Revisiting the thorny issue of missing values in single-cell proteomics

C Vanderaa, L Gatto - Journal of Proteome Research, 2023 - ACS Publications
Missing values are a notable challenge when analyzing mass spectrometry-based
proteomics data. While the field is still actively debating the best practices, the challenge …

scCAN: single-cell clustering using autoencoder and network fusion

B Tran, D Tran, H Nguyen, S Ro, T Nguyen - Scientific reports, 2022 - nature.com
Unsupervised clustering of single-cell RNA sequencing data (scRNA-seq) is important
because it allows us to identify putative cell types. However, the large number of cells (up to …

SAE-Impute: imputation for single-cell data via subspace regression and auto-encoders

L Bai, B Ji, S Wang - BMC bioinformatics, 2024 - Springer
Background Single-cell RNA sequencing (scRNA-seq) technology has emerged as a crucial
tool for studying cellular heterogeneity. However, dropouts are inherent to the sequencing …

scGAA: a general gated axial-attention model for accurate cell-type annotation of single-cell RNA-seq data

T Kong, T Yu, J Zhao, Z Hu, N **ong, J Wan, X Dong… - Scientific Reports, 2024 - nature.com
Single-cell RNA sequencing (scRNA-seq) is a key technology for investigating cell
development and analysing cell diversity across various diseases. However, the high …

Inferring single-cell trajectories via critical cell identification using graph centrality algorithm

Y Gan, J Chu, G Xu, C Yan, G Zou - Neurocomputing, 2025 - Elsevier
Trajectory inference (TI) aims to infer cell differentiation trajectories in biological processes.
Numerous computational methods have been developed to infer cell lineages from single …

Improved downstream functional analysis of single-cell RNA-sequence data using DGAN

D Pandey, PP Onkara - Scientific Reports, 2023 - nature.com
The dramatic increase in the number of single-cell RNA-sequence (scRNA-seq)
investigations is indeed an endorsement of the new-fangled proficiencies of next generation …

Imputation method for dropout in single-cell transcriptome data

C Jiang, L Hu, C Xu, Q Ge, X Zhao - Sheng wu yi xue Gong Cheng …, 2023 - europepmc.org
单细胞转录组测序 (scRNA-seq) 可以在单细胞精度下解析组织中细胞的表达特征,
使得研究人员能以更高的分辨率定量群体内的细胞异质性, 揭示潜在的异质细胞群体和复杂组织 …

Imputation method for single-cell RNA-seq data using neural topic model

Y Qi, S Han, L Tang, L Liu - GigaScience, 2023 - academic.oup.com
Single-cell RNA sequencing (scRNA-seq) technology studies transcriptome and cell-to-cell
differences from higher single-cell resolution and different perspectives. Despite the …

Dwen: A novel method for accurate estimation of cell type compositions from bulk data samples

D Tran, H Nguyen, H Nguyen… - 2022 14th International …, 2022 - ieeexplore.ieee.org
Advances in single-cell RNA sequencing (scRNAseq) technologies have allowed us to
study the heterogeneity of cell populations. The cell compositions of tissues from different …

Imputing Single-Cell Protein Abundance in Multiplex Tissue Imaging

R Kirchgaessner, C Watson, A Creason, K Keutler… - …, 2024 - pmc.ncbi.nlm.nih.gov
Multiplex tissue imaging are a collection of increasingly popular single-cell spatial
proteomics and transcriptomics assays for characterizing biological tissues both …