Single-cell omics: experimental workflow, data analyses and applications

F Sun, H Li, D Sun, S Fu, L Gu, X Shao, Q Wang… - Science China Life …, 2024 - Springer
Cells are the fundamental units of biological systems and exhibit unique development
trajectories and molecular features. Our exploration of how the genomes orchestrate the …

Deep single-cell RNA-seq data clustering with graph prototypical contrastive learning

J Lee, S Kim, D Hyun, N Lee, Y Kim, C Park - Bioinformatics, 2023 - academic.oup.com
Motivation Single-cell RNA sequencing enables researchers to study cellular heterogeneity
at single-cell level. To this end, identifying cell types of cells with clustering techniques …

scDCCA: deep contrastive clustering for single-cell RNA-seq data based on auto-encoder network

J Wang, J Xia, H Wang, Y Su… - Briefings in …, 2023 - academic.oup.com
The advances in single-cell ribonucleic acid sequencing (scRNA-seq) allow researchers to
explore cellular heterogeneity and human diseases at cell resolution. Cell clustering is a …

[HTML][HTML] Artificial intelligence and machine learning applications for cultured meat

ME Todhunter, S Jubair, R Verma, R Saqe… - Frontiers in Artificial …, 2024 - frontiersin.org
Cultured meat has the potential to provide a complementary meat industry with reduced
environmental, ethical, and health impacts. However, major technological challenges …

Deep learning in single-cell analysis

D Molho, J Ding, W Tang, Z Li, H Wen, Y Wang… - ACM Transactions on …, 2024 - dl.acm.org
Single-cell technologies are revolutionizing the entire field of biology. The large volumes of
data generated by single-cell technologies are high dimensional, sparse, and …

scLEGA: an attention-based deep clustering method with a tendency for low expression of genes on single-cell RNA-seq data

Z Liu, Y Liang, G Wang, T Zhang - Briefings in Bioinformatics, 2024 - academic.oup.com
Single-cell RNA sequencing (scRNA-seq) enables the exploration of biological
heterogeneity among different cell types within tissues at a resolution. Inferring cell types …

scGGAN: single-cell RNA-seq imputation by graph-based generative adversarial network

Z Huang, J Wang, X Lu, A Mohd Zain… - Briefings in …, 2023 - academic.oup.com
Single-cell RNA sequencing (scRNA-seq) data are typically with a large number of missing
values, which often results in the loss of critical gene signaling information and seriously …

Effective multi-modal clustering method via skip aggregation network for parallel scRNA-seq and scATAC-seq data

D Hu, K Liang, Z Dong, J Wang, Y Zhao… - Briefings in …, 2024 - academic.oup.com
In recent years, there has been a growing trend in the realm of parallel clustering analysis
for single-cell RNA-seq (scRNA) and single-cell Assay of Transposase Accessible …

A graph neural network approach for the analysis of siRNA-target biological networks

M La Rosa, A Fiannaca, L La Paglia… - International Journal of …, 2022 - mdpi.com
Many biological systems are characterised by biological entities, as well as their
relationships. These interaction networks can be modelled as graphs, with nodes …

scEGG: an exogenous gene-guided clustering method for single-cell transcriptomic data

D Hu, R Guan, K Liang, H Yu, H Quan… - Briefings in …, 2024 - academic.oup.com
In recent years, there has been significant advancement in the field of single-cell data
analysis, particularly in the development of clustering methods. Despite these …