Single-cell multiomics: technologies and data analysis methods

J Lee, DY Hyeon, D Hwang - Experimental & Molecular Medicine, 2020 - nature.com
Advances in single-cell isolation and barcoding technologies offer unprecedented
opportunities to profile DNA, mRNA, and proteins at a single-cell resolution. Recently, bulk …

Rethinking drug design in the artificial intelligence era

P Schneider, WP Walters, AT Plowright… - Nature reviews drug …, 2020 - nature.com
Artificial intelligence (AI) tools are increasingly being applied in drug discovery. While some
protagonists point to vast opportunities potentially offered by such tools, others remain …

The neutrotime transcriptional signature defines a single continuum of neutrophils across biological compartments

R Grieshaber-Bouyer, FA Radtke, P Cunin… - Nature …, 2021 - nature.com
Neutrophils are implicated in multiple homeostatic and pathological processes, but whether
functional diversity requires discrete neutrophil subsets is not known. Here, we apply single …

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

MD Luecken, FJ Theis - Molecular systems biology, 2019 - embopress.org
Single‐cell RNA‐seq has enabled gene expression to be studied at an unprecedented
resolution. The promise of this technology is attracting a growing user base for single‐cell …

Single-cell RNA sequencing technologies and bioinformatics pipelines

B Hwang, JH Lee, D Bang - Experimental & molecular medicine, 2018 - nature.com
Rapid progress in the development of next-generation sequencing (NGS) technologies in
recent years has provided many valuable insights into complex biological systems, ranging …

Principles and challenges of modeling temporal and spatial omics data

B Velten, O Stegle - Nature Methods, 2023 - nature.com
Studies with temporal or spatial resolution are crucial to understand the molecular dynamics
and spatial dependencies underlying a biological process or system. With advances in high …
AB Rosenberg, CM Roco, RA Muscat, A Kuchina… - Science, 2018 - science.org
To facilitate scalable profiling of single cells, we developed split-pool ligation-based
transcriptome sequencing (SPLiT-seq), a single-cell RNA-seq (scRNA-seq) method that …

PAGA: graph abstraction reconciles clustering with trajectory inference through a topology preserving map of single cells

FA Wolf, FK Hamey, M Plass, J Solana, JS Dahlin… - Genome biology, 2019 - Springer
Single-cell RNA-seq quantifies biological heterogeneity across both discrete cell types and
continuous cell transitions. Partition-based graph abstraction (PAGA) provides an …

SCENIC: single-cell regulatory network inference and clustering

S Aibar, CB González-Blas, T Moerman… - Nature …, 2017 - nature.com
We present SCENIC, a computational method for simultaneous gene regulatory network
reconstruction and cell-state identification from single-cell RNA-seq data (http://scenic …

Single-cell RNA sequencing to explore immune cell heterogeneity

E Papalexi, R Satija - Nature Reviews Immunology, 2018 - nature.com
Advances in single-cell RNA sequencing (scRNA-seq) have allowed for comprehensive
analysis of the immune system. In this Review, we briefly describe the available scRNA-seq …