Related papers: A stitch in time: Efficient computation of genomic…
Storing data in DNA is being explored as an efficient solution for archiving and in-object storage. Synthesis time and cost remain challenging, significantly limiting some applications at this stage. In this paper we investigate efficient…
We investigate the melting transition of non-supercoiled circular DNA of different lengths, employing Brownian dynamics simulation. In the absence of supercoiling, we find that melting of circular DNA is driven by a large bubble, which…
Detecting variation in the evolutionary process along chromosomes is increasingly important as whole-genome data becomes more widely available. For example, factors such as incomplete lineage sorting, horizontal gene transfer, and…
When a bug is detected by testing a quantum program on a quantum computer, we want to determine its location to fix it. To locate the bug, the quantum program is divided into several segments, and each segment is tested. However, to prepare…
Based on the Beylkin-Cramer summation rule, we introduce a new fast algorithm that enable us to explore the high order statistics efficiently in large data sets. Central to this technique is to make decomposition both of fields and…
Artificial synthesis of DNA molecules is an essential part of the study of biological mechanisms. The design of a synthetic DNA molecule usually involves many objectives. One of the important objectives is to eliminate short sequence…
Spectral clustering is a popular and effective algorithm designed to find $k$ clusters in a graph $G$. In the classical spectral clustering algorithm, the vertices of $G$ are embedded into $\mathbb{R}^k$ using $k$ eigenvectors of the graph…
Diffusion involving atom transport from one location to another governs many important processes and behaviors such as precipitation and phase nucleation. Local chemical complexity in compositionally complex alloys poses challenges for…
The maximum clique problem (MCP) is a fundamental problem in graph theory and in computational complexity. Given a graph G, the problem is that of finding the largest clique (complete subgraph) in G. The MCP has many important applications…
Genome engineering is undergoing unprecedented development and is now becoming widely available. To ensure responsible biotechnology innovation and to reduce misuse of engineered DNA sequences, it is vital to develop tools to identify the…
We demonstrate how the stochastic global optimization scheme of Simulated Annealing can be used to evaluate optimum parameters in the problem of DNA breathing dynamics. The breathing dynamics is followed in accordance with the stochastic…
Calculation of near-neighbor interactions among high dimensional, irregularly distributed data points is a fundamental task to many graph-based or kernel-based machine learning algorithms and applications. Such calculations, involving…
A matching algorithm for the identification of backbones in percolation problems is introduced. Using this procedure, percolation backbones are studied in two- to five-dimensional systems containing 1.7x10^7 sites, two orders of magnitude…
In this thesis, we address the problem of identifying and quantifying variants (alternative splicing and genomic polymorphism) in RNA-seq data when no reference genome is available, without assembling the full transcripts. Based on the…
Molecular dynamics simulations can generate atomically detailed trajectories of complex systems, but analyzing these dynamics can be challenging when systems lack well-established quantitative descriptors (features). Graph neural networks…
Network analysis has played a key role in knowledge discovery and data mining. In many real-world applications in recent years, we are interested in mining multilayer networks, where we have a number of edge sets called layers, which encode…
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…
We study the parameter sensitivity of hetero-polymeric DNA within the purview of DNA breathing dynamics. The degree of correlation between the mean bubble size and the model parameters are estimated for this purpose for three different DNA…
The first level of folding of DNA in eukaryotes is provided by the so called '10 nm chromatin fibre', where DNA wraps around histone proteins (approx. 10 nm in size) to form nucleosomes, which go on to create a zig zagging bead on a string…
In all state-of-the-art sketching and coreset techniques for clustering, as well as in the best known fixed-parameter tractable approximation algorithms, randomness plays a key role. For the classic $k$-median and $k$-means problems, there…