Briefings in functional genomics
Dec 6, 2024
Long-read sequencing technologies can capture entire RNA transcripts in a single sequencing read, reducing the ambiguity in constructing and quantifying transcript models in comparison to more common and earlier methods, such as short-read sequencing...
Zhongguo yi liao qi xie za zhi = Chinese journal of medical instrumentation
Nov 30, 2024
Intelligent medical devices are flourishing with the deep integration of modern information and artificial intelligence technologies into healthcare. Testing is an important means of performance evaluation and quality control for intelligent medical ...
Database : the journal of biological databases and curation
Nov 28, 2024
There is an ongoing need for scalable tools to aid researchers in both retrospective and prospective standardization of discrete entity types-such as disease names, cell types, or chemicals-that are used in metadata associated with biomedical data. W...
Bioinformatics (Oxford, England)
Nov 28, 2024
SUMMARY: Accurate drug response prediction is critical to advancing precision medicine and drug discovery. Recent advances in deep learning (DL) have shown promise in predicting drug response; however, the lack of convenient tools to support such mod...
Bioinformatics (Oxford, England)
Nov 28, 2024
MOTIVATION: For more than 25 years, learning-based eukaryotic gene predictors were driven by hidden Markov models (HMMs), which were directly inputted a DNA sequence. Recently, Holst et al. demonstrated with their program Helixer that the accuracy of...
Bioinformatics (Oxford, England)
Nov 28, 2024
MOTIVATION: RNA is implicated in numerous aberrant cellular functions and disease progressions, highlighting the crucial importance of RNA-targeted drugs. To accelerate the discovery of such drugs, it is essential to develop an effective computationa...
Bioinformatics (Oxford, England)
Nov 28, 2024
MOTIVATION: The advent of AlphaFold and other protein Artificial Intelligence (AI) models has transformed protein design, necessitating efficient handling of large-scale data and complex workflows. Using existing programming packages that predate rec...
Briefings in bioinformatics
Nov 22, 2024
The assay for transposase-accessible chromatin with sequencing (ATAC-seq) identifies chromatin accessibility across the genome, crucial for gene expression regulating. However, bulk ATAC-seq obscures cellular heterogeneity, while single-cell ATAC-seq...
Briefings in bioinformatics
Nov 22, 2024
Identifying the regulatory effects of noncoding variants presents a significant challenge. Recently, the accumulation of epigenomic profiling data in wheat has provided an opportunity to model the functional impacts of these variants. In this study, ...
Briefings in bioinformatics
Nov 22, 2024
Cell type annotation is a critical step in analyzing single-cell RNA sequencing (scRNA-seq) data. A large number of deep learning (DL)-based methods have been proposed to annotate cell types of scRNA-seq data and have achieved impressive results. How...