Intricacies of single-cell multi-omics data integration

Multi-domain translation between single-cell imaging and sequencing data using autoencoders

(2021) Karren Dai Yang et al.   Nature Communications

ArchR is a scalable software package for integrative single-cell chromatin accessibility analysis

(2021) Jeffrey M. Granja et al.   NATURE GENETICS

Joint profiling of histone modifications and transcriptome in single cells from mouse brain

(2021) Chenxu Zhu et al.   NATURE METHODS

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

(2021) Kevin E. Wu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Simultaneous trimodal single-cell measurement of transcripts, epitopes, and chromatin accessibility using TEA-seq

(2021) Elliott Swanson et al.   eLife

scAMACE: model-based approach to the joint analysis of single-cell data on chromatin accessibility, gene expression and methylation

(2021) Jiaxuan Wangwu et al.   BIOINFORMATICS

Manifold alignment for heterogeneous single-cell multi-omics data integration using Pamona

(2021) Kai Cao et al.   BIOINFORMATICS

Integrated analysis of multimodal single-cell data

(2021) Yuhan Hao et al.   CELL

Scalable, multimodal profiling of chromatin accessibility, gene expression and protein levels in single cells

(2021) Eleni P. Mimitou et al.   NATURE BIOTECHNOLOGY

coupleCoC+: An information-theoretic co-clustering-based transfer learning framework for the integrative analysis of single-cell genomic data

(2021) Pengcheng Zeng et al.   PLoS Computational Biology

Single-cell multimodal omics: the power of many

(2020) Chenxu Zhu et al.   NATURE METHODS

Model-Based Approach to the Joint Analysis of Single-Cell Data on Chromatin Accessibility and Gene Expression

(2020) Zhixiang Lin et al.   STATISTICAL SCIENCE

Single-cell analysis targeting the proteome

(2020) Mahmoud Labib et al.   Nature Reviews Chemistry

Lineage tracing meets single-cell omics: opportunities and challenges

(2020) Daniel E. Wagner et al.   NATURE REVIEWS GENETICS

Single‐Cell Multi‐Omics and Its Prospective Application in Cancer Biology

(2020) Anghui Peng et al.   PROTEOMICS

Integrative Methods and Practical Challenges for Single-Cell Multi-omics

(2020) Anjun Ma et al.   TRENDS IN BIOTECHNOLOGY

Unsupervised topological alignment for single-cell multi-omics integration

(2020) Kai Cao et al.   BIOINFORMATICS

Chromatin Potential Identified by Shared Single-Cell Profiling of RNA and Chromatin

(2020) Sai Ma et al.   CELL

Single-cell multiomics: technologies and data analysis methods

(2020) Jeongwoo Lee et al.   EXPERIMENTAL AND MOLECULAR MEDICINE

Jointly defining cell types from multiple single-cell datasets using LIGER

(2020) Jialin Liu et al.   Nature Protocols

Integrating genetic and non-genetic determinants of cancer evolution by single-cell multi-omics

(2020) Anna S. Nam et al.   NATURE REVIEWS GENETICS

Elucidation of Biological Networks across Complex Diseases Using Single-Cell Omics

(2020) Yang Li et al.   TRENDS IN GENETICS

Single-cell RNA cap and tail sequencing (scRCAT-seq) reveals subtype-specific isoforms differing in transcript demarcation

(2020) Youjin Hu et al.   Nature Communications

SCIM: universal single-cell matching with unpaired feature sets

(2020) Stefan G Stark et al.   BIOINFORMATICS

Deconvolution of single-cell multi-omics layers reveals regulatory heterogeneity

(2019) Longqi Liu et al.   Nature Communications

The single-cell transcriptional landscape of mammalian organogenesis

(2019) Junyue Cao et al.   NATURE

Corrupted coordination of epigenetic modifications leads to diverging chromatin states and transcriptional heterogeneity in CLL

(2019) Alessandro Pastore et al.   Nature Communications

Comprehensive Integration of Single-Cell Data

(2019) Tim Stuart et al.   CELL

Single-Cell Multi-omic Integration Compares and Contrasts Features of Brain Cell Identity

(2019) Joshua D. Welch et al.   CELL

Mapping chromatin modifications at the single cell level

(2019) Connor H. Ludwig et al.   DEVELOPMENT

Current best practices in single‐cell RNA‐seq analysis: a tutorial

(2019) Malte D Luecken et al.   Molecular Systems Biology

scSLAM-seq reveals core features of transcription dynamics in single cells

(2019) Florian Erhard et al.   NATURE

Joint analysis of heterogeneous single-cell RNA-seq dataset collections

(2019) Nikolas Barkas et al.   NATURE METHODS

A lineage-resolved molecular atlas of C. elegans embryogenesis at single-cell resolution

(2019) Jonathan S. Packer et al.   SCIENCE

Fast, sensitive and accurate integration of single-cell data with Harmony

(2019) Ilya Korsunsky et al.   NATURE METHODS

An ultra high-throughput method for single-cell joint analysis of open chromatin and transcriptome

(2019) Chenxu Zhu et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

DC3 is a method for deconvolution and coupled clustering from bulk and single-cell genomics data

(2019) Wanwen Zeng et al.   Nature Communications

Building gene regulatory networks from scATAC-seq and scRNA-seq using Linked Self Organizing Maps

(2019) Camden Jansen et al.   PLoS Computational Biology

Single-cell multiomic analysis identifies regulatory programs in mixed-phenotype acute leukemia

(2019) Jeffrey M. Granja et al.   NATURE BIOTECHNOLOGY

Integrated Single-Cell Analysis Maps the Continuous Regulatory Landscape of Human Hematopoietic Differentiation

(2018) Jason D. Buenrostro et al.   CELL

Batch effects in single-cell RNA-sequencing data are corrected by matching mutual nearest neighbors

(2018) Laleh Haghverdi et al.   NATURE BIOTECHNOLOGY

Integrating single-cell transcriptomic data across different conditions, technologies, and species

(2018) Andrew Butler et al.   NATURE BIOTECHNOLOGY

Integrative analysis of single-cell genomics data by coupled nonnegative matrix factorizations

(2018) Zhana Duren et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Single-Cell DNA Methylation Profiling: Technologies and Biological Applications

(2018) Ino D. Karemaker et al.   TRENDS IN BIOTECHNOLOGY

Joint profiling of chromatin accessibility and gene expression in thousands of single cells

(2018) Junyue Cao et al.   SCIENCE

Integrative single-cell analysis of transcriptional and epigenetic states in the human adult brain

(2017) Blue B Lake et al.   NATURE BIOTECHNOLOGY

Predicting cell-type-specific gene expression from regions of open chromatin

(2012) A. Natarajan et al.   GENOME RESEARCH