Computational principles and challenges in single-cell data integration
The development of single-cell multimodal assays provides a powerful tool for investigating
multiple dimensions of cellular heterogeneity, enabling new insights into development …
multiple dimensions of cellular heterogeneity, enabling new insights into development …
From reads to insight: a hitchhiker's guide to ATAC-seq data analysis
Abstract Assay of Transposase Accessible Chromatin sequencing (ATAC-seq) is widely
used in studying chromatin biology, but a comprehensive review of the analysis tools has …
used in studying chromatin biology, but a comprehensive review of the analysis tools has …
Multi-omics single-cell data integration and regulatory inference with graph-linked embedding
ZJ Cao, G Gao - Nature Biotechnology, 2022 - nature.com
Despite the emergence of experimental methods for simultaneous measurement of multiple
omics modalities in single cells, most single-cell datasets include only one modality. A major …
omics modalities in single cells, most single-cell datasets include only one modality. A major …
High-throughput sequencing of the transcriptome and chromatin accessibility in the same cell
Single-cell RNA sequencing can reveal the transcriptional state of cells, yet provides little
insight into the upstream regulatory landscape associated with open or accessible …
insight into the upstream regulatory landscape associated with open or accessible …
Integration of spatial and single-cell data across modalities with weakly linked features
Although single-cell and spatial sequencing methods enable simultaneous measurement of
more than one biological modality, no technology can capture all modalities within the same …
more than one biological modality, no technology can capture all modalities within the same …
scJoint integrates atlas-scale single-cell RNA-seq and ATAC-seq data with transfer learning
Single-cell multiomics data continues to grow at an unprecedented pace. Although several
methods have demonstrated promising results in integrating several data modalities from …
methods have demonstrated promising results in integrating several data modalities from …
Biologically informed deep learning to query gene programs in single-cell atlases
M Lotfollahi, S Rybakov, K Hrovatin… - Nature Cell …, 2023 - nature.com
The increasing availability of large-scale single-cell atlases has enabled the detailed
description of cell states. In parallel, advances in deep learning allow rapid analysis of newly …
description of cell states. In parallel, advances in deep learning allow rapid analysis of newly …
Integrative methods and practical challenges for single-cell multi-omics
Fast-developing single-cell multimodal omics (scMulti-omics) technologies enable the
measurement of multiple modalities, such as DNA methylation, chromatin accessibility, RNA …
measurement of multiple modalities, such as DNA methylation, chromatin accessibility, RNA …
BABEL enables cross-modality translation between multiomic profiles at single-cell resolution
Simultaneous profiling of multiomic modalities within a single cell is a grand challenge for
single-cell biology. While there have been impressive technical innovations demonstrating …
single-cell biology. While there have been impressive technical innovations demonstrating …
scAI: an unsupervised approach for the integrative analysis of parallel single-cell transcriptomic and epigenomic profiles
Simultaneous measurements of transcriptomic and epigenomic profiles in the same
individual cells provide an unprecedented opportunity to understand cell fates. However …
individual cells provide an unprecedented opportunity to understand cell fates. However …