Computational principles and challenges in single-cell data integration

R Argelaguet, ASE Cuomo, O Stegle… - Nature biotechnology, 2021 - nature.com
The development of single-cell multimodal assays provides a powerful tool for investigating
multiple dimensions of cellular heterogeneity, enabling new insights into development …

From reads to insight: a hitchhiker's guide to ATAC-seq data analysis

F Yan, DR Powell, DJ Curtis, NC Wong - Genome biology, 2020 - Springer
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 …

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 …

High-throughput sequencing of the transcriptome and chromatin accessibility in the same cell

S Chen, BB Lake, K Zhang - Nature biotechnology, 2019 - nature.com
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 …

Integration of spatial and single-cell data across modalities with weakly linked features

S Chen, B Zhu, S Huang, JW Hickey, KZ Lin… - Nature …, 2024 - nature.com
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 …

scJoint integrates atlas-scale single-cell RNA-seq and ATAC-seq data with transfer learning

Y Lin, TY Wu, S Wan, JYH Yang, WH Wong… - Nature …, 2022 - nature.com
Single-cell multiomics data continues to grow at an unprecedented pace. Although several
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 …

Integrative methods and practical challenges for single-cell multi-omics

A Ma, A McDermaid, J Xu, Y Chang, Q Ma - Trends in biotechnology, 2020 - cell.com
Fast-developing single-cell multimodal omics (scMulti-omics) technologies enable the
measurement of multiple modalities, such as DNA methylation, chromatin accessibility, RNA …

BABEL enables cross-modality translation between multiomic profiles at single-cell resolution

KE Wu, KE Yost, HY Chang… - Proceedings of the …, 2021 - National Acad Sciences
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 …

scAI: an unsupervised approach for the integrative analysis of parallel single-cell transcriptomic and epigenomic profiles

S Jin, L Zhang, Q Nie - Genome biology, 2020 - Springer
Simultaneous measurements of transcriptomic and epigenomic profiles in the same
individual cells provide an unprecedented opportunity to understand cell fates. However …