相关论文: ProtScan: Modeling and Prediction of RNA-Protein I…

Virtual screening, which identifies potential drugs from vast compound databases to bind with a particular protein pocket, is a critical step in AI-assisted drug discovery. Traditional docking methods are highly time-consuming, and can only…

Photoactivatable ribonucleoside-enhanced cross-linking and immunoprecipitation (PAR-CLIP) is an experimental method based on next-generation sequencing for identifying the RNA interaction sites of a given protein. The method deliberately…

Multi-modality pre-training paradigm that aligns protein sequences and biological descriptions has learned general protein representations and achieved promising performance in various downstream applications. However, these works were…

Prompt learning is a powerful technique for transferring Vision-Language Models (VLMs) such as CLIP to downstream tasks. However, the prompt-based methods that are fine-tuned solely with base classes may struggle to generalize to novel…

RNA/protein interactions play crucial roles in controlling gene expression. They are becoming important targets for pharmaceutical applications. Due to RNA flexibility and to the strength of electrostatic interactions, standard docking…

Isoform quantification is an important goal of RNA-seq experiments, yet it remains prob- lematic for genes with low expression or several isoforms. These difficulties may in principle be ameliorated by exploiting correlated experimental…

In the face of rapidly accumulating genomic data, our understanding of the RNA regulatory code remains incomplete. Recent self-supervised methods in other domains have demonstrated the ability to learn rules underlying the data-generating…

Motivation: Alternative splicing is an important mechanism in which the regions of pre-mRNAs are differentially joined in order to form different transcript isoforms. Alternative splicing is involved in the regulation of normal…

The development of novel high-throughput sequencing (HTS) methods for RNA (RNA-Seq) has provided a very powerful mean to study splicing under multiple conditions at unprecedented depth. However, the complexity of the information to be…

Alternative splicing is crucial in gene regulation, with significant implications in clinical settings and biotechnology. This review article compiles bioinformatics RNA-seq tools for investigating differential splicing; offering a detailed…

Virtual screening aims to efficiently identify active ligands from massive chemical libraries for a given target pocket. Recent CLIP-style models such as DrugCLIP enable scalable virtual screening by embedding pockets and ligands into a…

Contrastive Language-Image Pretraining (CLIP) has emerged as a novel paradigm to learn visual models from language supervision. While researchers continue to push the frontier of CLIP, reproducing these works remains challenging. This is…

RNA-Seq technology allows for studying the transcriptional state of the cell at an unprecedented level of detail. Beyond quantification of whole-gene expression, it is now possible to disentangle the abundance of individual alternatively…

Rapidly growing public gene expression databases contain a wealth of data for building an unprecedentedly detailed picture of human biology and disease. This data comes from many diverse measurement platforms that make integrating it all…

The recent advancements in Generative Adversarial Networks (GANs) and the emergence of Diffusion models have significantly streamlined the production of highly realistic and widely accessible synthetic content. As a result, there is a…

Molecular phenotyping by gene expression profiling is common in contemporary cancer research and in molecular diagnostics. However, molecular profiling remains costly and resource intense to implement, and is just starting to be introduced…

Background:Typically, proteins perform key biological functions by interacting with each other. As a consequence, predicting which protein pairs interact is a fundamental problem. Experimental methods are slow, expensive, and may be error…

Protein-DNA interaction is critical for life activities such as replication, transcription, and splicing. Identifying protein-DNA binding residues is essential for modeling their interaction and downstream studies. However, developing…

Identification and quantification of condition-specific transcripts using RNA-Seq is vital in transcriptomics research. While initial efforts using mathematical or statistical modeling of read counts or per-base exonic signal have been…

Computational screening of naturally occurring proteins has the potential to identify efficient catalysts among the hundreds of millions of sequences that remain uncharacterized. Current experimental methods remain time, cost and labor…