Machine learning integrative approaches to advance computational immunology

F Curion, FJ Theis - Genome Medicine, 2024 - Springer
The study of immunology, traditionally reliant on proteomics to evaluate individual immune
cells, has been revolutionized by single-cell RNA sequencing. Computational …

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 …

scmFormer integrates large‐scale single‐cell proteomics and transcriptomics data by multi‐task transformer

J Xu, DS Huang, X Zhang - Advanced Science, 2024 - Wiley Online Library
Transformer‐based models have revolutionized single cell RNA‐seq (scRNA‐seq) data
analysis. However, their applicability is challenged by the complexity and scale of single …

Applications of spatial transcriptomics and artificial intelligence to develop integrated management of pancreatic cancer

R Maurya, I Chug, V Vudatha… - Advances in cancer …, 2024 - pubmed.ncbi.nlm.nih.gov
Cancer is a complex disease intrinsically associated with cellular processes and gene
expression. With the development of techniques such as single-cell sequencing and …

Prediction of myocardial infarction using a combined generative adversarial network model and feature-enhanced loss function

S Yu, S Han, M Shi, M Harada, J Ge, X Li, X Cai… - Metabolites, 2024 - mdpi.com
Accurate risk prediction for myocardial infarction (MI) is crucial for preventive strategies,
given its significant impact on global mortality and morbidity. Here, we propose a novel deep …

Single-cell analysis reveals transcriptional dynamics in healthy primary parathyroid tissue

A Venkat, MJ Carlino, BR Lawton, ML Prasad… - Genome …, 2024 - genome.cshlp.org
Studies on human parathyroids are generally limited to hyperfunctioning glands owing to the
difficulty in obtaining normal human tissue. We therefore obtained non-human primate …

ZMGA: A ZINB-based multi-modal graph autoencoder enhancing topological consistency in single-cell clustering

J Yao, L Li, T Xu, Y Sun, H **g, C Wang - Biomedical Signal Processing …, 2024 - Elsevier
The topological structure has consistently been a focal point in single-cell clustering
research. Common methods often construct a k-nearest neighbors (KNN) graph from the cell …

Learning transcriptional and regulatory dynamics driving cancer cell plasticity using neural ODE-based optimal transport

A Tong, M Kuchroo, S Gupta, A Venkat, BP San Juan… - bioRxiv, 2023 - biorxiv.org
While single-cell technologies have allowed scientists to characterize cell states that emerge
during cancer progression through temporal sampling, connecting these samples over time …

Identification of cell-type-specific genes in multimodal single-cell data using deep neural network algorithm

W Qian, Z Yang - Computers in Biology and Medicine, 2023 - Elsevier
The emergence of single-cell RNA sequencing (scRNA-seq) technology makes it possible to
measure DNA, RNA, and protein in a single cell. Cellular Indexing of Transcriptomes and …

Scalable integration of multiomic single-cell data using generative adversarial networks

V Giansanti, F Giannese, OA Botrugno… - …, 2024 - academic.oup.com
Motivation Single-cell profiling has become a common practice to investigate the complexity
of tissues, organs, and organisms. Recent technological advances are expanding our …