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Single-cell multiomics: technologies and data analysis methods
Advances in single-cell isolation and barcoding technologies offer unprecedented
opportunities to profile DNA, mRNA, and proteins at a single-cell resolution. Recently, bulk …
opportunities to profile DNA, mRNA, and proteins at a single-cell resolution. Recently, bulk …
Rethinking drug design in the artificial intelligence era
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 …
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
Neutrophils are implicated in multiple homeostatic and pathological processes, but whether
functional diversity requires discrete neutrophil subsets is not known. Here, we apply single …
functional diversity requires discrete neutrophil subsets is not known. Here, we apply single …
Current best practices in single‐cell RNA‐seq analysis: a tutorial
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 …
resolution. The promise of this technology is attracting a growing user base for single‐cell …
Single-cell RNA sequencing technologies and bioinformatics pipelines
Rapid progress in the development of next-generation sequencing (NGS) technologies in
recent years has provided many valuable insights into complex biological systems, ranging …
recent years has provided many valuable insights into complex biological systems, ranging …
Principles and challenges of modeling temporal and spatial omics data
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 …
and spatial dependencies underlying a biological process or system. With advances in high …
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 …
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
Single-cell RNA-seq quantifies biological heterogeneity across both discrete cell types and
continuous cell transitions. Partition-based graph abstraction (PAGA) provides an …
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 …
reconstruction and cell-state identification from single-cell RNA-seq data (http://scenic …
Single-cell RNA sequencing to explore immune cell heterogeneity
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 …
analysis of the immune system. In this Review, we briefly describe the available scRNA-seq …