Related papers: Quadruplex detection in human cells
The proliferation of deep neural networks in various domains has seen an increased need for interpretability of these models. Preliminary work done along this line and papers that surveyed such, are focused on high-level representation…
Emerging evidence suggests that the introns and intergenic sequences of the genomes of higher eukaryotes (the ``junk'' DNA) codes for a vast, RNA-based, genetic regulatory network. It is believed that this network is responsible for the…
Cellular phenotypes are determined by the dynamical activity of networks of co-regulated genes. Elucidating such networks is crucial for the understanding of normal cell physiology as well as for the dissection of complex pathologic…
Molecular chaperones play a prominent role in signaling and transcriptional regulatory networks of the cell. Recent advances uncovered that chaperones act as genetic buffers stabilizing the phenotype of various cells and organisms and may…
Three coarse-grained models of the double-stranded DNA are proposed and compared in the context of mechanical manipulation such as twisting and various schemes of stretching. The models differ in the number of effective beads (between two…
Morphological profiling is a valuable tool in phenotypic drug discovery. The advent of high-throughput automated imaging has enabled the capturing of a wide range of morphological features of cells or organisms in response to perturbations…
Inferring functional relationships within complex networks from static snapshots of a subset of variables is a ubiquitous problem in science. For example, a key challenge of systems biology is to translate cellular heterogeneity data…
Cell counting is a ubiquitous, yet tedious task that would greatly benefit from automation. From basic biological questions to clinical trials, cell counts provide key quantitative feedback that drive research. Unfortunately, cell counting…
DNA-interacting proteins have roles multiple processes, many operating as molecular machines which undergo dynamic metastable transitions to bring about their biological function. To fully understand this molecular heterogeneity, DNA and…
Circular RNAs (circRNAs) are a class of RNA with an important role in micro RNA (miRNA) regulation recently discovered in Human and various other eukaryotes as well as in archaea. Here, we have analyzed RNA-seq data obtained from {\it…
Long non-coding RNA, microRNA, and messenger RNA enable key regulations of various biological processes through a variety of diverse interaction mechanisms. Identifying the interactions and cross-talk between these heterogeneous RNA classes…
Genomes contain rare guanine-rich sequences capable of assembling into four-stranded helical structures, termed G-quadruplexes, with potential roles in gene regulation and chromosome stability. Their mechanical unfolding has only been…
In many organisms, homologous (or repetitive) chromosomal regions can associate or/and undergo concerted epigenetic changes in the absence of DNA breakage and recombination. The direct specific pairing of DNA duplexes with similar…
Gene duplication is a fundamental evolutionary mechanism that contributes to biological complexity and diversity (Fortna et al., 2004). Traditionally, research has focused on the duplication of gene sequences (Zhang, 1914). However,…
Convolutional neural networks (CNNs) are the cutting edge model for supervised machine learning in computer vision. In recent years CNNs have outperformed traditional approaches in many computer vision tasks such as object detection, image…
Cell differentiation in multicellular organisms is a complex process whose mechanism can be understood by a reductionist approach, in which the individual processes that control the generation of different cell types are identified.…
Background: The evolution of microRNA regulation in metazoans is a mysterious process: MicroRNA sequences are highly conserved among distal organisms, but on the other hand, there is no evident conservation of their targets. Results: We…
New invariants for 2-dimensional cell complexes are defined, which can be interpreted as curvature bounds. These invariants are proved to be rational and computable in a companion article. This document is a survey that collects theorems…
Patient-specific therapies require that cells be manufactured in multiple batches of small volumes, making it a challenge for conventional modes of quality control. The added complexity of inherent variability (even within batches)…
Does quantum dynamics play a role in DNA replication? What type of tests would reveal that? Some statistical checks that distinguish classical and quantum dynamics in DNA replication are proposed.