Related papers: DCJVis: visualization of genome rearrangements usi…
We describe an algorithm for comparing two RNA secondary structures coded in the form of trees that introduces two new operations, called node fusion and edge fusion, besides the tree edit operations of deletion, insertion, and relabeling…
The decomposition of undirected graphs simplifies complex problems by breaking them into solvable subgraphs, following the philosophy of divide and conquer. This paper investigates the relationship between atom decomposition and the maximum…
We develop an algorithm based on three basic DNA editing operations suggested by a model for ciliate micronuclear decryption, to transform a given permutation into another. The number of ciliate operations performed by our algorithm during…
In applications where efficiency is critical, developers may examine their compiled binaries, seeking to understand how the compiler transformed their source code and what performance implications that transformation may have. This analysis…
The edit distance under the DCJ model can be computed in linear time for genomes with equal content or with Indels. But it becomes NP-Hard in the presence of duplications, a problem largely unsolved especially when Indels are considered. In…
The best way to understand complex data structures or algorithm is to see them in action. The present work presents a new tool, especially useful for students and lecturers in computer science. It is written in Java and developed at…
During the last decades, anatomy has become an interesting topic in education---even for laymen or schoolchildren. As medical imaging techniques become increasingly sophisticated, virtual anatomical education applications have emerged.…
Gene assembly in ciliates is one of the most involved DNA processings going on in any organism. This process transforms one nucleus (the micronucleus) into another functionally different nucleus (the macronucleus). We continue the…
Image fusion helps in merging two or more images to construct a more informative single fused image. Recently, unsupervised learning based convolutional neural networks (CNN) have been utilized for different types of image fusion tasks such…
In this paper, we propose a novel network named Vision Transformer for Biomedical Image Segmentation (ViTBIS). Our network splits the input feature maps into three parts with $1\times 1$, $3\times 3$ and $5\times 5$ convolutions in both…
Recent results on supercomputers show that beyond 65K cores, the efficiency of molecular dynamics simulations of interfacial systems decreases significantly. In this paper, we introduce a dynamic cutoff method (DCM) for interfacial systems…
Mesh reconstruction of the cardiac anatomy from medical images is useful for shape and motion measurements and biophysics simulations to facilitate the assessment of cardiac function and health. However, 3D medical images are often acquired…
Genome rearrangement is a common model for molecular evolution. In this paper, we consider the Pairwise Rearrangement problem, which takes as input two genomes and asks for the number of minimum-length sequences of permissible operations…
It has been shown that genome spatial structures largely affect both genome activity and DNA function. Knowing this, many researchers are currently attempting to accurately model genome structures. Despite these increased efforts there…
Program slicing is a technique for simplifying programs by focusing on selected aspects of their behaviour. Current mainstream static slicing methods operate on the PDG (program dependence graph) or SDG (system dependence graph), but these…
We propose a new compression scheme for genomic data given as sequence fragments called reads. The scheme uses a reference genome at the decoder side only, freeing the encoder from the burdens of storing references and performing…
Many imaging problems, such as total variation reconstruction of X-ray computed tomography (CT) and positron-emission tomography (PET), are solved via a convex optimization problem with near-circulant, but not actually circulant, linear…
Data visualization is a fundamental tool in genomics research, enabling the exploration, interpretation, and communication of complex genomic features. While machine learning models show promise for transforming data into insightful…
In many fields of science and technology we are confronted with complex networks. Making sense of these networks often require the ability to visualize and explore their intermingled structure consisting of nodes and links. To facilitate…
During the course of evolution, an organism's genome can undergo changes that affect the large-scale structure of the genome. These changes include gene gain, loss, duplication, chromosome fusion, fission, and rearrangement. When gene gain…