Multi-omics single-cell data integration and regulatory inference with graph-linked embedding

Probabilistic harmonization and annotation of single‐cell transcriptomics data with deep generative models

(2021) Chenling Xu et al.   Molecular Systems Biology

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

(2021) Karren Dai Yang et al.   Nature Communications

Single-cell multiomics sequencing reveals the functional regulatory landscape of early embryos

(2021) Yang Wang et al.   Nature Communications

Iterative single-cell multi-omic integration using online learning

(2021) Chao Gao et al.   NATURE BIOTECHNOLOGY

Computational principles and challenges in single-cell data integration

(2021) Ricard Argelaguet et al.   NATURE BIOTECHNOLOGY

Single-cell CUT&Tag profiles histone modifications and transcription factors in complex tissues

(2021) Marek Bartosovic et al.   NATURE BIOTECHNOLOGY

Single cell transcriptional and chromatin accessibility profiling redefine cellular heterogeneity in the adult human kidney

(2021) Yoshiharu Muto et al.   Nature Communications

Deep generative model embedding of single-cell RNA-Seq profiles on hyperspheres and hyperbolic spaces

(2021) Jiarui Ding et al.   Nature Communications

Mapping single-cell atlases throughout Metazoa unravels cell type evolution

(2021) Alexander J Tarashansky et al.   eLife

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

(2021) Kai Cao et al.   BIOINFORMATICS

A transcriptomic and epigenomic cell atlas of the mouse primary motor cortex

(2021) Zizhen Yao et al.   NATURE

A transcriptomic atlas of mouse cerebellar cortex comprehensively defines cell types

(2021) Velina Kozareva et al.   NATURE

Multiscale and integrative single-cell Hi-C analysis with Higashi

(2021) Ruochi Zhang et al.   NATURE BIOTECHNOLOGY

Benchmarking atlas-level data integration in single-cell genomics

(2021) Malte D. Luecken et al.   NATURE METHODS

Identification of genomic enhancers through spatial integration of single‐cell transcriptomics and epigenomics

(2020) Carmen Bravo González‐Blas et al.   Molecular Systems Biology

Unsupervised topological alignment for single-cell multi-omics integration

(2020) Kai Cao et al.   BIOINFORMATICS

Searching large-scale scRNA-seq databases via unbiased cell embedding with Cell BLAST

(2020) Zhi-Jie Cao et al.   Nature Communications

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

(2020) Sai Ma et al.   CELL

SCIM: universal single-cell matching with unpaired feature sets

(2020) Stefan G Stark et al.   BIOINFORMATICS

Adversarial deconfounding autoencoder for learning robust gene expression embeddings

(2020) Ayse B Dincer et al.   BIOINFORMATICS

Slide-seq: A scalable technology for measuring genome-wide expression at high spatial resolution

(2019) Samuel G. Rodriques et al.   SCIENCE

Integrative single-cell analysis

(2019) Tim Stuart et al.   NATURE REVIEWS GENETICS

Transcriptome-scale super-resolved imaging in tissues by RNA seqFISH+

(2019) Chee-Huat Linus Eng et al.   NATURE

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

A compendium of promoter-centered long-range chromatin interactions in the human genome

(2019) Inkyung Jung et al.   NATURE GENETICS

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

(2019) Song Chen et al.   NATURE BIOTECHNOLOGY

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

(2019) Ilya Korsunsky et al.   NATURE METHODS

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

(2019) Wanwen Zeng et al.   Nature Communications

Highly scalable generation of DNA methylation profiles in single cells

(2018) Ryan M Mulqueen et al.   NATURE BIOTECHNOLOGY

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

(2018) Andrew Butler et al.   NATURE BIOTECHNOLOGY

Exponential scaling of single-cell RNA-seq in the past decade

(2018) Valentine Svensson et al.   Nature Protocols

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 Multi-omics: An Engine for New Quantitative Models of Gene Regulation

(2018) Jonathan Packer et al.   TRENDS IN GENETICS

scNMT-seq enables joint profiling of chromatin accessibility DNA methylation and transcription in single cells

(2018) Stephen J. Clark et al.   Nature Communications

Molecular Diversity and Specializations among the Cells of the Adult Mouse Brain

(2018) Arpiar Saunders et al.   CELL

Cicero Predicts cis-Regulatory DNA Interactions from Single-Cell Chromatin Accessibility Data

(2018) Hannah A. Pliner et al.   MOLECULAR CELL

Deep generative modeling for single-cell transcriptomics

(2018) Romain Lopez et al.   NATURE METHODS

A rapid and robust method for single cell chromatin accessibility profiling

(2018) Xi Chen et al.   Nature Communications

Genetic effects on gene expression across human tissues

(2017) François Aguet et al.   NATURE

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

(2017) Blue B Lake et al.   NATURE BIOTECHNOLOGY

SCENIC: single-cell regulatory network inference and clustering

(2017) Sara Aibar et al.   NATURE METHODS

TRRUST v2: an expanded reference database of human and mouse transcriptional regulatory interactions

(2017) Heonjong Han et al.   NUCLEIC ACIDS RESEARCH

The Encyclopedia of DNA elements (ENCODE): data portal update

(2017) Carrie A Davis et al.   NUCLEIC ACIDS RESEARCH

Single-cell methylomes identify neuronal subtypes and regulatory elements in mammalian cortex

(2017) Chongyuan Luo et al.   SCIENCE

Massively parallel digital transcriptional profiling of single cells

(2017) Grace X. Y. Zheng et al.   Nature Communications

Lineage-Specific Genome Architecture Links Enhancers and Non-coding Disease Variants to Target Gene Promoters

(2016) Biola M. Javierre et al.   CELL

Molecular Identity of Human Outer Radial Glia during Cortical Development

(2015) Alex A. Pollen et al.   CELL

Disruption of DNA-methylation-dependent long gene repression in Rett syndrome

(2015) Harrison W. Gabel et al.   NATURE

Fixed single-cell transcriptomic characterization of human radial glial diversity

(2015) Elliot R Thomsen et al.   NATURE METHODS

Epigenomic Signatures of Neuronal Diversity in the Mammalian Brain

(2015) Alisa Mo et al.   NEURON

Multiplex single-cell profiling of chromatin accessibility by combinatorial cellular indexing

(2015) D. A. Cusanovich et al.   SCIENCE

Efficient Test and Visualization of Multi-Set Intersections

(2015) Minghui Wang et al.   Scientific Reports

Smart-seq2 for sensitive full-length transcriptome profiling in single cells

(2013) Simone Picelli et al.   NATURE METHODS

Exploring the three-dimensional organization of genomes: interpreting chromatin interaction data

(2013) Job Dekker et al.   NATURE REVIEWS GENETICS

Mass Cytometry: Technique for Real Time Single Cell Multitarget Immunoassay Based on Inductively Coupled Plasma Time-of-Flight Mass Spectrometry

(2009) Dmitry R. Bandura et al.   ANALYTICAL CHEMISTRY