Microglial research has advanced considerably in recent decades yet has been constrained
by a rolling series of dichotomies such as" resting versus activated" and" M1 versus M2." …

The joint analysis of the genome, epigenome, transcriptome, proteome and/or metabolome
from single cells is transforming our understanding of cell biology in health and disease. In …

Single-cell multi-omics technologies and methods characterize cell states and activities by
simultaneously integrating various single-modality omics methods that profile the …

The interplay between chromatin, transcription factors and genes generates complex
regulatory circuits that can be represented as gene regulatory networks (GRNs). The study …

Mapping single-cell sequencing profiles to comprehensive reference datasets provides a
powerful alternative to unsupervised analysis. However, most reference datasets are …

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 …

Joint profiling of chromatin accessibility and gene expression in individual cells provides an
opportunity to decipher enhancer-driven gene regulatory networks (GRNs). Here we present …

In the last decade, single-cell RNA sequencing routinely performed on large numbers of
single cells has greatly advanced our understanding of the underlying heterogeneity of …

The recent development of experimental methods for measuring chromatin state at single-
cell resolution has created a need for computational tools capable of analyzing these …

Emerging spatial technologies, including spatial transcriptomics and spatial epigenomics,
are becoming powerful tools for profiling of cellular states in the tissue context,,,–. However …