Related papers: DSBplot: Indels in DNA Double-strand Break Repair …
Advances in DNA nanotechnology have stimulated the search for simple motifs that can be used to control the properties of DNA nanostructures. One such motif, which has been used extensively in structures such as polyhedral cages,…
We present a calculation technique for modeling inhomogeneous DNA replication kinetics, where replication factors such as initiation rates or fork speeds can change with both position and time. We can use our model to simulate data sets…
Multi-modality (MM) semi-supervised learning (SSL) based medical image segmentation has recently gained increasing attention for its ability to utilize MM data and reduce reliance on labeled images. However, current methods face several…
The prevalent technique for DNA sequencing consists of two main steps: shotgun sequencing, where many randomly located fragments, called reads, are extracted from the overall sequence, followed by an assembly algorithm that aims to…
The cell cycle is an orderly sequence of events which ultimately lead to the division of a single cell into two daughter cells. In the case of DNA damage by radiation or chemicals, the damage checkpoints in the $G_{1}$ and $G_{2}$ phases of…
In this paper we study error-correcting codes for the storage of data in synthetic deoxyribonucleic acid (DNA). We investigate a storage model where a data set is represented by an unordered set of $M$ sequences, each of length $L$. Errors…
The development of novel high-throughput sequencing (HTS) methods for RNA (RNA-Seq) has provided a very powerful mean to study splicing under multiple conditions at unprecedented depth. However, the complexity of the information to be…
Extreme deformations of the DNA double helix attracted a lot of attention during the past decades. Particularly, the determination of the persistence length of DNA with extreme local disruptions, or kinks, has become a crucial problem in…
Multi-segment reconstruction (MSR) problem consists of recovering a signal from noisy segments with unknown positions of the observation windows. One example arises in DNA sequence assembly, which is typically solved by matching short reads…
The radiation-induced damages in bio-molecules are ubiquitous processes in radiotherapy, radio-biology and critical to space-projects. In this study we present a precise quantification of the fragmentation mechanisms of deoxyribonucleic…
Several neurodegenerative diseases involve the accumulation of cellular DNA damage. Comet assays are a popular way of estimating the extent of DNA damage. Current literature on the use of deep learning to quantify DNA damage presents an…
During mammalian embryo development, reprogramming of DNA methylation plays important roles in the erasure of parental epigenetic memory and the establishment of na\"{i}ve pluripogent cells. Multiple enzymes that regulate the processes of…
Modern high-throughput gene perturbation screens are key technologies at the forefront of genetic research. Combined with rich phenotypic descriptors they enable researchers to observe detailed cellular reactions to experimental…
DNA is an attractive medium for digital data storage. When data is stored on DNA, errors occur, which makes error-correcting coding techniques critical for reliable DNA data storage. To reduce the errors, a common technique is to include…
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…
It is not known how a cell manages to find a specific DNA sequence sufficiently fast to repair a broken chromosome through homologous recombination. I propose that the solution is based on a parallelized search implemented by freely…
We propose a combined experimental (Atomic Force Microscopy) and theoretical study of the structural and dynamical properties of nucleosomes. In contrast to biochemical approaches, this method allows to determine simultaneously the DNA…
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…
After the completion of human genome sequence was anounced, it is evident that interpretation of DNA sequences is an immediate task to work on. For understanding their signals, improvement of present sequence analysis tools and developing…
Multiply inverted balancer chromosomes that suppress exchange with their homologs are an essential part of the genetic toolkit in Drosophila melanogaster. Despite their widespread use, the organization of balancer chromosomes has not been…