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Article
3D printing and intelligent technology increase convenience, reliability, and patient acceptance of ostomy nursing: a randomized controlled trial
Traditional ostomy bags commonly cause skin allergy and inflammation around the stoma, as well as leakage. This study aimed to examine the effect of a 3D-printed ostomy bag with sensors and stimulators on stom...
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Article
Discrete latent embedding of single-cell chromatin accessibility sequencing data for uncovering cell heterogeneity
Single-cell epigenomic data has been growing continuously at an unprecedented pace, but their characteristics such as high dimensionality and sparsity pose substantial challenges to downstream analysis. Althou...
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Article
Open AccessscButterfly: a versatile single-cell cross-modality translation method via dual-aligned variational autoencoders
Recent advancements for simultaneously profiling multi-omics modalities within individual cells have enabled the interrogation of cellular heterogeneity and molecular hierarchy. However, technical limitations ...
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Article
SCREEN: predicting single-cell gene expression perturbation responses via optimal transport
In this study, we propose SCREEN, a novel method for predicting perturbation responses of scRNA-seq data. Through extensive experiments on various datasets, we validated the effectiveness and advantages of SCR...
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Article
Open AccessPublisher Correction: scCASE: accurate and interpretable enhancement for single-cell chromatin accessibility sequencing data
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Article
Open AccessscCASE: accurate and interpretable enhancement for single-cell chromatin accessibility sequencing data
Single-cell chromatin accessibility sequencing (scCAS) has emerged as a valuable tool for interrogating and elucidating epigenomic heterogeneity and gene regulation. However, scCAS data inherently suffers from...
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Article
Open AccessscIBD: a self-supervised iterative-optimizing model for boosting the detection of heterotypic doublets in single-cell chromatin accessibility data
Application of the widely used droplet-based microfluidic technologies in single-cell sequencing often yields doublets, introducing bias to downstream analyses. Especially, doublet-detection methods for single...
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Article
Cell type annotation of single-cell chromatin accessibility data via supervised Bayesian embedding
Recent advances in single-cell technologies have enabled the characterization of epigenomic heterogeneity at the cellular level. Computational methods for automatic cell type annotation are urgently needed giv...
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Article
Simultaneous deep generative modelling and clustering of single-cell genomic data
Recent advances in single-cell technologies, including single-cell ATAC-seq (scATAC-seq), have enabled large-scale profiling of the chromatin accessibility landscape at the single-cell level. However, the char...
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Article
Open AccessRA3 is a reference-guided approach for epigenetic characterization of single cells
The recent advancements in single-cell technologies, including single-cell chromatin accessibility sequencing (scCAS), have enabled profiling the epigenetic landscapes for thousands of individual cells. Howeve...
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Article
Open AccessEnClaSC: a novel ensemble approach for accurate and robust cell-type classification of single-cell transcriptomes
In recent years, the rapid development of single-cell RNA-sequencing (scRNA-seq) techniques enables the quantitative characterization of cell types at a single-cell resolution. With the explosive growth of the...
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Article
EpiFIT: functional interpretation of transcription factors based on combination of sequence and epigenetic information
Transcription factor is one of the most important regulators in the transcriptional process. Nevertheless, the functional interpretation of transcription factors is still a main challenge due to the poor perfo...
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Article
Open AccessVPAC: Variational projection for accurate clustering of single-cell transcriptomic data
Single-cell RNA-sequencing (scRNA-seq) technologies have advanced rapidly in recent years and enabled the quantitative characterization at a microscopic resolution. With the exponential growth of the number of...
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Article
Open AccessPredicting enhancers with deep convolutional neural networks
With the rapid development of deep sequencing techniques in the recent years, enhancers have been systematically identified in such projects as FANTOM and ENCODE, forming genome-wide landscapes in a series of ...
