Related papers: Quadruplex detection in human cells

RNA velocity is an important model that combines cellular spliced and unspliced RNA counts to infer dynamical properties of various regulatory functions. Despite its wide applicability and many variants used in practice, the model has not…

Genomic alterations lead to cancer complexity and form a major hurdle for a comprehensive understanding of the molecular mechanisms underlying oncogenesis. In this review, we describe the recent advances in studying cancer-associated genes…

The computer-aided folding of biomolecules, particularly RNAs, is one of the most difficult challenges in computational structural biology. RNA tetraloops are fundamental RNA motifs playing key roles in RNA folding and RNA-RNA and…

Biological systems, from a cell to the human brain, are inherently complex. A powerful representation of such systems, described by an intricate web of relationships across multiple scales, is provided by complex networks. Recently, several…

Biological cells, by definition, are the basic units which contain the fundamental molecules of life of which all living things are composed. Understanding how they function and differentiating cells from one another therefore is of…

This paper introduces the use of cable dynamics models as a means to explore the mechanics of DNA on long-length scales. It is on these length scales that DNA forms twisted and curved three-dimensional shapes known as supercoils and loops.…

MicroRNAs (miRNAs) critically modulate stem cell properties like pluripotency, but the fundamental mechanism remains largely unknown. This study systematically analyzes multiple-omics data and builds a systems physical network including…

Quaternions are an important tool to describe the orientation of a molecule. This paper considers the use of quaternions in matching two conformations of a molecule, in interpolating rotations, in performing statistics on orientational…

Identify the cells' nuclei is the important point for most medical analyses. To assist doctors finding the accurate cell' nuclei location automatically is highly demanded in the clinical practice. Recently, fully convolutional neural…

We study mathematically a method for discovering which gene is related to a cell phenotype of interest. The method is based on RNA interference -- a molecular process for gene deactivation -- and on coupling the phenotype with fluorescence…

Although in cellular networks full-duplex and dynamic time-division duplexing promise increased spectrum efficiency, their potential is so far challenged by increased interference. While previous studies have shown that self-interference…

Real networks exhibit heterogeneous nature with nodes playing far different roles in structure and function. To identify vital nodes is thus very significant, allowing us to control the outbreak of epidemics, to conduct advertisements for…

Understanding the morphological changes of primary neuronal cells induced by chemical compounds is essential for drug discovery. Using the data from a single high-throughput imaging assay, a classification model for predicting the…

Identifying the role of network units in deep neural networks (DNNs) is critical in many aspects including giving understandings on the mechanisms of DNNs and building basic connections between deep learning and neuroscience. However, there…

Neural networks in the real domain have been studied for a long time and achieved promising results in many vision tasks for recent years. However, the extensions of the neural network models in other number fields and their potential…

Diseases involve complex processes and modifications to the cellular machinery. The gene expression profile of the affected cells contains characteristic patterns linked to a disease. Hence, biological knowledge pertaining to a disease can…

RNA structure and functional dynamics play fundamental roles in controlling biological systems. Molecular dynamics simulation, which can characterize interactions at an atomistic level, can advance the understanding on new drug discovery,…

We study genetic networks that produce many species of non-coding RNA molecules that are present at a moderate density, as typically exists in the cell. The associations of the many species of these RNA are modeled physically, taking into…

The information capacity of double-crossover (DX) tiles was successfully increased beyond a binary representation to higher base representations. By controlling the length and the position of DNA hairpins on the DX tile, ternary and senary…

Microtubule networks (MTs) are a component of a cell that may indicate the presence of various chemical compounds and can be used to recognize properties such as treatment resistance. Therefore, the classification of MT images is of great…