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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…
Non-coding RNAs are ubiquitous, but the discovery of new RNA gene sequences far outpaces research on their structure and functional interactions. We mine the evolutionary sequence record to derive precise information about function and…
Accurate prediction of RNA properties, such as stability and interactions, is crucial for advancing our understanding of biological processes and developing RNA-based therapeutics. RNA structures can be represented as 1D sequences, 2D…
Predicting the secondary structure of RNA is a core challenge in computational biology, essential for understanding molecular function and designing novel therapeutics. The field has evolved from foundational but accuracy-limited…
Accurate prediction of RNA three-dimensional (3D) structure remains an unsolved challenge. Determining RNA 3D structures is crucial for understanding their functions and informing RNA-targeting drug development and synthetic biology design.…
RNA molecules are essential cellular machines performing a wide variety of functions for which a specific three-dimensional structure is required. Over the last several years, experimental determination of RNA structures through X-ray…
Non-coding RNA are functional molecules that are not translated into proteins. Their function comes as important regulators of biological function. Because they are not translated, they need not be as stable as other types of RNA. The TKF91…
Noncoding RNAs are integral to a wide range of biological processes, including translation, gene regulation, host-pathogen interactions and environmental sensing. While genomics is now a mature field, our capacity to identify noncoding RNA…
Accurate prediction of RNA secondary structure underpins transcriptome annotation, mechanistic analysis of non-coding RNAs, and RNA therapeutic design. Recent gains from deep learning and RNA foundation models are difficult to interpret…
Foundation models for single-cell RNA sequencing (scRNA-seq) have shown promising capabilities in capturing gene expression patterns. However, current approaches face critical limitations: they ignore biological prior knowledge encoded in…
The growing significance of RNA engineering in diverse biological applications has spurred interest in developing AI methods for structure-based RNA design. While diffusion models have excelled in protein design, adapting them for RNA…
Proteins, essential to biological systems, perform functions intricately linked to their three-dimensional structures. Understanding the relationship between protein structures and their amino acid sequences remains a core challenge in…
Pretraining with large-scale 3D volumes has a potential for improving the segmentation performance on a target medical image dataset where the training images and annotations are limited. Due to the high cost of acquiring pixel-level…
Structural prediction has long been considered critical in RNA research, especially following the success of AlphaFold2 in protein studies, which has drawn significant attention to the field. While recent advances in machine learning and…
RNA's diverse biological functions stem from its structural versatility, yet accurately predicting and designing RNA sequences given a 3D conformation (inverse folding) remains a challenge. Here, I introduce a deep learning framework that…
Biological foundation models (BioFMs), pretrained on large-scale biological sequences, have recently shown strong potential in providing meaningful representations for diverse downstream bioinformatics tasks. However, such models often rely…
Biological sequences encode fundamental instructions for the building blocks of life, in the form of DNA, RNA, and proteins. Modeling these sequences is key to understand disease mechanisms and is an active research area in computational…
The accurate prediction of protein-RNA binding affinity remains an unsolved problem in structural biology, limiting opportunities in understanding gene regulation and designing RNA-targeting therapeutics. A central obstacle is the…
RNA plays a pivotal role in diverse biological processes, ranging from gene regulation to catalysis. Recent advances in RNA design, such as RfamGen, Ribodiffusion and RDesign, have demonstrated promising results, with successful designs of…
RNA is a fundamental class of biomolecules that mediate a large variety of molecular processes within the cell. Computational algorithms can be of great help in the understanding of RNA structure-function relationship. One of the main…