A review of computational strategies for denoising and imputation of single-cell transcriptomic data

L Patruno, D Maspero, F Craighero… - Briefings in …, 2021 - academic.oup.com
Motivation The advancements of single-cell sequencing methods have paved the way for
the characterization of cellular states at unprecedented resolution, revolutionizing the …

Unraveling the heterogeneity and ontogeny of dendritic cells using single-cell RNA sequencing

B Chen, L Zhu, S Yang, W Su - Frontiers in Immunology, 2021 - frontiersin.org
Dendritic cells (DCs) play essential roles in innate and adaptive immunity and show high
heterogeneity and intricate ontogeny. Advances in high-throughput sequencing …

Imputation methods for scRNA sequencing data

M Wang, J Gan, C Han, Y Guo, K Chen, Y Shi… - Applied Sciences, 2022 - mdpi.com
More and more researchers use single-cell RNA sequencing (scRNA-seq) technology to
characterize the transcriptional map at the single-cell level. They use it to study the …

Imputing dropouts for single-cell RNA sequencing based on multi-objective optimization

K Jin, B Li, H Yan, XF Zhang - Bioinformatics, 2022 - academic.oup.com
Motivation Single-cell RNA sequencing (scRNA-seq) technologies have been testified
revolutionary for their promotion on the profiling of single-cell transcriptomes at single-cell …

SCDRHA: a scRNA-Seq data dimensionality reduction algorithm based on hierarchical autoencoder

J Zhao, N Wang, H Wang, C Zheng, Y Su - Frontiers in genetics, 2021 - frontiersin.org
Dimensionality reduction of high-dimensional data is crucial for single-cell RNA sequencing
(scRNA-seq) visualization and clustering. One prominent challenge in scRNA-seq studies …

High-throughput single-cell RNA-seq data imputation and characterization with surrogate-assisted automated deep learning

X Li, S Li, L Huang, S Zhang… - Briefings in …, 2022 - academic.oup.com
Single-cell RNA sequencing (scRNA-seq) technologies have been heavily developed to
probe gene expression profiles at single-cell resolution. Deep imputation methods have …

A framework for scRNA-seq data clustering based on multi-view feature integration

F Li, Y Liu, J Liu, D Ge, J Shang - Biomedical Signal Processing and Control, 2024 - Elsevier
Accurate and consistent estimation of cell-to-cell similarity is crucial for clustering single-cell
RNA-seq (scRNA-seq) data. However, the high sparsity of scRNA-seq data often leads to …

Graph quilting: graphical model selection from partially observed covariances

G Vinci, G Dasarathy, GI Allen - arXiv preprint arXiv:1912.05573, 2019 - arxiv.org
Graphical model selection is a seemingly impossible task when many pairs of variables are
never jointly observed; this requires inference of conditional dependencies with no …

Are dropout imputation methods for scRNA-seq effective for scATAC-seq data?

Y Liu, J Zhang, S Wang, X Zeng… - Briefings in …, 2022 - academic.oup.com
The tremendous progress of single-cell sequencing technology has given researchers the
opportunity to study cell development and differentiation processes at single-cell resolution …

SCMcluster: a high-precision cell clustering algorithm integrating marker gene set with single-cell RNA sequencing data

H Wu, H Zhou, B Zhou, M Wang - Briefings in Functional …, 2023 - academic.oup.com
Single-cell clustering is the most significant part of single-cell RNA sequencing (scRNA-seq)
data analysis. One main issue facing the scRNA-seq data is noise and sparsity, which poses …