相关论文: On the Mathematics of RNA Velocity II: Algorithmic…

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…

RNA design aims to identify RNA sequences that fold into a target secondary structure. This task is challenging in terms of computational efficiency. Most existing methods focus on either minimum free energy (MFE)-based or ensemble-based…

Single-cell RNA sequencing (scRNA-seq) technologies have enabled the profiling of gene expression for a collection of cells across time during a dynamic biological process. Given that each time point provides only a static snapshot,…

Background: Since the invention of next-generation RNA sequencing (RNA-seq) technologies, they have become a powerful tool to study the presence and quantity of RNA molecules in biological samples and have revolutionized transcriptomic…

Single-cell RNA sequencing (scRNA-seq) provides high-dimensional profiles of cellular states, enabling data-driven modeling of cellular dynamics over time. In practice, time-resolved scRNA-seq is collected at only a few discrete time points…

In single-cell RNA sequencing (scRNA-seq) analysis, a key challenge is inferring hidden cellular dynamics from static cell snapshots. Various computational methods have been developed to address this, focusing on perspectives like…

In this paper, we introduce the software suite, Hermes, which provides fast, novel algorithms for RNA secondary structure kinetics. Using the fast Fourier transform to efficiently compute the Boltzmann probability that a secondary structure…

Ab initio RNA secondary structure predictions have long dismissed helices interior to loops, so-called pseudoknots, despite their structural importance. Here, we report that many pseudoknots can be predicted through long time scales RNA…

This paper introduces a novel, fast atomic-snapshot protocol for asynchronous message-passing systems. In the process of defining what ``fast'' means exactly, we spot a few interesting issues that arise when conventional time metrics are…

The Regularized Nonlinear Acceleration (RNA) algorithm is an acceleration method capable of improving the rate of convergence of many optimization schemes such as gradient descend, SAGA or SVRG. Until now, its analysis is limited to convex…

Single-cell RNA sequencing (scRNA-seq), especially temporally resolved datasets, enables genome-wide profiling of gene expression dynamics at single-cell resolution across discrete time points. However, current technologies provide only…

RNA design, the task of finding a sequence that folds into a target secondary structure, has broad biological and biomedical impact but remains computationally challenging due to the exponentially large sequence space and exponentially many…

Large RNA molecules often carry multiple functional domains whose spatial arrangement is an important determinant of their function. Pre-mRNA splicing, furthermore, relies on the spatial proximity of the splice junctions that can be…

Single-cell RNA sequencing (scRNA-seq) has revolutionized our ability to analyze gene expression at the resolution of individual cells, providing unprecedented insights into cellular heterogeneity and complex biological systems. This paper…

Motivation: Predicting the secondary structure of an RNA sequence is useful in many applications. Existing algorithms (based on dynamic programming) suffer from a major limitation: their runtimes scale cubically with the RNA length, and…

RNA velocity is a model of gene expression dynamics designed to analyze single-cell RNA sequencing (scRNA-seq) data, and it has recently gained significant attention. However, despite its popularity, the model has raised several concerns,…

Understanding the dynamic nature of biological systems is fundamental to deciphering cellular behavior, developmental processes, and disease progression. Single-cell RNA sequencing (scRNA-seq) has provided static snapshots of gene…

Genes with similar transcriptional activation kinetics can display very different temporal mRNA profiles due to differences in transcription time, degradation rate and RNA processing kinetics. Recent studies have shown that a…

Histopathology whole-slide images (WSIs) are routinely acquired in clinical practice and contain rich tissue morphology but lack direct molecular architecture and functional programs defining pathological states, whereas RNA sequencing…

We describe a dynamic programming algorithm for predicting optimal RNA secondary structure, including pseudoknots. The algorithm has a worst case complexity of ${\cal O}(N^6)$ in time and ${\cal O}(N^4)$ in storage. The description of the…