Application of deep learning on single-cell RNA sequencing data analysis: a review
Single-cell RNA sequencing (scRNA-seq) has become a routinely used technique to
quantify the gene expression profile of thousands of single cells simultaneously. Analysis of …
quantify the gene expression profile of thousands of single cells simultaneously. Analysis of …
scGPT: toward building a foundation model for single-cell multi-omics using generative AI
Generative pretrained models have achieved remarkable success in various domains such
as language and computer vision. Specifically, the combination of large-scale diverse …
as language and computer vision. Specifically, the combination of large-scale diverse …
Optimal transport for single-cell and spatial omics
C Bunne, G Schiebinger, A Krause, A Regev… - Nature Reviews …, 2024 - nature.com
High-throughput single-cell profiling provides an unprecedented ability to uncover the
molecular states of millions of cells. These technologies are, however, destructive to cells …
molecular states of millions of cells. These technologies are, however, destructive to cells …
A fast, scalable and versatile tool for analysis of single-cell omics data
Single-cell omics technologies have revolutionized the study of gene regulation in complex
tissues. A major computational challenge in analyzing these datasets is to project the large …
tissues. A major computational challenge in analyzing these datasets is to project the large …
Universal DNA methylation age across mammalian tissues
Aging, often considered a result of random cellular damage, can be accurately estimated
using DNA methylation profiles, the foundation of pan-tissue epigenetic clocks. Here, we …
using DNA methylation profiles, the foundation of pan-tissue epigenetic clocks. Here, we …
Population-level integration of single-cell datasets enables multi-scale analysis across samples
C De Donno, S Hediyeh-Zadeh, AA Moinfar… - Nature …, 2023 - nature.com
The increasing generation of population-level single-cell atlases has the potential to link
sample metadata with cellular data. Constructing such references requires integration of …
sample metadata with cellular data. Constructing such references requires integration of …
Universal DNA methylation age across mammalian tissues
Aging is often perceived as a degenerative process resulting from random accrual of cellular
damage over time. Despite this, age can be accurately estimated by epigenetic clocks based …
damage over time. Despite this, age can be accurately estimated by epigenetic clocks based …
Explainable multi-task learning for multi-modality biological data analysis
Current biotechnologies can simultaneously measure multiple high-dimensional modalities
(eg, RNA, DNA accessibility, and protein) from the same cells. A combination of different …
(eg, RNA, DNA accessibility, and protein) from the same cells. A combination of different …
Multimodal single cell data integration challenge: results and lessons learned
Biology has become a data-intensive science. Recent technological advances in single-cell
genomics have enabled the measurement of multiple facets of cellular state, producing …
genomics have enabled the measurement of multiple facets of cellular state, producing …
Benchmarking algorithms for joint integration of unpaired and paired single-cell RNA-seq and ATAC-seq data
Background Single-cell RNA-sequencing (scRNA-seq) measures gene expression in single
cells, while single-nucleus ATAC-sequencing (snATAC-seq) quantifies chromatin …
cells, while single-nucleus ATAC-sequencing (snATAC-seq) quantifies chromatin …