Related papers: 3plex Web: An Interactive Platform for RNA:DNA Tri…
Given the importance of non-coding RNAs to cellular regulatory functions and rapid growth of RNA transcripts, computational prediction of RNA tertiary structure remains highly demanded yet significantly challenging. Even for a short RNA…
Automatically identifying data types of web structured data is a key step in the process of web data integration. Web structured data is usually associated with entities or objects in a particular domain. In this paper, we aim to map…
Multiplex networks are complex graph structures in which a set of entities are connected to each other via multiple types of relations, each relation representing a distinct layer. Such graphs are used to investigate many complex…
A full understanding of RNA-mediated biology would require the knowledge of three-dimensional (3D) structures, structural flexibility and stability of RNAs. To predict RNA 3D structures and stability, we have previously proposed a…
Motivation: Cell-biological processes are regulated through a complex network of interactions between genes and their products. The processes, their activating conditions, and the associated transcriptional responses are often unknown.…
Summary: Macromolecular assembly vertebrates essential cellular processes, such as gene regulation and signal transduction. A major challenge for conventional computational methods to study these processes is tackling the exponential…
Ribonucleic acid (RNA) is involved in many regulatory and catalytic processes in the cell. The function of any RNA molecule is intimately related with its structure. In-line probing experiments provide valuable structural datasets for a…
Elements composing complex systems usually interact in several different ways and as such the interaction architecture is well modelled by a multiplex network. However often this architecture is hidden, as one usually only has experimental…
Motivation: Spliced alignment refers to the alignment of messenger RNA (mRNA) or protein sequences to eukaryotic genomes. It plays a critical role in gene annotation and the study of gene functions. Accurate spliced alignment demands…
Single-cell RNA-sequencing (scRNA-seq) has become a routinely used technique to quantify the gene expression profile of thousands of single cells simultaneously. Analysis of scRNA-seq data plays an important role in the study of cell states…
A variety of real-world applications rely on far future information to make decisions, thus calling for efficient and accurate long sequence multivariate time series forecasting. While recent attention-based forecasting models show strong…
We propose HydraScreen, a deep-learning approach that aims to provide a framework for more robust machine-learning-accelerated drug discovery. HydraScreen utilizes a state-of-the-art 3D convolutional neural network, designed for the…
Recent progress on salient object detection mainly aims at exploiting how to effectively integrate multi-scale convolutional features in convolutional neural networks (CNNs). Many popular methods impose deep supervision to perform…
Gene regulation involves a hierarchy of events that extend from specific protein-DNA interactions to the combinatorial assembly of nucleoprotein complexes. The effects of DNA sequence on these processes have typically been studied based…
Direct cDNA preamplification protocols developed for single-cell RNA-seq have enabled transcriptome profiling of precious clinical samples and rare cells without sample pooling or RNA extraction. Currently, there is no algorithm optimized…
RNA interference (RNAi) is a mechanism whereby small RNAs (siRNAs) directly control gene expression without assistance from proteins. This mechanism consists of interactions between RNAs and small RNAs both of which may be single or double…
Diagnostic prediction and clinical reasoning are critical tasks in healthcare applications. While Large Language Models (LLMs) have shown strong capabilities in commonsense reasoning, they still struggle with diagnostic reasoning due to…
The Triple Pattern Fragment (TPF) interface is a recent proposal for reducing server load in Web-based approaches to execute SPARQL queries over public RDF datasets. The price for less overloaded servers is a higher client-side load and a…
Irregularly sampled time series data with missing values is observed in many fields like healthcare, astronomy, and climate science. Interpolation of these types of time series is crucial for tasks such as root cause analysis and medical…
Three-dimensional DNA networks, composed of tri- or higher valent nanostars with sticky, single-stranded DNA overhangs, have been previously studied in the context of designing thermally responsive, viscoelastic hydrogels. In this work, we…