Related papers: Modeling of two-dimensional DNA display
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…
Recent advances in deep learning have shown that learning robust feature representations is critical for the success of many computer vision tasks, including medical image segmentation. In particular, both transformer and…
Understanding the morphological structure of medical images and precisely segmenting the region of interest or abnormality is an important task that can assist in diagnosis. However, the unique properties of medical imaging make clear…
DNA nanotechnology uses predictable interactions of nucleic acids to precisely engineer complex nanostructures. Characterizing these self-assembled structures at the single-structure level is crucial for validating their design and…
A self-organizing approach is proposed for gene finding based on the model of codon usage for coding regions and positional preference for noncoding regions. The symmetry between the direct and reverse coding regions is adopted for reducing…
Automating classification and segmentation process of abnormal regions in different body organs has a crucial role in most of medical imaging applications such as funduscopy, endoscopy, and dermoscopy. Detecting multiple abnormalities in…
We propose a new abstraction set (SynopSet) that has a continuum of visual representations for the explanatory analysis of molecular dynamics simulations (MDS) in the DNA nanotechnology domain. By re-purposing the commonly used progress bar…
We represent 3D shape by structured 2D representations of fixed length making it feasible to apply well investigated 2D convolutional neural networks (CNN) for both discriminative and geometric tasks on 3D shapes. We first provide a general…
Conventional visualization media such as MRI prints and computer screens are inherently two dimensional, making them incapable of displaying true 3D volume data sets. By applying only transparency or intensity projection, and ignoring…
Two-dimensional coherent spectroscopy (2DCS) with terahertz radiation offers a promising new avenue for the exploration of many-body phenomena in quantum magnets. This includes the potential diagnosis of fractionalized excitations, for…
The oxDNA model of DNA has been applied widely to systems in biology, biophysics and nanotechnology. It is currently available via two independent open source packages. Here we present a set of clearly-documented exemplar simulations that…
Optical images of transparent three-dimensional objects can be different from a replica of the object's cross section in the image plane due to refraction at the surface or in the body of the object. Simulations of the object's image are…
DNA labeling is a powerful tool in molecular biology and biotechnology that allows for the visualization, detection, and study of DNA at the molecular level. Under this paradigm, a DNA molecule is being labeled by specific k patterns and is…
A difficult step in the process of karyotyping is segmenting chromosomes that touch or overlap. In an attempt to automate the process, previous studies turned to Deep Learning methods, with some formulating the task as a semantic…
Thanks to its capability of acquiring full-view frames at multiple kilohertz, ultrafast ultrasound imaging unlocked the analysis of rapidly changing physical phenomena in the human body, with pioneering applications such as ultrasensitive…
The goal of many computer vision systems is to transform image pixels into 3D representations. Recent popular models use neural networks to regress directly from pixels to 3D object parameters. Such an approach works well when supervision…
Genetic recombination can produce heterogeneous phylogenetic histories within a set of homologous genes. Delineating recombination events is important in the study of molecular evolution, as inference of such events provides a clearer…
Modern technology for producing extremely bright and coherent X-ray laser pulses provides the possibility to acquire a large number of diffraction patterns from individual biological nanoparticles, including proteins, viruses, and DNA.…
Plastic deformation In crystalline materials is controlled by the motion and interactions of dislocations [AND 17]. Discrete Dislocation Dynamics (DDD) simulations have now existed for about 25 years to investigate plastic flow at the…
DNA supercoiling, the under or overwinding of DNA, is a key physical mechanism both participating to compaction of bacterial genomes and making genomic sequences adopt various structural forms. DNA supercoiling may lead to the formation of…