomes has enabled investigation of a wide range of organisms and ecosystems. However, sampling variation in short-read data sets and…
Sequential Monte Carlo methods are a powerful framework for approximating the posterior distribution of a state variable in a sequential manner. They provide an attractive way of analyzing dynamic systems in real-time, taking into account…
With the rapid increase of available digital data, DNA storage is identified as a storage media with high density and capability of long-term preservation, especially for archival storage systems. However, the encoding density (i.e., how…
DNA-based storage is an emerging storage technology that provides high information density and long duration. Due to the physical constraints in the reading and writing processes, error correction in DNA storage poses several interesting…
Anomaly Detection (AD), as a critical problem, has been widely discussed. In this paper, we specialize in one specific problem, Visual Defect Detection (VDD), in many industrial applications. And in practice, defect image samples are very…
It is well known that the structural deformations (stressed states) of DNA molecule play a crucial role in its biological functions including gene expression. For instance, looping in DNA (often mediated by protein binding) is a crucial…
Modern approaches to supervised learning like deep neural networks (DNNs) typically implicitly assume that observed responses are statistically independent. In contrast, correlated data are prevalent in real-life large-scale applications,…
The yearly global production of data is growing exponentially, outpacing the capacity of existing storage media, such as tape and disk, and surpassing our ability to store it. DNA storage - the representation of arbitrary information as…
DNA storage systems face significant challenges, including insertion, deletion, and substitution (IDS) errors. Therefore, designing effective synchronization codes, i.e., codes capable of correcting IDS errors, is essential for DNA storage…
The short supercoiled circular DNA molecules are shown to be glassy systems and canonical Metropolis Monte Carlo simulations of the systems tend to get stuck in local metastable energy basins. A novel Monte Carlo algorithm is developed to…
DNA nanotechnology promises to provide controllable self-assembly on the nanoscale, allowing for the design of static structures, dynamic machines and computational architectures. In this article I review the state-of-the art of DNA…
The purpose of this work is to extend the Geant4-DNA Monte Carlo toolkit to include electron interactions with the four DNA bases using a set of cross sections recently implemented in Geant-DNA CPA100 models and available for liquid water.…
Chain-like macromolecules in solution, whether biological or synthetic, transform from a spatially extended conformation to a compact one upon change of temperature or solvent qualities. This sharp transition plays a key role in various…
Reconstructing transcriptional regulatory networks is an important task in functional genomics. Data obtained from experiments that perturb genes by knockouts or RNA interference contain useful information for addressing this reconstruction…
Heavy-ion collisions can be simulated by means of comprehensive approaches, to include the many different reaction mechanisms which may contribute. QMD models and their relativistic extensions are examples of these approaches based on Monte…
Models of core-collapse supernova explosions powered by the neutrino-driven mechanism have matured considerable in recent years. Explosions at the low-mass end of the progenitor spectrum can routinely be simulated in 1D, 2D, and 3D and…
Image domain prior models have been shown to improve the quality of reconstructed images, especially when data are limited. Pre-processing of raw data, through the implicit or explicit inclusion of data domain priors have separately also…
The effective DNA-DNA interaction force is calculated by computer simulations with explicit tetravalent counterions and monovalent salt. For overcharged DNA molecules, the interaction force shows a double-minimum structure. The positions…